Merge pull request #1025 from Codium-ai/tr/refresh

refresh message

.github/workflows/build-and-test.yaml

@@ -2,8 +2,11 @@ name: Build-and-test
 
 on:
   push:
+    branches:
+      - main
   pull_request:
-    types: [ opened, reopened ]
+    branches:
+      - main
 
 jobs:
   build-and-test:

.github/workflows/docs-ci.yaml

@@ -0,0 +1,33 @@
+name: docs-ci 
+on:
+  push:
+    branches:
+      - main
+      - add-docs-portal
+    paths:
+      - docs/**
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: pip install mkdocs-material 
+      - run: pip install "mkdocs-material[imaging]"
+      - run: pip install mkdocs-glightbox
+      - run: mkdocs gh-deploy -f docs/mkdocs.yml --force

.gitignore

@@ -1,9 +1,11 @@
 .idea/
+.lsp/
+.vscode/
 venv/
 pr_agent/settings/.secrets.toml
 __pycache__
 dist/
 *.egg-info/
 build/
-review.md
 .DS_Store
+docs/.cache/

.pr_agent.toml

@@ -1,7 +1,3 @@
 [pr_reviewer]
 enable_review_labels_effort = true
 enable_auto_approval = true
-
-
-[pr_code_suggestions]
-summarize=true

INSTALL.md

@@ -1,472 +0,0 @@
-
-## Installation
-
-To get started with PR-Agent quickly, you first need to acquire two tokens:
-
-1. An OpenAI key from [here](https://platform.openai.com/api-keys), with access to GPT-4.
-2. A GitHub\GitLab\BitBucket personal access token (classic), with the repo scope. [GitHub from [here](https://github.com/settings/tokens)]
-
-There are several ways to use PR-Agent:
-
-**Locally**
-- [Using Docker image (no installation required)](INSTALL.md#use-docker-image-no-installation-required)
-- [Run from source](INSTALL.md#run-from-source)
-
-**GitHub specific methods**
-- [Run as a GitHub Action](INSTALL.md#run-as-a-github-action)
-- [Run as a GitHub App](INSTALL.md#run-as-a-github-app)
-- [Deploy as a Lambda Function](INSTALL.md#deploy-as-a-lambda-function)
-- [AWS CodeCommit](INSTALL.md#aws-codecommit-setup)
-
-**GitLab specific methods**
-- [Run a GitLab webhook server](INSTALL.md#run-a-gitlab-webhook-server)
-
-**BitBucket specific methods**
-- [Run as a Bitbucket Pipeline](INSTALL.md#run-as-a-bitbucket-pipeline)
-- [Run on a hosted app](INSTALL.md#run-on-a-hosted-bitbucket-app)
-- [Bitbucket server and data center](INSTALL.md#bitbucket-server-and-data-center)
----
-
-### Use Docker image (no installation required)
-
-A list of the relevant tools can be found in the [tools guide](./docs/TOOLS_GUIDE.md).
-
-To invoke a tool (for example `review`), you can run directly from the Docker image. Here's how:
-
-- For GitHub:
-```
-docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
-```
-
-- For GitLab:
-```
-docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
-```
-
-Note: If you have a dedicated GitLab instance, you need to specify the custom url as variable:
-```
-docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> -e GITLAB.URL=<your gitlab instance url> codiumai/pr-agent:latest --pr_url <pr_url> review
-```
-
-- For BitBucket:
-```
-docker run --rm -it -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$OPENAI_API_KEY -e BITBUCKET.BEARER_TOKEN=$BITBUCKET_BEARER_TOKEN codiumai/pr-agent:latest --pr_url=<pr_url> review
-```
-
-For other git providers, update CONFIG.GIT_PROVIDER accordingly, and check the `pr_agent/settings/.secrets_template.toml` file for the environment variables expected names and values.
-
----
-
-
-If you want to ensure you're running a specific version of the Docker image, consider using the image's digest:
-```bash
-docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent@sha256:71b5ee15df59c745d352d84752d01561ba64b6d51327f97d46152f0c58a5f678 --pr_url <pr_url> review
-```
-
-Or you can run a [specific released versions](./RELEASE_NOTES.md) of pr-agent, for example:
-```
-codiumai/pr-agent@v0.9
-```
-
----
-
-### Run from source
-
-1. Clone this repository:
-
-```
-git clone https://github.com/Codium-ai/pr-agent.git
-```
-
-2. Navigate to the `/pr-agent` folder and install the requirements in your favorite virtual environment:
-
-```
-pip install -e .
-```
-
-*Note: If you get an error related to Rust in the dependency installation then make sure Rust is installed and in your `PATH`, instructions: https://rustup.rs*
-
-3. Copy the secrets template file and fill in your OpenAI key and your GitHub user token:
-
-```
-cp pr_agent/settings/.secrets_template.toml pr_agent/settings/.secrets.toml
-chmod 600 pr_agent/settings/.secrets.toml
-# Edit .secrets.toml file
-```
-
-4. Run the cli.py script:
-
-```
-python3 -m pr_agent.cli --pr_url <pr_url> review
-python3 -m pr_agent.cli --pr_url <pr_url> ask <your question>
-python3 -m pr_agent.cli --pr_url <pr_url> describe
-python3 -m pr_agent.cli --pr_url <pr_url> improve
-python3 -m pr_agent.cli --pr_url <pr_url> add_docs
-python3 -m pr_agent.cli --pr_url <pr_url> generate_labels
-python3 -m pr_agent.cli --issue_url <issue_url> similar_issue
-...
-```
-
-[Optional] Add the pr_agent folder to your PYTHONPATH
-```
-export PYTHONPATH=$PYTHONPATH:<PATH to pr_agent folder>
-```
-
----
-
-### Run as a GitHub Action
-
-You can use our pre-built Github Action Docker image to run PR-Agent as a Github Action.
-
-1. Add the following file to your repository under `.github/workflows/pr_agent.yml`:
-
-```yaml
-on:
-  pull_request:
-    types:
-      - opened
-      - reopened
-      - ready_for_review
-      - review_requested
-
-  issue_comment:
-    types:
-      - created
-      - edited
-jobs:
-  pr_agent_job:
-    runs-on: ubuntu-latest
-    permissions:
-      issues: write
-      pull-requests: write
-      contents: write
-    name: Run pr agent on every pull request, respond to user comments
-    steps:
-      - name: PR Agent action step
-        id: pragent
-        uses: Codium-ai/pr-agent@main
-        env:
-          OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-```
-** if you want to pin your action to a specific release (v0.7 for example) for stability reasons, use:
-```yaml
-on:
-  pull_request:
-    types:
-      - opened
-      - reopened
-      - ready_for_review
-      - review_requested
-
-  issue_comment:
-    types:
-      - created
-      - edited
-
-jobs:
-  pr_agent_job:
-    runs-on: ubuntu-latest
-    permissions:
-      issues: write
-      pull-requests: write
-      contents: write
-    name: Run pr agent on every pull request, respond to user comments
-    steps:
-      - name: PR Agent action step
-        id: pragent
-        uses: Codium-ai/pr-agent@v0.7
-        env:
-          OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-```
-2. Add the following secret to your repository under `Settings > Secrets and variables > Actions > New repository secret > Add secret`:
-
-```
-Name = OPENAI_KEY
-Secret = <your key>
-```
-
-The GITHUB_TOKEN secret is automatically created by GitHub.
-
-3. Merge this change to your main branch.
-When you open your next PR, you should see a comment from `github-actions` bot with a review of your PR, and instructions on how to use the rest of the tools.
-
-4. You may configure PR-Agent by adding environment variables under the env section corresponding to any configurable property in the [configuration](pr_agent/settings/configuration.toml) file. Some examples:
-```yaml
-      env:
-        # ... previous environment values
-        OPENAI.ORG: "<Your organization name under your OpenAI account>"
-        PR_REVIEWER.REQUIRE_TESTS_REVIEW: "false" # Disable tests review
-        PR_CODE_SUGGESTIONS.NUM_CODE_SUGGESTIONS: 6 # Increase number of code suggestions
-```
-
----
-
-### Run as a GitHub App
-Allowing you to automate the review process on your private or public repositories.
-
-1. Create a GitHub App from the [Github Developer Portal](https://docs.github.com/en/developers/apps/creating-a-github-app).
-
-   - Set the following permissions:
-     - Pull requests: Read & write
-     - Issue comment: Read & write
-     - Metadata: Read-only
-     - Contents: Read-only
-   - Set the following events:
-     - Issue comment
-     - Pull request
-     - Push (if you need to enable triggering on PR update)
-
-2. Generate a random secret for your app, and save it for later. For example, you can use:
-
-```
-WEBHOOK_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
-```
-
-3. Acquire the following pieces of information from your app's settings page:
-
-   - App private key (click "Generate a private key" and save the file)
-   - App ID
-
-4. Clone this repository:
-
-```
-git clone https://github.com/Codium-ai/pr-agent.git
-```
-
-5. Copy the secrets template file and fill in the following:
-    ```
-    cp pr_agent/settings/.secrets_template.toml pr_agent/settings/.secrets.toml
-    # Edit .secrets.toml file
-    ```
-   - Your OpenAI key.
-   - Copy your app's private key to the private_key field.
-   - Copy your app's ID to the app_id field.
-   - Copy your app's webhook secret to the webhook_secret field.
-   - Set deployment_type to 'app' in [configuration.toml](./pr_agent/settings/configuration.toml)
-
-> The .secrets.toml file is not copied to the Docker image by default, and is only used for local development.
-> If you want to use the .secrets.toml file in your Docker image, you can add remove it from the .dockerignore file.
-> In most production environments, you would inject the secrets file as environment variables or as mounted volumes.
-> For example, in order to inject a secrets file as a volume in a Kubernetes environment you can update your pod spec to include the following,
-> assuming you have a secret named `pr-agent-settings` with a key named `.secrets.toml`:
-```
-       volumes:
-        - name: settings-volume
-          secret:
-            secretName: pr-agent-settings
-// ...
-       containers:
-// ...
-          volumeMounts:
-            - mountPath: /app/pr_agent/settings_prod
-              name: settings-volume
-```
-
-> Another option is to set the secrets as environment variables in your deployment environment, for example `OPENAI.KEY` and `GITHUB.USER_TOKEN`.
-
-6. Build a Docker image for the app and optionally push it to a Docker repository. We'll use Dockerhub as an example:
-
-```
-docker build . -t codiumai/pr-agent:github_app --target github_app -f docker/Dockerfile
-docker push codiumai/pr-agent:github_app  # Push to your Docker repository
-```
-
-7. Host the app using a server, serverless function, or container environment. Alternatively, for development and
-   debugging, you may use tools like smee.io to forward webhooks to your local machine.
-    You can check [Deploy as a Lambda Function](#deploy-as-a-lambda-function)
-
-8. Go back to your app's settings, and set the following:
-
-   - Webhook URL: The URL of your app's server or the URL of the smee.io channel.
-   - Webhook secret: The secret you generated earlier.
-
-9. Install the app by navigating to the "Install App" tab and selecting your desired repositories.
-
-> **Note:** When running PR-Agent from GitHub App, the default configuration file (configuration.toml) will be loaded.<br>
-> However, you can override the default tool parameters by uploading a local configuration file `.pr_agent.toml`<br>
-> For more information please check out the [USAGE GUIDE](./Usage.md#working-with-github-app)
----
-
-### Deploy as a Lambda Function
-
-1. Follow steps 1-5 of [Method 5](#run-as-a-github-app).
-2. Build a docker image that can be used as a lambda function
-    ```shell
-    docker buildx build --platform=linux/amd64 . -t codiumai/pr-agent:serverless -f docker/Dockerfile.lambda
-   ```
-3. Push image to ECR
-    ```shell
-	docker tag codiumai/pr-agent:serverless <AWS_ACCOUNT>.dkr.ecr.<AWS_REGION>.amazonaws.com/codiumai/pr-agent:serverless
-	docker push <AWS_ACCOUNT>.dkr.ecr.<AWS_REGION>.amazonaws.com/codiumai/pr-agent:serverless
-    ```
-4. Create a lambda function that uses the uploaded image. Set the lambda timeout to be at least 3m.
-5. Configure the lambda function to have a Function URL.
-6. In the environment variables of the Lambda function, specify `AZURE_DEVOPS_CACHE_DIR` to a writable location such as /tmp. (see [link](https://github.com/Codium-ai/pr-agent/pull/450#issuecomment-1840242269))
-7. Go back to steps 8-9 of [Method 5](#run-as-a-github-app) with the function url as your Webhook URL.
-    The Webhook URL would look like `https://<LAMBDA_FUNCTION_URL>/api/v1/github_webhooks`
-
----
-
-### AWS CodeCommit Setup
-
-Not all features have been added to CodeCommit yet.  As of right now, CodeCommit has been implemented to run the pr-agent CLI on the command line, using AWS credentials stored in environment variables.  (More features will be added in the future.)  The following is a set of instructions to have pr-agent do a review of your CodeCommit pull request from the command line:
-
-1. Create an IAM user that you will use to read CodeCommit pull requests and post comments
-    * Note: That user should have CLI access only, not Console access
-2. Add IAM permissions to that user, to allow access to CodeCommit (see IAM Role example below)
-3. Generate an Access Key for your IAM user
-4. Set the Access Key and Secret using environment variables (see Access Key example below)
-5. Set the `git_provider` value to `codecommit` in the `pr_agent/settings/configuration.toml` settings file
-6. Set the `PYTHONPATH` to include your `pr-agent` project directory
-    * Option A: Add `PYTHONPATH="/PATH/TO/PROJECTS/pr-agent` to your `.env` file
-    * Option B: Set `PYTHONPATH` and run the CLI in one command, for example:
-        * `PYTHONPATH="/PATH/TO/PROJECTS/pr-agent python pr_agent/cli.py [--ARGS]`
-
-##### AWS CodeCommit IAM Role Example
-
-Example IAM permissions to that user to allow access to CodeCommit:
-
-* Note: The following is a working example of IAM permissions that has read access to the repositories and write access to allow posting comments
-* Note: If you only want pr-agent to review your pull requests, you can tighten the IAM permissions further, however this IAM example will work, and allow the pr-agent to post comments to the PR
-* Note: You may want to replace the `"Resource": "*"` with your list of repos, to limit access to only those repos
-
-```
-{
-    "Version": "2012-10-17",
-    "Statement": [
-        {
-            "Effect": "Allow",
-            "Action": [
-                "codecommit:BatchDescribe*",
-                "codecommit:BatchGet*",
-                "codecommit:Describe*",
-                "codecommit:EvaluatePullRequestApprovalRules",
-                "codecommit:Get*",
-                "codecommit:List*",
-                "codecommit:PostComment*",
-                "codecommit:PutCommentReaction",
-                "codecommit:UpdatePullRequestDescription",
-                "codecommit:UpdatePullRequestTitle"
-            ],
-            "Resource": "*"
-        }
-    ]
-}
-```
-
-##### AWS CodeCommit Access Key and Secret
-
-Example setting the Access Key and Secret using environment variables
-
-```sh
-export AWS_ACCESS_KEY_ID="XXXXXXXXXXXXXXXX"
-export AWS_SECRET_ACCESS_KEY="XXXXXXXXXXXXXXXX"
-export AWS_DEFAULT_REGION="us-east-1"
-```
-
-##### AWS CodeCommit CLI Example
-
-After you set up AWS CodeCommit using the instructions above, here is an example CLI run that tells pr-agent to **review** a given pull request.
-(Replace your specific PYTHONPATH and PR URL in the example)
-
-```sh
-PYTHONPATH="/PATH/TO/PROJECTS/pr-agent" python pr_agent/cli.py \
-  --pr_url https://us-east-1.console.aws.amazon.com/codesuite/codecommit/repositories/MY_REPO_NAME/pull-requests/321 \
-  review
-```
-
----
-
-### Run a GitLab webhook server
-
-1. From the GitLab workspace or group, create an access token. Enable the "api" scope only.
-2. Generate a random secret for your app, and save it for later. For example, you can use:
-
-```
-WEBHOOK_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
-```
-3. Follow the instructions to build the Docker image, setup a secrets file and deploy on your own server from [Method 5](#run-as-a-github-app) steps 4-7. Be sure to set the target to `gitlab_webhook` instead of `github_app` when building the Docker image.
-4. In the secrets file, fill in the following:
-    - Your OpenAI key.
-    - In the [gitlab] section, fill in personal_access_token and shared_secret. The access token can be a personal access token, or a group or project access token.
-    - Set deployment_type to 'gitlab' in [configuration.toml](./pr_agent/settings/configuration.toml)
-5. Create a webhook in GitLab. Set the URL to the URL of your app's server with the path `/webhook` (e.g. `http://pr-agent.example.com:3000/webhook`). Set the secret token to the generated secret from step 2.
-In the "Trigger" section, check the ‘comments’ and ‘merge request events’ boxes.
-6. Test your installation by opening a merge request or commenting on a merge request using one of CodiumAI's commands.
-
-
-
-### Run as a Bitbucket Pipeline
-
-
-You can use the Bitbucket Pipeline system to run PR-Agent on every pull request open or update.
-
-1. Add the following file in your repository bitbucket_pipelines.yml
-
-```yaml
-pipelines:
-    pull-requests:
-      '**':
-        - step:
-            name: PR Agent Review
-            image: python:3.10
-            services:
-              - docker
-            script:
-              - docker run -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$OPENAI_API_KEY -e BITBUCKET.BEARER_TOKEN=$BITBUCKET_BEARER_TOKEN codiumai/pr-agent:latest --pr_url=https://bitbucket.org/$BITBUCKET_WORKSPACE/$BITBUCKET_REPO_SLUG/pull-requests/$BITBUCKET_PR_ID review
-```
-
-2. Add the following secure variables to your repository under Repository settings > Pipelines > Repository variables.
-OPENAI_API_KEY: <your key>
-BITBUCKET_BEARER_TOKEN: <your token>
-
-You can get a Bitbucket token for your repository by following Repository Settings -> Security -> Access Tokens.
-
-Note that comments on a PR are not supported in Bitbucket Pipeline.
-
-
-### Run using CodiumAI-hosted Bitbucket app
-
-Please contact <support@codium.ai> or visit [CodiumAI pricing page](https://www.codium.ai/pricing/) if you're interested in a hosted BitBucket app solution that provides full functionality including PR reviews and comment handling. It's based on the [bitbucket_app.py](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/git_providers/bitbucket_provider.py) implementation.
-
-
-### Bitbucket Server and Data Center
-
-Login into your on-prem instance of Bitbucket with your service account username and password.
-Navigate to `Manage account`, `HTTP Access tokens`, `Create Token`.
-Generate the token and add it to .secret.toml under `bitbucket_server` section
-
-```toml
-[bitbucket_server]
-bearer_token = "<your key>"
-```
-
-#### Run it as CLI
-
-Modify `configuration.toml`:
-
-```toml
-git_provider="bitbucket_server"
-```
-
-and pass the Pull request URL:
-```shell
-python cli.py --pr_url https://git.onpreminstanceofbitbucket.com/projects/PROJECT/repos/REPO/pull-requests/1 review
-```
-
-#### Run it as service
-
-To run pr-agent as webhook, build the docker image:
-```
-docker build . -t codiumai/pr-agent:bitbucket_server_webhook --target bitbucket_server_webhook -f docker/Dockerfile
-docker push codiumai/pr-agent:bitbucket_server_webhook  # Push to your Docker repository
-```
-
-Navigate to `Projects` or `Repositories`, `Settings`, `Webhooks`, `Create Webhook`.
-Fill the name and URL, Authentication None select the Pull Request Opened checkbox to receive that event as webhook.
-
-The URL should end with `/webhook`, for example: https://domain.com/webhook
-
-=======

MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include pr_agent *.toml
+recursive-exclude pr_agent *.secrets.toml

README.md

@@ -6,13 +6,16 @@
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="https://codium.ai/images/pr_agent/logo-dark.png" width="330">
   <source media="(prefers-color-scheme: light)" srcset="https://codium.ai/images/pr_agent/logo-light.png" width="330">
-  <img alt="logo">
+  <img src="https://codium.ai/images/pr_agent/logo-light.png" alt="logo" width="330">
+
 </picture>
 <br/>
-Making pull requests less painful with an AI agent
+CodiumAI PR-Agent aims to help efficiently review and handle pull requests, by providing AI feedbacks and suggestions
 </div>
 
 [![GitHub license](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://github.com/Codium-ai/pr-agent/blob/main/LICENSE)
+[![Static Badge](https://img.shields.io/badge/Chrome-Extension-violet)](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl)
+[![Static Badge](https://img.shields.io/badge/Code-Benchmark-blue)](https://pr-agent-docs.codium.ai/finetuning_benchmark/)
 [![Discord](https://badgen.net/badge/icon/discord?icon=discord&label&color=purple)](https://discord.com/channels/1057273017547378788/1126104260430528613)
 [![Twitter](https://img.shields.io/twitter/follow/codiumai)](https://twitter.com/codiumai)
     <a href="https://github.com/Codium-ai/pr-agent/commits/main">
@@ -20,112 +23,116 @@ Making pull requests less painful with an AI agent
     </a>
 </div>
 
+### [Documentation](https://pr-agent-docs.codium.ai/)
+- See the [Installation Guide](https://pr-agent-docs.codium.ai/installation/) for instructions on installing PR-Agent on different platforms.
+
+- See the [Usage Guide](https://pr-agent-docs.codium.ai/usage-guide/) for instructions on running PR-Agent tools via different interfaces, such as CLI, PR Comments, or by automatically triggering them when a new PR is opened.
+
+- See the [Tools Guide](https://pr-agent-docs.codium.ai/tools/) for a detailed description of the different tools, and the available configurations for each tool.
+
+
 ## Table of Contents
 - [News and Updates](#news-and-updates)
 - [Overview](#overview)
 - [Example results](#example-results)
 - [Try it now](#try-it-now)
-- [Installation](#installation)
 - [PR-Agent Pro 💎](#pr-agent-pro-)
 - [How it works](#how-it-works)
 - [Why use PR-Agent?](#why-use-pr-agent)
   
 ## News and Updates
 
-### Feb 29, 2024
-- You can now use the repo's [wiki page](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#configuration-options) to set configurations for PR-Agent 💎
+### July 4, 2024
 
-<kbd><img src="https://codium.ai/images/pr_agent/wiki_configuration.png" width="512"></kbd>
+Added improved support for claude-sonnet-3.5 model (anthropic, vertex, bedrock), including dedicated prompts.
 
+### June 17, 2024
 
-### Feb 21, 2024
-- Added a new command, `/help`, to easily provide a list of available tools and their descriptions, and run them interactively.
+New option for a self-review checkbox is now available for the `/improve` tool, along with the ability(💎) to enable auto-approve, or demand self-review in addition to human reviewer. See more [here](https://pr-agent-docs.codium.ai/tools/improve/#self-review).
 
-<kbd>
+<kbd><img src="https://www.codium.ai/images/pr_agent/self_review_1.png" width="512"></kbd>
 
-<img src="https://www.codium.ai/images/pr_agent/help.png" width="512">
+### June 6, 2024
 
-</kbd>
+New option now available (💎) - **apply suggestions**:
+
+<kbd><img src="https://www.codium.ai/images/pr_agent/apply_suggestion_1.png" width="512"></kbd>
+
+&rarr;
+
+<kbd><img src="https://www.codium.ai/images/pr_agent/apply_suggestion_2.png" width="512"></kbd>
 
-### Feb 18, 2024
-- Introducing the `CI Feedback` tool 💎. The tool automatically triggers when a PR has a failed check. It analyzes the failed check, and provides summarized logs and analysis. Note that this feature requires read access to GitHub 'checks' and 'actions'. See [here](./docs/CI_FEEDBACK.md) for more details.
-- New ability - you can run `/ask` on specific lines of code in the PR from the PR's diff view. See [here](./docs/ASK.md#ask-lines) for more details.
-- Introducing support for [Azure DevOps Webhooks](./Usage.md#azure-devops-webhook), as well as bug fixes and improved support for several ADO commands.
 
 
 ## Overview
 <div style="text-align:left;">
 
-CodiumAI PR-Agent is an open-source tool to help efficiently review and handle pull requests.
-
-- See the [Installation Guide](./INSTALL.md) for instructions on installing and running the tool on different git platforms.
-
-- See the [Usage Guide](./Usage.md) for instructions on running the PR-Agent commands via different interfaces, including _CLI_, _online usage_, or by _automatically triggering_ them when a new PR is opened.
-
-- See the [Tools Guide](./docs/TOOLS_GUIDE.md) for a detailed description of the different tools (tools are run via the commands).
-
 Supported commands per platform:
 
-|       |                                                                                                                                         | GitHub             | Gitlab             | Bitbucket          | Azure DevOps       |
-|-------|-----------------------------------------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:--------------------:|:--------------------:|
-| TOOLS | Review                                                                                                                                  | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | ⮑ Incremental                                                                                                                           | :white_check_mark: |                    |                    |                    |
-|       | ⮑ [SOC2 Compliance](https://github.com/Codium-ai/pr-agent/blob/main/docs/REVIEW.md#soc2-ticket-compliance-) 💎                           | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Describe                                                                                                                                | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | ⮑ [Inline File Summary](https://github.com/Codium-ai/pr-agent/blob/main/docs/DESCRIBE.md#inline-file-summary-) 💎                        | :white_check_mark: |                    |                    |                    |
-|       | Improve                                                                                                                                 | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | ⮑ Extended                                                                                                                              | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Ask                                                                                                                                     | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | ⮑ [Ask on code lines](./docs/ASK.md#ask-lines)                                                                                          | :white_check_mark: | :white_check_mark: |                    |                    |
-|       | [Custom Suggestions](https://github.com/Codium-ai/pr-agent/blob/main/docs/CUSTOM_SUGGESTIONS.md) 💎                                      | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | [Test](https://github.com/Codium-ai/pr-agent/blob/main/docs/TEST.md) 💎                                                                  | :white_check_mark: | :white_check_mark: |                    | :white_check_mark: |
-|       | Reflect and Review                                                                                                                      | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Update CHANGELOG.md                                                                                                                     | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Find Similar Issue                                                                                                                      | :white_check_mark: |                    |                    |                    |
-|       | [Add PR Documentation](https://github.com/Codium-ai/pr-agent/blob/main/docs/ADD_DOCUMENTATION.md) 💎                                     | :white_check_mark: | :white_check_mark: |                   | :white_check_mark: |
-|       | [Custom Labels](https://github.com/Codium-ai/pr-agent/blob/main/docs/DESCRIBE.md#handle-custom-labels-from-the-repos-labels-page-gem) 💎 | :white_check_mark: | :white_check_mark: |                    | :white_check_mark: |
-|       | [Analyze](https://github.com/Codium-ai/pr-agent/blob/main/docs/Analyze.md) 💎                                                            | :white_check_mark: | :white_check_mark: |                    | :white_check_mark: |
-|       | [CI Feedback](https://github.com/Codium-ai/pr-agent/blob/main/docs/CI_FEEDBACK.md) 💎                                                    | :white_check_mark: |                    |                    |                    |
-|       |                                                                                                                                         |                    |                    |                    |                    |
-| USAGE | CLI                                                                                                                                     | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | App / webhook                                                                                                                           | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Tagging bot                                                                                                                             | :white_check_mark: |                    |                    |                    |
-|       | Actions                                                                                                                                 | :white_check_mark: |                    | :white_check_mark: |                    |
-|       |                                                                                                                                         |                    |                    |                    |                    |
-| CORE  | PR compression                                                                                                                          | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Repo language prioritization                                                                                                            | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Adaptive and token-aware file patch fitting                                                                                             | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Multiple models support                                                                                                                 | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | [Static code analysis](https://github.com/Codium-ai/pr-agent/blob/main/docs/Analyze.md) 💎                                               | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | [Global and wiki configurations](./Usage.md#configuration) 💎                           | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | [PR Actions](https://www.codium.ai/images/pr_agent/pr-actions.mp4) 💎                                                                    | :white_check_mark: |                    |                    |                    |
+|       |                                                                                                         | GitHub             | Gitlab             | Bitbucket          | Azure DevOps       |
+|-------|---------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:--------------------:|:--------------------:|
+| TOOLS | Review                                                                                                  | ✅ | ✅ | ✅ | ✅ |
+|       | ⮑ Incremental                                                                                           | ✅ |                    |                    |                    |
+|       | ⮑ [SOC2 Compliance](https://pr-agent-docs.codium.ai/tools/review/#soc2-ticket-compliance) 💎            | ✅ | ✅ | ✅ | ✅ |
+|       | Describe                                                                                                | ✅ | ✅ | ✅ | ✅ |
+|       | ⮑ [Inline File Summary](https://pr-agent-docs.codium.ai/tools/describe#inline-file-summary) 💎          | ✅ |                    |                    |                    |
+|       | Improve                                                                                                 | ✅ | ✅ | ✅ | ✅ |
+|       | ⮑ Extended                                                                                              | ✅ | ✅ | ✅ | ✅ |
+|       | Ask                                                                                                     | ✅ | ✅ | ✅ | ✅ |
+|       | ⮑ [Ask on code lines](https://pr-agent-docs.codium.ai/tools/ask#ask-lines)                              | ✅ | ✅ |                    |                    |
+|       | [Custom Prompt](https://pr-agent-docs.codium.ai/tools/custom_prompt/) 💎                                | ✅ | ✅ | ✅ | ✅ |
+|       | [Test](https://pr-agent-docs.codium.ai/tools/test/) 💎                                                  | ✅ | ✅ |                    | ✅ |
+|       | Reflect and Review                                                                                      | ✅ | ✅ | ✅ | ✅ |
+|       | Update CHANGELOG.md                                                                                     | ✅ | ✅ | ✅ | ✅ |
+|       | Find Similar Issue                                                                                      | ✅ |                    |                    |                    |
+|       | [Add PR Documentation](https://pr-agent-docs.codium.ai/tools/documentation/) 💎                         | ✅ | ✅ |                   | ✅ |
+|       | [Custom Labels](https://pr-agent-docs.codium.ai/tools/custom_labels/) 💎                                | ✅ | ✅ |                    | ✅ |
+|       | [Analyze](https://pr-agent-docs.codium.ai/tools/analyze/) 💎                                            | ✅ | ✅ |                    | ✅ |
+|       | [CI Feedback](https://pr-agent-docs.codium.ai/tools/ci_feedback/) 💎                                    | ✅ |                    |                    |                    |
+|       | [Similar Code](https://pr-agent-docs.codium.ai/tools/similar_code/) 💎                                  | ✅ |                    |                    |                    |
+|       |                                                                                                         |                    |                    |                    |                    |
+| USAGE | CLI                                                                                                     | ✅ | ✅ | ✅ | ✅ |
+|       | App / webhook                                                                                           | ✅ | ✅ | ✅ | ✅ |
+|       | Tagging bot                                                                                             | ✅ |                    |                    |                    |
+|       | Actions                                                                                                 | ✅ |                    | ✅ |                    |
+|       |                                                                                                         |                    |                    |                    |                    |
+| CORE  | PR compression                                                                                          | ✅ | ✅ | ✅ | ✅ |
+|       | Repo language prioritization                                                                            | ✅ | ✅ | ✅ | ✅ |
+|       | Adaptive and token-aware file patch fitting                                                             | ✅ | ✅ | ✅ | ✅ |
+|       | Multiple models support                                                                                 | ✅ | ✅ | ✅ | ✅ |
+|       | [Static code analysis](https://pr-agent-docs.codium.ai/core-abilities/#static-code-analysis) 💎         | ✅ | ✅ | ✅ | ✅ |
+|       | [Global and wiki configurations](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/) 💎 | ✅ | ✅ | ✅ | ✅ |
+|       | [PR interactive actions](https://www.codium.ai/images/pr_agent/pr-actions.mp4) 💎                       | ✅ |                    |                    |                    |
 - 💎 means this feature is available only in [PR-Agent Pro](https://www.codium.ai/pricing/)
-- Support for additional git providers is described in [here](./docs/Full_environments.md)
+
+[//]: # (- Support for additional git providers is described in [here]&#40;./docs/Full_environments.md&#41;)
 ___
 
-‣ **Auto Description ([`/describe`](./docs/DESCRIBE.md))**: Automatically generating PR description - title, type, summary, code walkthrough and labels.
+‣ **Auto Description ([`/describe`](https://pr-agent-docs.codium.ai/tools/describe/))**: Automatically generating PR description - title, type, summary, code walkthrough and labels.
 \
-‣ **Auto Review ([`/review`](./docs/REVIEW.md))**: Adjustable feedback about the PR, possible issues, security concerns, review effort and more.
+‣ **Auto Review ([`/review`](https://pr-agent-docs.codium.ai/tools/review/))**: Adjustable feedback about the PR, possible issues, security concerns, review effort and more.
 \
-‣ **Question Answering ([`/ask ...`](./docs/ASK.md))**: Answering free-text questions about the PR.
+‣ **Code Suggestions ([`/improve`](https://pr-agent-docs.codium.ai/tools/improve/))**: Code suggestions for improving the PR.
 \
-‣ **Code Suggestions ([`/improve`](./docs/IMPROVE.md))**: Code suggestions for improving the PR.
+‣ **Question Answering ([`/ask ...`](https://pr-agent-docs.codium.ai/tools/ask/))**: Answering free-text questions about the PR.
 \
-‣ **Update Changelog ([`/update_changelog`](./docs/UPDATE_CHANGELOG.md))**: Automatically updating the CHANGELOG.md file with the PR changes.
+‣ **Update Changelog ([`/update_changelog`](https://pr-agent-docs.codium.ai/tools/update_changelog/))**: Automatically updating the CHANGELOG.md file with the PR changes.
 \
-‣ **Find Similar Issue ([`/similar_issue`](./docs/SIMILAR_ISSUE.md))**: Automatically retrieves and presents similar issues.
+‣ **Find Similar Issue ([`/similar_issue`](https://pr-agent-docs.codium.ai/tools/similar_issues/))**: Automatically retrieves and presents similar issues.
 \
-‣ **Add Documentation 💎  ([`/add_docs`](./docs/ADD_DOCUMENTATION.md))**: Generates documentation to methods/functions/classes that changed in the PR.
+‣ **Add Documentation 💎  ([`/add_docs`](https://pr-agent-docs.codium.ai/tools/documentation/))**: Generates documentation to methods/functions/classes that changed in the PR.
 \
-‣ **Generate Custom Labels 💎 ([`/generate_labels`](./docs/GENERATE_CUSTOM_LABELS.md))**: Generates custom labels for the PR, based on specific guidelines defined by the user.
+‣ **Generate Custom Labels 💎 ([`/generate_labels`](https://pr-agent-docs.codium.ai/tools/custom_labels/))**: Generates custom labels for the PR, based on specific guidelines defined by the user.
 \
-‣ **Analyze 💎 ([`/analyze`](./docs/Analyze.md))**: Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component.
+‣ **Analyze 💎 ([`/analyze`](https://pr-agent-docs.codium.ai/tools/analyze/))**: Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component.
 \
-‣ **Custom Suggestions 💎 ([`/custom_suggestions`](./docs/CUSTOM_SUGGESTIONS.md))**: Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user.
+‣ **Custom Prompt 💎 ([`/custom_prompt`](https://pr-agent-docs.codium.ai/tools/custom_prompt/))**: Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user.
 \
-‣ **Generate Tests 💎 ([`/test component_name`](./docs/TEST.md))**: Automatically generates unit tests for a selected component, based on the PR code changes.
+‣ **Generate Tests 💎 ([`/test component_name`](https://pr-agent-docs.codium.ai/tools/test/))**: Generates unit tests for a selected component, based on the PR code changes.
 \
-‣ **CI Feedback 💎 ([`/checks ci_job`](./docs/CI_FEEDBACK.md))**: Automatically generates feedback and analysis for a failed CI job.
+‣ **CI Feedback 💎 ([`/checks ci_job`](https://pr-agent-docs.codium.ai/tools/ci_feedback/))**: Automatically generates feedback and analysis for a failed CI job.
+\
+‣ **Similar Code 💎 ([`/find_similar_component`](https://pr-agent-docs.codium.ai/tools/similar_code/))**: Retrieves the most similar code components from inside the organization's codebase, or from open-source code.
 ___
 
 ## Example results
@@ -219,46 +226,56 @@ and the agent will respond with a review of your PR
 ![Review generation process](https://www.codium.ai/images/demo-2.gif)
 
 
-To set up your own PR-Agent, see the [Installation](#installation) section below.
+To set up your own PR-Agent, see the [Installation](https://pr-agent-docs.codium.ai/installation/) section below.
 Note that when you set your own PR-Agent or use CodiumAI hosted PR-Agent, there is no need to mention `@CodiumAI-Agent ...`. Instead, directly start with the command, e.g., `/ask ...`.
 
 ---
 
-## Installation
-To use your own version of PR-Agent, you first need to acquire two tokens:
+[//]: # (## Installation)
 
-1. An OpenAI key from [here](https://platform.openai.com/), with access to GPT-4.
-2. A GitHub personal access token (classic) with the repo scope.
+[//]: # (To use your own version of PR-Agent, you first need to acquire two tokens:)
 
-There are several ways to use PR-Agent:
+[//]: # ()
+[//]: # (1. An OpenAI key from [here]&#40;https://platform.openai.com/&#41;, with access to GPT-4.)
 
-**Locally**
-- [Use Docker image (no installation required)](./INSTALL.md#use-docker-image-no-installation-required)
-- [Run from source](./INSTALL.md#run-from-source)
+[//]: # (2. A GitHub personal access token &#40;classic&#41; with the repo scope.)
 
-**GitHub specific methods**
-- [Run as a GitHub Action](./INSTALL.md#run-as-a-github-action)
-- [Run as a GitHub App](./INSTALL.md#run-as-a-github-app)
+[//]: # ()
+[//]: # (There are several ways to use PR-Agent:)
 
-**GitLab specific methods**
-- [Run a GitLab webhook server](./INSTALL.md#run-a-gitlab-webhook-server)
+[//]: # ()
+[//]: # (**Locally**)
 
-**BitBucket specific methods**
-- [Run as a Bitbucket Pipeline](./INSTALL.md#run-as-a-bitbucket-pipeline)
+[//]: # (- [Using pip package]&#40;https://pr-agent-docs.codium.ai/installation/locally/#using-pip-package&#41;)
+
+[//]: # (- [Using Docker image]&#40;https://pr-agent-docs.codium.ai/installation/locally/#using-docker-image&#41;)
+
+[//]: # (- [Run from source]&#40;https://pr-agent-docs.codium.ai/installation/locally/#run-from-source&#41;)
+
+[//]: # ()
+[//]: # (**GitHub specific methods**)
+
+[//]: # (- [Run as a GitHub Action]&#40;https://pr-agent-docs.codium.ai/installation/github/#run-as-a-github-action&#41;)
+
+[//]: # (- [Run as a GitHub App]&#40;https://pr-agent-docs.codium.ai/installation/github/#run-as-a-github-app&#41;)
+
+[//]: # ()
+[//]: # (**GitLab specific methods**)
+
+[//]: # (- [Run a GitLab webhook server]&#40;https://pr-agent-docs.codium.ai/installation/gitlab/&#41;)
+
+[//]: # ()
+[//]: # (**BitBucket specific methods**)
+
+[//]: # (- [Run as a Bitbucket Pipeline]&#40;https://pr-agent-docs.codium.ai/installation/bitbucket/&#41;)
 
 ## PR-Agent Pro 💎
 [PR-Agent Pro](https://www.codium.ai/pricing/) is a hosted version of PR-Agent, provided by CodiumAI. It is available for a monthly fee, and provides the following benefits:
-1. **Fully managed** - We take care of everything for you - hosting, models, regular updates, and more. Installation is as simple as signing up and adding the PR-Agent app to your GitHub\BitBucket repo.
+1. **Fully managed** - We take care of everything for you - hosting, models, regular updates, and more. Installation is as simple as signing up and adding the PR-Agent app to your GitHub\GitLab\BitBucket repo.
 2. **Improved privacy** - No data will be stored or used to train models. PR-Agent Pro will employ zero data retention, and will use an OpenAI account with zero data retention.
 3. **Improved support** - PR-Agent Pro users will receive priority support, and will be able to request new features and capabilities.
-4. **Extra features** -In addition to the benefits listed above, PR-Agent Pro will emphasize more customization, and the usage of static code analysis, in addition to LLM logic, to improve results. It has the following additional tools and features:
-    - [**Analyze PR components**](https://github.com/Codium-ai/pr-agent/blob/main/docs/Analyze.md)
-    - [**Custom Code Suggestions**](https://github.com/Codium-ai/pr-agent/blob/main/docs/CUSTOM_SUGGESTIONS.md)
-    - [**Tests**](https://github.com/Codium-ai/pr-agent/blob/main/docs/TEST.md)
-    - [**PR documentation**](https://github.com/Codium-ai/pr-agent/blob/main/docs/ADD_DOCUMENTATION.md)
-    - [**SOC2 compliance check**](https://github.com/Codium-ai/pr-agent/blob/main/docs/REVIEW.md#soc2-ticket-compliance-)
-    - [**Custom labels**](https://github.com/Codium-ai/pr-agent/blob/main/docs/DESCRIBE.md#handle-custom-labels-from-the-repos-labels-page-gem)
-    - [**Global configuration**](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#global-configuration-file-)
+4. **Extra features** -In addition to the benefits listed above, PR-Agent Pro will emphasize more customization, and the usage of static code analysis, in addition to LLM logic, to improve results. 
+See [here](https://pr-agent-docs.codium.ai/#pr-agent-pro) for a list of features available in PR-Agent Pro.
 
 
 
@@ -268,7 +285,7 @@ The following diagram illustrates PR-Agent tools and their flow:
 
 ![PR-Agent Tools](https://codium.ai/images/pr_agent/diagram-v0.9.png)
 
-Check out the [PR Compression strategy](./PR_COMPRESSION.md) page for more details on how we convert a code diff to a manageable LLM prompt
+Check out the [PR Compression strategy](https://pr-agent-docs.codium.ai/core-abilities/#pr-compression-strategy) page for more details on how we convert a code diff to a manageable LLM prompt
 
 ## Why use PR-Agent?
 
@@ -277,18 +294,29 @@ A reasonable question that can be asked is: `"Why use PR-Agent? What makes it st
 Here are some advantages of PR-Agent:
 
 - We emphasize **real-life practical usage**. Each tool (review, improve, ask, ...) has a single GPT-4 call, no more. We feel that this is critical for realistic team usage - obtaining an answer quickly (~30 seconds) and affordably.
-- Our [PR Compression strategy](./PR_COMPRESSION.md)  is a core ability that enables to effectively tackle both short and long PRs.
+- Our [PR Compression strategy](https://pr-agent-docs.codium.ai/core-abilities/#pr-compression-strategy)  is a core ability that enables to effectively tackle both short and long PRs.
 - Our JSON prompting strategy enables to have **modular, customizable tools**. For example, the '/review' tool categories can be controlled via the [configuration](pr_agent/settings/configuration.toml) file. Adding additional categories is easy and accessible.
 - We support **multiple git providers** (GitHub, Gitlab, Bitbucket), **multiple ways** to use the tool (CLI, GitHub Action, GitHub App, Docker, ...), and **multiple models** (GPT-4, GPT-3.5, Anthropic, Cohere, Llama2).
 
 
 ## Data privacy
 
-If you host PR-Agent with your OpenAI API key, it is between you and OpenAI. You can read their API data privacy policy here:
+### Self-hosted PR-Agent
+
+- If you host PR-Agent with your OpenAI API key, it is between you and OpenAI. You can read their API data privacy policy here:
 https://openai.com/enterprise-privacy
 
-When using PR-Agent Pro 💎, hosted by CodiumAI, we will not store any of your data, nor will we use it for training.
-You will also benefit from an OpenAI account with zero data retention.
+### CodiumAI-hosted PR-Agent Pro 💎
+
+- When using PR-Agent Pro 💎, hosted by CodiumAI, we will not store any of your data, nor will we use it for training. You will also benefit from an OpenAI account with zero data retention.
+
+- For certain clients, CodiumAI-hosted PR-Agent Pro will use CodiumAI’s proprietary models — if this is the case, you will be notified.
+
+- No passive collection of Code and Pull Requests’ data — PR-Agent will be active only when you invoke it, and it will then extract and analyze only data relevant to the executed command and queried pull request.
+
+### PR-Agent Chrome extension
+
+- The [PR-Agent Chrome extension](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl) serves solely to modify the visual appearance of a GitHub PR screen. It does not transmit any user's repo or pull request code. Code is only sent for processing when a user submits a GitHub comment that activates a PR-Agent tool, in accordance with the standard privacy policy of PR-Agent.
 
 ## Links
 

Usage.md

@@ -1,529 +0,0 @@
-## Usage Guide
-
-### Table of Contents
-- [Introduction](#introduction)
-- [Configuration Options](#configuration-options)
-- [Managing Mail Notifications](#managing-mail-notifications)
-- [Usage Types](#usage-types)
-  - [Local Repo (CLI)](#working-from-a-local-repo-cli)
-  - [Online Usage](#online-usage)
-  - [GitHub App](#working-with-github-app)
-  - [GitHub Action](#working-with-github-action)
-  - [GitLab Webhook](#working-with-gitlab-webhook)
-  - [BitBucket App](#working-with-bitbucket-self-hosted-app)
-  - [Azure DevOps Provider](#azure-devops-provider)
-- [Additional Configurations Walkthrough](#appendix---additional-configurations-walkthrough)
-  - [Ignoring files from analysis](#ignoring-files-from-analysis)
-  - [Extra instructions](#extra-instructions)
-  - [Working with large PRs](#working-with-large-prs)
-  - [Changing a model](#changing-a-model)
-  - [Patch Extra Lines](#patch-extra-lines)
-  - [Editing the prompts](#editing-the-prompts)
-
-## Introduction
-
-After [installation](/INSTALL.md), there are three basic ways to invoke CodiumAI PR-Agent:
-1. Locally running a CLI command
-2. Online usage - by [commenting](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021901) on a PR
-3. Enabling PR-Agent tools to run automatically when a new PR is opened
-
-
-Specifically, CLI commands can be issued by invoking a pre-built [docker image](/INSTALL.md#running-from-source), or by invoking a [locally cloned repo](INSTALL.md#method-2-run-from-source).
-For online usage, you will need to setup either a [GitHub App](INSTALL.md#method-5-run-as-a-github-app), or a [GitHub Action](INSTALL.md#method-3-run-as-a-github-action).
-GitHub App and GitHub Action also enable to run PR-Agent specific tool automatically when a new PR is opened.
-
-
-### git provider
-The [git_provider](pr_agent/settings/configuration.toml#L4) field in the configuration file determines the GIT provider that will be used by PR-Agent. Currently, the following providers are supported:
-`
-"github", "gitlab", "bitbucket", "azure", "codecommit", "local", "gerrit"
-`
-
-## Configuration Options
-
-The different tools and sub-tools used by CodiumAI PR-Agent are adjustable via the **[configuration file](pr_agent/settings/configuration.toml)**.
-
-In addition to general configuration options, each tool has its own configurations. For example, the `review` tool will use parameters from the [pr_reviewer](/pr_agent/settings/configuration.toml#L16) section in the configuration file.
-See the [Tools Guide](./docs/TOOLS_GUIDE.md) for a detailed description of the different tools and their configurations.
-
-There are three ways to set persistent configurations:
-1. Wiki configuration page 💎
-2. Local configuration file
-3. Global configuration file 💎
-
-In terms of precedence, wiki configurations will override local configurations, and local configurations will override global configurations.
-
-### Wiki configuration file 💎
-
-Specifically for GitHub, with PR-Agent-Pro you can set configurations by creating a page called `.pr_agent.toml` in the [wiki](https://github.com/Codium-ai/pr-agent/wiki/pr_agent.toml) of the repo. 
-The advantage of this method is that it allows to set configurations without needing to commit new content to the repo - just edit the wiki page and **save**.
-
-<kbd><img src="https://codium.ai/images/pr_agent/wiki_configuration.png" width="512"></kbd>
-
-Click [here](https://codium.ai/images/pr_agent/wiki_configuration_pr_agent.mp4) to see a short instructional video. We recommend surrounding the configuration content with triple-quotes, to allow better presentation when displayed in the wiki as markdown.
-An example content:
-
-\`\`\`<br>
-[pr_description] # /describe #<br>
-keep_original_user_title=false<br>
-\`\`\`
-
-PR-Agent will know to remove the triple-quotes when reading the configuration content.
-
-### Local configuration file
-
-By uploading a local `.pr_agent.toml` file to the root of the repo's main branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
-
-For example, if you set in `.pr_agent.toml`:
-
-```
-[pr_reviewer]
-extra_instructions="""\
-- instruction a
-- instruction b
-...
-"""
-```
-
-Then you can give a list of extra instructions to the `review` tool.
-
-
-### Global configuration file 💎
-
-If you create a repo called `pr-agent-settings` in your **organization**, it's configuration file `.pr_agent.toml` will be used as a global configuration file for any other repo that belongs to the same organization.
-Parameters from a local `.pr_agent.toml` file, in a specific repo, will override the global configuration parameters.
-
-For example, in the GitHub organization `Codium-ai`:
-- The repo [`https://github.com/Codium-ai/pr-agent-settings`](https://github.com/Codium-ai/pr-agent-settings/blob/main/.pr_agent.toml) contains a `.pr_agent.toml` file that serves as a global configuration file for all the repos in the GitHub organization `Codium-ai`.
-- The repo [`https://github.com/Codium-ai/pr-agent`](https://github.com/Codium-ai/pr-agent/blob/main/.pr_agent.toml) inherits the global configuration file from `pr-agent-settings`.
-
-
-## Managing mail notifications
-Unfortunately, it is not possible in GitHub to disable mail notifications from a specific user.
-If you are subscribed to notifications for a repo with PR-Agent, we recommend turning off notifications for PR comments, to avoid lengthy emails:
-
-<kbd><img src="https://codium.ai/images/pr_agent/notifications.png" width="512"></kbd>
-
-As an alternative, you can filter in your mail provider the notifications specifically from the PR-Agent bot:
-https://www.quora.com/How-can-you-filter-emails-for-specific-people-in-Gmail#:~:text=On%20the%20Filters%20and%20Blocked,the%20body%20of%20the%20email
-
-<kbd><img src="https://codium.ai/images/pr_agent/filter_mail_notifications.png" width="512"></kbd>
-
-## Usage Types
-
-### Working from a local repo (CLI)
-When running from your local repo (CLI), your local configuration file will be used.
-Examples of invoking the different tools via the CLI:
-
-- **Review**:       `python -m pr_agent.cli --pr_url=<pr_url>  review`
-- **Describe**:     `python -m pr_agent.cli --pr_url=<pr_url>  describe`
-- **Improve**:      `python -m pr_agent.cli --pr_url=<pr_url>  improve`
-- **Ask**:          `python -m pr_agent.cli --pr_url=<pr_url>  ask "Write me a poem about this PR"`
-- **Reflect**:      `python -m pr_agent.cli --pr_url=<pr_url>  reflect`
-- **Update Changelog**:      `python -m pr_agent.cli --pr_url=<pr_url>  update_changelog`
-
-`<pr_url>` is the url of the relevant PR (for example: https://github.com/Codium-ai/pr-agent/pull/50).
-
-**Notes:**
-
-(1) in addition to editing your local configuration file, you can also change any configuration value by adding it to the command line:
-```
-python -m pr_agent.cli --pr_url=<pr_url>  /review --pr_reviewer.extra_instructions="focus on the file: ..."
-```
-
-(2) You can print results locally, without publishing them, by setting in `configuration.toml`:
-```
-[config]
-publish_output=false
-verbosity_level=2
-```
-This is useful for debugging or experimenting with different tools.
-
-
-### Online usage
-
-Online usage means invoking PR-Agent tools by [comments](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021901) on a PR.
-Commands for invoking the different tools via comments:
-
-- **Review**:       `/review`
-- **Describe**:     `/describe`
-- **Improve**:      `/improve`
-- **Ask**:          `/ask "..."`
-- **Reflect**:      `/reflect`
-- **Update Changelog**:      `/update_changelog`
-
-
-To edit a specific configuration value, just add `--config_path=<value>` to any command.
-For example, if you want to edit the `review` tool configurations, you can run:
-```
-/review --pr_reviewer.extra_instructions="..." --pr_reviewer.require_score_review=false
-```
-Any configuration value in [configuration file](pr_agent/settings/configuration.toml) file can be similarly edited. Comment `/config` to see the list of available configurations.
-
-
-### Working with GitHub App
-
-#### GitHub app automatic tools when a new PR is opened
-
-The [github_app](pr_agent/settings/configuration.toml#L108) section defines GitHub app specific configurations.  
-
-The configuration parameter `pr_commands` defines the list of tools that will be **run automatically** when a new PR is opened.
-```
-[github_app]
-pr_commands = [
-    "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
-    "/review --pr_reviewer.num_code_suggestions=0",
-    "/improve",
-]
-```
-This means that when a new PR is opened/reopened or marked as ready for review, PR-Agent will run the `describe`, `review` and `improve` tools.  
-For the `describe` tool, for example, the `add_original_user_description` and `keep_original_user_title` parameters will be set to true.
-
-You can override the default tool parameters by using one the three options for a [configuration file](#configuration-options): **wiki**, **local**, or **global**. 
-For example, if your local `.pr_agent.toml` file contains:
-```
-[pr_description]
-add_original_user_description = false
-keep_original_user_title = false
-```
-When a new PR is opened, PR-Agent will run the `describe` tool with the above parameters.
-
-To cancel the automatic run of all the tools, set:
-```
-[github_app]
-handle_pr_actions = []
-```
-
-You can also disable automatic runs for PRs with specific titles, by setting the `ignore_pr_titles` parameter with the relevant regex. For example:
-```
-[github_app]
-ignore_pr_title = ["^[Auto]", ".*ignore.*"]
-```
-will ignore PRs with titles that start with "Auto" or contain the word "ignore".
-
-#### GitHub app automatic tools for push actions (commits to an open PR)
-
-In addition to running automatic tools when a PR is opened, the GitHub app can also respond to new code that is pushed to an open PR.
-
-The configuration toggle `handle_push_trigger` can be used to enable this feature.  
-The configuration parameter `push_commands` defines the list of tools that will be **run automatically** when new code is pushed to the PR.
-```
-[github_app]
-handle_push_trigger = true
-push_commands = [
-    "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
-    "/review  --pr_reviewer.num_code_suggestions=0",
-]
-```
-This means that when new code is pushed to the PR, the PR-Agent will run the `describe` and `review` tools, with the specified parameters.
-
-### Working with GitHub Action
-`GitHub Action` is a different way to trigger PR-Agent tools, and uses a different configuration mechanism than `GitHub App`.
-You can configure settings for `GitHub Action` by adding environment variables under the env section in `.github/workflows/pr_agent.yml` file. 
-Specifically, start by setting the following environment variables:
-```yaml
-      env:
-        OPENAI_KEY: ${{ secrets.OPENAI_KEY }} # Make sure to add your OpenAI key to your repo secrets
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Make sure to add your GitHub token to your repo secrets
-        github_action_config.auto_review: "true" # enable\disable auto review
-        github_action_config.auto_describe: "true" # enable\disable auto describe
-        github_action_config.auto_improve: "true" # enable\disable auto improve
-```
-`github_action_config.auto_review`, `github_action_config.auto_describe` and `github_action_config.auto_improve` are used to enable/disable automatic tools that run when a new PR is opened.
-If not set, the default configuration is for all three tools to run automatically when a new PR is opened.
-
-Note that you can give additional config parameters by adding environment variables to `.github/workflows/pr_agent.yml`, or by using a `.pr_agent.toml` file in the root of your repo, similar to the GitHub App usage.
-
-For example, you can set an environment variable: `pr_description.add_original_user_description=false`, or add a `.pr_agent.toml` file with the following content:
-```
-[pr_description]
-add_original_user_description = false
-```
-
-### Working with GitLab Webhook
-After setting up a GitLab webhook, to control which commands will run automatically when a new PR is opened, you can set the `pr_commands` parameter in the configuration file, similar to the GitHub App:
-```
-[gitlab]
-pr_commands = [
-    "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
-    "/review --pr_reviewer.num_code_suggestions=0",
-    "/improve",
-]
-```
-
-### Working with BitBucket Self-Hosted App
-Similar to GitHub app, when running PR-Agent from BitBucket App, the default [configuration file](pr_agent/settings/configuration.toml) from a pre-built docker will be initially loaded.
-
-By uploading a local `.pr_agent.toml` file to the root of the repo's main branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
-
-For example, if your local `.pr_agent.toml` file contains:
-```
-[pr_reviewer]
-inline_code_comments = true
-```
-
-Each time you invoke a `/review` tool, it will use inline code comments.
-
-#### BitBucket Self-Hosted App automatic tools
-You can configure in your local `.pr_agent.toml` file which tools will **run automatically** when a new PR is opened.
-
-Specifically, set the following values:
-```yaml
-[bitbucket_app]
-auto_review = true    # set as config var in .pr_agent.toml
-auto_describe = true  # set as config var in .pr_agent.toml
-auto_improve = true   # set as config var in .pr_agent.toml
-```
-
-`bitbucket_app.auto_review`, `bitbucket_app.auto_describe` and `bitbucket_app.auto_improve` are used to enable/disable automatic tools.
-If not set, the default option is that only the `review` tool will run automatically when a new PR is opened.
-
-Note that due to limitations of the bitbucket platform, the `auto_describe` tool will be able to publish a PR description only as a comment. 
-In addition, some subsections like `PR changes walkthrough` will not appear, since they require the usage of collapsible sections, which are not supported by bitbucket.
-
-### Azure DevOps provider
-
-To use Azure DevOps provider use the following settings in configuration.toml:
-```
-[config]
-git_provider="azure"
-use_repo_settings_file=false
-```
-
-Azure DevOps provider supports [PAT token](https://learn.microsoft.com/en-us/azure/devops/organizations/accounts/use-personal-access-tokens-to-authenticate?view=azure-devops&tabs=Windows) or [DefaultAzureCredential](https://learn.microsoft.com/en-us/azure/developer/python/sdk/authentication-overview#authentication-in-server-environments) authentication.
-PAT is faster to create, but has build in experation date, and will use the user identity for API calls. 
-Using DefaultAzureCredential you can use managed identity or Service principle, which are more secure and will create seperate ADO user identity (via AAD) to the agent.
-
-If PAT was choosen, you can assign the value in .secrets.toml. 
-If DefaultAzureCredential was choosen, you can assigned the additional env vars like AZURE_CLIENT_SECRET directly, 
-or use managed identity/az cli (for local develpment) without any additional configuration.
-in any case, 'org' value must be assigned in .secrets.toml:
-```
-[azure_devops]
-org = "https://dev.azure.com/YOUR_ORGANIZATION/"
-# pat = "YOUR_PAT_TOKEN" needed only if using PAT for authentication
-```
-
-##### Azure DevOps Webhook
-To trigger from an Azure webhook, you need to manually [add a webhook](https://learn.microsoft.com/en-us/azure/devops/service-hooks/services/webhooks?view=azure-devops). 
-Use the "Pull request created" type to trigger a review, or "Pull request commented on" to trigger any supported comment with /<command> <args> comment on the relevant PR. Note that for the "Pull request commented on" trigger, only API v2.0 is supported.
-
-To control which commands will run automatically when a new PR is opened, you can set the `pr_commands` parameter in the configuration file, similar to the GitHub App:
-```
-[azure_devops_server]
-pr_commands = [
-    "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
-    "/review --pr_reviewer.num_code_suggestions=0",
-    "/improve",
-]
-```
-
-For webhook security, create a sporadic username/password pair and configure the webhook username and password on both the server and Azure DevOps webhook. These will be sent as basic Auth data by the webhook with each request:
-```
-[azure_devops_server]
-webhook_username = "<basic auth user>"
-webhook_password = "<basic auth password>"
-```
-> :warning: **Ensure that the webhook endpoint is only accessible over HTTPS** to mitigate the risk of credential interception when using basic authentication.
-
-
-## Appendix - additional configurations walkthrough
-
-
-#### Ignoring files from analysis
-In some cases, you may want to exclude specific files or directories from the analysis performed by CodiumAI PR-Agent. This can be useful, for example, when you have files that are generated automatically or files that shouldn't be reviewed, like vendored code.
-
-To ignore files or directories, edit the **[ignore.toml](/pr_agent/settings/ignore.toml)** configuration file. This setting also exposes the following environment variables:
-
- - `IGNORE.GLOB`
- - `IGNORE.REGEX`
-
-For example, to ignore python files in a PR with online usage, comment on a PR:
-`/review --ignore.glob=['*.py']`
-
-To ignore python files in all PRs, set in a configuration file:
-```
-[ignore]
-glob = ['*.py']
-```
-
-#### Extra instructions
-All PR-Agent tools have a parameter called `extra_instructions`, that enables to add free-text extra instructions. Example usage:
-```
-/update_changelog --pr_update_changelog.extra_instructions="Make sure to update also the version ..."
-```
-
-#### Working with large PRs
-
-The default mode of CodiumAI is to have a single call per tool, using GPT-4, which has a token limit of 8000 tokens.
-This mode provide a very good speed-quality-cost tradeoff, and can handle most PRs successfully.
-When the PR is above the token limit, it employs a [PR Compression strategy](./PR_COMPRESSION.md).
-
-However, for very large PRs, or in case you want to emphasize quality over speed and cost, there are 2 possible solutions:
-1) [Use a model](#changing-a-model) with larger context, like GPT-32K, or claude-100K. This solution will be applicable for all the tools.
-2) For the `/improve` tool, there is an ['extended' mode](./docs/IMPROVE.md) (`/improve --extended`),
-which divides the PR to chunks, and process each chunk separately. With this mode, regardless of the model, no compression will be done (but for large PRs, multiple model calls may occur)
-
-
-#### Changing a model
-
-See [here](pr_agent/algo/__init__.py) for the list of available models.
-To use a different model than the default (GPT-4), you need to edit [configuration file](pr_agent/settings/configuration.toml#L2).
-For models and environments not from OPENAI, you might need to provide additional keys and other parameters. See below for instructions.
-
-##### Azure
-To use Azure, set in your `.secrets.toml` (working from CLI), or in the GitHub `Settings > Secrets and variables` (working from GitHub App or GitHub Action):
-```
-[openai]
-key = "" # your azure api key
-api_type = "azure"
-api_version = '2023-05-15'  # Check Azure documentation for the current API version
-api_base = ""  # The base URL for your Azure OpenAI resource. e.g. "https://<your resource name>.openai.azure.com"
-deployment_id = ""  # The deployment name you chose when you deployed the engine
-```
-
-and set in your configuration file:
-```
-[config]
-model="" # the OpenAI model you've deployed on Azure (e.g. gpt-3.5-turbo)
-```
-
-##### Huggingface
-
-**Local**
-You can run Huggingface models locally through either [VLLM](https://docs.litellm.ai/docs/providers/vllm) or [Ollama](https://docs.litellm.ai/docs/providers/ollama)
-
-E.g. to use a new Huggingface model locally via Ollama, set:
-```
-[__init__.py]
-MAX_TOKENS = {
-    "model-name-on-ollama": <max_tokens>
-}
-e.g.
-MAX_TOKENS={
-    ...,
-    "ollama/llama2": 4096
-}
-
-
-[config] # in configuration.toml
-model = "ollama/llama2"
-
-[ollama] # in .secrets.toml
-api_base = ... # the base url for your huggingface inference endpoint
-# e.g. if running Ollama locally, you may use:
-api_base = "http://localhost:11434/"
-```
-
-**Inference Endpoints**
-
-To use a new model with Huggingface Inference Endpoints, for example, set:
-```
-[__init__.py]
-MAX_TOKENS = {
-    "model-name-on-huggingface": <max_tokens>
-}
-e.g.
-MAX_TOKENS={
-    ...,
-    "meta-llama/Llama-2-7b-chat-hf": 4096
-}
-[config] # in configuration.toml
-model = "huggingface/meta-llama/Llama-2-7b-chat-hf"
-
-[huggingface] # in .secrets.toml
-key = ... # your huggingface api key
-api_base = ... # the base url for your huggingface inference endpoint
-```
-(you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
-
-##### Replicate
-
-To use Llama2 model with Replicate, for example, set:
-```
-[config] # in configuration.toml
-model = "replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"
-[replicate] # in .secrets.toml
-key = ...
-```
-(you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
-
-
-Also review the [AiHandler](pr_agent/algo/ai_handler.py) file for instruction how to set keys for other models.
-
-##### Vertex AI
-
-To use Google's Vertex AI platform and its associated models (chat-bison/codechat-bison) set:
-
-``` 
-[config] # in configuration.toml
-model = "vertex_ai/codechat-bison"
-fallback_models="vertex_ai/codechat-bison"
-
-[vertexai] # in .secrets.toml
-vertex_project = "my-google-cloud-project"
-vertex_location = ""
-```
-
-Your [application default credentials](https://cloud.google.com/docs/authentication/application-default-credentials) will be used for authentication so there is no need to set explicit credentials in most environments.
-
-If you do want to set explicit credentials then you can use the `GOOGLE_APPLICATION_CREDENTIALS` environment variable set to a path to a json credentials file.
-
-##### Amazon Bedrock
-
-To use Amazon Bedrock and its foundational models, add the below configuration:
-
-``` 
-[config] # in configuration.toml
-model = "anthropic.claude-v2"
-fallback_models="anthropic.claude-instant-v1"
-
-[aws] # in .secrets.toml
-bedrock_region = "us-east-1"
-```
-
-Note that you have to add access to foundational models before using them. Please refer to [this document](https://docs.aws.amazon.com/bedrock/latest/userguide/setting-up.html) for more details.
-
-AWS session is automatically authenticated from your environment, but you can also explicitly set `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` environment variables.
-
-
-#### Patch Extra Lines
-By default, around any change in your PR, git patch provides 3 lines of context above and below the change.
-```
-@@ -12,5 +12,5 @@ def func1():
- code line that already existed in the file...
- code line that already existed in the file...
- code line that already existed in the file....
--code line that was removed in the PR
-+new code line added in the PR
- code line that already existed in the file...
- code line that already existed in the file...
- code line that already existed in the file...
-```
-
-For the `review`, `describe`, `ask` and `add_docs` tools, if the token budget allows, PR-Agent tries to increase the number of lines of context, via the parameter:
-```
-[config]
-patch_extra_lines=3
-```
-
-Increasing this number provides more context to the model, but will also increase the token budget.
-If the PR is too large (see [PR Compression strategy](./PR_COMPRESSION.md)), PR-Agent automatically sets this number to 0, using the original git patch.
-
-
-#### Editing the prompts
-The prompts for the various PR-Agent tools are defined in the `pr_agent/settings` folder.
-In practice, the prompts are loaded and stored as a standard setting object.
-Hence, editing them is similar to editing any other configuration value - just place the relevant key in `.pr_agent.toml`file, and override the default value.
-
-For example, if you want to edit the prompts of the [describe](./pr_agent/settings/pr_description_prompts.toml) tool, you can add the following to your `.pr_agent.toml` file:
-```
-[pr_description_prompt]
-system="""
-...
-"""
-user="""
-...
-"""
-```
-Note that the new prompt will need to generate an output compatible with the relevant [post-process function](./pr_agent/tools/pr_description.py#L137).

docker/Dockerfile

@@ -8,7 +8,7 @@ ENV PYTHONPATH=/app
 
 FROM base as github_app
 ADD pr_agent pr_agent
-CMD ["python", "pr_agent/servers/github_app.py"]
+CMD ["python", "-m", "gunicorn", "-k", "uvicorn.workers.UvicornWorker", "-c", "pr_agent/servers/gunicorn_config.py", "--forwarded-allow-ips", "*", "pr_agent.servers.github_app:app"]
 
 FROM base as bitbucket_app
 ADD pr_agent pr_agent

docker/Dockerfile.lambda

@@ -1,10 +1,10 @@
 FROM public.ecr.aws/lambda/python:3.10
 
 RUN yum update -y && \
-    yum install -y gcc python3-devel && \
+    yum install -y gcc python3-devel git && \
     yum clean all
 
-ADD pyproject.toml .
+ADD pyproject.toml requirements.txt .
 RUN pip install . && rm pyproject.toml
 RUN pip install mangum==0.17.0
 COPY pr_agent/ ${LAMBDA_TASK_ROOT}/pr_agent/

docs/ADD_DOCUMENTATION.md

@@ -1,24 +0,0 @@
-# Add Documentation Tool 💎
-The `add_docs` tool scans the PR code changes, and automatically suggests documentation for any code components that changed in the PR (functions, classes, etc.).
-
-It can be invoked manually by commenting on any PR:
-```
-/add_docs
-```
-For example:
-
-<kbd><img src=https://codium.ai/images/pr_agent/docs_command.png width="768"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/docs_components.png width="768"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/docs_single_component.png width="768"></kbd>
-
-### Configuration options
- - `docs_style`: The exact style of the documentation (for python docstring). you can choose between: `google`, `numpy`, `sphinx`, `restructuredtext`, `plain`. Default is `sphinx`.
- - `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
-
-Notes 
-- Language that are currently fully supported: Python, Java, C++, JavaScript, TypeScript.
-- For languages that are not fully supported, the tool will suggest documentation only for new components in the PR.
-- A previous version of the tool, that offered support only for new components, was deprecated.
-

docs/ASK.md

@@ -1,24 +0,0 @@
-# ASK Tool
-
-The `ask` tool answers questions about the PR, based on the PR code changes. Make sure to be specific and clear in your questions.
-It can be invoked manually by commenting on any PR:
-```
-/ask "..."
-```
-For example:
-___
-<kbd><img src="https://codium.ai/images/pr_agent/ask_comment.png" width="768"></kbd>
-___
-<kbd><img src="https://codium.ai/images/pr_agent/ask.png" width="768"></kbd>
-___
-
-## Ask lines
-You can run `/ask` on specific lines of code in the PR from the PR's diff view. The tool will answer questions based on the code changes in the selected lines.
-- Click on the '+' sign next to the line number to select the line.
-- To select multiple lines, click on the '+' sign of the first line and then hold and drag to select the rest of the lines. 
-- write `/ask "..."` in the comment box and press `Add single comment` button.
-
-<kbd><img src="https://codium.ai/images/pr_agent/Ask_line.png" width="768"></kbd>
-
-
-Note that the tool does not have "memory" of previous questions, and answers each question independently.

docs/Analyze.md

@@ -1,21 +0,0 @@
-# Analyze Tool 💎
-The `analyze` tool combines static code analysis with LLM capabilities to provide a comprehensive analysis of the PR code changes.
-
-The tool scans the PR code changes, find the code components (methods, functions, classes) that changed, and summarizes the changes in each component.
-
-It can be invoked manually by commenting on any PR:
-```
-/analyze
-```
-
-An example [result](https://github.com/Codium-ai/pr-agent/pull/546#issuecomment-1868524805):
-
-<kbd><img src=https://codium.ai/images/pr_agent/analyze_1.png width="768"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/analyze_2.png width="768"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/analyze_3.png width="768"></kbd>
-
-
-Notes 
-- Language that are currently supported: Python, Java, C++, JavaScript, TypeScript.

docs/CUSTOM_SUGGESTIONS.md

@@ -1,65 +0,0 @@
-# Custom Suggestions Tool 💎
-
-## Table of Contents
-- [Overview](#overview)
-- [Example usage](#example-usage)
-- [Configuration options](#configuration-options)
-
-
-## Overview
-The `custom_suggestions` tool scans the PR code changes, and automatically generates custom suggestions for improving the PR code.
-It shares similarities with the `improve` tool, but with one main difference: the `custom_suggestions` tool will only propose suggestions that follow specific guidelines defined by the prompt in: `pr_custom_suggestions.prompt` configuration.
-
-The tool can be triggered [automatically](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools) every time a new PR is opened, or can be invoked manually by commenting on a PR.
-
-When commenting, use the following template:
-
-```
-/custom_suggestions --pr_custom_suggestions.prompt="The suggestions should focus only on the following:\n-...\n-...\n-..."
-```
-
-With a [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-app), use the following template:
-
-```
-[pr_custom_suggestions]
-prompt="""\
-The suggestions should focus only on the following:
--...
--...
--...
-"""
-```
-Using a configuration file is recommended, since it allows to use multi-line instructions.
-
-Don't forget - with this tool, you are the prompter. Be specific, clear, and concise in the instructions. Specify relevant aspects that you want the model to focus on. \
-You might benefit from several trial-and-error iterations, until you get the correct prompt for your use case.
-
-## Example usage
-
-Here is an example of a possible prompt:
-```
-[pr_custom_suggestions]
-prompt="""\
-The suggestions should focus only on the following:
-- look for edge cases when implementing a new function
-- make sure every variable has a meaningful name
-- make sure the code is efficient
-"""
-```     
-
-The instructions above are just an example. We want to emphasize that the prompt should be specific and clear, and be tailored to the needs of your project.
-
-Results obtained with the prompt above:
-___
-<kbd><img src=https://codium.ai/images/pr_agent/custom_suggestions_prompt.png width="512"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/custom_suggestions_result.png width="768"></kbd>
-___
-
-## Configuration options
-
-`prompt`: the prompt for the tool. It should be a multi-line string.
-
-`num_code_suggestions`: number of code suggestions provided by the 'custom_suggestions' tool. Default is 4.
-
-`enable_help_text`: if set to true, the tool will display a help text in the comment. Default is true.

docs/DESCRIBE.md

@@ -1,163 +0,0 @@
-# Describe Tool
-## Table of Contents
-- [Overview](#overview)
-  - [Configuration options](#configuration-options)
-  - [Inline file summary 💎](#inline-file-summary-)
-  - [Handle custom labels from the Repo's labels page :gem:](#handle-custom-labels-from-the-repos-labels-page-gem)
-  - [Markers template](#markers-template)
-- [Usage Tips](#usage-tips)
-  - [Automation](#automation)
-  - [Custom labels](#custom-labels)
-
-## Overview
-The `describe` tool scans the PR code changes, and generates a description for the PR - title, type, summary, walkthrough and labels.
-
-The tool can be triggered automatically every time a new PR is [opened](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools), or it can be invoked manually by commenting on any PR:
-```
-/describe
-```
-For example:
-___
-<kbd><img src=https://codium.ai/images/pr_agent/describe_comment.png width="768"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/describe_new.png width="768"></kbd>
-___
-  
-### Configuration options
-To edit [configurations](./../pr_agent/settings/configuration.toml#L46) related to the describe tool (`pr_description` section), use the following template:
-```
-/describe --pr_description.some_config1=... --pr_description.some_config2=...
-```
-
-**Possible configurations:**
-- `publish_labels`: if set to true, the tool will publish the labels to the PR. Default is true.
-
-- `publish_description_as_comment`: if set to true, the tool will publish the description as a comment to the PR. If false, it will overwrite the origianl description. Default is false.
-
-- `add_original_user_description`: if set to true, the tool will add the original user description to the generated description. Default is true.
-
-- `keep_original_user_title`: if set to true, the tool will keep the original PR title, and won't change it. Default is true.
-
-- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
-
-- To enable `custom labels`, apply the configuration changes described [here](./GENERATE_CUSTOM_LABELS.md#configuration-changes)
-
-- `enable_pr_type`: if set to false, it will not show the `PR type` as a text value in the description content. Default is true.
-
-- `final_update_message`: if set to true, it will add a comment message [`PR Description updated to latest commit...`](https://github.com/Codium-ai/pr-agent/pull/499#issuecomment-1837412176) after finishing calling `/describe`. Default is true.
-
-- `enable_semantic_files_types`: if set to true, "Changes walkthrough" section will be generated. Default is true.
-- `collapsible_file_list`: if set to true, the file list in the "Changes walkthrough" section will be collapsible. If set to "adaptive", the file list will be collapsible only if there are more than 8 files. Default is "adaptive".
-  
-### Inline file summary 💎
-> This feature is available only in PR-Agent Pro
-
-This feature will enable you to quickly understand the changes in each file while reviewing the code changes (diff view).
-
-To add the walkthrough table to the "Files changed" tab, you can click on the checkbox that appears PR Description status message below the main PR Description:
-
-<kbd><img src=https://codium.ai/images/pr_agent/add_table_checkbox.png width="512"></kbd>
-
-If you prefer to have the file summaries appear in the "Files changed" tab on every PR, change the `pr_description.inline_file_summary` parameter in the configuration file, possible values are:
-
-- `'table'`: File changes walkthrough table will be displayed on the top of the "Files changed" tab, in addition to the "Conversation" tab.
-<kbd><img src=https://codium.ai/images/pr_agent/diffview-table.png width="768"></kbd>
-
-- `true`: A collapsable file comment with changes title and a changes summary for each file in the PR.
-<kbd><img src=https://codium.ai/images/pr_agent/diffview_changes.png width="768"></kbd>
-
-- `false` (`default`): File changes walkthrough will be added only to the "Conversation" tab.
-
-Note that this feature is currently available only for GitHub.
-
-
-### Handle custom labels from the Repo's labels page :gem:
-> This feature is available only in PR-Agent Pro 
-
-You can control  the custom labels that will be suggested by the `describe` tool, from the repo's labels page:
-
-* GitHub : go to `https://github.com/{owner}/{repo}/labels` (or click on the "Labels" tab in the issues or PRs page)
-* GitLab : go to `https://gitlab.com/{owner}/{repo}/-/labels` (or click on "Manage" -> "Labels" on the left menu)
-
-Now add/edit the custom labels. they should be formatted as follows:
-* Label name: The name of the custom label.
-* Description: Start the description of with prefix `pr_agent:`, for example: `pr_agent: Description of when AI should suggest this label`.<br>
-
-The description should be comprehensive and detailed, indicating when to add the desired label. For example:
-<kbd><img src=https://codium.ai/images/pr_agent/add_native_custom_labels.png width="880"></kbd>
-
-
-### Markers template
-To enable markers, set `pr_description.use_description_markers=true`.
-Markers enable to easily integrate user's content and auto-generated content, with a template-like mechanism.
-
-For example, if the PR original description was:
-```
-User content...
-
-## PR Type:
-pr_agent:type
-
-## PR Description:
-pr_agent:summary
-
-## PR Walkthrough:
-pr_agent:walkthrough
-```
-The marker `pr_agent:type` will be replaced with the PR type, `pr_agent:summary` will be replaced with the PR summary, and `pr_agent:walkthrough` will be replaced with the PR walkthrough.
-
-<kbd><img src=https://codium.ai/images/pr_agent/describe_markers_before.png width="768"></kbd>
-
-==>
-
-<kbd><img src=https://codium.ai/images/pr_agent/describe_markers_after.png width="768"></kbd>
-
-**Configuration params:**
-
-- `use_description_markers`: if set to true, the tool will use markers template. It replaces every marker of the form `pr_agent:marker_name` with the relevant content. Default is false.
-- `include_generated_by_header`: if set to true, the tool will add a dedicated header: 'Generated by PR Agent at ...' to any automatic content. Default is true.
-
-
-## Usage Tips
-1)  [Automation](#automation)
-2) [Custom labels](#custom-labels)
-### Automation
-- When you first install the app, the [default mode](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools) for the describe tool is:
-```
-pr_commands = ["/describe --pr_description.add_original_user_description=true" 
-                         "--pr_description.keep_original_user_title=true", ...]
-```
-meaning the `describe` tool will run automatically on every PR, will keep the original title, and will add the original user description above the generated description. 
-<br> This default settings aim to strike a good balance between automation and control:
-If you want more automation, just give the PR a title, and the tool will auto-write a full description; If you want more control, you can add a detailed description, and the tool will add the complementary description below it.
-- For maximal automation, you can change the default mode to:
-```
-pr_commands = ["/describe --pr_description.add_original_user_description=false" 
-                         "--pr_description.keep_original_user_title=true", ...]
-```
-so the title will be auto-generated as well.
-- Markers are an alternative way to control the generated description, to give maximal control to the user. If you set:
-```
-pr_commands = ["/describe --pr_description.use_description_markers=true", ...]
-```
-the tool will replace every marker of the form `pr_agent:marker_name` in the PR description with the relevant content, where `marker_name` is one of the following:
-  - `type`: the PR type.
-  - `summary`: the PR summary.
-  - `walkthrough`: the PR walkthrough.
-
-Note that when markers are enabled, if the original PR description does not contain any markers, the tool will not alter the description at all.
-
-### Custom labels
-The default labels of the describe tool are quite generic, since they are meant to be used in any repo: [`Bug fix`, `Tests`, `Enhancement`, `Documentation`, `Other`].
-
-If you specify [custom labels](#handle-custom-labels-from-the-repos-labels-page-gem) in the repo's labels page, you can get tailored labels for your use cases.
-Examples for custom labels:
-- `Main topic:performance` -  pr_agent:The main topic of this PR is performance
-- `New endpoint` -  pr_agent:A new endpoint was added in this PR
-- `SQL query` -  pr_agent:A new SQL query was added in this PR
-- `Dockerfile changes` - pr_agent:The PR contains changes in the Dockerfile
-- ...
-
-The list above is eclectic, and aims to give an idea of different possibilities. Define custom labels that are relevant for your repo and use cases.
-Note that Labels are not mutually exclusive, so you can add multiple label categories.
-<br>Make sure to provide proper title, and a detailed and well-phrased description for each label, so the tool will know when to suggest it.

docs/Full_environments.md

@@ -1,27 +0,0 @@
-## Overview
-`PR-Agent` offers extensive pull request functionalities across various git providers:
-|       |                                             | GitHub | Gitlab | Bitbucket | CodeCommit | Azure DevOps | Gerrit |
-|-------|---------------------------------------------|:------:|:------:|:---------:|:----------:|:----------:|:----------:|
-| TOOLS | Review                                      |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:    |
-|       | ⮑ Incremental                              |   :white_check_mark:    |       |           |       |          |     |
-|       | Ask                                         |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:          |   :white_check_mark:          | :white_check_mark: |  :white_check_mark:    |
-|       | Auto-Description                            |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:        |   :white_check_mark:    |   :white_check_mark:    | :white_check_mark:    |
-|       | Improve Code                                |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:        |   :white_check_mark:    |          |    :white_check_mark:    |
-|       | ⮑ Extended                             |   :white_check_mark:    |   :white_check_mark:    |        :white_check_mark:   |   :white_check_mark:    |          | :white_check_mark:    |
-|       | Reflect and Review                          |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:        |          |   :white_check_mark:    |    :white_check_mark:    |
-|       | Update CHANGELOG.md                         |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:        |   :white_check_mark:    |          |       |
-|       | Find similar issue                          |   :white_check_mark:    |                         |                             |          |          |       |
-|       | Add Documentation                           |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:        |   :white_check_mark:    |          |    :white_check_mark:    |
-|       | Generate Custom Labels 💎                   |   :white_check_mark:    |   :white_check_mark:    |         |     |          |      |
-|       |                                             |        |        |      |      |      |
-| USAGE | CLI                                         |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |   :white_check_mark:    |   :white_check_mark:    |
-|       | App / webhook                               |   :white_check_mark:    |   :white_check_mark:    |           |         |      :white_check_mark:     |
-|       | Tagging bot                                 |   :white_check_mark:    |        |           |          |          |
-|       | Actions                                     |   :white_check_mark:    |        |           |          |          |
-|       | Web server                                  |       |        |           |          |          |  :white_check_mark:   |
-|       |                                             |        |        |      |      |      |
-| CORE  | PR compression                              |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       | :white_check_mark: |   :white_check_mark:       | :white_check_mark:       |
-|       | Repo language prioritization                |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       | :white_check_mark: |   :white_check_mark:       | :white_check_mark:       |
-|       | Adaptive and token-aware<br />file patch fitting |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       | :white_check_mark: |   :white_check_mark:       | :white_check_mark:       |
-|       | Multiple models support |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       | :white_check_mark: |   :white_check_mark:       | :white_check_mark:       |
-|       | Incremental PR Review |   :white_check_mark:    |      |      |      |      |      |

docs/IMPROVE.md

@@ -1,97 +0,0 @@
-# Improve Tool
-
-## Table of Contents
-- [Overview](#overview)
-  - [Configuration options](#configuration-options)
-- [Usage Tips](#usage-tips)
-    - [Extra instructions](#extra-instructions)
-    - [PR footprint - regular vs summarize mode](#pr-footprint---regular-vs-summarize-mode)
-    - [A note on code suggestions quality](#a-note-on-code-suggestions-quality)
-
-## Overview
-The `improve` tool scans the PR code changes, and automatically generates suggestions for improving the PR code.
-The tool can be triggered automatically every time a new PR is [opened](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools), or it can be invoked manually by commenting on any PR:
-```
-/improve
-```
-
-### Summarized vs committable code suggestions
-
-The code suggestions can be presented as a single comment (via `pr_code_suggestions.summarize=true`):
-___
-<kbd><img src=https://codium.ai/images/pr_agent/code_suggestions_as_comment.png width="768"></kbd>
-___
-
-Or as a separate commitable code comment for each suggestion:
-___
-<kbd><img src=https://codium.ai/images/pr_agent/improve.png width="768"></kbd>
-
----
-Note that a single comment has a significantly smaller PR footprint. We recommend this mode for most cases.
-Also note that collapsible are not supported in _Bitbucket_. Hence, the suggestions are presented there as code comments.
-
-### Extended mode
-
-An extended mode, which does not involve PR Compression and provides more comprehensive suggestions, can be invoked by commenting on any PR:
-```
-/improve --extended
-```
-
-or by setting:
-```
-[pr_code_suggestions]
-auto_extended_mode=true
-```
-(True by default).
-
-Note that the extended mode divides the PR code changes into chunks, up to the token limits, where each chunk is handled separately (might use multiple calls to GPT-4 for large PRs).
-Hence, the total number of suggestions is proportional to the number of chunks, i.e., the size of the PR.
-
-### Configuration options
-
-To edit [configurations](./../pr_agent/settings/configuration.toml#L66) related to the improve tool (`pr_code_suggestions` section), use the following template:
-```
-/improve --pr_code_suggestions.some_config1=... --pr_code_suggestions.some_config2=...
-```
-
-#### General options
-- `num_code_suggestions`: number of code suggestions provided by the 'improve' tool. Default is 4.
-- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
-- `rank_suggestions`: if set to true, the tool will rank the suggestions, based on importance. Default is false.
-- `summarize`: if set to true, the tool will display the suggestions in a single comment. Default is false.
-- `enable_help_text`: if set to true, the tool will display a help text in the comment. Default is true.
-#### params for '/improve --extended' mode
-- `auto_extended_mode`: enable extended mode automatically (no need for the `--extended` option). Default is true.
-- `num_code_suggestions_per_chunk`: number of code suggestions provided by the 'improve' tool, per chunk. Default is 8.
-- `rank_extended_suggestions`: if set to true, the tool will rank the suggestions, based on importance. Default is true.
-- `max_number_of_calls`: maximum number of chunks. Default is 5.
-- `final_clip_factor`: factor to remove suggestions with low confidence. Default is 0.9.
-
-
-## Usage Tips
-
-### Extra instructions
-Extra instructions are very important for the `imrpove` tool, since they enable you to guide the model to suggestions that are more relevant to the specific needs of the project.
-
-Be specific, clear, and concise in the instructions. With extra instructions, you are the prompter. Specify relevant aspects that you want the model to focus on.
-
-Examples for extra instructions:
-```
-[pr_code_suggestions] # /improve #
-extra_instructions="""
-Emphasize the following aspects:
-- Does the code logic cover relevant edge cases?
-- Is the code logic clear and easy to understand?
-- Is the code logic efficient?
-...
-"""
-```
-Use triple quotes to write multi-line instructions. Use bullet points to make the instructions more readable.
-
-### A note on code suggestions quality
-
-- While the current AI for code is getting better and better (GPT-4), it's not flawless. Not all the suggestions will be perfect, and a user should not accept all of them automatically.
-- Suggestions are not meant to be [simplistic](./../pr_agent/settings/pr_code_suggestions_prompts.toml#L34). Instead, they aim to give deep feedback and raise questions, ideas and thoughts to the user, who can then use his judgment, experience, and understanding of the code base.
-- Recommended to use the `exra_instructions` field to guide the model to suggestions that are more relevant to the specific needs of the project.
-- Consider also trying the [Custom Suggestions Tool](https://github.com/Codium-ai/pr-agent/blob/main/docs/CUSTOM_SUGGESTIONS.md) 💎, that will **only** propose suggestions that follow specific guidelines defined by user.
-

docs/README.md

@@ -0,0 +1 @@
+# [Visit Our Docs Portal](https://pr-agent-docs.codium.ai/)

docs/REVIEW.md

@@ -1,176 +0,0 @@
-# Review Tool
-
-## Table of Contents
-- [Overview](#overview)
-  - [Configuration options](#configuration-options)
-  - [Incremental Mode](#incremental-mode)
-  - [PR Reflection](#pr-reflection)
-- [Usage Tips](#usage-tips)
-  - [General guidelines](#general-guidelines)
-  - [Code suggestions](#code-suggestions)
-  - [Automation](#automation)
-  - [Auto-labels](#auto-labels)
-  - [Extra instructions](#extra-instructions)
-  - [Auto-approval](#auto-approval-1)
-
-## Overview
-The `review` tool scans the PR code changes, and automatically generates a PR review.
-The tool can be triggered automatically every time a new PR is [opened](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools), or can be invoked manually by commenting on any PR:
-```
-/review
-```
-For example:
-___
-<kbd><img src=https://codium.ai/images/pr_agent/review_comment.png width="768"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/review.png width="768"></kbd>
-___
-
-### Configuration options
-
-To edit [configurations](./../pr_agent/settings/configuration.toml#L19)  related to the review tool (`pr_reviewer` section), use the following template:
-```
-/review --pr_reviewer.some_config1=... --pr_reviewer.some_config2=...
-```
-
-#### General options
-- `num_code_suggestions`: number of code suggestions provided by the 'review' tool. For manual comments, default is 4. For [PR-Agent app](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L142) auto tools, default is 0, meaning no code suggestions will be provided by the review tool, unless you manually edit `pr_commands`.
-- `inline_code_comments`: if set to true, the tool will publish the code suggestions as comments on the code diff. Default is false.
-- `persistent_comment`: if set to true, the review comment will be persistent, meaning that every new review request will edit the previous one. Default is true.
-- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
-#### Enable\\disable features
-- `require_focused_review`: if set to true, the tool will add a section - 'is the PR a focused one'. Default is false.
-- `require_score_review`: if set to true, the tool will add a section that scores the PR. Default is false.
-- `require_tests_review`: if set to true, the tool will add a section that checks if the PR contains tests. Default is true.
-- `require_estimate_effort_to_review`: if set to true, the tool will add a section that estimates the effort needed to review the PR. Default is true.
-#### SOC2 ticket compliance 💎
-This sub-tool checks if the PR description properly contains a ticket to a project management system (e.g., Jira, Asana, Trello, etc.), as required by SOC2 compliance. If not, it will add a label to the PR: "Missing SOC2 ticket".
-- `require_soc2_ticket`: If set to true, the SOC2 ticket checker sub-tool will be enabled. Default is false.
-- `soc2_ticket_prompt`: The prompt for the SOC2 ticket review. Default is: `Does the PR description include a link to ticket in a project management system (e.g., Jira, Asana, Trello, etc.) ?`. Edit this field if your compliance requirements are different.
-#### Adding PR labels
-- `enable_review_labels_security`: if set to true, the tool will publish a 'possible security issue' label if it detects a security issue. Default is true.
-- `enable_review_labels_effort`: if set to true, the tool will publish a 'Review effort [1-5]: x' label. Default is true.
-#### Auto-approval
-- `enable_auto_approval`: if set to true, the tool will approve the PR when invoked with the 'auto_approve' command. Default is false. This flag can be changed only from configuration file.
-- `maximal_review_effort`: maximal effort level for auto-approval. If the PR's estimated review effort is above this threshold, the auto-approval will not run. Default is 5.
-
-###  Incremental Mode
-Incremental review only considers changes since the last PR-Agent review. This can be useful when working on the PR in an iterative manner, and you want to focus on the changes since the last review instead of reviewing the entire PR again.
-For invoking the incremental mode, the following command can be used:
-```
-/review -i
-```
-Note that the incremental mode is only available for GitHub.
-
-<kbd><img src=https://codium.ai/images/pr_agent/incremental_review.png width="768"></kbd>
-
-Under the section 'pr_reviewer', the [configuration file](./../pr_agent/settings/configuration.toml#L19) contains options to customize the 'review -i' tool.  
-These configurations can be used to control the rate at which the incremental review tool will create new review comments when invoked automatically, to prevent making too much noise in the PR.
-- `minimal_commits_for_incremental_review`: Minimal number of commits since the last review that are required to create incremental review.
-If there are less than the specified number of commits since the last review, the tool will not perform any action.
-Default is 0 - the tool will always run, no matter how many commits since the last review.
-- `minimal_minutes_for_incremental_review`: Minimal number of minutes that need to pass since the last reviewed commit to create incremental review.
-If less than the specified number of minutes have passed between the last reviewed commit and running this command, the tool will not perform any action. 
-Default is 0 - the tool will always run, no matter how much time have passed since the last reviewed commit.
-- `require_all_thresholds_for_incremental_review`: If set to true, all the previous thresholds must be met for incremental review to run. If false, only one is enough to run the tool.
-For example, if `minimal_commits_for_incremental_review=2` and `minimal_minutes_for_incremental_review=2`, and we have 3 commits since the last review, but the last reviewed commit is from 1 minute ago:
-When `require_all_thresholds_for_incremental_review=true` the incremental review __will not__ run, because only 1 out of 2 conditions were met (we have enough commits but the last review is too recent),
-but when `require_all_thresholds_for_incremental_review=false` the incremental review __will__ run, because one condition is enough (we have 3 commits which is more than the configured 2).
-Default is false - the tool will run as long as at least once conditions is met.
-
-### PR Reflection
-By invoking:
-```
-/reflect_and_review
-```
-The tool will first ask the author questions about the PR, and will guide the review based on their answers.
-
-<kbd><img src=https://codium.ai/images/pr_agent/reflection_questions.png width="768"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/reflection_answers.png width="768"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/reflection_insights.png width="768"></kbd>
-___
-
-
-## Usage Tips
-1) [General guidelines](#general-guidelines)
-2) [Code suggestions](#code-suggestions)
-3) [Automation](#automation)
-4) [Auto-labels](#auto-labels)
-5) [Extra instructions](#extra-instructions)
-6) [Auto-approval](#auto-approval)
-
-### General guidelines
-The `review` tool provides a collection of possible feedbacks about a PR.
-It is recommended to review the [Configuration options](#configuration-options) section, and choose the relevant options for your use case.
-
-Some of the features that are disabled by default are quite useful, and should be considered for enabling. For example: 
-`require_score_review`, `require_soc2_ticket`, and more.
-
-On the other hand, if you find one of the enabled features to be irrelevant for your use case, disable it. No default configuration can fit all use cases.
-
-### Code suggestions
-If you set `num_code_suggestions`>0 , the `review` tool will also provide code suggestions.
-
-Notice If you are interested **only** in the code suggestions, it is recommended to use the [`improve`](./IMPROVE.md) feature instead, since it is a dedicated only to code suggestions, and usually gives better results.
-Use the `review` tool if you want to get more comprehensive feedback, which includes code suggestions as well.
-
-### Automation
-- When you first install the app, the [default mode](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools) for the `review` tool is:
-```
-pr_commands = ["/review", ...]
-```
-Meaning the `review` tool will run automatically on every PR, with the default configuration.
-Edit this field to enable/disable the tool, or to change the used configurations.
-
-### Auto-labels
-The `review` tool can auto-generate two specific types of labels for a PR:
-- a `possible security issue` label that detects a possible [security issue](https://github.com/Codium-ai/pr-agent/blob/tr/user_description/pr_agent/settings/pr_reviewer_prompts.toml#L136) (`enable_review_labels_security` flag)
-- a `Review effort [1-5]: x` label, where x is the estimated effort to review the PR (`enable_review_labels_effort` flag)
-
-Both modes are useful, and we recommended to enable them.
-
-### Extra instructions
-Extra instructions are important.
-The `review` tool can be configured with extra instructions, which can be used to guide the model to a feedback tailored to the needs of your project.
-
-Be specific, clear, and concise in the instructions. With extra instructions, you are the prompter. Specify the relevant sub-tool, and the relevant aspects of the PR that you want to emphasize.
-
-Examples for extra instructions:
-```
-[pr_reviewer] # /review #
-extra_instructions="""
-In the code feedback section, emphasize the following:
-- Does the code logic cover relevant edge cases?
-- Is the code logic clear and easy to understand?
-- Is the code logic efficient?
-...
-"""
-```
-Use triple quotes to write multi-line instructions. Use bullet points to make the instructions more readable.
-
-
-### Auto-approval
-PR-Agent can approve a PR when a specific comment is invoked.
-
-To ensure safety, the auto-approval feature is disabled by default. To enable auto-approval, you need to actively set in a pre-defined configuration file the following:
-```
-[pr_reviewer]
-enable_auto_approval = true
-```
-(this specific flag cannot be set with a command line argument, only in the configuration file, committed to the repository)
-
-
-After enabling, by commenting on a PR:
-```
-/review auto_approve
-```
-PR-Agent will automatically approve the PR, and add a comment with the approval.
-
-
-You can also enable auto-approval only if the PR meets certain requirements, such as that the `estimated_review_effort` label is equal or below a certain threshold, by adjusting the flag:
-```
-[pr_reviewer]
-maximal_review_effort = 5
-```

docs/TOOLS_GUIDE.md

@@ -1,15 +0,0 @@
-## Tools Guide
-- [DESCRIBE](./DESCRIBE.md)
-- [REVIEW](./REVIEW.md)
-- [IMPROVE](./IMPROVE.md)
-- [ASK](./ASK.md)
-- [SIMILAR_ISSUE](./SIMILAR_ISSUE.md)
-- [UPDATE CHANGELOG](./UPDATE_CHANGELOG.md)
-- [CUSTOM SUGGESTIONS](./CUSTOM_SUGGESTIONS.md) 💎
-- [ADD DOCUMENTATION](./ADD_DOCUMENTATION.md) 💎
-- [GENERATE CUSTOM LABELS](./GENERATE_CUSTOM_LABELS.md) 💎
-- [Analyze](./Analyze.md) 💎
-- [Test](./TEST.md) 💎
-- [CI Feedback](./CI_FEEDBACK.md) 💎
-
-See the **[installation guide](/INSTALL.md)** for instructions on setting up PR-Agent.

docs/UPDATE_CHANGELOG.md

@@ -1,19 +0,0 @@
-# Update Changelog Tool
-
-The `update_changelog` tool automatically updates the CHANGELOG.md file with the PR changes.
-It can be invoked manually by commenting on any PR:
-```
-/update_changelog
-```
-For example:
-
-<kbd><img src=https://codium.ai/images/pr_agent/update_changelog_comment.png width="768"></kbd>
-<kbd><img src=https://codium.ai/images/pr_agent/update_changelog.png width="768"></kbd>
-
-
-### Configuration options
-
-Under the section 'pr_update_changelog', the [configuration file](./../pr_agent/settings/configuration.toml#L50) contains options to customize the 'update changelog' tool:
-
-- `push_changelog_changes`: whether to push the changes to CHANGELOG.md, or just print them. Default is false (print only).
-- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...

docs/docs/CNAME

@@ -0,0 +1 @@
+pr-agent-docs.codium.ai

docs/docs/assets/logo.svg

@@ -0,0 +1,140 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 28.1.0, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+	 width="64px" height="64px" viewBox="0 0 64 64" enable-background="new 0 0 64 64" xml:space="preserve">
+<g>
+	<defs>
+		<rect id="SVGID_1_" x="0.4" y="0.1" width="63.4" height="63.4"/>
+	</defs>
+	<clipPath id="SVGID_00000008836131916906499950000015813697852011234749_">
+		<use xlink:href="#SVGID_1_"  overflow="visible"/>
+	</clipPath>
+	<g clip-path="url(#SVGID_00000008836131916906499950000015813697852011234749_)">
+		<path fill="#05E5AD" d="M21.4,9.8c3,0,5.9,0.7,8.5,1.9c-5.7,3.4-9.8,11.1-9.8,20.1c0,9,4,16.7,9.8,20.1c-2.6,1.2-5.5,1.9-8.5,1.9
+			c-11.6,0-21-9.8-21-22S9.8,9.8,21.4,9.8z"/>
+		
+			<radialGradient id="SVGID_00000150822754378345238340000008985053211526864828_" cx="-140.0905" cy="350.1757" r="4.8781" gradientTransform="matrix(-4.7708 -6.961580e-02 -0.1061 7.2704 -601.3099 -2523.8489)" gradientUnits="userSpaceOnUse">
+			<stop  offset="0" style="stop-color:#6447FF"/>
+			<stop  offset="6.666670e-02" style="stop-color:#6348FE"/>
+			<stop  offset="0.1333" style="stop-color:#614DFC"/>
+			<stop  offset="0.2" style="stop-color:#5C54F8"/>
+			<stop  offset="0.2667" style="stop-color:#565EF3"/>
+			<stop  offset="0.3333" style="stop-color:#4E6CEC"/>
+			<stop  offset="0.4" style="stop-color:#447BE4"/>
+			<stop  offset="0.4667" style="stop-color:#3A8DDB"/>
+			<stop  offset="0.5333" style="stop-color:#2F9FD1"/>
+			<stop  offset="0.6" style="stop-color:#25B1C8"/>
+			<stop  offset="0.6667" style="stop-color:#1BC0C0"/>
+			<stop  offset="0.7333" style="stop-color:#13CEB9"/>
+			<stop  offset="0.8" style="stop-color:#0DD8B4"/>
+			<stop  offset="0.8667" style="stop-color:#08DFB0"/>
+			<stop  offset="0.9333" style="stop-color:#06E4AE"/>
+			<stop  offset="1" style="stop-color:#05E5AD"/>
+		</radialGradient>
+		<path fill="url(#SVGID_00000150822754378345238340000008985053211526864828_)" d="M21.4,9.8c3,0,5.9,0.7,8.5,1.9
+			c-5.7,3.4-9.8,11.1-9.8,20.1c0,9,4,16.7,9.8,20.1c-2.6,1.2-5.5,1.9-8.5,1.9c-11.6,0-21-9.8-21-22S9.8,9.8,21.4,9.8z"/>
+		
+			<radialGradient id="SVGID_00000022560571240417802950000012439139323268113305_" cx="-191.7649" cy="385.7387" r="4.8781" gradientTransform="matrix(-2.5514 -0.7616 -0.8125 2.7217 -130.733 -1180.2209)" gradientUnits="userSpaceOnUse">
+			<stop  offset="0" style="stop-color:#6447FF"/>
+			<stop  offset="6.666670e-02" style="stop-color:#6348FE"/>
+			<stop  offset="0.1333" style="stop-color:#614DFC"/>
+			<stop  offset="0.2" style="stop-color:#5C54F8"/>
+			<stop  offset="0.2667" style="stop-color:#565EF3"/>
+			<stop  offset="0.3333" style="stop-color:#4E6CEC"/>
+			<stop  offset="0.4" style="stop-color:#447BE4"/>
+			<stop  offset="0.4667" style="stop-color:#3A8DDB"/>
+			<stop  offset="0.5333" style="stop-color:#2F9FD1"/>
+			<stop  offset="0.6" style="stop-color:#25B1C8"/>
+			<stop  offset="0.6667" style="stop-color:#1BC0C0"/>
+			<stop  offset="0.7333" style="stop-color:#13CEB9"/>
+			<stop  offset="0.8" style="stop-color:#0DD8B4"/>
+			<stop  offset="0.8667" style="stop-color:#08DFB0"/>
+			<stop  offset="0.9333" style="stop-color:#06E4AE"/>
+			<stop  offset="1" style="stop-color:#05E5AD"/>
+		</radialGradient>
+		<path fill="url(#SVGID_00000022560571240417802950000012439139323268113305_)" d="M38,18.3c-2.1-2.8-4.9-5.1-8.1-6.6
+			c2-1.2,4.2-1.9,6.6-1.9c2.2,0,4.3,0.6,6.2,1.7C40.8,12.9,39.2,15.3,38,18.3L38,18.3z"/>
+		
+			<radialGradient id="SVGID_00000143611122169386473660000017673587931016751800_" cx="-194.7918" cy="395.2442" r="4.8781" gradientTransform="matrix(-2.5514 -0.7616 -0.8125 2.7217 -130.733 -1172.9556)" gradientUnits="userSpaceOnUse">
+			<stop  offset="0" style="stop-color:#6447FF"/>
+			<stop  offset="6.666670e-02" style="stop-color:#6348FE"/>
+			<stop  offset="0.1333" style="stop-color:#614DFC"/>
+			<stop  offset="0.2" style="stop-color:#5C54F8"/>
+			<stop  offset="0.2667" style="stop-color:#565EF3"/>
+			<stop  offset="0.3333" style="stop-color:#4E6CEC"/>
+			<stop  offset="0.4" style="stop-color:#447BE4"/>
+			<stop  offset="0.4667" style="stop-color:#3A8DDB"/>
+			<stop  offset="0.5333" style="stop-color:#2F9FD1"/>
+			<stop  offset="0.6" style="stop-color:#25B1C8"/>
+			<stop  offset="0.6667" style="stop-color:#1BC0C0"/>
+			<stop  offset="0.7333" style="stop-color:#13CEB9"/>
+			<stop  offset="0.8" style="stop-color:#0DD8B4"/>
+			<stop  offset="0.8667" style="stop-color:#08DFB0"/>
+			<stop  offset="0.9333" style="stop-color:#06E4AE"/>
+			<stop  offset="1" style="stop-color:#05E5AD"/>
+		</radialGradient>
+		<path fill="url(#SVGID_00000143611122169386473660000017673587931016751800_)" d="M38,45.2c1.2,3,2.9,5.3,4.7,6.8
+			c-1.9,1.1-4,1.7-6.2,1.7c-2.3,0-4.6-0.7-6.6-1.9C33.1,50.4,35.8,48.1,38,45.2L38,45.2z"/>
+		<path fill="#684BFE" d="M20.1,31.8c0-9,4-16.7,9.8-20.1c3.2,1.5,6,3.8,8.1,6.6c-1.5,3.7-2.5,8.4-2.5,13.5s0.9,9.8,2.5,13.5
+			c-2.1,2.8-4.9,5.1-8.1,6.6C24.1,48.4,20.1,40.7,20.1,31.8z"/>
+		
+			<radialGradient id="SVGID_00000147942998054305738810000004710078864578628519_" cx="-212.7358" cy="363.2475" r="4.8781" gradientTransform="matrix(-2.3342 -1.063 -1.623 3.5638 149.3813 -1470.1027)" gradientUnits="userSpaceOnUse">
+			<stop  offset="0" style="stop-color:#6447FF"/>
+			<stop  offset="6.666670e-02" style="stop-color:#6348FE"/>
+			<stop  offset="0.1333" style="stop-color:#614DFC"/>
+			<stop  offset="0.2" style="stop-color:#5C54F8"/>
+			<stop  offset="0.2667" style="stop-color:#565EF3"/>
+			<stop  offset="0.3333" style="stop-color:#4E6CEC"/>
+			<stop  offset="0.4" style="stop-color:#447BE4"/>
+			<stop  offset="0.4667" style="stop-color:#3A8DDB"/>
+			<stop  offset="0.5333" style="stop-color:#2F9FD1"/>
+			<stop  offset="0.6" style="stop-color:#25B1C8"/>
+			<stop  offset="0.6667" style="stop-color:#1BC0C0"/>
+			<stop  offset="0.7333" style="stop-color:#13CEB9"/>
+			<stop  offset="0.8" style="stop-color:#0DD8B4"/>
+			<stop  offset="0.8667" style="stop-color:#08DFB0"/>
+			<stop  offset="0.9333" style="stop-color:#06E4AE"/>
+			<stop  offset="1" style="stop-color:#05E5AD"/>
+		</radialGradient>
+		<path fill="url(#SVGID_00000147942998054305738810000004710078864578628519_)" d="M50.7,42.5c0.6,3.3,1.5,6.1,2.5,8
+			c-1.8,2-3.8,3.1-6,3.1c-1.6,0-3.1-0.6-4.5-1.7C46.1,50.2,48.9,46.8,50.7,42.5L50.7,42.5z"/>
+		
+			<radialGradient id="SVGID_00000083770737908230256670000016126156495859285174_" cx="-208.5327" cy="357.2025" r="4.8781" gradientTransform="matrix(-2.3342 -1.063 -1.623 3.5638 149.3813 -1476.8097)" gradientUnits="userSpaceOnUse">
+			<stop  offset="0" style="stop-color:#6447FF"/>
+			<stop  offset="6.666670e-02" style="stop-color:#6348FE"/>
+			<stop  offset="0.1333" style="stop-color:#614DFC"/>
+			<stop  offset="0.2" style="stop-color:#5C54F8"/>
+			<stop  offset="0.2667" style="stop-color:#565EF3"/>
+			<stop  offset="0.3333" style="stop-color:#4E6CEC"/>
+			<stop  offset="0.4" style="stop-color:#447BE4"/>
+			<stop  offset="0.4667" style="stop-color:#3A8DDB"/>
+			<stop  offset="0.5333" style="stop-color:#2F9FD1"/>
+			<stop  offset="0.6" style="stop-color:#25B1C8"/>
+			<stop  offset="0.6667" style="stop-color:#1BC0C0"/>
+			<stop  offset="0.7333" style="stop-color:#13CEB9"/>
+			<stop  offset="0.8" style="stop-color:#0DD8B4"/>
+			<stop  offset="0.8667" style="stop-color:#08DFB0"/>
+			<stop  offset="0.9333" style="stop-color:#06E4AE"/>
+			<stop  offset="1" style="stop-color:#05E5AD"/>
+		</radialGradient>
+		<path fill="url(#SVGID_00000083770737908230256670000016126156495859285174_)" d="M42.7,11.5c1.4-1.1,2.9-1.7,4.5-1.7
+			c2.2,0,4.3,1.1,6,3.1c-1,2-1.9,4.7-2.5,8C48.9,16.7,46.1,13.4,42.7,11.5L42.7,11.5z"/>
+		<path fill="#684BFE" d="M38,45.2c2.8-3.7,4.4-8.4,4.4-13.5c0-5.1-1.7-9.8-4.4-13.5c1.2-3,2.9-5.3,4.7-6.8c3.4,1.9,6.2,5.3,8,9.5
+			c-0.6,3.2-0.9,6.9-0.9,10.8s0.3,7.6,0.9,10.8c-1.8,4.3-4.6,7.6-8,9.5C40.8,50.6,39.2,48.2,38,45.2L38,45.2z"/>
+		<path fill="#321BB2" d="M38,45.2c-1.5-3.7-2.5-8.4-2.5-13.5S36.4,22,38,18.3c2.8,3.7,4.4,8.4,4.4,13.5S40.8,41.5,38,45.2z"/>
+		<path fill="#05E6AD" d="M53.2,12.9c1.1-2,2.3-3.1,3.6-3.1c3.9,0,7,9.8,7,22s-3.1,22-7,22c-1.3,0-2.6-1.1-3.6-3.1
+			c3.4-3.8,5.7-10.8,5.7-18.8C58.8,23.8,56.6,16.8,53.2,12.9z"/>
+		
+			<radialGradient id="SVGID_00000009565123575973598080000009335550354766300606_" cx="-7.8671" cy="278.2442" r="4.8781" gradientTransform="matrix(1.5187 0 0 -7.8271 69.237 2209.3281)" gradientUnits="userSpaceOnUse">
+			<stop  offset="0" style="stop-color:#05E5AD"/>
+			<stop  offset="0.32" style="stop-color:#05E5AD;stop-opacity:0"/>
+			<stop  offset="0.9028" style="stop-color:#6447FF"/>
+		</radialGradient>
+		<path fill="url(#SVGID_00000009565123575973598080000009335550354766300606_)" d="M53.2,12.9c1.1-2,2.3-3.1,3.6-3.1
+			c3.9,0,7,9.8,7,22s-3.1,22-7,22c-1.3,0-2.6-1.1-3.6-3.1c3.4-3.8,5.7-10.8,5.7-18.8C58.8,23.8,56.6,16.8,53.2,12.9z"/>
+		<path fill="#684BFE" d="M52.8,31.8c0-3.9-0.8-7.6-2.1-10.8c0.6-3.3,1.5-6.1,2.5-8c3.4,3.8,5.7,10.8,5.7,18.8c0,8-2.3,15-5.7,18.8
+			c-1-2-1.9-4.7-2.5-8C52,39.3,52.8,35.7,52.8,31.8z"/>
+		<path fill="#321BB2" d="M50.7,42.5c-0.6-3.2-0.9-6.9-0.9-10.8s0.3-7.6,0.9-10.8c1.3,3.2,2.1,6.9,2.1,10.8S52,39.3,50.7,42.5z"/>
+	</g>
+</g>
+</svg>

docs/docs/chrome-extension/index.md

@@ -0,0 +1,49 @@
+## PR-Agent chrome extension
+PR-Agent Chrome extension is a collection of tools that integrates seamlessly with your GitHub environment, aiming to enhance your PR-Agent usage experience, and providing additional features.
+
+## Features
+
+### Toolbar extension
+With PR-Agent Chrome extension, it's [easier than ever](https://www.youtube.com/watch?v=gT5tli7X4H4) to interactively configure and experiment with the different tools and configuration options.
+
+After you found the setup that works for you, you can also easily export it as a persistent configuration file, and use it for automatic commands.
+
+<img src="https://codium.ai/images/pr_agent/toolbar1.png" width="512">
+
+<img src="https://codium.ai/images/pr_agent/toolbar2.png" width="512">
+
+### PR-Agent filters
+
+PR-Agent filters is a sidepanel option. that allows you to filter different message in the conversation tab.
+
+For example, you can choose to present only message from PR-Agent, or filter those messages, focusing only on user's comments.
+
+<img src="https://codium.ai/images/pr_agent/pr_agent_filters1.png" width="256">
+
+<img src="https://codium.ai/images/pr_agent/pr_agent_filters2.png" width="256">
+
+
+### Enhanced code suggestions
+
+PR-Agent Chrome extension adds the following capabilities to code suggestions tool's comments:
+
+- Auto-expand the table when you are viewing a code block, to avoid clipping.
+- Adding a "quote-and-reply" button, that enables to address and comment on a specific suggestion (for example, asking the author to fix the issue)
+
+
+<img src="https://codium.ai/images/pr_agent/chrome_extension_code_suggestion1.png" width="512">
+
+<img src="https://codium.ai/images/pr_agent/chrome_extension_code_suggestion2.png" width="512">
+
+## Installation
+
+Go to the marketplace and install the extension:
+[PR-Agent Chrome Extension](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl)
+
+## Pre-requisites
+
+The PR-Agent Chrome extension will work on any repo where you have previously [installed PR-Agent](https://pr-agent-docs.codium.ai/installation/).
+
+## Data privacy and security
+
+The PR-Agent Chrome extension only modifies the visual appearance of a GitHub PR screen. It does not transmit any user's repo or pull request code. Code is only sent for processing when a user submits a GitHub comment that activates a PR-Agent tool, in accordance with the standard privacy policy of PR-Agent.

docs/docs/core-abilities/index.md

@@ -1,42 +1,52 @@
-# PR Compression Strategy
+## PR Compression Strategy
 There are two scenarios:
+
 1. The PR is small enough to fit in a single prompt (including system and user prompt)
 2. The PR is too large to fit in a single prompt (including system and user prompt)
 
 For both scenarios, we first use the following strategy
-#### Repo language prioritization strategy
 
+#### Repo language prioritization strategy
 We prioritize the languages of the repo based on the following criteria:
+
 1. Exclude binary files and non code files (e.g. images, pdfs, etc)
 2. Given the main languages used in the repo
-2. We sort the PR files by the most common languages in the repo (in descending order): 
+3. We sort the PR files by the most common languages in the repo (in descending order): 
    * ```[[file.py, file2.py],[file3.js, file4.jsx],[readme.md]]```
    
 
-## Small PR
+### Small PR
 In this case, we can fit the entire PR in a single prompt:
 1. Exclude binary files and non code files (e.g. images, pdfs, etc)
 2. We Expand the surrounding context of each patch to 3 lines above and below the patch
-## Large PR
 
-### Motivation
+### Large PR
+
+#### Motivation
 Pull Requests can be very long and contain a lot of information with varying degree of relevance to the pr-agent.
 We want to be able to pack as much information as possible in a single LMM prompt, while keeping the information relevant to the pr-agent.
 
-
-
 #### Compression strategy
 We prioritize additions over deletions:
  - Combine all deleted files into a single list (`deleted files`)
  - File patches are a list of hunks, remove all hunks of type deletion-only from the hunks in the file patch
+
 ####  Adaptive and token-aware file patch fitting
 We use [tiktoken](https://github.com/openai/tiktoken) to tokenize the patches after the modifications described above, and we use the following strategy to fit the patches into the prompt:
-1. Within each language we sort the files by the number of tokens in the file (in descending order):
-   * ```[[file2.py, file.py],[file4.jsx, file3.js],[readme.md]]```
-2. Iterate through the patches in the order described above
-2. Add the patches to the prompt until the prompt reaches a certain buffer from the max token length
-3. If there are still patches left, add the remaining patches as a list called `other modified files` to the prompt until the prompt reaches the max token length (hard stop), skip the rest of the patches.
-4. If we haven't reached the max token length, add the `deleted files` to the prompt until the prompt reaches the max token length (hard stop), skip the rest of the patches.
 
-### Example
-<kbd><img src=https://codium.ai/images/git_patch_logic.png width="768"></kbd>
+1. Within each language we sort the files by the number of tokens in the file (in descending order):
+    - ```[[file2.py, file.py],[file4.jsx, file3.js],[readme.md]]```
+2. Iterate through the patches in the order described above
+3. Add the patches to the prompt until the prompt reaches a certain buffer from the max token length
+4. If there are still patches left, add the remaining patches as a list called `other modified files` to the prompt until the prompt reaches the max token length (hard stop), skip the rest of the patches.
+5. If we haven't reached the max token length, add the `deleted files` to the prompt until the prompt reaches the max token length (hard stop), skip the rest of the patches.
+
+#### Example
+
+![Core Abilities](https://codium.ai/images/git_patch_logic.png){width=768}
+
+## YAML Prompting
+TBD
+
+## Static Code Analysis 💎
+TBD

docs/docs/css/custom.css

@@ -0,0 +1,36 @@
+
+
+:root {
+    --md-primary-fg-color: #765bfa;
+    --md-accent-fg-color: #AEA1F1;
+  }
+
+.md-nav--primary {
+    .md-nav__link {
+    font-size: 18px; /* Change the font size as per your preference */
+    }
+}
+
+/*.md-nav__title, .md-nav__link  {*/
+/*    font-size: 18px;*/
+/*    margin-top: 14px; !* Adjust the space as needed *!*/
+/*    margin-bottom: 14px; !* Adjust the space as needed *!*/
+/*}*/
+
+.md-tabs__link  {
+    font-size: 18px;
+}
+
+.md-header__title {
+    font-size: 20px;
+    margin-left: 0px !important;
+}
+
+.md-content img {
+    border-width: 1px;
+    border-style: solid;
+    border-color: black;
+    outline-width: 1px;
+    outline-style: solid;
+    outline-color: darkgray;
+  }

docs/docs/finetuning_benchmark/index.md

@@ -0,0 +1,92 @@
+# PR-Agent Code Fine-tuning Benchmark
+
+On coding tasks, the gap between open-source models and top closed-source models such as GPT4 is significant.
+<br>
+In practice, open-source models are unsuitable for most real-world code tasks, and require further fine-tuning to produce acceptable results.
+
+_PR-Agent fine-tuning benchmark_ aims to benchmark open-source models on their ability to be fine-tuned for a coding task.
+Specifically, we chose to fine-tune open-source models on the task of analyzing a pull request, and providing useful feedback and code suggestions.
+
+Here are the results:
+<br>
+<br>
+
+**Model performance:**
+
+| Model name                  | Model size [B] | Better than gpt-4 rate, after fine-tuning [%] |
+|-----------------------------|----------------|----------------------------------------------|
+| **DeepSeek 34B-instruct**   | **34**         | **40.7**                                     |
+| DeepSeek 34B-base           | 34             | 38.2                                         |
+| Phind-34b                   | 34             | 38                                           |
+| Granite-34B                 | 34             | 37.6                                         |
+| Codestral-22B-v0.1          | 22             | 32.7                                         |
+| QWEN-1.5-32B                | 32             | 29                                           |
+|                             |                |                                              |
+| **CodeQwen1.5-7B**          | **7**          | **35.4**                                     |
+| Granite-8b-code-instruct    | 8              | 34.2                                         |
+| CodeLlama-7b-hf             | 7              | 31.8                                         |
+| Gemma-7B                    | 7              | 27.2                                         |
+| DeepSeek coder-7b-instruct  | 7              | 26.8                                         |
+| Llama-3-8B-Instruct         | 8              | 26.8                                         |
+| Mistral-7B-v0.1             | 7              | 16.1                                         |
+
+<br>
+
+**Fine-tuning impact:**
+
+| Model name                | Model size [B] | Fine-tuned | Better than gpt-4 rate [%] |
+|---------------------------|----------------|------------|----------------------------|
+| DeepSeek 34B-instruct     | 34             | yes        | 40.7                       |
+| DeepSeek 34B-instruct     | 34             | no         | 3.6                        |
+
+## Results analysis
+
+- **Fine-tuning is a must** - without fine-tuning, open-source models provide poor results on most real-world code tasks, which include complicated prompt and lengthy context. We clearly see that without fine-tuning, deepseek model was 96.4% of the time inferior to GPT-4, while after fine-tuning, it is better 40.7% of the time.
+- **Always start from a code-dedicated model** — When fine-tuning, always start from a code-dedicated model, and not from a general-usage model. The gaps in downstream results are very big.
+- **Don't believe the hype** —newer models, or models from big-tech companies (Llama3, Gemma, Mistral), are not always better for fine-tuning.
+- **The best large model** - For large 34B code-dedicated models, the gaps when doing proper fine-tuning are small. The current top model is **DeepSeek 34B-instruct**
+- **The best small model** - For small 7B code-dedicated models, the gaps when fine-tuning are much larger. **CodeQWEN 1.5-7B** is by far the best model for fine-tuning.
+- **Base vs. instruct** - For the top model (deepseek), we saw small advantage when starting from the instruct version. However, we recommend testing both versions on each specific task, as the base model is generally considered more suitable for fine-tuning.
+
+## The dataset
+
+### Training dataset
+
+Our training dataset comprises 25,000 pull requests, aggregated from permissive license repos. For each pull request, we generated responses for the three main tools of PR-Agent:
+[Describe](https://pr-agent-docs.codium.ai/tools/describe/), [Review](https://pr-agent-docs.codium.ai/tools/improve/) and [Improve](https://pr-agent-docs.codium.ai/tools/improve/).
+
+On the raw data collected, we employed various automatic and manual cleaning techniques to ensure the outputs were of the highest quality, and suitable for instruct-tuning.
+
+Here are the prompts, and example outputs, used as input-output pairs to fine-tune the models:
+
+| Tool     | Prompt                                                                                                     | Example output |
+|----------|------------------------------------------------------------------------------------------------------------|----------------|
+| Describe | [link](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/pr_description_prompts.toml) | [link](https://github.com/Codium-ai/pr-agent/pull/910#issue-2303989601)           |
+| Review   | [link](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml) | [link](https://github.com/Codium-ai/pr-agent/pull/910#issuecomment-2118761219)           |
+| Improve  | [link](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/pr_code_suggestions_prompts.toml) | [link](https://github.com/Codium-ai/pr-agent/pull/910#issuecomment-2118761309)           |
+
+### Evaluation dataset
+
+- For each tool, we aggregated 100 additional examples to be used for evaluation. These examples were not used in the training dataset, and were manually selected to represent diverse real-world use-cases.
+- For each test example, we generated two responses: one from the fine-tuned model, and one from the best code model in the world, `gpt-4-turbo-2024-04-09`.
+
+- We used a third LLM to judge which response better answers the prompt, and will likely be perceived by a human as better response.
+<br>
+
+We experimented with three model as judges: `gpt-4-turbo-2024-04-09`, `gpt-4o`, and `claude-3-opus-20240229`. All three produced similar results, with the same ranking order. This strengthens the validity of our testing protocol.
+The evaluation prompt can be found [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/pr_evaluate_prompt_response.toml)
+
+Here is an example of a judge model feedback:
+
+```
+command: improve
+model1_score: 9,
+model2_score: 6,
+why: |
+  Response 1 is better because it provides more actionable and specific suggestions that directly 
+  enhance the code's maintainability, performance, and best practices. For example, it suggests 
+  using a variable for reusable widget instances and using named routes for navigation, which 
+  are practical improvements. In contrast, Response 2 focuses more on general advice and less 
+  actionable suggestions, such as changing variable names and adding comments, which are less 
+  critical for immediate code improvement."
+```

docs/docs/index.md

@@ -0,0 +1,81 @@
+# Overview
+
+CodiumAI PR-Agent is an open-source tool to help efficiently review and handle pull requests.
+
+- See the [Installation Guide](./installation/index.md) for instructions on installing and running the tool on different git platforms.
+
+- See the [Usage Guide](./usage-guide/index.md) for instructions on running the PR-Agent commands via different interfaces, including _CLI_, _online usage_, or by _automatically triggering_ them when a new PR is opened.
+
+- See the [Tools Guide](./tools/index.md) for a detailed description of the different tools.
+
+
+## PR-Agent Features
+PR-Agent offers extensive pull request functionalities across various git providers.
+
+|       |                                                                                                                       | GitHub | Gitlab | Bitbucket | Azure DevOps |
+|-------|-----------------------------------------------------------------------------------------------------------------------|:------:|:------:|:---------:|:------------:|
+| TOOLS | Review                                                                                                                |   ✅    |   ✅    |   ✅       |      ✅      |
+|       | ⮑ Incremental                                                                                                         |   ✅    |        |            |              |
+|       | ⮑ [SOC2 Compliance](https://pr-agent-docs.codium.ai/tools/review/#soc2-ticket-compliance){:target="_blank"} 💎        |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | Ask                                                                                                                   |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | Describe                                                                                                              |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | ⮑ [Inline file summary](https://pr-agent-docs.codium.ai/tools/describe/#inline-file-summary){:target="_blank"} 💎     |   ✅    |   ✅    |           |      ✅      |
+|       | Improve                                                                                                               |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | ⮑ Extended                                                                                                            |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | [Custom Prompt](./tools/custom_prompt.md){:target="_blank"} 💎                                                        |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | Reflect and Review                                                                                                    |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | Update CHANGELOG.md                                                                                                   |   ✅    |   ✅    |   ✅        |      ️       |
+|       | Find Similar Issue                                                                                                    |   ✅    |        |             |      ️       |
+|       | [Add PR Documentation](./tools/documentation.md){:target="_blank"} 💎                                                 |   ✅    |   ✅    |          |      ✅      |
+|       | [Generate Custom Labels](./tools/describe.md#handle-custom-labels-from-the-repos-labels-page-💎){:target="_blank"} 💎 |   ✅    |   ✅    |            |      ✅      |
+|       | [Analyze PR Components](./tools/analyze.md){:target="_blank"} 💎                                                      |   ✅    |   ✅    |       |      ✅      |
+|       |                                                                                                                       |        |        |            |      ️       |
+| USAGE | CLI                                                                                                                   |   ✅    |   ✅    |   ✅       |      ✅      |
+|       | App / webhook                                                                                                         |   ✅    |   ✅    |    ✅        |      ✅      |
+|       | Actions                                                                                                               |   ✅    |        |            |      ️       |
+|       |                                                                                                                       |        |        |            |
+| CORE  | PR compression                                                                                                        |   ✅    |   ✅    |   ✅       |   ✅        |
+|       | Repo language prioritization                                                                                          |   ✅    |   ✅    |   ✅       |   ✅        |
+|       | Adaptive and token-aware file patch fitting                                                                           |   ✅    |   ✅    |   ✅     |   ✅        |
+|       | Multiple models support                                                                                               |   ✅    |   ✅    |   ✅       |   ✅        |
+|       | Incremental PR review                                                                                                 |   ✅    |        |            |           |
+|       | [Static code analysis](./tools/analyze.md/){:target="_blank"} 💎                                                      |   ✅    |   ✅     |    ✅    |   ✅        |
+|       | [Multiple configuration options](./usage-guide/configuration_options.md){:target="_blank"} 💎                         |   ✅    |   ✅     |    ✅    |   ✅        |
+
+💎 marks a feature available only in [PR-Agent Pro](https://www.codium.ai/pricing/){:target="_blank"}
+
+
+## Example Results
+<hr>
+
+#### [/describe](https://github.com/Codium-ai/pr-agent/pull/530)
+<figure markdown="1">
+![/describe](https://www.codium.ai/images/pr_agent/describe_new_short_main.png){width=512}
+</figure>
+<hr>
+
+#### [/review](https://github.com/Codium-ai/pr-agent/pull/732#issuecomment-1975099151)
+<figure markdown="1">
+![/review](https://www.codium.ai/images/pr_agent/review_new_short_main.png){width=512}
+</figure>
+<hr>
+
+#### [/improve](https://github.com/Codium-ai/pr-agent/pull/732#issuecomment-1975099159)
+<figure markdown="1">
+![/improve](https://www.codium.ai/images/pr_agent/improve_new_short_main.png){width=512}
+</figure>
+<hr>
+
+#### [/generate_labels](https://github.com/Codium-ai/pr-agent/pull/530)
+<figure markdown="1">
+![/generate_labels](https://www.codium.ai/images/pr_agent/geneare_custom_labels_main_short.png){width=300}
+</figure>
+<hr>
+
+## How it Works
+
+The following diagram illustrates PR-Agent tools and their flow:
+
+![PR-Agent Tools](https://codium.ai/images/pr_agent/diagram-v0.9.png)
+
+Check out the [PR Compression strategy](core-abilities/index.md) page for more details on how we convert a code diff to a manageable LLM prompt

docs/docs/installation/azure.md

@@ -0,0 +1,35 @@
+## Azure DevOps provider
+
+To use Azure DevOps provider use the following settings in configuration.toml:
+```
+[config]
+git_provider="azure"
+```
+
+Azure DevOps provider supports [PAT token](https://learn.microsoft.com/en-us/azure/devops/organizations/accounts/use-personal-access-tokens-to-authenticate?view=azure-devops&tabs=Windows) or [DefaultAzureCredential](https://learn.microsoft.com/en-us/azure/developer/python/sdk/authentication-overview#authentication-in-server-environments) authentication.
+PAT is faster to create, but has build in expiration date, and will use the user identity for API calls. 
+Using DefaultAzureCredential you can use managed identity or Service principle, which are more secure and will create separate ADO user identity (via AAD) to the agent.
+
+If PAT was chosen, you can assign the value in .secrets.toml. 
+If DefaultAzureCredential was chosen, you can assigned the additional env vars like AZURE_CLIENT_SECRET directly, 
+or use managed identity/az cli (for local development) without any additional configuration.
+in any case, 'org' value must be assigned in .secrets.toml:
+```
+[azure_devops]
+org = "https://dev.azure.com/YOUR_ORGANIZATION/"
+# pat = "YOUR_PAT_TOKEN" needed only if using PAT for authentication
+```
+
+### Azure DevOps Webhook
+
+To trigger from an Azure webhook, you need to manually [add a webhook](https://learn.microsoft.com/en-us/azure/devops/service-hooks/services/webhooks?view=azure-devops). 
+Use the "Pull request created" type to trigger a review, or "Pull request commented on" to trigger any supported comment with /<command> <args> comment on the relevant PR. Note that for the "Pull request commented on" trigger, only API v2.0 is supported.
+
+
+For webhook security, create a sporadic username/password pair and configure the webhook username and password on both the server and Azure DevOps webhook. These will be sent as basic Auth data by the webhook with each request:
+```
+[azure_devops_server]
+webhook_username = "<basic auth user>"
+webhook_password = "<basic auth password>"
+```
+> :warning: **Ensure that the webhook endpoint is only accessible over HTTPS** to mitigate the risk of credential interception when using basic authentication.

docs/docs/installation/bitbucket.md

@@ -0,0 +1,70 @@
+## Run as a Bitbucket Pipeline
+
+
+You can use the Bitbucket Pipeline system to run PR-Agent on every pull request open or update.
+
+1. Add the following file in your repository bitbucket_pipelines.yml
+
+```yaml
+pipelines:
+    pull-requests:
+      '**':
+        - step:
+            name: PR Agent Review
+            image: python:3.10
+            services:
+              - docker
+            script:
+              - docker run -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$OPENAI_API_KEY -e BITBUCKET.BEARER_TOKEN=$BITBUCKET_BEARER_TOKEN codiumai/pr-agent:latest --pr_url=https://bitbucket.org/$BITBUCKET_WORKSPACE/$BITBUCKET_REPO_SLUG/pull-requests/$BITBUCKET_PR_ID review
+```
+
+2. Add the following secure variables to your repository under Repository settings > Pipelines > Repository variables.
+OPENAI_API_KEY: `<your key>`
+BITBUCKET_BEARER_TOKEN: `<your token>`
+
+You can get a Bitbucket token for your repository by following Repository Settings -> Security -> Access Tokens.
+
+Note that comments on a PR are not supported in Bitbucket Pipeline.
+
+
+## Run using CodiumAI-hosted Bitbucket app
+
+Please contact [support@codium.ai](mailto:support@codium.ai) or visit [CodiumAI pricing page](https://www.codium.ai/pricing/) if you're interested in a hosted BitBucket app solution that provides full functionality including PR reviews and comment handling. It's based on the [bitbucket_app.py](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/git_providers/bitbucket_provider.py) implementation.
+
+
+## Bitbucket Server and Data Center
+
+Login into your on-prem instance of Bitbucket with your service account username and password.
+Navigate to `Manage account`, `HTTP Access tokens`, `Create Token`.
+Generate the token and add it to .secret.toml under `bitbucket_server` section
+
+```toml
+[bitbucket_server]
+bearer_token = "<your key>"
+```
+
+### Run it as CLI
+
+Modify `configuration.toml`:
+
+```toml
+git_provider="bitbucket_server"
+```
+
+and pass the Pull request URL:
+```shell
+python cli.py --pr_url https://git.onpreminstanceofbitbucket.com/projects/PROJECT/repos/REPO/pull-requests/1 review
+```
+
+### Run it as service
+
+To run pr-agent as webhook, build the docker image:
+```
+docker build . -t codiumai/pr-agent:bitbucket_server_webhook --target bitbucket_server_webhook -f docker/Dockerfile
+docker push codiumai/pr-agent:bitbucket_server_webhook  # Push to your Docker repository
+```
+
+Navigate to `Projects` or `Repositories`, `Settings`, `Webhooks`, `Create Webhook`.
+Fill the name and URL, Authentication None select the Pull Request Opened checkbox to receive that event as webhook.
+
+The URL should end with `/webhook`, for example: https://domain.com/webhook

docs/docs/installation/github.md

@@ -0,0 +1,242 @@
+## Run as a GitHub Action
+
+You can use our pre-built Github Action Docker image to run PR-Agent as a Github Action.
+
+1) Add the following file to your repository under `.github/workflows/pr_agent.yml`:
+
+```yaml
+on:
+  pull_request:
+    types: [opened, reopened, ready_for_review]
+  issue_comment:
+jobs:
+  pr_agent_job:
+    if: ${{ github.event.sender.type != 'Bot' }}
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+      contents: write
+    name: Run pr agent on every pull request, respond to user comments
+    steps:
+      - name: PR Agent action step
+        id: pragent
+        uses: Codium-ai/pr-agent@main
+        env:
+          OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+```
+** if you want to pin your action to a specific release (v2.0 for example) for stability reasons, use:
+```yaml
+...
+    steps:
+      - name: PR Agent action step
+        id: pragent
+        uses: Codium-ai/pr-agent@v2.0
+...
+```
+2) Add the following secret to your repository under `Settings > Secrets and variables > Actions > New repository secret > Add secret`:
+
+```
+Name = OPENAI_KEY
+Secret = <your key>
+```
+
+The GITHUB_TOKEN secret is automatically created by GitHub.
+
+3) Merge this change to your main branch.
+When you open your next PR, you should see a comment from `github-actions` bot with a review of your PR, and instructions on how to use the rest of the tools.
+
+4) You may configure PR-Agent by adding environment variables under the env section corresponding to any configurable property in the [configuration](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) file. Some examples:
+```yaml
+      env:
+        # ... previous environment values
+        OPENAI.ORG: "<Your organization name under your OpenAI account>"
+        PR_REVIEWER.REQUIRE_TESTS_REVIEW: "false" # Disable tests review
+        PR_CODE_SUGGESTIONS.NUM_CODE_SUGGESTIONS: 6 # Increase number of code suggestions
+```
+See detailed usage instructions in the [USAGE GUIDE](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#github-action)
+
+---
+
+## Run as a GitHub App
+Allowing you to automate the review process on your private or public repositories.
+
+1) Create a GitHub App from the [Github Developer Portal](https://docs.github.com/en/developers/apps/creating-a-github-app).
+
+   - Set the following permissions:
+     - Pull requests: Read & write
+     - Issue comment: Read & write
+     - Metadata: Read-only
+     - Contents: Read-only
+   - Set the following events:
+     - Issue comment
+     - Pull request
+     - Push (if you need to enable triggering on PR update)
+
+2) Generate a random secret for your app, and save it for later. For example, you can use:
+
+```
+WEBHOOK_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
+```
+
+3) Acquire the following pieces of information from your app's settings page:
+
+   - App private key (click "Generate a private key" and save the file)
+   - App ID
+
+4) Clone this repository:
+
+```
+git clone https://github.com/Codium-ai/pr-agent.git
+```
+
+5) Copy the secrets template file and fill in the following:
+    
+```
+cp pr_agent/settings/.secrets_template.toml pr_agent/settings/.secrets.toml
+# Edit .secrets.toml file
+```
+
+   - Your OpenAI key.
+   - Copy your app's private key to the private_key field.
+   - Copy your app's ID to the app_id field.
+   - Copy your app's webhook secret to the webhook_secret field.
+   - Set deployment_type to 'app' in [configuration.toml](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml)
+
+    > The .secrets.toml file is not copied to the Docker image by default, and is only used for local development.
+    > If you want to use the .secrets.toml file in your Docker image, you can add remove it from the .dockerignore file.
+    > In most production environments, you would inject the secrets file as environment variables or as mounted volumes.
+    > For example, in order to inject a secrets file as a volume in a Kubernetes environment you can update your pod spec to include the following,
+    > assuming you have a secret named `pr-agent-settings` with a key named `.secrets.toml`:
+    ```
+           volumes:
+            - name: settings-volume
+              secret:
+                secretName: pr-agent-settings
+    // ...
+           containers:
+    // ...
+              volumeMounts:
+                - mountPath: /app/pr_agent/settings_prod
+                  name: settings-volume
+    ```
+    
+    > Another option is to set the secrets as environment variables in your deployment environment, for example `OPENAI.KEY` and `GITHUB.USER_TOKEN`.
+
+6) Build a Docker image for the app and optionally push it to a Docker repository. We'll use Dockerhub as an example:
+
+    ```
+    docker build . -t codiumai/pr-agent:github_app --target github_app -f docker/Dockerfile
+    docker push codiumai/pr-agent:github_app  # Push to your Docker repository
+    ```
+
+7. Host the app using a server, serverless function, or container environment. Alternatively, for development and
+   debugging, you may use tools like smee.io to forward webhooks to your local machine.
+    You can check [Deploy as a Lambda Function](#deploy-as-a-lambda-function)
+
+8. Go back to your app's settings, and set the following:
+
+   - Webhook URL: The URL of your app's server or the URL of the smee.io channel.
+   - Webhook secret: The secret you generated earlier.
+
+9. Install the app by navigating to the "Install App" tab and selecting your desired repositories.
+
+> **Note:** When running PR-Agent from GitHub App, the default configuration file (configuration.toml) will be loaded.
+> However, you can override the default tool parameters by uploading a local configuration file `.pr_agent.toml`
+> For more information please check out the [USAGE GUIDE](../usage-guide/automations_and_usage.md#github-app)
+---
+
+## Deploy as a Lambda Function
+
+Note that since AWS Lambda env vars cannot have "." in the name, you can replace each "." in an env variable with "__".<br>
+For example: `GITHUB.WEBHOOK_SECRET` --> `GITHUB__WEBHOOK_SECRET`
+
+1. Follow steps 1-5 from [here](#run-as-a-github-app).
+2. Build a docker image that can be used as a lambda function
+    ```shell
+    docker buildx build --platform=linux/amd64 . -t codiumai/pr-agent:serverless -f docker/Dockerfile.lambda
+   ```
+3. Push image to ECR
+    ```shell
+	docker tag codiumai/pr-agent:serverless <AWS_ACCOUNT>.dkr.ecr.<AWS_REGION>.amazonaws.com/codiumai/pr-agent:serverless
+	docker push <AWS_ACCOUNT>.dkr.ecr.<AWS_REGION>.amazonaws.com/codiumai/pr-agent:serverless
+    ```
+4. Create a lambda function that uses the uploaded image. Set the lambda timeout to be at least 3m.
+5. Configure the lambda function to have a Function URL.
+6. In the environment variables of the Lambda function, specify `AZURE_DEVOPS_CACHE_DIR` to a writable location such as /tmp. (see [link](https://github.com/Codium-ai/pr-agent/pull/450#issuecomment-1840242269))
+7. Go back to steps 8-9 of [Method 5](#run-as-a-github-app) with the function url as your Webhook URL.
+    The Webhook URL would look like `https://<LAMBDA_FUNCTION_URL>/api/v1/github_webhooks`
+
+---
+
+## AWS CodeCommit Setup
+
+Not all features have been added to CodeCommit yet.  As of right now, CodeCommit has been implemented to run the pr-agent CLI on the command line, using AWS credentials stored in environment variables.  (More features will be added in the future.)  The following is a set of instructions to have pr-agent do a review of your CodeCommit pull request from the command line:
+
+1. Create an IAM user that you will use to read CodeCommit pull requests and post comments
+    * Note: That user should have CLI access only, not Console access
+2. Add IAM permissions to that user, to allow access to CodeCommit (see IAM Role example below)
+3. Generate an Access Key for your IAM user
+4. Set the Access Key and Secret using environment variables (see Access Key example below)
+5. Set the `git_provider` value to `codecommit` in the `pr_agent/settings/configuration.toml` settings file
+6. Set the `PYTHONPATH` to include your `pr-agent` project directory
+    * Option A: Add `PYTHONPATH="/PATH/TO/PROJECTS/pr-agent` to your `.env` file
+    * Option B: Set `PYTHONPATH` and run the CLI in one command, for example:
+        * `PYTHONPATH="/PATH/TO/PROJECTS/pr-agent python pr_agent/cli.py [--ARGS]`
+
+---
+
+
+#### AWS CodeCommit IAM Role Example
+
+Example IAM permissions to that user to allow access to CodeCommit:
+
+* Note: The following is a working example of IAM permissions that has read access to the repositories and write access to allow posting comments
+* Note: If you only want pr-agent to review your pull requests, you can tighten the IAM permissions further, however this IAM example will work, and allow the pr-agent to post comments to the PR
+* Note: You may want to replace the `"Resource": "*"` with your list of repos, to limit access to only those repos
+
+```
+{
+    "Version": "2012-10-17",
+    "Statement": [
+        {
+            "Effect": "Allow",
+            "Action": [
+                "codecommit:BatchDescribe*",
+                "codecommit:BatchGet*",
+                "codecommit:Describe*",
+                "codecommit:EvaluatePullRequestApprovalRules",
+                "codecommit:Get*",
+                "codecommit:List*",
+                "codecommit:PostComment*",
+                "codecommit:PutCommentReaction",
+                "codecommit:UpdatePullRequestDescription",
+                "codecommit:UpdatePullRequestTitle"
+            ],
+            "Resource": "*"
+        }
+    ]
+}
+```
+
+#### AWS CodeCommit Access Key and Secret
+
+Example setting the Access Key and Secret using environment variables
+
+```sh
+export AWS_ACCESS_KEY_ID="XXXXXXXXXXXXXXXX"
+export AWS_SECRET_ACCESS_KEY="XXXXXXXXXXXXXXXX"
+export AWS_DEFAULT_REGION="us-east-1"
+```
+
+#### AWS CodeCommit CLI Example
+
+After you set up AWS CodeCommit using the instructions above, here is an example CLI run that tells pr-agent to **review** a given pull request.
+(Replace your specific PYTHONPATH and PR URL in the example)
+
+```sh
+PYTHONPATH="/PATH/TO/PROJECTS/pr-agent" python pr_agent/cli.py \
+  --pr_url https://us-east-1.console.aws.amazon.com/codesuite/codecommit/repositories/MY_REPO_NAME/pull-requests/321 \
+  review
+```

docs/docs/installation/gitlab.md

@@ -0,0 +1,20 @@
+## Run a GitLab webhook server
+
+1. From the GitLab workspace or group, create an access token. Enable the "api" scope only.
+
+2. Generate a random secret for your app, and save it for later. For example, you can use:
+
+```
+WEBHOOK_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
+```
+3. Follow the instructions to build the Docker image, setup a secrets file and deploy on your own server from [here](https://pr-agent-docs.codium.ai/installation/github/#run-as-a-github-app) steps 4-7.
+
+4. In the secrets file, fill in the following:
+    - Your OpenAI key.
+    - In the [gitlab] section, fill in personal_access_token and shared_secret. The access token can be a personal access token, or a group or project access token.
+    - Set deployment_type to 'gitlab' in [configuration.toml](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml)
+   
+5. Create a webhook in GitLab. Set the URL to the URL of your app's server. Set the secret token to the generated secret from step 2.
+In the "Trigger" section, check the ‘comments’ and ‘merge request events’ boxes.
+
+6. Test your installation by opening a merge request or commenting or a merge request using one of CodiumAI's commands.

docs/docs/installation/index.md

@@ -0,0 +1,22 @@
+# Installation
+
+## Self-hosted PR-Agent
+If you choose to host you own PR-Agent, you first need to acquire two tokens:
+
+1. An OpenAI key from [here](https://platform.openai.com/api-keys), with access to GPT-4 (or a key for [other models](../usage-guide/additional_configurations.md/#changing-a-model), if you prefer).
+2. A GitHub\GitLab\BitBucket personal access token (classic), with the repo scope. [GitHub from [here](https://github.com/settings/tokens)]
+
+There are several ways to use self-hosted PR-Agent:
+
+- [Locally](./locally.md)
+- [GitHub](./github.md)
+- [GitLab](./gitlab.md)
+- [BitBucket](./bitbucket.md)
+- [Azure DevOps](./azure.md)
+
+## PR-Agent Pro 💎
+PR-Agent Pro, an app for GitHub\GitLab\BitBucket hosted by CodiumAI, is also available. 
+<br>
+With PR-Agent Pro Installation is as simple as signing up and adding the PR-Agent app to your relevant repo.
+<br>
+See [here](./pr_agent_pro.md) for more details.

docs/docs/installation/locally.md

@@ -0,0 +1,121 @@
+## Using pip package
+
+Install the package:
+
+```
+pip install pr-agent
+```
+
+Then run the relevant tool with the script below.
+<br>
+Make sure to fill in the required parameters (`user_token`, `openai_key`, `pr_url`, `command`):
+
+```python
+from pr_agent import cli
+from pr_agent.config_loader import get_settings
+
+def main():
+    # Fill in the following values
+    provider = "github" # GitHub provider
+    user_token = "..."  # GitHub user token
+    openai_key = "..."  # OpenAI key
+    pr_url = "..."      # PR URL, for example 'https://github.com/Codium-ai/pr-agent/pull/809'
+    command = "/review" # Command to run (e.g. '/review', '/describe', '/ask="What is the purpose of this PR?"', ...)
+
+    # Setting the configurations
+    get_settings().set("CONFIG.git_provider", provider)
+    get_settings().set("openai.key", openai_key)
+    get_settings().set("github.user_token", user_token)
+
+    # Run the command. Feedback will appear in GitHub PR comments
+    cli.run_command(pr_url, command)
+
+
+if __name__ == '__main__':
+    main()
+```
+
+## Using Docker image
+
+A list of the relevant tools can be found in the [tools guide](../tools/ask.md).
+
+To invoke a tool (for example `review`), you can run directly from the Docker image. Here's how:
+
+- For GitHub:
+```
+docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
+```
+
+- For GitLab:
+```
+docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
+```
+
+Note: If you have a dedicated GitLab instance, you need to specify the custom url as variable:
+```
+docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> -e GITLAB.URL=<your gitlab instance url> codiumai/pr-agent:latest --pr_url <pr_url> review
+```
+
+- For BitBucket:
+```
+docker run --rm -it -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$OPENAI_API_KEY -e BITBUCKET.BEARER_TOKEN=$BITBUCKET_BEARER_TOKEN codiumai/pr-agent:latest --pr_url=<pr_url> review
+```
+
+For other git providers, update CONFIG.GIT_PROVIDER accordingly, and check the `pr_agent/settings/.secrets_template.toml` file for the environment variables expected names and values.
+
+---
+
+
+If you want to ensure you're running a specific version of the Docker image, consider using the image's digest:
+```bash
+docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent@sha256:71b5ee15df59c745d352d84752d01561ba64b6d51327f97d46152f0c58a5f678 --pr_url <pr_url> review
+```
+
+Or you can run a [specific released versions](https://github.com/Codium-ai/pr-agent/blob/main/RELEASE_NOTES.md) of pr-agent, for example:
+```
+codiumai/pr-agent@v0.9
+```
+
+---
+
+## Run from source
+
+1. Clone this repository:
+
+```
+git clone https://github.com/Codium-ai/pr-agent.git
+```
+
+2. Navigate to the `/pr-agent` folder and install the requirements in your favorite virtual environment:
+
+```
+pip install -e .
+```
+
+*Note: If you get an error related to Rust in the dependency installation then make sure Rust is installed and in your `PATH`, instructions: https://rustup.rs*
+
+3. Copy the secrets template file and fill in your OpenAI key and your GitHub user token:
+
+```
+cp pr_agent/settings/.secrets_template.toml pr_agent/settings/.secrets.toml
+chmod 600 pr_agent/settings/.secrets.toml
+# Edit .secrets.toml file
+```
+
+4. Run the cli.py script:
+
+```
+python3 -m pr_agent.cli --pr_url <pr_url> review
+python3 -m pr_agent.cli --pr_url <pr_url> ask <your question>
+python3 -m pr_agent.cli --pr_url <pr_url> describe
+python3 -m pr_agent.cli --pr_url <pr_url> improve
+python3 -m pr_agent.cli --pr_url <pr_url> add_docs
+python3 -m pr_agent.cli --pr_url <pr_url> generate_labels
+python3 -m pr_agent.cli --issue_url <issue_url> similar_issue
+...
+```
+
+[Optional] Add the pr_agent folder to your PYTHONPATH
+```
+export PYTHONPATH=$PYTHONPATH:<PATH to pr_agent folder>
+```

docs/docs/installation/pr_agent_pro.md

@@ -0,0 +1,64 @@
+
+## Getting Started with PR-Agent Pro
+
+PR-Agent Pro is a versatile application compatible with GitHub, GitLab, and BitBucket, hosted by CodiumAI.
+See [here](https://pr-agent-docs.codium.ai/#pr-agent-pro) for more details about the benefits of using PR-Agent Pro.
+
+Interested parties can subscribe to PR-Agent Pro through the following [link](https://www.codium.ai/pricing/). 
+After subscribing, you are granted the ability to easily install the application across any of your repositories.
+
+![PR Agent Pro](https://codium.ai/images/pr_agent/pr_agent_pro_install.png){width=468}
+
+Each user who wants to use PR-Agent pro needs to buy a seat. 
+Initially, CodiumAI offers a two-week trial period at no cost, after which continued access requires each user to secure a personal seat.
+Once a user acquires a seat, they gain the flexibility to use PR-Agent Pro across any repository where it was enabled.
+
+Users without a purchased seat who interact with a repository featuring PR-Agent Pro are entitled to receive up to five complimentary feedbacks.
+Beyond this limit, PR-Agent Pro will cease to respond to their inquiries unless a seat is purchased.
+
+
+## Install PR-Agent Pro for GitLab (Teams & Enterprise)
+
+Since GitLab platform does not support apps, installing PR-Agent Pro for GitLab is a bit more involved, and requires the following steps:
+
+### Step 1
+
+Acquire a personal, project or group level access token. Enable the “api” scope in order to allow PR-Agent to read pull requests, comment and respond to requests.
+
+<figure markdown="1">
+![Step 1](https://www.codium.ai/images/pr_agent/gitlab_pro_pat.png){width=750}
+</figure>
+
+Store the token in a safe place, you won’t be able to access it again after it was generated.
+
+### Step 2
+
+Generate a shared secret and link it to the access token. Browse to [https://register.gitlab.pr-agent.codium.ai](https://register.gitlab.pr-agent.codium.ai).
+Fill in your generated GitLab token and your company or personal name in the appropriate fields and click "Submit".
+
+You should see "Success!" displayed above the Submit button, and a shared secret will be generated. Store it in a safe place, you won’t be able to access it again after it was generated.
+
+### Step 3
+
+Install a webhook for your repository or groups, by clicking “webhooks” on the settings menu. Click the “Add new webhook” button.
+
+<figure markdown="1">
+![Step 3.1](https://www.codium.ai/images/pr_agent/gitlab_pro_add_webhook.png)
+</figure>
+
+In the webhook definition form, fill in the following fields:
+URL: https://pro.gitlab.pr-agent.codium.ai/webhook
+
+Secret token: Your CodiumAI key
+Trigger: Check the ‘comments’ and ‘merge request events’ boxes.
+Enable SSL verification: Check the box.
+
+<figure markdown="1">
+![Step 3.2](https://www.codium.ai/images/pr_agent/gitlab_pro_webhooks.png){width=750}
+</figure>
+
+### Step 4
+
+You’re all set!
+
+Open a new merge request or add a MR comment with one of PR-Agent’s commands such as /review, /describe or /improve.

docs/docs/overview/data_privacy.md

@@ -0,0 +1,17 @@
+## Self-hosted PR-Agent
+
+- If you host PR-Agent with your OpenAI API key, it is between you and OpenAI. You can read their API data privacy policy here:
+https://openai.com/enterprise-privacy
+
+## PR-Agent Pro 💎
+
+- When using PR-Agent Pro 💎, hosted by CodiumAI, we will not store any of your data, nor will we use it for training. You will also benefit from an OpenAI account with zero data retention.
+
+- For certain clients, CodiumAI-hosted PR-Agent Pro will use CodiumAI’s proprietary models. If this is the case, you will be notified.
+
+- No passive collection of Code and Pull Requests’ data — PR-Agent will be active only when you invoke it, and it will then extract and analyze only data relevant to the executed command and queried pull request.
+
+
+## PR-Agent Chrome extension
+
+- The [PR-Agent Chrome extension](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl) serves solely to modify the visual appearance of a GitHub PR screen. It does not transmit any user's repo or pull request code. Code is only sent for processing when a user submits a GitHub comment that activates a PR-Agent tool, in accordance with the standard privacy policy of PR-Agent.

docs/docs/overview/index.md

@@ -0,0 +1,81 @@
+# Overview
+
+CodiumAI PR-Agent is an open-source tool to help efficiently review and handle pull requests.
+
+- See the [Installation Guide](./installation/index.md) for instructions on installing and running the tool on different git platforms.
+
+- See the [Usage Guide](./usage-guide/index.md) for instructions on running the PR-Agent commands via different interfaces, including _CLI_, _online usage_, or by _automatically triggering_ them when a new PR is opened.
+
+- See the [Tools Guide](./tools/index.md) for a detailed description of the different tools.
+
+
+## PR-Agent Features
+PR-Agent offers extensive pull request functionalities across various git providers.
+
+|       |                                                                                                                       | GitHub | Gitlab | Bitbucket | Azure DevOps |
+|-------|-----------------------------------------------------------------------------------------------------------------------|:------:|:------:|:---------:|:------------:|
+| TOOLS | Review                                                                                                                |   ✅    |   ✅    |   ✅       |      ✅      |
+|       | ⮑ Incremental                                                                                                         |   ✅    |        |            |              |
+|       | ⮑ [SOC2 Compliance](https://pr-agent-docs.codium.ai/tools/review/#soc2-ticket-compliance){:target="_blank"} 💎        |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | Ask                                                                                                                   |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | Describe                                                                                                              |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | ⮑ [Inline file summary](https://pr-agent-docs.codium.ai/tools/describe/#inline-file-summary){:target="_blank"} 💎     |   ✅    |   ✅    |           |      ✅      |
+|       | Improve                                                                                                               |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | ⮑ Extended                                                                                                            |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | [Custom Prompt](./tools/custom_prompt.md){:target="_blank"} 💎                                                        |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | Reflect and Review                                                                                                    |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | Update CHANGELOG.md                                                                                                   |   ✅    |   ✅    |   ✅        |      ️       |
+|       | Find Similar Issue                                                                                                    |   ✅    |        |             |      ️       |
+|       | [Add PR Documentation](./tools/documentation.md){:target="_blank"} 💎                                                 |   ✅    |   ✅    |          |      ✅      |
+|       | [Generate Custom Labels](./tools/describe.md#handle-custom-labels-from-the-repos-labels-page-💎){:target="_blank"} 💎 |   ✅    |   ✅    |            |      ✅      |
+|       | [Analyze PR Components](./tools/analyze.md){:target="_blank"} 💎                                                      |   ✅    |   ✅    |       |      ✅      |
+|       |                                                                                                                       |        |        |            |      ️       |
+| USAGE | CLI                                                                                                                   |   ✅    |   ✅    |   ✅       |      ✅      |
+|       | App / webhook                                                                                                         |   ✅    |   ✅    |    ✅        |      ✅      |
+|       | Actions                                                                                                               |   ✅    |        |            |      ️       |
+|       |                                                                                                                       |        |        |            |
+| CORE  | PR compression                                                                                                        |   ✅    |   ✅    |   ✅       |   ✅        |
+|       | Repo language prioritization                                                                                          |   ✅    |   ✅    |   ✅       |   ✅        |
+|       | Adaptive and token-aware file patch fitting                                                                           |   ✅    |   ✅    |   ✅     |   ✅        |
+|       | Multiple models support                                                                                               |   ✅    |   ✅    |   ✅       |   ✅        |
+|       | Incremental PR review                                                                                                 |   ✅    |        |            |           |
+|       | [Static code analysis](./tools/analyze.md/){:target="_blank"} 💎                                                      |   ✅    |   ✅     |    ✅    |   ✅        |
+|       | [Multiple configuration options](./usage-guide/configuration_options.md){:target="_blank"} 💎                         |   ✅    |   ✅     |    ✅    |   ✅        |
+
+💎 marks a feature available only in [PR-Agent Pro](https://www.codium.ai/pricing/){:target="_blank"}
+
+
+## Example Results
+<hr>
+
+#### [/describe](https://github.com/Codium-ai/pr-agent/pull/530)
+<figure markdown="1">
+![/describe](https://www.codium.ai/images/pr_agent/describe_new_short_main.png){width=512}
+</figure>
+<hr>
+
+#### [/review](https://github.com/Codium-ai/pr-agent/pull/732#issuecomment-1975099151)
+<figure markdown="1">
+![/review](https://www.codium.ai/images/pr_agent/review_new_short_main.png){width=512}
+</figure>
+<hr>
+
+#### [/improve](https://github.com/Codium-ai/pr-agent/pull/732#issuecomment-1975099159)
+<figure markdown="1">
+![/improve](https://www.codium.ai/images/pr_agent/improve_new_short_main.png){width=512}
+</figure>
+<hr>
+
+#### [/generate_labels](https://github.com/Codium-ai/pr-agent/pull/530)
+<figure markdown="1">
+![/generate_labels](https://www.codium.ai/images/pr_agent/geneare_custom_labels_main_short.png){width=300}
+</figure>
+<hr>
+
+## How it Works
+
+The following diagram illustrates PR-Agent tools and their flow:
+
+![PR-Agent Tools](https://codium.ai/images/pr_agent/diagram-v0.9.png)
+
+Check out the [PR Compression strategy](core-abilities/index.md) page for more details on how we convert a code diff to a manageable LLM prompt

docs/docs/overview/pr_agent_pro.md

@@ -0,0 +1,18 @@
+[PR-Agent Pro](https://www.codium.ai/pricing/) is a hosted version of PR-Agent, provided by CodiumAI. It is available for a monthly fee, and provides the following benefits:
+
+1. **Fully managed** - We take care of everything for you - hosting, models, regular updates, and more. Installation is as simple as signing up and adding the PR-Agent app to your GitHub\GitLab\BitBucket repo.
+2. **Improved privacy** - No data will be stored or used to train models. PR-Agent Pro will employ zero data retention, and will use an OpenAI account with zero data retention.
+3. **Improved support** - PR-Agent Pro users will receive priority support, and will be able to request new features and capabilities.
+4. **Extra features** -In addition to the benefits listed above, PR-Agent Pro will emphasize more customization, and the usage of static code analysis, in addition to LLM logic, to improve results. It has the following additional tools and features:
+    - (Tool): [**Analyze PR components**](./tools/analyze.md/)
+    - (Tool): [**Custom Prompt Suggestions**](./tools/custom_prompt.md/)
+    - (Tool): [**Tests**](./tools/test.md/)
+    - (Tool): [**PR documentation**](./tools/documentation.md/)
+    - (Tool): [**Improve Component**](https://pr-agent-docs.codium.ai/tools/improve_component/)
+    - (Tool): [**Similar code search**](https://pr-agent-docs.codium.ai/tools/similar_code/)
+    - (Tool): [**CI feedback**](./tools/ci_feedback.md/)
+    - (Feature): [**Interactive triggering**](./usage-guide/automations_and_usage.md/#interactive-triggering)
+    - (Feature): [**SOC2 compliance check**](./tools/review.md/#soc2-ticket-compliance)
+    - (Feature): [**Custom labels**](./tools/describe.md/#handle-custom-labels-from-the-repos-labels-page)
+    - (Feature): [**Global and wiki configuration**](./usage-guide/configuration_options.md/#wiki-configuration-file)
+    - (Feature): [**Inline file summary**](https://pr-agent-docs.codium.ai/tools/describe/#inline-file-summary)

docs/docs/tools/analyze.md

@@ -0,0 +1,19 @@
+## Overview
+The `analyze` tool combines advanced static code analysis with LLM capabilities to provide a comprehensive analysis of the PR code changes.
+
+The tool scans the PR code changes, find the code components (methods, functions, classes) that changed, and enables to interactively generate tests, docs, code suggestions and similar code search for each component.
+
+It can be invoked manually by commenting on any PR:
+```
+/analyze
+```
+
+## Example usage
+
+An example result:
+
+![Analyze 1](https://codium.ai/images/pr_agent/analyze_1.png){width=750}
+
+**Notes**
+
+- Language that are currently supported: Python, Java, C++, JavaScript, TypeScript, C#.

docs/docs/tools/ask.md

@@ -0,0 +1,59 @@
+## Overview
+
+The `ask` tool answers questions about the PR, based on the PR code changes. Make sure to be specific and clear in your questions.
+It can be invoked manually by commenting on any PR:
+```
+/ask "..."
+```
+
+## Example usage
+
+![Ask Comment](https://codium.ai/images/pr_agent/ask_comment.png){width=512}
+
+![Ask](https://codium.ai/images/pr_agent/ask.png){width=512}
+
+## Ask lines
+
+You can run `/ask` on specific lines of code in the PR from the PR's diff view. The tool will answer questions based on the code changes in the selected lines.
+- Click on the '+' sign next to the line number to select the line.
+- To select multiple lines, click on the '+' sign of the first line and then hold and drag to select the rest of the lines. 
+- write `/ask "..."` in the comment box and press `Add single comment` button.
+
+![Ask Line](https://codium.ai/images/pr_agent/Ask_line.png){width=512}
+
+Note that the tool does not have "memory" of previous questions, and answers each question independently.
+
+## Ask on images
+
+You can also ask questions about images that appear in the comment, where the entire PR code will be used as context.
+<br>
+The basic syntax is:
+```
+/ask "..."
+
+[Image](https://real_link_to_image)
+```
+where `https://real_link_to_image` is the direct link to the image.
+
+Note that GitHub has a built-in mechanism of pasting images in comments. However, pasted image does not provide a direct link.
+To get a direct link to an image, we recommend using the following scheme:
+
+1) First, post a comment that contains **only** the image:
+
+![Ask image1](https://codium.ai/images/pr_agent/ask_images1.png){width=512}
+
+2) Quote reply to that comment:
+
+![Ask image2](https://codium.ai/images/pr_agent/ask_images2.png){width=512}
+
+3) In the screen opened, type the question below the image:
+
+![Ask image3](https://codium.ai/images/pr_agent/ask_images3.png){width=512}
+![Ask image4](https://codium.ai/images/pr_agent/ask_images4.png){width=512}
+
+4) Post the comment, and receive the answer:
+
+![Ask image5](https://codium.ai/images/pr_agent/ask_images5.png){width=512}
+
+
+See a full video tutorial [here](https://codium.ai/images/pr_agent/ask_image_video.mov)

docs/docs/tools/ci_feedback.md

@@ -1,20 +1,19 @@
-# CI Feedback Tool
+## Overview
 
 The CI feedback tool (`/checks)` automatically triggers when a PR has a failed check.
 The tool analyzes the failed checks and provides several feedbacks:
+
 - Failed stage
 - Failed test name
 - Failure summary
 - Relevant error logs
 
-<kbd>
-<img src="https://www.codium.ai/images/pr_agent/failed_check1.png" width="768">
-</kbd>
+## Example usage
+
+![Failed Check 1](https://www.codium.ai/images/pr_agent/failed_check1.png){width=768}
 
 &rarr;
-<kbd>
-<img src="https://www.codium.ai/images/pr_agent/failed_check2.png" width="768">
-</kbd>
+![Failed Check 2](https://www.codium.ai/images/pr_agent/failed_check2.png){width=768}
 
 ___
 
@@ -24,8 +23,17 @@ In addition to being automatically triggered, the tool can also be invoked manua
 ```
 where `{repo_name}` is the name of the repository, `{run_number}` is the run number of the failed check, and `{job_number}` is the job number of the failed check.
 
-### Configuration options
+## Disabling the tool from running automatically
+
+If you wish to disable the tool from running automatically, you can do so by adding the following configuration to the configuration file:
+```
+[checks]
+enable_auto_checks_feedback = false
+```
+
+## Configuration options
 - `enable_auto_checks_feedback` - if set to true, the tool will automatically provide feedback when a check is failed. Default is true.
 - `excluded_checks_list` - a list of checks to exclude from the feedback, for example: ["check1", "check2"]. Default is an empty list.
 - `persistent_comment` - if set to true, the tool will overwrite a previous checks comment with the new feedback. Default is true.
 - `enable_help_text=true` - if set to true, the tool will provide a help message when a user comments "/checks" on a PR. Default is true.
+- `final_update_message` - if `persistent_comment` is true and updating a previous checks message, the tool will also create a new message: "Persistent checks updated to latest commit". Default is true.

docs/docs/tools/custom_labels.md

@@ -1,18 +1,20 @@
-# Generate Custom Labels 💎
+## Overview
 The `generate_labels` tool scans the PR code changes, and given a list of labels and their descriptions, it automatically suggests labels that match the PR code changes.
 
 It can be invoked manually by commenting on any PR:
 ```
 /generate_labels
 ```
-For example:
+
+## Example usage
 
 If we wish to add detect changes to SQL queries in a given PR, we can add the following custom label along with its description:
 
-<kbd><img src=https://codium.ai/images/pr_agent/custom_labels_list.png width="768"></kbd>
+![Custom labels list](https://codium.ai/images/pr_agent/custom_labels_list.png){width=768}
 
 When running the `generate_labels` tool on a PR that includes changes in SQL queries, it will automatically suggest the custom label:
-<kbd><img src=https://codium.ai/images/pr_agent/custom_label_published.png width="768"></kbd>
+
+![Custom labels published](https://codium.ai/images/pr_agent/custom_label_published.png){width=768}
 
 Note that in addition to the dedicated tool `generate_labels`, the custom labels will also be used by the `describe` tool.
 
@@ -20,13 +22,14 @@ Note that in addition to the dedicated tool `generate_labels`, the custom labels
 There are 3 ways to enable custom labels:
 
 #### 1. CLI (local configuration file)
-When working from CLI, you need to apply the [configuration changes](#configuration-changes) to the [custom_labels file](./../pr_agent/settings/custom_labels.toml):
+When working from CLI, you need to apply the [configuration changes](#configuration-options) to the [custom_labels file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/custom_labels.toml):
 
 #### 2. Repo configuration file
-To enable custom labels, you need to apply the [configuration changes](#configuration-changes) to the local `.pr_agent.toml` file in you repository.
+To enable custom labels, you need to apply the [configuration changes](#configuration-options) to the local `.pr_agent.toml` file in you repository.
 
-#### 3. Handle custom labels from the Repo's labels page 
+#### 3. Handle custom labels from the Repo's labels page 💎
 > This feature is available only in PR-Agent Pro 
+
 * GitHub : `https://github.com/{owner}/{repo}/labels`, or click on the "Labels" tab in the issues or PRs page.
 * GitLab : `https://gitlab.com/{owner}/{repo}/-/labels`, or click on "Manage" -> "Labels" on the left menu.
 
@@ -34,13 +37,14 @@ b. Add/edit the custom labels. It should be formatted as follows:
 * Label name: The name of the custom label.
 * Description: Start the description of with prefix `pr_agent:`, for example: `pr_agent: Description of when AI should suggest this label`.<br>
 The description should be comprehensive and detailed, indicating when to add the desired label.
-<kbd><img src=https://codium.ai/images/pr_agent/add_native_custom_labels.png width="880"></kbd>
+
+![Add native custom labels](https://codium.ai/images/pr_agent/add_native_custom_labels.png){width=880}
 
 c. Now the custom labels will be included in the `generate_labels` tool.
 
-*This feature is supported in GitHub and GitLab.
+> This feature is supported in GitHub and GitLab.
 
-#### Configuration changes
+## Configuration options
  - Change `enable_custom_labels` to True: This will turn off the default labels and enable the custom labels provided in the custom_labels.toml file.
  - Add the custom labels. It should be formatted as follows:
 
@@ -53,5 +57,4 @@ description = "Description of when AI should suggest this label"
 
 [custom_labels."Custom Label 2"]
 description = "Description of when AI should suggest this label 2"
-```
-
+```

docs/docs/tools/custom_prompt.md

@@ -0,0 +1,58 @@
+## Overview
+The `custom_prompt` tool scans the PR code changes, and automatically generates suggestions for improving the PR code.
+It shares similarities with the `improve` tool, but with one main difference: the `custom_prompt` tool will **only propose suggestions that follow specific guidelines defined by the prompt** in: `pr_custom_prompt.prompt` configuration.
+
+The tool can be triggered [automatically](../usage-guide/automations_and_usage.md#github-app-automatic-tools-when-a-new-pr-is-opened) every time a new PR is opened, or can be invoked manually by commenting on a PR.
+
+When commenting, use the following template:
+
+```
+/custom_prompt --pr_custom_prompt.prompt="
+The code suggestions should focus only on the following:
+- ...
+- ...
+
+"
+```
+
+With a [configuration file](../usage-guide/automations_and_usage.md#github-app), use the following template:
+
+```
+[pr_custom_prompt]
+prompt="""\
+The suggestions should focus only on the following:
+-...
+-...
+
+"""
+```
+
+Remember - with this tool, you are the prompter. Be specific, clear, and concise in the instructions. Specify relevant aspects that you want the model to focus on. \
+You might benefit from several trial-and-error iterations, until you get the correct prompt for your use case.
+
+## Example usage
+
+Here is an example of a possible prompt, defined in the configuration file:
+```
+[pr_custom_prompt]
+prompt="""\
+The code suggestions should focus only on the following:
+- look for edge cases when implementing a new function
+- make sure every variable has a meaningful name
+- make sure the code is efficient
+"""
+```     
+
+(The instructions above are just an example. We want to emphasize that the prompt should be specific and clear, and be tailored to the needs of your project)
+
+Results obtained with the prompt above:
+
+![Custom prompt results](https://codium.ai/images/pr_agent/custom_suggestions_result.png){width=768}
+
+## Configuration options
+
+`prompt`: the prompt for the tool. It should be a multi-line string.
+
+`num_code_suggestions`: number of code suggestions provided by the 'custom_prompt' tool. Default is 4.
+
+`enable_help_text`: if set to true, the tool will display a help text in the comment. Default is true.

docs/docs/tools/describe.md

@@ -0,0 +1,224 @@
+## Overview
+The `describe` tool scans the PR code changes, and generates a description for the PR - title, type, summary, walkthrough and labels.
+
+The tool can be triggered automatically every time a new PR is [opened](../usage-guide/automations_and_usage.md#github-app-automatic-tools-when-a-new-pr-is-opened), or it can be invoked manually by commenting on any PR:
+```
+/describe
+```
+
+## Example usage
+
+### Manual triggering
+
+Invoke the tool manually by commenting `/describe` on any PR:
+
+![Describe comment](https://codium.ai/images/pr_agent/describe_comment.png){width=512}
+
+After ~30 seconds, the tool will generate a description for the PR:
+
+![Describe New](https://codium.ai/images/pr_agent/describe_new.png){width=512}
+
+If you want to edit [configurations](#configuration-options), add the relevant ones to the command:
+```
+/describe --pr_description.some_config1=... --pr_description.some_config2=...
+```
+
+### Automatic triggering
+
+To run the `describe` automatically when a PR is opened, define in a [configuration file](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/#wiki-configuration-file):
+```
+[github_app]
+pr_commands = [
+    "/describe",
+    ...
+]
+
+[pr_description]
+publish_labels = ...
+...
+```
+
+- The `pr_commands` lists commands that will be executed automatically when a PR is opened.
+- The `[pr_description]` section contains the configurations for the `describe` tool you want to edit (if any).
+
+
+## Configuration options
+
+!!! example "Possible configurations"
+
+<table>
+  <tr>
+    <td><b>publish_labels</b></td>
+    <td>If set to true, the tool will publish the labels to the PR. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>publish_description_as_comment</b></td>
+    <td>If set to true, the tool will publish the description as a comment to the PR. If false, it will overwrite the original description. Default is false.</td>
+  </tr>
+  <tr>
+    <td><b>publish_description_as_comment_persistent</b></td>
+    <td>If set to true and `publish_description_as_comment` is true, the tool will publish the description as a persistent comment to the PR. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>add_original_user_description</b></td>
+    <td>If set to true, the tool will add the original user description to the generated description. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>generate_ai_title</b></td>
+    <td>If set to true, the tool will also generate an AI title for the PR. Default is false.</td>
+  </tr>
+  <tr>
+    <td><b>extra_instructions</b></td>
+    <td>Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ..."</td>
+  </tr>
+  <tr>
+    <td><b>enable_pr_type</b></td>
+    <td>If set to false, it will not show the `PR type` as a text value in the description content. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>final_update_message</b></td>
+    <td>If set to true, it will add a comment message [`PR Description updated to latest commit...`](https://github.com/Codium-ai/pr-agent/pull/499#issuecomment-1837412176) after finishing calling `/describe`. Default is false.</td>
+  </tr>
+  <tr>
+    <td><b>enable_semantic_files_types</b></td>
+    <td>If set to true, "Changes walkthrough" section will be generated. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>collapsible_file_list</b></td>
+    <td>If set to true, the file list in the "Changes walkthrough" section will be collapsible. If set to "adaptive", the file list will be collapsible only if there are more than 8 files. Default is "adaptive".</td>
+  </tr>
+  <tr>
+    <td><b>enable_large_pr_handling</b></td>
+    <td>Pro feature. If set to true, in case of a large PR the tool will make several calls to the AI and combine them to be able to cover more files. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>enable_help_text</b></td>
+    <td>If set to true, the tool will display a help text in the comment. Default is false.</td>
+  </tr>
+</table>
+
+
+## Inline file summary 💎
+
+This feature enables you to copy the `changes walkthrough` table to the "Files changed" tab, so you can quickly understand the changes in each file while reviewing the code changes (diff view).
+
+To copy the `changes walkthrough` table to the "Files changed" tab, you can click on the checkbox that appears PR Description status message below the main PR Description:
+
+![Add table checkbox](https://codium.ai/images/pr_agent/add_table_checkbox.png){width=512}
+
+If you prefer to have the file summaries appear in the "Files changed" tab on every PR, change the `pr_description.inline_file_summary` parameter in the configuration file, possible values are:
+
+- `'table'`: File changes walkthrough table will be displayed on the top of the "Files changed" tab, in addition to the "Conversation" tab.
+
+![Diffview table](https://codium.ai/images/pr_agent/diffview-table.png){width=512}
+
+- `true`: A collapsible file comment with changes title and a changes summary for each file in the PR.
+
+![Diffview changes](https://codium.ai/images/pr_agent/diffview_changes.png){width=512}
+
+- `false` (`default`): File changes walkthrough will be added only to the "Conversation" tab.
+
+**Note**: that this feature is currently available only for GitHub.
+
+
+## Markers template
+
+To enable markers, set `pr_description.use_description_markers=true`.
+Markers enable to easily integrate user's content and auto-generated content, with a template-like mechanism.
+
+For example, if the PR original description was:
+```
+User content...
+
+## PR Type:
+pr_agent:type
+
+## PR Description:
+pr_agent:summary
+
+## PR Walkthrough:
+pr_agent:walkthrough
+```
+The marker `pr_agent:type` will be replaced with the PR type, `pr_agent:summary` will be replaced with the PR summary, and `pr_agent:walkthrough` will be replaced with the PR walkthrough.
+
+![Describe markers before](https://codium.ai/images/pr_agent/describe_markers_before.png){width=512}
+
+&rarr;
+
+![Describe markers after](https://codium.ai/images/pr_agent/describe_markers_after.png){width=512}
+
+
+**Configuration params**:
+
+- `use_description_markers`: if set to true, the tool will use markers template. It replaces every marker of the form `pr_agent:marker_name` with the relevant content. Default is false.
+- `include_generated_by_header`: if set to true, the tool will add a dedicated header: 'Generated by PR Agent at ...' to any automatic content. Default is true.
+
+## Custom labels
+The default labels of the describe tool are quite generic, since they are meant to be used in any repo: [`Bug fix`, `Tests`, `Enhancement`, `Documentation`, `Other`].
+
+You can define custom labels that are relevant for your repo and use cases.
+Custom labels can be defined in a [configuration file](https://pr-agent-docs.codium.ai/tools/custom_labels/#configuration-options), or directly in the repo's [labels page](#handle-custom-labels-from-the-repos-labels-page).
+
+Make sure to provide proper title, and a detailed and well-phrased description for each label, so the tool will know when to suggest it.
+Each label description should be a **conditional statement**, that indicates if to add the label to the PR or not, according to the PR content.
+
+### Handle custom labels from a configuration file
+Example for a custom labels configuration setup in a configuration file:
+```
+[config]
+enable_custom_labels=true
+
+
+[custom_labels."sql_changes"]
+description = "Use when a PR contains changes to SQL queries"
+
+[custom_labels."test"]
+description = "use when a PR primarily contains new tests"
+
+...
+```
+
+### Handle custom labels from the Repo's labels page 💎
+
+You can also control the custom labels that will be suggested by the `describe` tool from the repo's labels page:
+
+* GitHub : go to `https://github.com/{owner}/{repo}/labels` (or click on the "Labels" tab in the issues or PRs page)
+* GitLab : go to `https://gitlab.com/{owner}/{repo}/-/labels` (or click on "Manage" -> "Labels" on the left menu)
+
+Now add/edit the custom labels. they should be formatted as follows:
+
+* Label name: The name of the custom label.
+* Description: Start the description of with prefix `pr_agent:`, for example: `pr_agent: Description of when AI should suggest this label`.<br>
+
+Examples for custom labels:
+
+  - `Main topic:performance` -  pr_agent:The main topic of this PR is performance
+  - `New endpoint` -  pr_agent:A new endpoint was added in this PR
+  - `SQL query` -  pr_agent:A new SQL query was added in this PR
+  - `Dockerfile changes` - pr_agent:The PR contains changes in the Dockerfile
+  - ...
+
+The description should be comprehensive and detailed, indicating when to add the desired label. For example:
+![Add native custom labels](https://codium.ai/images/pr_agent/add_native_custom_labels.png){width=768}
+
+
+## Usage Tips
+
+!!! tip "Automation"
+    - When you first install PR-Agent app, the [default mode](../usage-guide/automations_and_usage.md#github-app) for the describe tool is:
+    ```
+    pr_commands = ["/describe", ...]
+    ```
+    meaning the `describe` tool will run automatically on every PR, with the default configurations.
+
+
+   - Markers are an alternative way to control the generated description, to give maximal control to the user. If you set:
+   ```
+   pr_commands = ["/describe --pr_description.use_description_markers=true", ...]
+   ```
+   the tool will replace every marker of the form `pr_agent:marker_name` in the PR description with the relevant content, where `marker_name` is one of the following:
+         * `type`: the PR type.
+         * `summary`: the PR summary.
+         * `walkthrough`: the PR walkthrough.
+
+   - Note that when markers are enabled, if the original PR description does not contain any markers, the tool will not alter the description at all.

docs/docs/tools/documentation.md

@@ -0,0 +1,33 @@
+## Overview
+The `add_docs` tool scans the PR code changes, and automatically suggests documentation for any code components that changed in the PR (functions, classes, etc.).
+
+It can be invoked manually by commenting on any PR:
+```
+/add_docs
+```
+
+## Example usage
+
+Invoke the tool manually by commenting `/add_docs` on any PR:
+
+![Docs command](https://codium.ai/images/pr_agent/docs_command.png){width=768}
+
+The tool will generate documentation for all the components that changed in the PR:
+
+![Docs component](https://codium.ai/images/pr_agent/docs_components.png){width=768}
+
+![Docs single component](https://codium.ai/images/pr_agent/docs_single_component.png){width=768}
+
+You can state a name of a specific component in the PR to get documentation only for that component:
+```
+/add_docs component_name
+```
+
+## Configuration options
+ - `docs_style`: The exact style of the documentation (for python docstring). you can choose between: `google`, `numpy`, `sphinx`, `restructuredtext`, `plain`. Default is `sphinx`.
+ - `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
+
+**Notes**
+
+- Language that are currently fully supported: Python, Java, C++, JavaScript, TypeScript, C#.
+- This tool can also be triggered interactively by using the [`analyze`](./analyze.md) tool.

docs/docs/tools/help.md

@@ -0,0 +1,17 @@
+## Overview
+The `help` tool provides a list of all the available tools and their descriptions.
+For PR-Agent Pro users, it also enables to trigger each tool by checking the relevant box.
+
+It can be invoked manually by commenting on any PR:
+```
+/help
+```
+
+## Example usage
+An example [result](https://github.com/Codium-ai/pr-agent/pull/546#issuecomment-1868524805):
+
+![Help 1](https://codium.ai/images/pr_agent/help1.png){width=750}
+
+→
+
+![Analyze 2](https://codium.ai/images/pr_agent/help2.png){width=750}

docs/docs/tools/improve.md

@@ -0,0 +1,195 @@
+## Overview
+The `improve` tool scans the PR code changes, and automatically generates suggestions for improving the PR code.
+The tool can be triggered automatically every time a new PR is [opened](../usage-guide/automations_and_usage.md#github-app-automatic-tools-when-a-new-pr-is-opened), or it can be invoked manually by commenting on any PR:
+```
+/improve
+```
+
+## Example usage
+
+### Manual triggering
+
+Invoke the tool manually by commenting `/improve` on any PR. The code suggestions by default are presented as a single comment:
+
+![code suggestions as comment](https://codium.ai/images/pr_agent/code_suggestions_as_comment.png){width=512}
+
+To edit [configurations](#configuration-options) related to the improve tool, use the following template:
+```
+/improve --pr_code_suggestions.some_config1=... --pr_code_suggestions.some_config2=...
+```
+
+For example, you can choose to present the suggestions as commitable code comments, by running the following command:
+```
+/improve --pr_code_suggestions.commitable_code_suggestions=true
+```
+
+![improve](https://codium.ai/images/pr_agent/improve.png){width=512}
+
+
+Note that a single comment has a significantly smaller PR footprint. We recommend this mode for most cases.
+Also note that collapsible are not supported in _Bitbucket_. Hence, the suggestions are presented there as code comments.
+
+### Automatic triggering
+
+To run the `improve` automatically when a PR is opened, define in a [configuration file](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/#wiki-configuration-file):
+```
+[github_app]
+pr_commands = [
+    "/improve",
+    ...
+]
+
+[pr_code_suggestions]
+num_code_suggestions_per_chunk = ...
+...
+```
+
+- The `pr_commands` lists commands that will be executed automatically when a PR is opened.
+- The `[pr_code_suggestions]` section contains the configurations for the `improve` tool you want to edit (if any)
+
+### Extended mode
+
+An extended mode, which does not involve PR Compression and provides more comprehensive suggestions, can be invoked by commenting on any PR by setting:
+```
+[pr_code_suggestions]
+auto_extended_mode=true
+```
+(This mode is true by default).
+
+Note that the extended mode divides the PR code changes into chunks, up to the token limits, where each chunk is handled separately (might use multiple calls to GPT-4 for large PRs).
+Hence, the total number of suggestions is proportional to the number of chunks, i.e., the size of the PR.
+
+### Self-review
+If you set in a configuration file:
+```
+[pr_code_suggestions]
+demand_code_suggestions_self_review = true
+```
+The `improve` tool will add a checkbox below the suggestions, prompting user to acknowledge that they have reviewed the suggestions.
+You can set the content of the checkbox text via:
+```
+[pr_code_suggestions]
+code_suggestions_self_review_text = "... (your text here) ..."
+```
+![self_review_1](https://codium.ai/images/pr_agent/self_review_1.png){width=512}
+
+💎 In addition, by setting:
+```
+[pr_code_suggestions]
+approve_pr_on_self_review = true
+```
+the tool can automatically approve the PR when the user checks the self-review checkbox.
+
+!!! tip "Demanding self-review from the PR author"
+  If you set the number of required reviewers for a PR to 2, this effectively means that the PR author must click the self-review checkbox before the PR can be merged (in addition to a human reviewer).
+  ![self_review_2](https://codium.ai/images/pr_agent/self_review_2.png){width=512}
+
+
+## Configuration options
+
+!!! example "General options"
+
+<table>
+  <tr>
+    <td><b>num_code_suggestions</b></td>
+    <td>Number of code suggestions provided by the 'improve' tool. Default is 4 for CLI, 0 for auto tools.</td>
+  </tr>
+  <tr>
+    <td><b>extra_instructions</b></td>
+    <td>Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".</td>
+  </tr>
+  <tr>
+    <td><b>rank_suggestions</b></td>
+    <td>If set to true, the tool will rank the suggestions, based on importance. Default is false.</td>
+  </tr>
+  <tr>
+    <td><b>commitable_code_suggestions</b></td>
+    <td>If set to true, the tool will display the suggestions as commitable code comments. Default is false.</td>
+  </tr>
+  <tr>
+    <td><b>persistent_comment</b></td>
+    <td>If set to true, the improve comment will be persistent, meaning that every new improve request will edit the previous one. Default is false.</td>
+  </tr>
+  <tr>
+    <td><b>self_reflect_on_suggestions</b></td>
+    <td>If set to true, the improve tool will calculate an importance score for each suggestion [1-10], and sort the suggestion labels group based on this score. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>suggestions_score_threshold</b></td>
+    <td> Any suggestion with importance score less than this threshold will be removed. Default is 0. Highly recommend not to set this value above 7-8, since above it may clip relevant suggestions that can be useful. </td>
+  </tr>
+  <tr>
+    <td><b>apply_suggestions_checkbox</b></td>
+    <td> Enable the checkbox to create a committable suggestion. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>enable_help_text</b></td>
+    <td>If set to true, the tool will display a help text in the comment. Default is true.</td>
+  </tr>
+</table>
+
+!!! example "params for 'extended' mode"
+
+<table>
+  <tr>
+    <td><b>auto_extended_mode</b></td>
+    <td>Enable extended mode automatically (no need for the --extended option). Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>num_code_suggestions_per_chunk</b></td>
+    <td>Number of code suggestions provided by the 'improve' tool, per chunk. Default is 5.</td>
+  </tr>
+  <tr>
+    <td><b>rank_extended_suggestions</b></td>
+    <td>If set to true, the tool will rank the suggestions, based on importance. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>max_number_of_calls</b></td>
+    <td>Maximum number of chunks. Default is 5.</td>
+  </tr>
+  <tr>
+    <td><b>final_clip_factor</b></td>
+    <td>Factor to remove suggestions with low confidence. Default is 0.9.</td>
+  </tr>
+</table>
+
+## Usage Tips
+
+!!! tip "Extra instructions"
+
+    Extra instructions are very important for the `improve` tool, since they enable you to guide the model to suggestions that are more relevant to the specific needs of the project.
+    
+    Be specific, clear, and concise in the instructions. With extra instructions, you are the prompter. Specify relevant aspects that you want the model to focus on.
+    
+    Examples for extra instructions:
+    ```
+    [pr_code_suggestions] # /improve #
+    extra_instructions="""\
+    Emphasize the following aspects:
+    - Does the code logic cover relevant edge cases?
+    - Is the code logic clear and easy to understand?
+    - Is the code logic efficient?
+    ...
+    """
+    ```
+    Use triple quotes to write multi-line instructions. Use bullet points to make the instructions more readable.
+
+!!! tip "Review vs. Improve tools comparison"
+
+    - The [review](https://pr-agent-docs.codium.ai/tools/review/) tool includes a section called 'Possible issues', that also provide feedback on the PR Code.
+    In this section, the model is instructed to focus **only** on [major bugs and issues](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml#L71).
+    - The `improve` tool, on the other hand, has a broader mandate, and in addition to bugs and issues, it can also give suggestions for improving code quality and making the code more efficient, readable, and maintainable (see [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/pr_code_suggestions_prompts.toml#L34)).
+    - Hence, if you are interested only in feedback about clear bugs, the `review` tool might suffice. If you want a more detailed feedback, including broader suggestions for improving the PR code, also enable the `improve` tool to run on each PR.
+
+## A note on code suggestions quality
+
+- While the current AI for code is getting better and better (GPT-4), it's not flawless. Not all the suggestions will be perfect, and a user should not accept all of them automatically. Critical reading and judgment are required.
+- While mistakes of the AI are rare but can happen, a real benefit from the suggestions of the `improve` (and [`review`](https://pr-agent-docs.codium.ai/tools/review/)) tool is to catch, with high probability, **mistakes or bugs done by the PR author**, when they happen. So, it's a good practice to spend the needed ~30-60 seconds to review the suggestions, even if not all of them are always relevant.
+- The hierarchical structure of the suggestions is designed to help the user to _quickly_ understand them, and to decide which ones are relevant and which are not:
+
+    - Only if the `Category` header is relevant, the user should move to the summarized suggestion description
+    - Only if the summarized suggestion description is relevant, the user should click on the collapsible, to read the full suggestion description with a code preview example.
+
+In addition, we recommend to use the `extra_instructions` field to guide the model to suggestions that are more relevant to the specific needs of the project. 
+<br>
+Consider also trying the [Custom Prompt Tool](./custom_prompt.md) 💎, that will **only** propose code suggestions that follow specific guidelines defined by user.

docs/docs/tools/improve_component.md

@@ -0,0 +1,29 @@
+## Overview
+The `improve_component` tool generates code suggestions for a specific code component that changed in the PR.
+it can be invoked manually by commenting on any PR:
+```
+/improve_component component_name
+```
+
+To get a list of the components that changed in the PR and choose the relevant component interactively, use the [`analyze`](./analyze.md) tool.
+
+
+## Example usage
+
+Invoke the tool manually by commenting `/improve_component` on any PR:
+
+![improve_component1](https://codium.ai/images/pr_agent/improve_component1.png){width=768}
+
+The tool will generate code suggestions for the selected component (if no component is stated, it will generate code suggestions for the largest component):
+
+![improve_component2](https://codium.ai/images/pr_agent/improve_component2.png){width=768}
+
+**Notes**
+- Language that are currently supported by the tool: Python, Java, C++, JavaScript, TypeScript, C#.
+- This tool can also be triggered interactively by using the [`analyze`](./analyze.md) tool.
+
+## Configuration options
+- `num_code_suggestions`: number of code suggestions to provide. Default is 4
+- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on ...".
+- `file`: in case there are several components with the same name, you can specify the relevant file.
+- `class_name`: in case there are several methods with the same name in the same file, you can specify the relevant class name.

docs/docs/tools/index.md

@@ -0,0 +1,22 @@
+# Tools
+
+Here is a list of PR-Agent tools, each with a dedicated page that explains how to use it:
+
+| Tool                                                                                     | Description                                                                                                                                 |
+|------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------|
+| **[PR Description (`/describe`](./describe.md))**                                        | Automatically generating PR description - title, type, summary, code walkthrough and labels                                                 |
+| **[PR Review (`/review`](./review.md))**                                                 | Adjustable feedback about the PR, possible issues, security concerns, review effort and more                                                |
+| **[Code Suggestions (`/improve`](./improve.md))**                                        | Code suggestions for improving the PR                                                                                                       |
+| **[Question Answering (`/ask ...`](./ask.md))**                                          | Answering free-text questions about the PR, or on specific code lines                                                                       |
+| **[Update Changelog (`/update_changelog`](./update_changelog.md))**                      | Automatically updating the CHANGELOG.md file with the PR changes                                                                            |
+| **[Find Similar Issue (`/similar_issue`](./similar_issues.md))**                         | Automatically retrieves and presents similar issues                                                                                         |
+| **[Help (`/help`](./help.md))**                                                          | Provides a list of all the available tools. Also enables to trigger them interactively (💎)                                                 |
+| **💎 [Add Documentation (`/add_docs`](./documentation.md))**                             | Generates documentation to methods/functions/classes that changed in the PR                                                                 |
+| **💎 [Generate Custom Labels (`/generate_labels`](./custom_labels.md))**                 | Generates custom labels for the PR, based on specific guidelines defined by the user                                                        |
+| **💎 [Analyze (`/analyze`](./analyze.md))**                                              | Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component |
+| **💎 [Custom Prompt (`/custom_prompt`](./custom_prompt.md))**                            | Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user                      |
+| **💎 [Generate Tests (`/test component_name`](./test.md))**                              | Automatically generates unit tests for a selected component, based on the PR code changes                                                   |
+| **💎 [Improve Component (`/improve_component component_name`](./improve_component.md))** | Generates code suggestions for a specific code component that changed in the PR                                                             |
+| **💎 [CI Feedback (`/checks ci_job`](./ci_feedback.md))**                                | Automatically generates feedback and analysis for a failed CI job                                                                           |
+
+Note that the tools marked with 💎 are available only for PR-Agent Pro users.

docs/docs/tools/review.md

@@ -0,0 +1,261 @@
+## Overview
+The `review` tool scans the PR code changes, and generates a list of feedbacks about the PR, aiming to aid the reviewing process.
+<br>
+The tool can be triggered automatically every time a new PR is [opened](../usage-guide/automations_and_usage.md#github-app-automatic-tools-when-a-new-pr-is-opened), or can be invoked manually by commenting on any PR:
+```
+/review
+```
+
+Note that the main purpose of the `review` tool is to provide the **PR reviewer** with useful feedbacks and insights. The PR author, in contrast, may prefer to save time and focus on the output of the [improve](./improve.md) tool, which provides actionable code suggestions.
+
+## Example usage
+
+### Manual triggering
+
+Invoke the tool manually by commenting `/review` on any PR:
+
+![review comment](https://codium.ai/images/pr_agent/review_comment.png){width=512}
+
+After ~30 seconds, the tool will generate a review for the PR:
+
+![review](https://codium.ai/images/pr_agent/review3.png){width=512}
+
+If you want to edit [configurations](#configuration-options), add the relevant ones to the command:
+```
+/review --pr_reviewer.some_config1=... --pr_reviewer.some_config2=...
+```
+
+### Automatic triggering
+
+To run the `review` automatically when a PR is opened, define in a [configuration file](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/#wiki-configuration-file):
+```
+[github_app]
+pr_commands = [
+    "/review",
+    ...
+]
+
+[pr_reviewer]
+num_code_suggestions = ...
+...
+```
+
+- The `pr_commands` lists commands that will be executed automatically when a PR is opened.
+- The `[pr_reviewer]` section contains the configurations for the `review` tool you want to edit (if any).
+
+### Incremental Mode
+Incremental review only considers changes since the last PR-Agent review. This can be useful when working on the PR in an iterative manner, and you want to focus on the changes since the last review instead of reviewing the entire PR again.
+For invoking the incremental mode, the following command can be used:
+```
+/review -i
+```
+Note that the incremental mode is only available for GitHub.
+
+![incremental review](https://codium.ai/images/pr_agent/incremental_review_2.png){width=512}
+
+[//]: # (### PR Reflection)
+
+[//]: # ()
+[//]: # (By invoking:)
+
+[//]: # (```)
+
+[//]: # (/reflect_and_review)
+
+[//]: # (```)
+
+[//]: # (The tool will first ask the author questions about the PR, and will guide the review based on their answers.)
+
+[//]: # ()
+[//]: # (![reflection questions]&#40;https://codium.ai/images/pr_agent/reflection_questions.png&#41;{width=512})
+
+[//]: # ()
+[//]: # (![reflection answers]&#40;https://codium.ai/images/pr_agent/reflection_answers.png&#41;{width=512})
+
+[//]: # ()
+[//]: # (![reflection insights]&#40;https://codium.ai/images/pr_agent/reflection_insights.png&#41;{width=512})
+
+
+
+## Configuration options
+
+!!! example "General options"
+
+<table>
+  <tr>
+    <td><b>num_code_suggestions</b></td>
+    <td>Number of code suggestions provided by the 'review' tool. For manual comments, default is 4. For PR-Agent app auto tools, default is 0, meaning no code suggestions will be provided by the review tool, unless you manually edit pr_commands.</td>
+  </tr>
+  <tr>
+    <td><b>inline_code_comments</b></td>
+    <td>If set to true, the tool will publish the code suggestions as comments on the code diff. Default is false.</td>
+  </tr>
+  <tr>
+    <td><b>persistent_comment</b></td>
+    <td>If set to true, the review comment will be persistent, meaning that every new review request will edit the previous one. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>extra_instructions</b></td>
+    <td>Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".</td>
+  </tr>
+  <tr>
+    <td><b>enable_help_text</b></td>
+    <td>If set to true, the tool will display a help text in the comment. Default is true.</td>
+  </tr>
+</table>
+
+!!! example "Enable\\disable specific sub-sections"
+
+<table>
+  <tr>
+    <td><b>require_score_review</b></td>
+    <td>If set to true, the tool will add a section that scores the PR. Default is false.</td>
+  </tr>
+  <tr>
+    <td><b>require_tests_review</b></td>
+    <td>If set to true, the tool will add a section that checks if the PR contains tests. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>require_estimate_effort_to_review</b></td>
+    <td>If set to true, the tool will add a section that estimates the effort needed to review the PR. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>require_can_be_split_review</b></td>
+    <td>If set to true, the tool will add a section that checks if the PR contains several themes, and can be split into smaller PRs. Default is false.</td>
+  </tr>
+  <tr>
+    <td><b>require_security_review</b></td>
+    <td>If set to true, the tool will add a section that checks if the PR contains a possible security or vulnerability issue. Default is true.</td>
+  </tr>
+</table>
+
+!!! example "SOC2 ticket compliance 💎"
+
+This sub-tool checks if the PR description properly contains a ticket to a project management system (e.g., Jira, Asana, Trello, etc.), as required by SOC2 compliance. If not, it will add a label to the PR: "Missing SOC2 ticket".
+    
+<table>
+  <tr>
+    <td><b>require_soc2_ticket</b></td>
+    <td>If set to true, the SOC2 ticket checker sub-tool will be enabled. Default is false.</td>
+  </tr>
+  <tr>
+    <td><b>soc2_ticket_prompt</b></td>
+    <td>The prompt for the SOC2 ticket review. Default is: `Does the PR description include a link to ticket in a project management system (e.g., Jira, Asana, Trello, etc.) ?`. Edit this field if your compliance requirements are different.</td>
+  </tr>
+</table>
+
+!!! example "Adding PR labels"
+
+You can enable\disable the `review` tool to add specific labels to the PR:
+
+<table>
+  <tr>
+    <td><b>enable_review_labels_security</b></td>
+    <td>If set to true, the tool will publish a 'possible security issue' label if it detects a security issue. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>enable_review_labels_effort</b></td>
+    <td>If set to true, the tool will publish a 'Review effort [1-5]: x' label. Default is true.</td>
+  </tr>
+</table>
+
+!!! example "Auto-approval"
+
+If enabled, the `review` tool can approve a PR when a specific comment, `/review auto_approve`, is invoked.
+
+<table>
+  <tr>
+    <td><b>enable_auto_approval</b></td>
+    <td>If set to true, the tool will approve the PR when invoked with the 'auto_approve' command. Default is false. This flag can be changed only from configuration file.</td>
+  </tr>
+  <tr>
+    <td><b>maximal_review_effort</b></td>
+    <td>Maximal effort level for auto-approval. If the PR's estimated review effort is above this threshold, the auto-approval will not run. Default is 5.</td>
+  </tr>
+</table>
+
+## Usage Tips
+
+!!! tip "General guidelines"
+
+    The `review` tool provides a collection of configurable feedbacks about a PR.
+    It is recommended to review the [Configuration options](#configuration-options) section, and choose the relevant options for your use case.
+    
+    Some of the features that are disabled by default are quite useful, and should be considered for enabling. For example: 
+    `require_score_review`, `require_soc2_ticket`, and more.
+    
+    On the other hand, if you find one of the enabled features to be irrelevant for your use case, disable it. No default configuration can fit all use cases.
+
+!!! tip "Automation"
+    When you first install PR-Agent app, the [default mode](../usage-guide/automations_and_usage.md#github-app-automatic-tools-when-a-new-pr-is-opened) for the `review` tool is:
+    ```
+    pr_commands = ["/review --pr_reviewer.num_code_suggestions=0", ...]
+    ```
+    Meaning the `review` tool will run automatically on every PR, without providing code suggestions.
+    Edit this field to enable/disable the tool, or to change the used configurations.
+
+!!! tip "Possible labels from the review tool"
+
+    The `review` tool can auto-generate two specific types of labels for a PR:
+    
+    - a `possible security issue` label that detects if a possible [security issue](https://github.com/Codium-ai/pr-agent/blob/tr/user_description/pr_agent/settings/pr_reviewer_prompts.toml#L136) exists in the PR code (`enable_review_labels_security` flag)
+    - a `Review effort [1-5]: x` label, where x is the estimated effort to review the PR (`enable_review_labels_effort` flag)
+    
+    Both modes are useful, and we recommended to enable them.
+
+!!! tip "Extra instructions"
+
+    Extra instructions are important.
+    The `review` tool can be configured with extra instructions, which can be used to guide the model to a feedback tailored to the needs of your project.
+    
+    Be specific, clear, and concise in the instructions. With extra instructions, you are the prompter. Specify the relevant sub-tool, and the relevant aspects of the PR that you want to emphasize.
+    
+    Examples for extra instructions:
+    ```
+    [pr_reviewer]
+    extra_instructions="""\
+    In the code feedback section, emphasize the following:
+    - Does the code logic cover relevant edge cases?
+    - Is the code logic clear and easy to understand?
+    - Is the code logic efficient?
+    ...
+    """
+    ```
+    Use triple quotes to write multi-line instructions. Use bullet points to make the instructions more readable.
+
+
+!!! tip "Auto-approval"
+
+    PR-Agent can approve a PR when a specific comment is invoked.
+    
+    To ensure safety, the auto-approval feature is disabled by default. To enable auto-approval, you need to actively set in a pre-defined configuration file the following:
+    ```
+    [pr_reviewer]
+    enable_auto_approval = true
+    ```
+    (this specific flag cannot be set with a command line argument, only in the configuration file, committed to the repository)
+    
+    
+    After enabling, by commenting on a PR:
+    ```
+    /review auto_approve
+    ```
+    PR-Agent will automatically approve the PR, and add a comment with the approval.
+    
+    
+    You can also enable auto-approval only if the PR meets certain requirements, such as that the `estimated_review_effort` label is equal or below a certain threshold, by adjusting the flag:
+    ```
+    [pr_reviewer]
+    maximal_review_effort = 5
+    ```
+
+[//]: # (!!! tip  "Code suggestions")
+
+[//]: # ()
+[//]: # (    If you set `num_code_suggestions`>0 , the `review` tool will also provide code suggestions.)
+
+[//]: # (    )
+[//]: # (    Notice If you are interested **only** in the code suggestions, it is recommended to use the [`improve`]&#40;./improve.md&#41; feature instead, since it is a dedicated only to code suggestions, and usually gives better results.)
+
+[//]: # (    Use the `review` tool if you want to get more comprehensive feedback, which includes code suggestions as well.)
+

docs/docs/tools/similar_code.md

@@ -0,0 +1,63 @@
+## Overview
+The similar code tool retrieves the most similar code components from inside the organization's codebase, or from open-source code.
+
+For example:
+
+`Global Search` for a method called `chat_completion`:
+
+![similar code global](https://codium.ai/images/pr_agent/similar_code_global2.png){width=768}
+
+
+PR-Agent will examine the code component and will extract the most relevant keywords to search for similar code:
+
+- `extracted keywords`: the keywords that were extracted from the code by PR-Agent. the link will open a search page with the extracted keywords, to allow the user to modify the search if needed.
+- `search context`: the context in which the search will be performed, organization's codebase or open-source code (Global).
+- `similar code`: the most similar code components found. the link will open the code component in the relevant file.
+- `relevant repositories`: the open-source repositories in which that are relevant to the searched code component and it's keywords.
+
+Search result link example:
+
+![code search result single](https://codium.ai/images/pr_agent/code_search_result_single.png){width=768}
+
+
+`Organization Search`:
+
+![similar code org](https://codium.ai/images/pr_agent/similar_code_org.png){width=768}
+
+
+## How to use
+### Manually
+To invoke the `similar code` tool manually, comment on the PR:
+```
+/find_similar_component COMPONENT_NAME
+```
+Where `COMPONENT_NAME` should be the name of a code component in the PR (class, method, function).
+
+If there is a name ambiguity, there are two configurations that will help the tool to find the correct component:
+
+- `--pr_find_similar_component.file`: in case there are several components with the same name, you can specify the relevant file.
+- `--pr_find_similar_component.class_name`: in case there are several methods with the same name in the same file, you can specify the relevant class name.
+
+example:
+```
+/find_similar_component COMPONENT_NAME --pr_find_similar_component.file=FILE_NAME
+```
+
+### Automatically (via Analyze table)
+It can be invoked automatically from the analyze table, can be accessed by:
+```
+/analyze
+```
+Choose the components you want to find similar code for, and click on the `similar` checkbox.
+![analyze similar](https://codium.ai/images/pr_agent/analyze_similar.png){width=768}
+
+If you are looking to search for similar code in the organization's codebase, you can click on the `Organization` checkbox, and it will invoke a new search command just for the organization's codebase. 
+
+![similar code global](https://codium.ai/images/pr_agent/similar_code_global.png){width=768}
+
+
+## Configuration options
+
+- `search_from_org`: if set to true, the tool will search for similar code in the organization's codebase. Default is false.
+- `number_of_keywords`: number of keywords to use for the search. Default is 5.
+- `number_of_results`: the maximum number of results to present. Default is 5.

docs/docs/tools/similar_issues.md

@@ -1,14 +1,18 @@
-# Similar Issue Tool
+## Overview
 The similar issue tool retrieves the most similar issues to the current issue.
 It can be invoked manually by commenting on any PR:
 ```
 /similar_issue
 ```
-For example:
 
-<kbd><img src=https://codium.ai/images/pr_agent/similar_issue_original_issue.png width="768"></kbd>
-<kbd><img src=https://codium.ai/images/pr_agent/similar_issue_comment.png width="768"></kbd>
-<kbd><img src=https://codium.ai/images/pr_agent/similar_issue.png width="768"></kbd>
+
+## Example usage
+
+![similar_issue_original_issue](https://codium.ai/images/pr_agent/similar_issue_original_issue.png){width=768}
+
+![similar_issue_comment](https://codium.ai/images/pr_agent/similar_issue_comment.png){width=768}
+
+![similar_issue](https://codium.ai/images/pr_agent/similar_issue.png){width=768}
 
 Note that to perform retrieval, the `similar_issue` tool indexes all the repo previous issues (once).
 
@@ -29,11 +33,11 @@ environment = "..."
 These parameters can be obtained by registering to [Pinecone](https://app.pinecone.io/?sessionType=signup/).
 
 
-### How to use:
+## How to use
 - To invoke the 'similar issue' tool from **CLI**, run:
 `python3 cli.py --issue_url=... similar_issue`
 
 - To invoke the 'similar' issue tool via online usage, [comment](https://github.com/Codium-ai/pr-agent/issues/178#issuecomment-1716934893) on a PR:
 `/similar_issue`
 
-- You can also enable the 'similar issue' tool to run automatically when a new issue is opened, by adding it to the [pr_commands list in the github_app section](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L66)
+- You can also enable the 'similar issue' tool to run automatically when a new issue is opened, by adding it to the [pr_commands list in the github_app section](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L66)

docs/docs/tools/test.md

@@ -1,26 +1,32 @@
-# Test Tool 💎
+## Overview
 By combining LLM abilities with static code analysis, the `test` tool  generate tests for a selected component, based on the PR code changes.
 It can be invoked manually by commenting on any PR:
 ```
 /test component_name
 ```
 where 'component_name' is the name of a specific component in the PR.
-To get a list of the components that changed in the PR, use the [`analyze`](https://github.com/Codium-ai/pr-agent/blob/main/docs/Analyze.md) tool.
+To get a list of the components that changed in the PR and choose the relevant component interactively, use the [`analyze`](./analyze.md) tool.
+
+## Example usage
+
+Invoke the tool manually by commenting `/test` on any PR:
+
+![test1](https://codium.ai/images/pr_agent/test1.png){width=704}
+
+The tool will generate tests for the selected component (if no component is stated, it will generate tests for largest component):
+
+![test2](https://codium.ai/images/pr_agent/test2.png){width=768}
+
+![test3](https://codium.ai/images/pr_agent/test3.png){width=768}
+
+(Example taken from [here](https://github.com/Codium-ai/pr-agent/pull/598#issuecomment-1913679429)):
+
+**Notes**
+- Language that are currently supported by the tool: Python, Java, C++, JavaScript, TypeScript, C#.
+- This tool can also be triggered interactively by using the [`analyze`](./analyze.md) tool.
 
 
-An example [result](https://github.com/Codium-ai/pr-agent/pull/598#issuecomment-1913679429):
-
-<kbd><img src=https://codium.ai/images/pr_agent/test1.png width="704"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/test2.png width="768"></kbd>
-___
-<kbd><img src=https://codium.ai/images/pr_agent/test3.png width="768"></kbd>
-
-Language that are currently supported by the tool: Python, Java, C++, JavaScript, TypeScript.
-
-
-
-### Configuration options
+## Configuration options
 - `num_tests`: number of tests to generate. Default is 3.
 - `testing_framework`: the testing framework to use. If not set, for Python it will use `pytest`, for Java it will use `JUnit`, for C++ it will use `Catch2`, and for JavaScript and TypeScript it will use `jest`.
 - `avoid_mocks`: if set to true, the tool will try to avoid using mocks in the generated tests. Note that even if this option is set to true, the tool might still use mocks if it cannot generate a test without them. Default is true.

docs/docs/tools/update_changelog.md

@@ -0,0 +1,19 @@
+## Overview
+The `update_changelog` tool automatically updates the CHANGELOG.md file with the PR changes.
+It can be invoked manually by commenting on any PR:
+```
+/update_changelog
+```
+
+## Example usage
+
+![update_changelog_comment](https://codium.ai/images/pr_agent/update_changelog_comment.png){width=768}
+
+![update_changelog](https://codium.ai/images/pr_agent/update_changelog.png){width=768}
+
+## Configuration options
+
+Under the section `pr_update_changelog`, the [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L50) contains options to customize the 'update changelog' tool:
+
+- `push_changelog_changes`: whether to push the changes to CHANGELOG.md, or just print them. Default is false (print only).
+- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...

docs/docs/usage-guide/additional_configurations.md

@@ -0,0 +1,254 @@
+## Ignoring files from analysis
+
+In some cases, you may want to exclude specific files or directories from the analysis performed by CodiumAI PR-Agent. This can be useful, for example, when you have files that are generated automatically or files that shouldn't be reviewed, like vendored code.
+
+You can ignore files or folders using the following methods:
+ - `IGNORE.GLOB`
+ - `IGNORE.REGEX`
+
+which you can edit to ignore files or folders based on glob or regex patterns.
+
+### Example usage
+
+Let's look at an example where we want to ignore all files with `.py` extension from the analysis.
+
+To ignore Python files in a PR with online usage, comment on a PR:
+`/review --ignore.glob="['*.py']"`
+
+
+To ignore Python files in all PRs using `glob` pattern, set in a configuration file:
+```
+[ignore]
+glob = ['*.py']
+```
+
+And to ignore Python files in all PRs using `regex` pattern, set in a configuration file:
+```
+[regex]
+regex = ['.*\.py$']
+```
+
+## Extra instructions
+
+All PR-Agent tools have a parameter called `extra_instructions`, that enables to add free-text extra instructions. Example usage:
+```
+/update_changelog --pr_update_changelog.extra_instructions="Make sure to update also the version ..."
+```
+
+## Working with large PRs
+
+The default mode of CodiumAI is to have a single call per tool, using GPT-4, which has a token limit of 8000 tokens.
+This mode provides a very good speed-quality-cost tradeoff, and can handle most PRs successfully.
+When the PR is above the token limit, it employs a [PR Compression strategy](../core-abilities/index.md).
+
+However, for very large PRs, or in case you want to emphasize quality over speed and cost, there are two possible solutions:
+1) [Use a model](https://codium-ai.github.io/Docs-PR-Agent/usage-guide/#changing-a-model) with larger context, like GPT-32K, or claude-100K. This solution will be applicable for all the tools.
+2) For the `/improve` tool, there is an ['extended' mode](https://codium-ai.github.io/Docs-PR-Agent/tools/#improve) (`/improve --extended`),
+which divides the PR to chunks, and processes each chunk separately. With this mode, regardless of the model, no compression will be done (but for large PRs, multiple model calls may occur)
+
+
+## Changing a model
+
+See [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/algo/__init__.py) for the list of available models.
+To use a different model than the default (GPT-4), you need to edit [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L2).
+For models and environments not from OPENAI, you might need to provide additional keys and other parameters. See below for instructions.
+
+### Azure
+
+To use Azure, set in your `.secrets.toml` (working from CLI), or in the GitHub `Settings > Secrets and variables` (working from GitHub App or GitHub Action):
+```
+[openai]
+key = "" # your azure api key
+api_type = "azure"
+api_version = '2023-05-15'  # Check Azure documentation for the current API version
+api_base = ""  # The base URL for your Azure OpenAI resource. e.g. "https://<your resource name>.openai.azure.com"
+deployment_id = ""  # The deployment name you chose when you deployed the engine
+```
+
+and set in your configuration file:
+```
+[config]
+model="" # the OpenAI model you've deployed on Azure (e.g. gpt-3.5-turbo)
+```
+
+### Hugging Face
+
+**Local**
+You can run Hugging Face models locally through either [VLLM](https://docs.litellm.ai/docs/providers/vllm) or [Ollama](https://docs.litellm.ai/docs/providers/ollama)
+
+E.g. to use a new Hugging Face model locally via Ollama, set:
+```
+[__init__.py]
+MAX_TOKENS = {
+    "model-name-on-ollama": <max_tokens>
+}
+e.g.
+MAX_TOKENS={
+    ...,
+    "ollama/llama2": 4096
+}
+
+
+[config] # in configuration.toml
+model = "ollama/llama2"
+model_turbo = "ollama/llama2"
+
+[ollama] # in .secrets.toml
+api_base = ... # the base url for your Hugging Face inference endpoint
+# e.g. if running Ollama locally, you may use:
+api_base = "http://localhost:11434/"
+```
+
+### Inference Endpoints
+
+To use a new model with Hugging Face Inference Endpoints, for example, set:
+```
+[__init__.py]
+MAX_TOKENS = {
+    "model-name-on-huggingface": <max_tokens>
+}
+e.g.
+MAX_TOKENS={
+    ...,
+    "meta-llama/Llama-2-7b-chat-hf": 4096
+}
+[config] # in configuration.toml
+model = "huggingface/meta-llama/Llama-2-7b-chat-hf"
+model_turbo = "huggingface/meta-llama/Llama-2-7b-chat-hf"
+
+[huggingface] # in .secrets.toml
+key = ... # your Hugging Face api key
+api_base = ... # the base url for your Hugging Face inference endpoint
+```
+(you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
+
+### Replicate
+
+To use Llama2 model with Replicate, for example, set:
+```
+[config] # in configuration.toml
+model = "replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"
+model_turbo = "replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"
+[replicate] # in .secrets.toml
+key = ...
+```
+(you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
+
+
+Also, review the [AiHandler](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/algo/ai_handler.py) file for instructions on how to set keys for other models.
+
+### Groq
+
+To use Llama3 model with Groq, for example, set:
+```
+[config] # in configuration.toml
+model = "llama3-70b-8192"
+model_turbo = "llama3-70b-8192"
+fallback_models = ["groq/llama3-70b-8192"] 
+[groq] # in .secrets.toml
+key = ... # your Groq api key
+```
+(you can obtain a Groq key from [here](https://console.groq.com/keys))
+
+### Vertex AI
+
+To use Google's Vertex AI platform and its associated models (chat-bison/codechat-bison) set:
+
+``` 
+[config] # in configuration.toml
+model = "vertex_ai/codechat-bison"
+model_turbo = "vertex_ai/codechat-bison"
+fallback_models="vertex_ai/codechat-bison"
+
+[vertexai] # in .secrets.toml
+vertex_project = "my-google-cloud-project"
+vertex_location = ""
+```
+
+Your [application default credentials](https://cloud.google.com/docs/authentication/application-default-credentials) will be used for authentication so there is no need to set explicit credentials in most environments.
+
+If you do want to set explicit credentials then you can use the `GOOGLE_APPLICATION_CREDENTIALS` environment variable set to a path to a json credentials file.
+
+### Anthropic
+
+To use Anthropic models, set the relevant models in the configuration section of the configuration file:
+```
+[config]
+model="anthropic/claude-3-opus-20240229"
+model_turbo="anthropic/claude-3-opus-20240229"
+fallback_models=["anthropic/claude-3-opus-20240229"]
+```
+
+And also set the api key in the .secrets.toml file:
+```
+[anthropic]
+KEY = "..."
+```
+
+### Amazon Bedrock
+
+To use Amazon Bedrock and its foundational models, add the below configuration:
+
+``` 
+[config] # in configuration.toml
+model="bedrock/anthropic.claude-3-sonnet-20240229-v1:0"
+model_turbo="bedrock/anthropic.claude-3-sonnet-20240229-v1:0"
+fallback_models=["bedrock/anthropic.claude-v2:1"]
+
+[aws] # in .secrets.toml
+bedrock_region = "us-east-1"
+```
+
+Note that you have to add access to foundational models before using them. Please refer to [this document](https://docs.aws.amazon.com/bedrock/latest/userguide/setting-up.html) for more details.
+
+If you are using the claude-3 model, please configure the following settings as there are parameters incompatible with claude-3.
+```
+[litellm]
+drop_params = true
+```
+
+AWS session is automatically authenticated from your environment, but you can also explicitly set `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` environment variables.
+
+
+## Patch Extra Lines
+
+By default, around any change in your PR, git patch provides three lines of context above and below the change.
+```
+@@ -12,5 +12,5 @@ def func1():
+ code line that already existed in the file...
+ code line that already existed in the file...
+ code line that already existed in the file....
+-code line that was removed in the PR
++new code line added in the PR
+ code line that already existed in the file...
+ code line that already existed in the file...
+ code line that already existed in the file...
+```
+
+For the `review`, `describe`, `ask` and `add_docs` tools, if the token budget allows, PR-Agent tries to increase the number of lines of context, via the parameter:
+```
+[config]
+patch_extra_lines=3
+```
+
+Increasing this number provides more context to the model, but will also increase the token budget.
+If the PR is too large (see [PR Compression strategy](https://github.com/Codium-ai/pr-agent/blob/main/PR_COMPRESSION.md)), PR-Agent automatically sets this number to 0, using the original git patch.
+
+
+## Editing the prompts
+
+The prompts for the various PR-Agent tools are defined in the `pr_agent/settings` folder.
+In practice, the prompts are loaded and stored as a standard setting object.
+Hence, editing them is similar to editing any other configuration value - just place the relevant key in `.pr_agent.toml`file, and override the default value.
+
+For example, if you want to edit the prompts of the [describe](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/pr_description_prompts.toml) tool, you can add the following to your `.pr_agent.toml` file:
+```
+[pr_description_prompt]
+system="""
+...
+"""
+user="""
+...
+"""
+```
+Note that the new prompt will need to generate an output compatible with the relevant [post-process function](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/tools/pr_description.py#L137).

docs/docs/usage-guide/automations_and_usage.md

@@ -0,0 +1,223 @@
+## Local repo (CLI)
+When running from your locally cloned PR-Agent repo (CLI), your local configuration file will be used.
+Examples of invoking the different tools via the CLI:
+
+- **Review**:       `python -m pr_agent.cli --pr_url=<pr_url>  review`
+- **Describe**:     `python -m pr_agent.cli --pr_url=<pr_url>  describe`
+- **Improve**:      `python -m pr_agent.cli --pr_url=<pr_url>  improve`
+- **Ask**:          `python -m pr_agent.cli --pr_url=<pr_url>  ask "Write me a poem about this PR"`
+- **Reflect**:      `python -m pr_agent.cli --pr_url=<pr_url>  reflect`
+- **Update Changelog**:      `python -m pr_agent.cli --pr_url=<pr_url>  update_changelog`
+
+`<pr_url>` is the url of the relevant PR (for example: [#50](https://github.com/Codium-ai/pr-agent/pull/50)).
+
+**Notes:**
+
+(1) in addition to editing your local configuration file, you can also change any configuration value by adding it to the command line:
+```
+python -m pr_agent.cli --pr_url=<pr_url>  /review --pr_reviewer.extra_instructions="focus on the file: ..."
+```
+
+(2) You can print results locally, without publishing them, by setting in `configuration.toml`:
+```
+[config]
+publish_output=false
+verbosity_level=2
+```
+This is useful for debugging or experimenting with different tools.
+
+
+### Online usage
+
+Online usage means invoking PR-Agent tools by [comments](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021901) on a PR.
+Commands for invoking the different tools via comments:
+
+- **Review**:       `/review`
+- **Describe**:     `/describe`
+- **Improve**:      `/improve`
+- **Ask**:          `/ask "..."`
+- **Reflect**:      `/reflect`
+- **Update Changelog**:      `/update_changelog`
+
+
+To edit a specific configuration value, just add `--config_path=<value>` to any command.
+For example, if you want to edit the `review` tool configurations, you can run:
+```
+/review --pr_reviewer.extra_instructions="..." --pr_reviewer.require_score_review=false
+```
+Any configuration value in [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) file can be similarly edited. Comment `/config` to see the list of available configurations.
+
+
+## GitHub App
+
+!!! note "Configurations for PR-Agent Pro"
+    PR-Agent Pro for GitHub is an App, hosted by CodiumAI. So all the instructions below are relevant also for PR-Agent Pro users.
+    Same goes for [GitLab webhook](#gitlab-webhook) and [BitBucket App](#bitbucket-app) sections.
+
+### GitHub app automatic tools when a new PR is opened
+
+The [github_app](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L108) section defines GitHub app specific configurations.  
+
+The configuration parameter `pr_commands` defines the list of tools that will be **run automatically** when a new PR is opened.
+```
+[github_app]
+pr_commands = [
+    "/describe --pr_description.final_update_message=false",
+    "/review --pr_reviewer.num_code_suggestions=0",
+    "/improve",
+]
+```
+This means that when a new PR is opened/reopened or marked as ready for review, PR-Agent will run the `describe`, `review` and `improve` tools.  
+For the `review` tool, for example, the `num_code_suggestions` parameter will be set to 0.
+
+You can override the default tool parameters by using one the three options for a [configuration file](https://codium-ai.github.io/Docs-PR-Agent/usage-guide/#configuration-options): **wiki**, **local**, or **global**. 
+For example, if your local `.pr_agent.toml` file contains:
+```
+[pr_description]
+generate_ai_title = true
+```
+Every time you run the `describe` tool, including automatic runs, the PR title will be generated by the AI.
+
+To cancel the automatic run of all the tools, set:
+```
+[github_app]
+pr_commands = []
+```
+
+You can also disable automatic runs for PRs with specific titles, by setting the `ignore_pr_titles` parameter with the relevant regex. For example:
+```
+[github_app]
+ignore_pr_title = ["^[Auto]", ".*ignore.*"]
+```
+will ignore PRs with titles that start with "Auto" or contain the word "ignore".
+
+### GitHub app automatic tools for push actions (commits to an open PR)
+
+In addition to running automatic tools when a PR is opened, the GitHub app can also respond to new code that is pushed to an open PR.
+
+The configuration toggle `handle_push_trigger` can be used to enable this feature.  
+The configuration parameter `push_commands` defines the list of tools that will be **run automatically** when new code is pushed to the PR.
+```
+[github_app]
+handle_push_trigger = true
+push_commands = [
+    "/describe",
+    "/review  --pr_reviewer.num_code_suggestions=0 --pr_reviewer.final_update_message=false",
+]
+```
+This means that when new code is pushed to the PR, the PR-Agent will run the `describe` and `review` tools, with the specified parameters.
+
+## GitHub Action
+`GitHub Action` is a different way to trigger PR-Agent tools, and uses a different configuration mechanism than `GitHub App`.<br>
+You can configure settings for `GitHub Action` by adding environment variables under the env section in `.github/workflows/pr_agent.yml` file. 
+Specifically, start by setting the following environment variables:
+```yaml
+      env:
+        OPENAI_KEY: ${{ secrets.OPENAI_KEY }} # Make sure to add your OpenAI key to your repo secrets
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Make sure to add your GitHub token to your repo secrets
+        github_action_config.auto_review: "true" # enable\disable auto review
+        github_action_config.auto_describe: "true" # enable\disable auto describe
+        github_action_config.auto_improve: "true" # enable\disable auto improve
+```
+`github_action_config.auto_review`, `github_action_config.auto_describe` and `github_action_config.auto_improve` are used to enable/disable automatic tools that run when a new PR is opened.
+If not set, the default configuration is for all three tools to run automatically when a new PR is opened.
+
+`github_action_config.enable_output` are used to enable/disable github actions [output parameter](https://docs.github.com/en/actions/creating-actions/metadata-syntax-for-github-actions#outputs-for-docker-container-and-javascript-actions) (default is `true`). 
+Review result is output as JSON to `steps.{step-id}.outputs.review` property.
+The JSON structure is equivalent to the yaml data structure defined in [pr_reviewer_prompts.toml](https://github.com/idubnori/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml).
+
+Note that you can give additional config parameters by adding environment variables to `.github/workflows/pr_agent.yml`, or by using a `.pr_agent.toml` [configuration file](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/#global-configuration-file) in the root of your repo
+
+For example, you can set an environment variable: `pr_description.publish_labels=false`, or add a `.pr_agent.toml` file with the following content:
+```
+[pr_description]
+publish_labels = false
+```
+to prevent PR-Agent from publishing labels when running the `describe` tool.
+
+## GitLab Webhook
+After setting up a GitLab webhook, to control which commands will run automatically when a new MR is opened, you can set the `pr_commands` parameter in the configuration file, similar to the GitHub App:
+```
+[gitlab]
+pr_commands = [
+    "/describe",
+    "/review --pr_reviewer.num_code_suggestions=0",
+    "/improve",
+]
+```
+
+the GitLab webhook can also respond to new code that is pushed to an open MR.
+The configuration toggle `handle_push_trigger` can be used to enable this feature.  
+The configuration parameter `push_commands` defines the list of tools that will be **run automatically** when new code is pushed to the MR.
+```
+[gitlab]
+handle_push_trigger = true
+push_commands = [
+    "/describe",
+    "/review  --pr_reviewer.num_code_suggestions=0 --pr_reviewer.final_update_message=false",
+]
+```
+
+Note that to use the 'handle_push_trigger' feature, you need to give the gitlab webhook also the "Push events" scope.
+
+## BitBucket App
+Similar to GitHub app, when running PR-Agent from BitBucket App, the default [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) from a pre-built docker will be initially loaded.
+
+By uploading a local `.pr_agent.toml` file to the root of the repo's main branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
+
+For example, if your local `.pr_agent.toml` file contains:
+```
+[pr_reviewer]
+inline_code_comments = true
+```
+
+Each time you invoke a `/review` tool, it will use inline code comments.
+
+### BitBucket Self-Hosted App automatic tools
+
+To control which commands will run automatically when a new PR is opened, you can set the `pr_commands` parameter in the configuration file:
+Specifically, set the following values:
+
+```
+[bitbucket_app]
+pr_commands = [
+    "/review --pr_reviewer.num_code_suggestions=0",
+    "/improve --pr_code_suggestions.commitable_code_suggestions=true --pr_code_suggestions.suggestions_score_threshold=7",
+]
+```
+Note that we set specifically for bitbucket, we recommend using: `--pr_code_suggestions.suggestions_score_threshold=7` and that is the default value we set for bitbucket.
+Since this platform only supports inline code suggestions, we want to limit the number of suggestions, and only present a limited number.
+
+## Azure DevOps provider
+
+To use Azure DevOps provider use the following settings in configuration.toml:
+```
+[config]
+git_provider="azure"
+```
+
+Azure DevOps provider supports [PAT token](https://learn.microsoft.com/en-us/azure/devops/organizations/accounts/use-personal-access-tokens-to-authenticate?view=azure-devops&tabs=Windows) or [DefaultAzureCredential](https://learn.microsoft.com/en-us/azure/developer/python/sdk/authentication-overview#authentication-in-server-environments) authentication.
+PAT is faster to create, but has build in expiration date, and will use the user identity for API calls. 
+Using DefaultAzureCredential you can use managed identity or Service principle, which are more secure and will create separate ADO user identity (via AAD) to the agent.
+
+If PAT was chosen, you can assign the value in .secrets.toml. 
+If DefaultAzureCredential was chosen, you can assigned the additional env vars like AZURE_CLIENT_SECRET directly, 
+or use managed identity/az cli (for local development) without any additional configuration.
+in any case, 'org' value must be assigned in .secrets.toml:
+```
+[azure_devops]
+org = "https://dev.azure.com/YOUR_ORGANIZATION/"
+# pat = "YOUR_PAT_TOKEN" needed only if using PAT for authentication
+```
+
+### Azure DevOps Webhook
+
+To control which commands will run automatically when a new PR is opened, you can set the `pr_commands` parameter in the configuration file, similar to the GitHub App:
+```
+[azure_devops_server]
+pr_commands = [
+    "/describe",
+    "/review --pr_reviewer.num_code_suggestions=0",
+    "/improve",
+]
+```

docs/docs/usage-guide/configuration_options.md

@@ -0,0 +1,61 @@
+The different tools and sub-tools used by CodiumAI PR-Agent are adjustable via the **[configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml)**.
+
+In addition to general configuration options, each tool has its own configurations. For example, the `review` tool will use parameters from the [pr_reviewer](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L16) section in the configuration file.
+See the [Tools Guide](https://codium-ai.github.io/Docs-PR-Agent/tools/) for a detailed description of the different tools and their configurations.
+
+There are three ways to set persistent configurations:
+
+1. Wiki configuration page 💎
+2. Local configuration file
+3. Global configuration file 💎
+
+In terms of precedence, wiki configurations will override local configurations, and local configurations will override global configurations.
+
+!!! tip "Tip1: edit only what you need"
+    Your configuration file should be minimal, and edit only the relevant values. Don't copy the entire configuration options, since it can lead to legacy problems when something changes.
+!!! tip "Tip2: show relevant configurations"
+    If you set `config.output_relevant_configurations=true`, each tool will also output in a collapsible section its relevant configurations. This can be useful for debugging, or getting to know the configurations better.
+
+## Wiki configuration file 💎
+
+For GitHub and GitLab, with PR-Agent-Pro you can set configurations by creating a page called `.pr_agent.toml` in the [wiki](https://github.com/Codium-ai/pr-agent/wiki/pr_agent.toml) of the repo. 
+The advantage of this method is that it allows to set configurations without needing to commit new content to the repo - just edit the wiki page and **save**.
+
+![wiki_configuration](https://codium.ai/images/pr_agent/wiki_configuration.png){width=512}
+
+Click [here](https://codium.ai/images/pr_agent/wiki_configuration_pr_agent.mp4) to see a short instructional video. We recommend surrounding the configuration content with triple-quotes, to allow better presentation when displayed in the wiki as markdown.
+An example content:
+
+```
+[pr_description]
+generate_ai_title=true
+```
+
+PR-Agent will know to remove the triple-quotes when reading the configuration content.
+
+## Local configuration file
+
+By uploading a local `.pr_agent.toml` file to the root of the repo's main branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
+
+For example, if you set in `.pr_agent.toml`:
+
+```
+[pr_reviewer]
+extra_instructions="""\
+- instruction a
+- instruction b
+...
+"""
+```
+
+Then you can give a list of extra instructions to the `review` tool.
+
+
+## Global configuration file 💎
+
+If you create a repo called `pr-agent-settings` in your **organization**, it's configuration file `.pr_agent.toml` will be used as a global configuration file for any other repo that belongs to the same organization.
+Parameters from a local `.pr_agent.toml` file, in a specific repo, will override the global configuration parameters.
+
+For example, in the GitHub organization `Codium-ai`:
+- The repo [`https://github.com/Codium-ai/pr-agent-settings`](https://github.com/Codium-ai/pr-agent-settings/blob/main/.pr_agent.toml) contains a `.pr_agent.toml` file that serves as a global configuration file for all the repos in the GitHub organization `Codium-ai`.
+- The repo [`https://github.com/Codium-ai/pr-agent`](https://github.com/Codium-ai/pr-agent/blob/main/.pr_agent.toml) inherits the global configuration file from `pr-agent-settings`.

docs/docs/usage-guide/index.md

@@ -0,0 +1,23 @@
+# Usage guide
+
+This page provides a detailed guide on how to use PR-Agent. It includes information on how to adjust PR-Agent configurations, define which tools will run automatically, manage mail notifications, and other advanced configurations.
+
+
+- [Introduction](./introduction.md)
+- [Configuration Options](./configuration_options.md)
+- [Usage and Automation](./automations_and_usage.md)
+    - [Local Repo (CLI)](./automations_and_usage.md#local-repo-cli)
+    - [Online Usage](./automations_and_usage.md#online-usage)
+    - [GitHub App](./automations_and_usage.md#github-app)
+    - [GitHub Action](./automations_and_usage.md#github-action)
+    - [GitLab Webhook](./automations_and_usage.md#gitlab-webhook)
+    - [BitBucket App](./automations_and_usage.md#bitbucket-app)
+    - [Azure DevOps Provider](./automations_and_usage.md#azure-devops-provider)
+- [Managing Mail Notifications](./mail_notifications.md)
+- [Additional Configurations Walkthrough](./additional_configurations.md)
+    - [Ignoring files from analysis](./additional_configurations.md#ignoring-files-from-analysis)
+    - [Extra instructions](./additional_configurations.md#extra-instructions)
+    - [Working with large PRs](./additional_configurations.md#working-with-large-prs)
+    - [Changing a model](./additional_configurations.md#changing-a-model)
+    - [Patch Extra Lines](./additional_configurations.md#patch-extra-lines)
+    - [Editing the prompts](./additional_configurations.md#editing-the-prompts)

docs/docs/usage-guide/introduction.md

@@ -0,0 +1,18 @@
+
+After [installation](https://pr-agent-docs.codium.ai/installation/), there are three basic ways to invoke CodiumAI PR-Agent:
+
+1. Locally running a CLI command
+2. Online usage - by [commenting](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021901) on a PR
+3. Enabling PR-Agent tools to run automatically when a new PR is opened
+
+
+Specifically, CLI commands can be issued by invoking a pre-built [docker image](https://pr-agent-docs.codium.ai/installation/locally/#using-docker-image), or by invoking a [locally cloned repo](https://pr-agent-docs.codium.ai/installation/locally/#run-from-source).
+For online usage, you will need to setup either a [GitHub App](https://pr-agent-docs.codium.ai/installation/github/#run-as-a-github-app), or a [GitHub Action](https://pr-agent-docs.codium.ai/installation/github/#run-as-a-github-action).
+GitHub App and GitHub Action also enable to run PR-Agent specific tool automatically when a new PR is opened.
+
+
+**git provider**: The [git_provider](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L5) field in the configuration file determines the GIT provider that will be used by PR-Agent. Currently, the following providers are supported:
+`
+"github", "gitlab", "bitbucket", "azure", "codecommit", "local", "gerrit"
+`
+

docs/docs/usage-guide/mail_notifications.md

@@ -0,0 +1,18 @@
+
+Unfortunately, it is not possible in GitHub to disable mail notifications from a specific user.
+If you are subscribed to notifications for a repo with PR-Agent, we recommend turning off notifications for PR comments, to avoid lengthy emails:
+
+![notifications](https://codium.ai/images/pr_agent/notifications.png){width=512}
+
+As an alternative, you can filter in your mail provider the notifications specifically from the PR-Agent bot, [see how](https://www.quora.com/How-can-you-filter-emails-for-specific-people-in-Gmail#:~:text=On%20the%20Filters%20and%20Blocked,the%20body%20of%20the%20email).
+
+![filter_mail_notifications](https://codium.ai/images/pr_agent/filter_mail_notifications.png){width=512}
+
+
+Another option to reduce the mail overload, yet still receive notifications on PR-Agent tools, is to disable the help collapsible section in PR-Agent bot comments. 
+This can done by setting `enable_help_text=false` for the relevant tool in the configuration file.
+For example, to disable the help text for the `pr_reviewer` tool, set:
+```
+[pr_reviewer]
+enable_help_text = false
+```

docs/mkdocs.yml

@@ -0,0 +1,139 @@
+site_name: PR-Agent Documentation
+repo_url: https://github.com/Codium-ai/pr-agent
+repo_name: Codium-ai/pr-agent
+
+nav:
+  - Overview:
+    - 'index.md'
+    - 💎 PR-Agent Pro: 'overview/pr_agent_pro.md'
+    - Data Privacy: 'overview/data_privacy.md'
+  - Installation:
+    - 'installation/index.md'
+    - Locally: 'installation/locally.md'
+    - GitHub: 'installation/github.md'
+    - GitLab: 'installation/gitlab.md'
+    - BitBucket: 'installation/bitbucket.md'
+    - Azure DevOps: 'installation/azure.md'
+    - 💎 PR-Agent Pro: 'installation/pr_agent_pro.md'
+  - Usage Guide:
+    - 'usage-guide/index.md'
+    - Introduction: 'usage-guide/introduction.md'
+    - Configuration Options: 'usage-guide/configuration_options.md'
+    - Managing Mail Notifications: 'usage-guide/mail_notifications.md'
+    - Usage and Automation: 'usage-guide/automations_and_usage.md'
+    - Additional Configurations: 'usage-guide/additional_configurations.md'
+  - Tools:
+    - 'tools/index.md'
+    - Describe: 'tools/describe.md'
+    - Review: 'tools/review.md'
+    - Improve: 'tools/improve.md'
+    - Ask: 'tools/ask.md'
+    - Update Changelog: 'tools/update_changelog.md'
+    - Similar Issues: 'tools/similar_issues.md'
+    - Help: 'tools/help.md'
+    - 💎 Analyze: 'tools/analyze.md'
+    - 💎 Test: 'tools/test.md'
+    - 💎 Improve Component: 'tools/improve_component.md'
+    - 💎 Documentation: 'tools/documentation.md'
+    - 💎 Custom Labels: 'tools/custom_labels.md'
+    - 💎 Custom Prompt: 'tools/custom_prompt.md'
+    - 💎 CI Feedback: 'tools/ci_feedback.md'
+    - 💎 Similar Code: 'tools/similar_code.md'
+  - Core Abilities: 'core-abilities/index.md'
+  - Chrome Extension: 'chrome-extension/index.md'
+  - Code Fine-tuning Benchmark: 'finetuning_benchmark/index.md'
+
+theme:
+  logo: assets/logo.svg
+  favicon: assets/favicon.ico
+  name: material
+  icon:
+    repo: fontawesome/brands/github
+  features:
+    - navigation.tabs
+    - navigation.expand
+    - navigation.path
+    - navigation.top
+    - navigation.tracking
+    - navigation.indexes
+    - search.suggest
+    - search.highlight
+    - content.tabs.link
+    - content.code.annotation
+    - content.code.copy
+    - content.tabs.link
+  language: en
+  custom_dir: overrides
+
+  palette:
+    - media: "(prefers-color-scheme)"
+      toggle:
+        icon: material/brightness-auto
+        name: Switch to light mode
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
+      toggle:
+        icon: material/toggle-switch-off-outline
+        name: Switch to dark mode
+      primary: custom
+      accent: custom
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      toggle:
+        icon: material/toggle-switch
+        name: Switch to light mode
+      primary: custom
+      accent: custom
+
+plugins:
+  - social
+  - search
+  - glightbox
+
+extra:
+  generator: false
+  social:
+    - icon: fontawesome/brands/github
+      link: https://github.com/Codium-ai
+    - icon: fontawesome/brands/discord
+      link: https://discord.com/invite/SgSxuQ65GF
+    - icon: fontawesome/brands/youtube
+      link: https://www.youtube.com/@Codium-AI
+    - icon: fontawesome/brands/linkedin
+      link: https://www.linkedin.com/company/codiumai
+    - icon: fontawesome/brands/twitter
+      link: https://twitter.com/CodiumAI
+    - icon: fontawesome/brands/instagram
+      link: https://www.instagram.com/codiumai/
+  analytics:
+    provider: custom
+    property: ${{ secrets.GOOGLE_ANALYTICS_ID }}
+
+extra_css:
+  - css/custom.css
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - admonition
+  - pymdownx.arithmatex:
+      generic: true
+  - footnotes
+  - pymdownx.details
+  - pymdownx.superfences
+  - pymdownx.mark
+  - md_in_html
+  - attr_list
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+  - toc:
+      title: On this page
+      toc_depth: 2
+      permalink: true
+
+
+copyright: |
+  &copy; 2024 <a href="https://www.codium.ai/"  target="_blank" rel="noopener">CodiumAI</a>

docs/overrides/main.html

@@ -0,0 +1,10 @@
+{% extends "base.html" %}
+
+{% block scripts %}
+  {{ super() }}
+  
+    <!-- Google Tag Manager (noscript) -->
+    <noscript><iframe src="https://www.googletagmanager.com/ns.html?id=GTM-5C9KZBM3"
+    height="0" width="0" style="display:none;visibility:hidden"></iframe></noscript>
+    <!-- End Google Tag Manager (noscript) -->
+{% endblock %}

docs/overrides/partials/footer.html

@@ -0,0 +1,115 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+<meta charset="UTF-8">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<title>Footer</title>
+<style>
+  body {
+    margin: 0;
+    padding: 0;
+    font-family: Arial, sans-serif;
+    font-size: 16px;
+  }
+
+  .wrapper {
+    background-color: #171518;
+  }
+
+  .container {
+    display: flex;
+    flex-direction: row;
+    align-items: center;
+    justify-content: space-between;
+    color: white;
+    padding: 20px;
+    max-width: 61rem;
+    margin-left: auto;
+    margin-right: auto;
+  }
+
+  .footer-links, .social-icons {
+    padding: 0;
+    list-style-type: none;
+    display: flex;
+    justify-content: center;
+    gap: 20px;
+    align-items: center;
+  }
+
+  .footer-links a:hover, .social-icons a:hover {
+    color: #AEA1F1;
+  }
+
+  .social-icons svg {
+    width: 24px; 
+    height: auto;
+    fill: white;
+  }
+
+  .footer-text {
+    width: 240px;
+  }
+
+  @media (max-width: 768px) {
+    .container {
+      flex-direction: column;
+      align-items: center;
+      text-align: center;
+    }
+
+    .footer-links, .social-icons, .footer-text {
+      width: 100%;
+      justify-content: center;
+      margin: 10px 0;
+    }
+
+    .footer-links {
+      order: 1;
+    }
+
+    .social-icons {
+      order: 2;
+    }
+
+    .footer-text {
+      order: 3;
+    }
+  }
+</style>
+</head>
+<body>
+
+<footer class="wrapper">
+  <div class="container">
+    <p class="footer-text">© 2024 <a href="https://www.codium.ai/" target="_blank" rel="noopener">CodiumAI</a></p>
+    <div class="footer-links">
+      <a href="https://codiumate-docs.codium.ai/">Codiumate</a>
+      <p>|</p>
+      <a href="https://alpha-codium-docs.codium.ai/">AlphaCodium</a>
+    </div>
+    <div class="social-icons">
+      <a href="https://github.com/Codium-ai" target="_blank" rel="noopener" title="github.com" class="social-link">
+        <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg>
+      </a>
+      <a href="https://discord.com/invite/SgSxuQ65GF" target="_blank" rel="noopener" title="discord.com" class="social-link">
+        <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 640 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M524.531 69.836a1.5 1.5 0 0 0-.764-.7A485.065 485.065 0 0 0 404.081 32.03a1.816 1.816 0 0 0-1.923.91 337.461 337.461 0 0 0-14.9 30.6 447.848 447.848 0 0 0-134.426 0 309.541 309.541 0 0 0-15.135-30.6 1.89 1.89 0 0 0-1.924-.91 483.689 483.689 0 0 0-119.688 37.107 1.712 1.712 0 0 0-.788.676C39.068 183.651 18.186 294.69 28.43 404.354a2.016 2.016 0 0 0 .765 1.375 487.666 487.666 0 0 0 146.825 74.189 1.9 1.9 0 0 0 2.063-.676A348.2 348.2 0 0 0 208.12 430.4a1.86 1.86 0 0 0-1.019-2.588 321.173 321.173 0 0 1-45.868-21.853 1.885 1.885 0 0 1-.185-3.126 251.047 251.047 0 0 0 9.109-7.137 1.819 1.819 0 0 1 1.9-.256c96.229 43.917 200.41 43.917 295.5 0a1.812 1.812 0 0 1 1.924.233 234.533 234.533 0 0 0 9.132 7.16 1.884 1.884 0 0 1-.162 3.126 301.407 301.407 0 0 1-45.89 21.83 1.875 1.875 0 0 0-1 2.611 391.055 391.055 0 0 0 30.014 48.815 1.864 1.864 0 0 0 2.063.7A486.048 486.048 0 0 0 610.7 405.729a1.882 1.882 0 0 0 .765-1.352c12.264-126.783-20.532-236.912-86.934-334.541ZM222.491 337.58c-28.972 0-52.844-26.587-52.844-59.239s23.409-59.241 52.844-59.241c29.665 0 53.306 26.82 52.843 59.239 0 32.654-23.41 59.241-52.843 59.241Zm195.38 0c-28.971 0-52.843-26.587-52.843-59.239s23.409-59.241 52.843-59.241c29.667 0 53.307 26.82 52.844 59.239 0 32.654-23.177 59.241-52.844 59.241Z"></path></svg>
+      </a>
+      <a href="https://www.youtube.com/@Codium-AI" target="_blank" rel="noopener" title="www.youtube.com" class="social-link">
+        <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 576 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M549.655 124.083c-6.281-23.65-24.787-42.276-48.284-48.597C458.781 64 288 64 288 64S117.22 64 74.629 75.486c-23.497 6.322-42.003 24.947-48.284 48.597-11.412 42.867-11.412 132.305-11.412 132.305s0 89.438 11.412 132.305c6.281 23.65 24.787 41.5 48.284 47.821C117.22 448 288 448 288 448s170.78 0 213.371-11.486c23.497-6.321 42.003-24.171 48.284-47.821 11.412-42.867 11.412-132.305 11.412-132.305s0-89.438-11.412-132.305zm-317.51 213.508V175.185l142.739 81.205-142.739 81.201z"></path></svg>
+      </a>
+      <a href="https://www.linkedin.com/company/codiumai" target="_blank" rel="noopener" title="www.linkedin.com" class="social-link">
+        <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M416 32H31.9C14.3 32 0 46.5 0 64.3v383.4C0 465.5 14.3 480 31.9 480H416c17.6 0 32-14.5 32-32.3V64.3c0-17.8-14.4-32.3-32-32.3zM135.4 416H69V202.2h66.5V416zm-33.2-243c-21.3 0-38.5-17.3-38.5-38.5S80.9 96 102.2 96c21.2 0 38.5 17.3 38.5 38.5 0 21.3-17.2 38.5-38.5 38.5zm282.1 243h-66.4V312c0-24.8-.5-56.7-34.5-56.7-34.6 0-39.9 27-39.9 54.9V416h-66.4V202.2h63.7v29.2h.9c8.9-16.8 30.6-34.5 62.9-34.5 67.2 0 79.7 44.3 79.7 101.9V416z"></path></svg>
+      </a>
+      <a href="https://twitter.com/CodiumAI" target="_blank" rel="noopener" title="twitter.com" class="social-link">
+        <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg>
+      </a>
+      <a href="https://www.instagram.com/codiumai/" target="_blank" rel="noopener" title="www.instagram.com" class="social-link">
+        <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M224.1 141c-63.6 0-114.9 51.3-114.9 114.9s51.3 114.9 114.9 114.9S339 319.5 339 255.9 287.7 141 224.1 141zm0 189.6c-41.1 0-74.7-33.5-74.7-74.7s33.5-74.7 74.7-74.7 74.7 33.5 74.7 74.7-33.6 74.7-74.7 74.7zm146.4-194.3c0 14.9-12 26.8-26.8 26.8-14.9 0-26.8-12-26.8-26.8s12-26.8 26.8-26.8 26.8 12 26.8 26.8zm76.1 27.2c-1.7-35.9-9.9-67.7-36.2-93.9-26.2-26.2-58-34.4-93.9-36.2-37-2.1-147.9-2.1-184.9 0-35.8 1.7-67.6 9.9-93.9 36.1s-34.4 58-36.2 93.9c-2.1 37-2.1 147.9 0 184.9 1.7 35.9 9.9 67.7 36.2 93.9s58 34.4 93.9 36.2c37 2.1 147.9 2.1 184.9 0 35.9-1.7 67.7-9.9 93.9-36.2 26.2-26.2 34.4-58 36.2-93.9 2.1-37 2.1-147.8 0-184.8zM398.8 388c-7.8 19.6-22.9 34.7-42.6 42.6-29.5 11.7-99.5 9-132.1 9s-102.7 2.6-132.1-9c-19.6-7.8-34.7-22.9-42.6-42.6-11.7-29.5-9-99.5-9-132.1s-2.6-102.7 9-132.1c7.8-19.6 22.9-34.7 42.6-42.6 29.5-11.7 99.5-9 132.1-9s102.7-2.6 132.1 9c19.6 7.8 34.7 22.9 42.6 42.6 11.7 29.5 9 99.5 9 132.1s2.7 102.7-9 132.1z"></path></svg>
+      </a>
+    </div>
+  </div>
+</footer>
+
+</body>
+</html>

docs/overrides/partials/integrations/analytics/custom.html

@@ -0,0 +1,7 @@
+<!-- Google Tag Manager -->
+<script>(function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':
+    new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],
+    j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src=
+    'https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);
+    })(window,document,'script','dataLayer','GTM-5C9KZBM3');</script>
+    <!-- End Google Tag Manager -->

pr_agent/agent/pr_agent.py

@@ -46,9 +46,10 @@ command2class = {
 
 commands = list(command2class.keys())
 
+
 class PRAgent:
     def __init__(self, ai_handler: partial[BaseAiHandler,] = LiteLLMAIHandler):
-        self.ai_handler = ai_handler # will be initialized in run_action
+        self.ai_handler = ai_handler  # will be initialized in run_action
         self.forbidden_cli_args = ['enable_auto_approval']
 
     async def handle_request(self, pr_url, request, notify=None) -> bool:
@@ -68,11 +69,16 @@ class PRAgent:
             for forbidden_arg in self.forbidden_cli_args:
                 for arg in args:
                     if forbidden_arg in arg:
-                        get_logger().error(f"CLI argument for param '{forbidden_arg}' is forbidden. Use instead a configuration file.")
+                        get_logger().error(
+                            f"CLI argument for param '{forbidden_arg}' is forbidden. Use instead a configuration file."
+                        )
                         return False
         args = update_settings_from_args(args)
 
         action = action.lstrip("/").lower()
+        if action not in command2class:
+            get_logger().debug(f"Unknown command: {action}")
+            return False
         with get_logger().contextualize(command=action):
             get_logger().info("PR-Agent request handler started", analytics=True)
             if action == "reflect_and_review":
@@ -91,4 +97,3 @@ class PRAgent:
             else:
                 return False
             return True
-

pr_agent/algo/__init__.py

@@ -1,15 +1,21 @@
 MAX_TOKENS = {
     'text-embedding-ada-002': 8000,
-    'gpt-3.5-turbo': 4000,
+    'gpt-3.5-turbo': 16000,
+    'gpt-3.5-turbo-0125': 16000,
     'gpt-3.5-turbo-0613': 4000,
-    'gpt-3.5-turbo-0301': 4000,
+    'gpt-3.5-turbo-1106': 16000,
     'gpt-3.5-turbo-16k': 16000,
     'gpt-3.5-turbo-16k-0613': 16000,
     'gpt-4': 8000,
     'gpt-4-0613': 8000,
     'gpt-4-32k': 32000,
-    'gpt-4-1106-preview': 128000, # 128K, but may be limited by config.max_model_tokens
+    'gpt-4-1106-preview': 128000,  # 128K, but may be limited by config.max_model_tokens
     'gpt-4-0125-preview': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'gpt-4o': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'gpt-4o-2024-05-13': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'gpt-4-turbo-preview': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'gpt-4-turbo-2024-04-09': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'gpt-4-turbo': 128000,  # 128K, but may be limited by config.max_model_tokens
     'claude-instant-1': 100000,
     'claude-2': 100000,
     'command-nightly': 4096,
@@ -17,9 +23,25 @@ MAX_TOKENS = {
     'meta-llama/Llama-2-7b-chat-hf': 4096,
     'vertex_ai/codechat-bison': 6144,
     'vertex_ai/codechat-bison-32k': 32000,
+    'vertex_ai/claude-3-haiku@20240307': 100000,
+    'vertex_ai/claude-3-sonnet@20240229': 100000,
+    'vertex_ai/claude-3-opus@20240229': 100000,
+    'vertex_ai/claude-3-5-sonnet@20240620': 100000,
+    'vertex_ai/gemini-1.5-pro': 1048576,
     'codechat-bison': 6144,
     'codechat-bison-32k': 32000,
-    'anthropic.claude-v2': 100000,
     'anthropic.claude-instant-v1': 100000,
     'anthropic.claude-v1': 100000,
+    'anthropic.claude-v2': 100000,
+    'anthropic/claude-3-opus-20240229': 100000,
+    'anthropic/claude-3-5-sonnet-20240620': 100000,
+    'bedrock/anthropic.claude-instant-v1': 100000,
+    'bedrock/anthropic.claude-v2': 100000,
+    'bedrock/anthropic.claude-v2:1': 100000,
+    'bedrock/anthropic.claude-3-sonnet-20240229-v1:0': 100000,
+    'bedrock/anthropic.claude-3-haiku-20240307-v1:0': 100000,
+    'bedrock/anthropic.claude-3-5-sonnet-20240620-v1:0': 100000,
+    'groq/llama3-8b-8192': 8192,
+    'groq/llama3-70b-8192': 8192,
+    'ollama/llama3': 4096,
 }

pr_agent/algo/ai_handlers/base_ai_handler.py

@@ -1,5 +1,6 @@
 from abc import ABC, abstractmethod
 
+
 class BaseAiHandler(ABC):
     """
     This class defines the interface for an AI handler to be used by the PR Agents.  
@@ -14,8 +15,8 @@ class BaseAiHandler(ABC):
     def deployment_id(self):
         pass
 
-    @abstractmethod   
-    async def chat_completion(self, model: str, system: str, user: str, temperature: float = 0.2):
+    @abstractmethod
+    async def chat_completion(self, model: str, system: str, user: str, temperature: float = 0.2, img_path: str = None):
         """
         This method should be implemented to return a chat completion from the AI model.
         Args:
@@ -25,4 +26,3 @@ class BaseAiHandler(ABC):
             temperature (float): the temperature to use for the chat completion    
         """
         pass
-

pr_agent/algo/ai_handlers/langchain_ai_handler.py

@@ -1,19 +1,20 @@
 try:
-    from langchain.chat_models import ChatOpenAI, AzureChatOpenAI
-    from langchain.schema import SystemMessage, HumanMessage
-except: # we don't enforce langchain as a dependency, so if it's not installed, just move on
+    from langchain_openai import ChatOpenAI, AzureChatOpenAI
+    from langchain_core.messages import SystemMessage, HumanMessage
+except:  # we don't enforce langchain as a dependency, so if it's not installed, just move on
     pass
 
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 
-from openai.error import APIError, RateLimitError, Timeout, TryAgain
+from openai import APIError, RateLimitError, Timeout
 from retry import retry
 import functools
 
 OPENAI_RETRIES = 5
 
+
 class LangChainOpenAIHandler(BaseAiHandler):
     def __init__(self):
         # Initialize OpenAIHandler specific attributes here
@@ -30,20 +31,24 @@ class LangChainOpenAIHandler(BaseAiHandler):
                     openai_api_version=get_settings().openai.api_version,
                 )
             else:
-                self._chat = ChatOpenAI(openai_api_key=get_settings().openai.key)
+                # for llms that compatible with openai, should use custom api base
+                openai_api_base = get_settings().get("OPENAI.API_BASE", None)
+                if openai_api_base is None or len(openai_api_base) == 0:
+                    self._chat = ChatOpenAI(openai_api_key=get_settings().openai.key)
+                else:
+                    self._chat = ChatOpenAI(openai_api_key=get_settings().openai.key, openai_api_base=openai_api_base)
         except AttributeError as e:
             if getattr(e, "name"):
                 raise ValueError(f"OpenAI {e.name} is required") from e
             else:
                 raise e
-    
-    @property
-    def chat(self):
+
+    def chat(self, messages: list, model: str, temperature: float):
         if self.azure:
             # we must set the deployment_id only here (instead of the __init__ method) to support fallback_deployments
-            return self._chat(deployment_name=self.deployment_id)
+            return self._chat.invoke(input = messages, model=model, temperature=temperature, deployment_name=self.deployment_id)
         else:
-            return self._chat
+            return self._chat.invoke(input = messages, model=model, temperature=temperature)
 
     @property
     def deployment_id(self):
@@ -51,17 +56,18 @@ class LangChainOpenAIHandler(BaseAiHandler):
         Returns the deployment ID for the OpenAI API.
         """
         return get_settings().get("OPENAI.DEPLOYMENT_ID", None)
-    @retry(exceptions=(APIError, Timeout, TryAgain, AttributeError, RateLimitError),
+
+    @retry(exceptions=(APIError, Timeout, AttributeError, RateLimitError),
            tries=OPENAI_RETRIES, delay=2, backoff=2, jitter=(1, 3))
     async def chat_completion(self, model: str, system: str, user: str, temperature: float = 0.2):
         try:
-            messages=[SystemMessage(content=system), HumanMessage(content=user)]
-            
+            messages = [SystemMessage(content=system), HumanMessage(content=user)]
+
             # get a chat completion from the formatted messages
             resp = self.chat(messages, model=model, temperature=temperature)
-            finish_reason="completed"
+            finish_reason = "completed"
             return resp.content, finish_reason
-        
+
         except (Exception) as e:
             get_logger().error("Unknown error during OpenAI inference: ", e)
-            raise e
+            raise e

pr_agent/algo/ai_handlers/litellm_ai_handler.py

@@ -1,11 +1,10 @@
 import os
-
+import requests
 import boto3
 import litellm
 import openai
 from litellm import acompletion
-from openai.error import APIError, RateLimitError, Timeout, TryAgain
-from retry import retry
+from tenacity import retry, retry_if_exception_type, stop_after_attempt
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
@@ -26,16 +25,25 @@ class LiteLLMAIHandler(BaseAiHandler):
         Raises a ValueError if the OpenAI key is missing.
         """
         self.azure = False
-        self.aws_bedrock_client = None
-
+        self.api_base = None
+        self.repetition_penalty = None
         if get_settings().get("OPENAI.KEY", None):
             openai.api_key = get_settings().openai.key
             litellm.openai_key = get_settings().openai.key
+        elif 'OPENAI_API_KEY' not in os.environ:
+            litellm.api_key = "dummy_key"
+        if get_settings().get("aws.AWS_ACCESS_KEY_ID"):
+            assert get_settings().aws.AWS_SECRET_ACCESS_KEY and get_settings().aws.AWS_REGION_NAME, "AWS credentials are incomplete"
+            os.environ["AWS_ACCESS_KEY_ID"] = get_settings().aws.AWS_ACCESS_KEY_ID
+            os.environ["AWS_SECRET_ACCESS_KEY"] = get_settings().aws.AWS_SECRET_ACCESS_KEY
+            os.environ["AWS_REGION_NAME"] = get_settings().aws.AWS_REGION_NAME
         if get_settings().get("litellm.use_client"):
             litellm_token = get_settings().get("litellm.LITELLM_TOKEN")
             assert litellm_token, "LITELLM_TOKEN is required"
             os.environ["LITELLM_TOKEN"] = litellm_token
             litellm.use_client = True
+        if get_settings().get("LITELLM.DROP_PARAMS", None):
+            litellm.drop_params = get_settings().litellm.drop_params
         if get_settings().get("OPENAI.ORG", None):
             litellm.organization = get_settings().openai.org
         if get_settings().get("OPENAI.API_TYPE", None):
@@ -50,25 +58,36 @@ class LiteLLMAIHandler(BaseAiHandler):
             litellm.anthropic_key = get_settings().anthropic.key
         if get_settings().get("COHERE.KEY", None):
             litellm.cohere_key = get_settings().cohere.key
-        if get_settings().get("REPLICATE.KEY", None):
-            litellm.replicate_key = get_settings().replicate.key
+        if get_settings().get("GROQ.KEY", None):
+            litellm.api_key = get_settings().groq.key
         if get_settings().get("REPLICATE.KEY", None):
             litellm.replicate_key = get_settings().replicate.key
         if get_settings().get("HUGGINGFACE.KEY", None):
             litellm.huggingface_key = get_settings().huggingface.key
-            if get_settings().get("HUGGINGFACE.API_BASE", None):
-                litellm.api_base = get_settings().huggingface.api_base
+        if get_settings().get("HUGGINGFACE.API_BASE", None) and 'huggingface' in get_settings().config.model:
+            litellm.api_base = get_settings().huggingface.api_base
+            self.api_base = get_settings().huggingface.api_base
+        if get_settings().get("OLLAMA.API_BASE", None):
+            litellm.api_base = get_settings().ollama.api_base
+            self.api_base = get_settings().ollama.api_base
+        if get_settings().get("HUGGINGFACE.REPETITION_PENALTY", None):
+            self.repetition_penalty = float(get_settings().huggingface.repetition_penalty)
         if get_settings().get("VERTEXAI.VERTEX_PROJECT", None):
             litellm.vertex_project = get_settings().vertexai.vertex_project
             litellm.vertex_location = get_settings().get(
                 "VERTEXAI.VERTEX_LOCATION", None
             )
-        if get_settings().get("AWS.BEDROCK_REGION", None):
-            litellm.AmazonAnthropicConfig.max_tokens_to_sample = 2000
-            self.aws_bedrock_client = boto3.client(
-                service_name="bedrock-runtime",
-                region_name=get_settings().aws.bedrock_region,
-            )
+    def prepare_logs(self, response, system, user, resp, finish_reason):
+        response_log = response.dict().copy()
+        response_log['system'] = system
+        response_log['user'] = user
+        response_log['output'] = resp
+        response_log['finish_reason'] = finish_reason
+        if hasattr(self, 'main_pr_language'):
+            response_log['main_pr_language'] = self.main_pr_language
+        else:
+            response_log['main_pr_language'] = 'unknown'
+        return response_log
 
     @property
     def deployment_id(self):
@@ -77,62 +96,71 @@ class LiteLLMAIHandler(BaseAiHandler):
         """
         return get_settings().get("OPENAI.DEPLOYMENT_ID", None)
 
-    @retry(exceptions=(APIError, Timeout, TryAgain, AttributeError, RateLimitError),
-           tries=OPENAI_RETRIES, delay=2, backoff=2, jitter=(1, 3))
-    async def chat_completion(self, model: str, system: str, user: str, temperature: float = 0.2):
-        """
-        Performs a chat completion using the OpenAI ChatCompletion API.
-        Retries in case of API errors or timeouts.
-        
-        Args:
-            model (str): The model to use for chat completion.
-            temperature (float): The temperature parameter for chat completion.
-            system (str): The system message for chat completion.
-            user (str): The user message for chat completion.
-        
-        Returns:
-            tuple: A tuple containing the response and finish reason from the API.
-        
-        Raises:
-            TryAgain: If the API response is empty or there are no choices in the response.
-            APIError: If there is an error during OpenAI inference.
-            Timeout: If there is a timeout during OpenAI inference.
-            TryAgain: If there is an attribute error during OpenAI inference.
-        """
+    @retry(
+        retry=retry_if_exception_type((openai.APIError, openai.APIConnectionError, openai.APITimeoutError)), # No retry on RateLimitError
+        stop=stop_after_attempt(OPENAI_RETRIES)
+    )
+    async def chat_completion(self, model: str, system: str, user: str, temperature: float = 0.2, img_path: str = None):
         try:
             resp, finish_reason = None, None
             deployment_id = self.deployment_id
             if self.azure:
                 model = 'azure/' + model
             messages = [{"role": "system", "content": system}, {"role": "user", "content": user}]
+            if img_path:
+                try:
+                    # check if the image link is alive
+                    r = requests.head(img_path, allow_redirects=True)
+                    if r.status_code == 404:
+                        error_msg = f"The image link is not [alive](img_path).\nPlease repost the original image as a comment, and send the question again with 'quote reply' (see [instructions](https://pr-agent-docs.codium.ai/tools/ask/#ask-on-images-using-the-pr-code-as-context))."
+                        get_logger().error(error_msg)
+                        return f"{error_msg}", "error"
+                except Exception as e:
+                    get_logger().error(f"Error fetching image: {img_path}", e)
+                    return f"Error fetching image: {img_path}", "error"
+                messages[1]["content"] = [{"type": "text", "text": messages[1]["content"]},
+                                          {"type": "image_url", "image_url": {"url": img_path}}]
+
             kwargs = {
                 "model": model,
                 "deployment_id": deployment_id,
                 "messages": messages,
                 "temperature": temperature,
                 "force_timeout": get_settings().config.ai_timeout,
+                "api_base": self.api_base,
             }
-            if self.aws_bedrock_client:
-                kwargs["aws_bedrock_client"] = self.aws_bedrock_client
+            if self.repetition_penalty:
+                kwargs["repetition_penalty"] = self.repetition_penalty
 
             get_logger().debug("Prompts", artifact={"system": system, "user": user})
+
+            if get_settings().config.verbosity_level >= 2:
+                get_logger().info(f"\nSystem prompt:\n{system}")
+                get_logger().info(f"\nUser prompt:\n{user}")
+
             response = await acompletion(**kwargs)
-        except (APIError, Timeout, TryAgain) as e:
+        except (openai.APIError, openai.APITimeoutError) as e:
             get_logger().error("Error during OpenAI inference: ", e)
             raise
-        except (RateLimitError) as e:
+        except (openai.RateLimitError) as e:
             get_logger().error("Rate limit error during OpenAI inference: ", e)
             raise
         except (Exception) as e:
             get_logger().error("Unknown error during OpenAI inference: ", e)
-            raise TryAgain from e
+            raise openai.APIError from e
         if response is None or len(response["choices"]) == 0:
-            raise TryAgain
+            raise openai.APIError
         else:
             resp = response["choices"][0]['message']['content']
             finish_reason = response["choices"][0]["finish_reason"]
-            # usage = response.get("usage")
             get_logger().debug(f"\nAI response:\n{resp}")
-            get_logger().debug("Full_response", artifact=response)
 
-        return resp, finish_reason
+            # log the full response for debugging
+            response_log = self.prepare_logs(response, system, user, resp, finish_reason)
+            get_logger().debug("Full_response", artifact=response_log)
+
+            # for CLI debugging
+            if get_settings().config.verbosity_level >= 2:
+                get_logger().info(f"\nAI response:\n{resp}")
+
+        return resp, finish_reason

pr_agent/algo/ai_handlers/openai_ai_handler.py

@@ -28,13 +28,14 @@ class OpenAIHandler(BaseAiHandler):
 
         except AttributeError as e:
             raise ValueError("OpenAI key is required") from e
+
     @property
     def deployment_id(self):
         """
         Returns the deployment ID for the OpenAI API.
         """
         return get_settings().get("OPENAI.DEPLOYMENT_ID", None)
-    
+
     @retry(exceptions=(APIError, Timeout, TryAgain, AttributeError, RateLimitError),
            tries=OPENAI_RETRIES, delay=2, backoff=2, jitter=(1, 3))
     async def chat_completion(self, model: str, system: str, user: str, temperature: float = 0.2):
@@ -54,8 +55,8 @@ class OpenAIHandler(BaseAiHandler):
             finish_reason = chat_completion["choices"][0]["finish_reason"]
             usage = chat_completion.get("usage")
             get_logger().info("AI response", response=resp, messages=messages, finish_reason=finish_reason,
-                            model=model, usage=usage)
-            return resp, finish_reason       
+                              model=model, usage=usage)
+            return resp, finish_reason
         except (APIError, Timeout, TryAgain) as e:
             get_logger().error("Error during OpenAI inference: ", e)
             raise
@@ -64,4 +65,4 @@ class OpenAIHandler(BaseAiHandler):
             raise
         except (Exception) as e:
             get_logger().error("Unknown error during OpenAI inference: ", e)
-            raise TryAgain from e        
+            raise TryAgain from e

pr_agent/algo/file_filter.py

@@ -3,7 +3,8 @@ import re
 
 from pr_agent.config_loader import get_settings
 
-def filter_ignored(files):
+
+def filter_ignored(files, platform = 'github'):
     """
     Filter out files that match the ignore patterns.
     """
@@ -14,7 +15,7 @@ def filter_ignored(files):
         if isinstance(patterns, str):
             patterns = [patterns]
         glob_setting = get_settings().ignore.glob
-        if isinstance(glob_setting, str): # --ignore.glob=[.*utils.py], --ignore.glob=.*utils.py
+        if isinstance(glob_setting, str):  # --ignore.glob=[.*utils.py], --ignore.glob=.*utils.py
             glob_setting = glob_setting.strip('[]').split(",")
         patterns += [fnmatch.translate(glob) for glob in glob_setting]
 
@@ -27,8 +28,16 @@ def filter_ignored(files):
                 pass
 
         # keep filenames that _don't_ match the ignore regex
-        for r in compiled_patterns:
-            files = [f for f in files if (f.filename and not r.match(f.filename))]
+        if files and isinstance(files, list):
+            for r in compiled_patterns:
+                if platform == 'github':
+                    files = [f for f in files if (f.filename and not r.match(f.filename))]
+                elif platform == 'bitbucket':
+                    files = [f for f in files if (f.new.path and not r.match(f.new.path))]
+                elif platform == 'gitlab':
+                    files = [f for f in files if (f['new_path'] and not r.match(f['new_path']))]
+                elif platform == 'azure':
+                    files = [f for f in files if not r.match(f)]
 
     except Exception as e:
         print(f"Could not filter file list: {e}")

pr_agent/algo/git_patch_processing.py

@@ -23,7 +23,10 @@ def extend_patch(original_file_str, patch_str, num_lines) -> str:
         return patch_str
 
     if type(original_file_str) == bytes:
-        original_file_str = original_file_str.decode('utf-8')
+        try:
+            original_file_str = original_file_str.decode('utf-8')
+        except UnicodeDecodeError:
+            return ""
 
     original_lines = original_file_str.splitlines()
     patch_lines = patch_str.splitlines()
@@ -133,7 +136,7 @@ def handle_patch_deletions(patch: str, original_file_content_str: str,
         str: The modified patch with deletion hunks omitted.
 
     """
-    if not new_file_content_str and edit_type != EDIT_TYPE.ADDED:
+    if not new_file_content_str and (edit_type == EDIT_TYPE.DELETED or edit_type == EDIT_TYPE.UNKNOWN):
         # logic for handling deleted files - don't show patch, just show that the file was deleted
         if get_settings().config.verbosity_level > 0:
             get_logger().info(f"Processing file: {file_name}, minimizing deletion file")

pr_agent/algo/language_handler.py

@@ -5,17 +5,20 @@ from pr_agent.config_loader import get_settings
 
 
 
-# Bad Extensions, source: https://github.com/EleutherAI/github-downloader/blob/345e7c4cbb9e0dc8a0615fd995a08bf9d73b3fe6/download_repo_text.py  # noqa: E501
-bad_extensions = get_settings().bad_extensions.default
-if get_settings().config.use_extra_bad_extensions:
-    bad_extensions += get_settings().bad_extensions.extra
-
 
 def filter_bad_extensions(files):
-    return [f for f in files if f.filename is not None and is_valid_file(f.filename)]
+    # Bad Extensions, source: https://github.com/EleutherAI/github-downloader/blob/345e7c4cbb9e0dc8a0615fd995a08bf9d73b3fe6/download_repo_text.py  # noqa: E501
+    bad_extensions = get_settings().bad_extensions.default
+    if get_settings().config.use_extra_bad_extensions:
+        bad_extensions += get_settings().bad_extensions.extra
+    return [f for f in files if f.filename is not None and is_valid_file(f.filename, bad_extensions)]
 
 
-def is_valid_file(filename):
+def is_valid_file(filename, bad_extensions=None):
+    if not bad_extensions:
+        bad_extensions = get_settings().bad_extensions.default
+        if get_settings().config.use_extra_bad_extensions:
+            bad_extensions += get_settings().bad_extensions.extra
     return filename.split('.')[-1] not in bad_extensions
 
 

pr_agent/algo/pr_processing.py

@@ -9,7 +9,7 @@ from pr_agent.algo.git_patch_processing import convert_to_hunks_with_lines_numbe
 from pr_agent.algo.language_handler import sort_files_by_main_languages
 from pr_agent.algo.file_filter import filter_ignored
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import get_max_tokens, ModelType
+from pr_agent.algo.utils import get_max_tokens, clip_tokens, ModelType
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.git_provider import GitProvider
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
@@ -21,29 +21,17 @@ MORE_MODIFIED_FILES_ = "Additional modified files (insufficient token budget to
 
 ADDED_FILES_ = "Additional added files (insufficient token budget to process):\n"
 
-OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD = 1000
-OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD = 600
+OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD = 1500
+OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD = 1000
 
-def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler, model: str,
-                add_line_numbers_to_hunks: bool = False, disable_extra_lines: bool = False) -> str:
-    """
-    Returns a string with the diff of the pull request, applying diff minimization techniques if needed.
 
-    Args:
-        git_provider (GitProvider): An object of the GitProvider class representing the Git provider used for the pull
-        request.
-        token_handler (TokenHandler): An object of the TokenHandler class used for handling tokens in the context of the
-        pull request.
-        model (str): The name of the model used for tokenization.
-        add_line_numbers_to_hunks (bool, optional): A boolean indicating whether to add line numbers to the hunks in the
-        diff. Defaults to False.
-        disable_extra_lines (bool, optional): A boolean indicating whether to disable the extension of each patch with
-        extra lines of context. Defaults to False.
-
-    Returns:
-        str: A string with the diff of the pull request, applying diff minimization techniques if needed.
-    """
 
+def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler,
+                model: str,
+                add_line_numbers_to_hunks: bool = False,
+                disable_extra_lines: bool = False,
+                large_pr_handling=False,
+                return_remaining_files=False):
     if disable_extra_lines:
         PATCH_EXTRA_LINES = 0
     else:
@@ -87,25 +75,100 @@ def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler, model: s
     # if we are over the limit, start pruning
     get_logger().info(f"Tokens: {total_tokens}, total tokens over limit: {get_max_tokens(model)}, "
                       f"pruning diff.")
-    patches_compressed, modified_file_names, deleted_file_names, added_file_names = \
-        pr_generate_compressed_diff(pr_languages, token_handler, model, add_line_numbers_to_hunks)
+    patches_compressed_list, total_tokens_list, deleted_files_list, remaining_files_list, file_dict, files_in_patches_list = \
+        pr_generate_compressed_diff(pr_languages, token_handler, model, add_line_numbers_to_hunks, large_pr_handling)
 
+    if large_pr_handling and len(patches_compressed_list) > 1:
+        get_logger().info(f"Large PR handling mode, and found {len(patches_compressed_list)} patches with original diff.")
+        return "" # return empty string, as we generate multiple patches with a different prompt
+
+    # return the first patch
+    patches_compressed = patches_compressed_list[0]
+    total_tokens_new = total_tokens_list[0]
+    files_in_patch = files_in_patches_list[0]
+
+    # Insert additional information about added, modified, and deleted files if there is enough space
+    max_tokens = get_max_tokens(model) - OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD
+    curr_token = total_tokens_new  # == token_handler.count_tokens(final_diff)+token_handler.prompt_tokens
     final_diff = "\n".join(patches_compressed)
-    if added_file_names:
-        added_list_str = ADDED_FILES_ + "\n".join(added_file_names)
+    delta_tokens = 10
+    added_list_str = modified_list_str = deleted_list_str = ""
+    unprocessed_files = []
+    # generate the added, modified, and deleted files lists
+    if (max_tokens - curr_token) > delta_tokens:
+        for filename, file_values in file_dict.items():
+            if filename in files_in_patch:
+                continue
+            if file_values['edit_type'] == EDIT_TYPE.ADDED:
+                unprocessed_files.append(filename)
+                if not added_list_str:
+                    added_list_str = ADDED_FILES_ + f"\n{filename}"
+                else:
+                    added_list_str = added_list_str + f"\n{filename}"
+            elif file_values['edit_type'] == EDIT_TYPE.MODIFIED or EDIT_TYPE.RENAMED:
+                unprocessed_files.append(filename)
+                if not modified_list_str:
+                    modified_list_str = MORE_MODIFIED_FILES_ + f"\n{filename}"
+                else:
+                    modified_list_str = modified_list_str + f"\n{filename}"
+            elif file_values['edit_type'] == EDIT_TYPE.DELETED:
+                # unprocessed_files.append(filename) # not needed here, because the file was deleted, so no need to process it
+                if not deleted_list_str:
+                    deleted_list_str = DELETED_FILES_ + f"\n{filename}"
+                else:
+                    deleted_list_str = deleted_list_str + f"\n{filename}"
+
+    # prune the added, modified, and deleted files lists, and add them to the final diff
+    added_list_str = clip_tokens(added_list_str, max_tokens - curr_token)
+    if added_list_str:
         final_diff = final_diff + "\n\n" + added_list_str
-    if modified_file_names:
-        modified_list_str = MORE_MODIFIED_FILES_ + "\n".join(modified_file_names)
+        curr_token += token_handler.count_tokens(added_list_str) + 2
+    modified_list_str = clip_tokens(modified_list_str, max_tokens - curr_token)
+    if modified_list_str:
         final_diff = final_diff + "\n\n" + modified_list_str
-    if deleted_file_names:
-        deleted_list_str = DELETED_FILES_ + "\n".join(deleted_file_names)
+        curr_token += token_handler.count_tokens(modified_list_str) + 2
+    deleted_list_str = clip_tokens(deleted_list_str, max_tokens - curr_token)
+    if deleted_list_str:
         final_diff = final_diff + "\n\n" + deleted_list_str
+
+    get_logger().debug(f"After pruning, added_list_str: {added_list_str}, modified_list_str: {modified_list_str}, "
+                       f"deleted_list_str: {deleted_list_str}")
+    if not return_remaining_files:
+        return final_diff
+    else:
+        return final_diff, remaining_files_list
+
+
+def get_pr_diff_multiple_patchs(git_provider: GitProvider, token_handler: TokenHandler, model: str,
+                add_line_numbers_to_hunks: bool = False, disable_extra_lines: bool = False):
     try:
-        get_logger().debug(f"After pruning, added_list_str: {added_list_str}, modified_list_str: {modified_list_str}, "
-                          f"deleted_list_str: {deleted_list_str}")
-    except Exception as e:
-        pass
-    return final_diff
+        diff_files_original = git_provider.get_diff_files()
+    except RateLimitExceededException as e:
+        get_logger().error(f"Rate limit exceeded for git provider API. original message {e}")
+        raise
+
+    diff_files = filter_ignored(diff_files_original)
+    if diff_files != diff_files_original:
+        try:
+            get_logger().info(f"Filtered out {len(diff_files_original) - len(diff_files)} files")
+            new_names = set([a.filename for a in diff_files])
+            orig_names = set([a.filename for a in diff_files_original])
+            get_logger().info(f"Filtered out files: {orig_names - new_names}")
+        except Exception as e:
+            pass
+
+    # get pr languages
+    pr_languages = sort_files_by_main_languages(git_provider.get_languages(), diff_files)
+    if pr_languages:
+        try:
+            get_logger().info(f"PR main language: {pr_languages[0]['language']}")
+        except Exception as e:
+            pass
+
+    patches_compressed_list, total_tokens_list, deleted_files_list, remaining_files_list, file_dict, files_in_patches_list = \
+        pr_generate_compressed_diff(pr_languages, token_handler, model, add_line_numbers_to_hunks, large_pr_handling=True)
+
+    return patches_compressed_list, total_tokens_list, deleted_files_list, remaining_files_list, file_dict, files_in_patches_list
 
 
 def pr_generate_extended_diff(pr_languages: list,
@@ -134,6 +197,9 @@ def pr_generate_extended_diff(pr_languages: list,
 
             # extend each patch with extra lines of context
             extended_patch = extend_patch(original_file_content_str, patch, num_lines=patch_extra_lines)
+            if not extended_patch:
+                get_logger().warning(f"Failed to extend patch for file: {file.filename}")
+                continue
             full_extended_patch = f"\n\n## {file.filename}\n\n{extended_patch}\n"
 
             if add_line_numbers_to_hunks:
@@ -149,41 +215,17 @@ def pr_generate_extended_diff(pr_languages: list,
 
 
 def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, model: str,
-                                convert_hunks_to_line_numbers: bool) -> Tuple[list, list, list, list]:
-    """
-    Generate a compressed diff string for a pull request, using diff minimization techniques to reduce the number of
-    tokens used.
-    Args:
-        top_langs (list): A list of dictionaries representing the languages used in the pull request and their
-        corresponding files.
-        token_handler (TokenHandler): An object of the TokenHandler class used for handling tokens in the context of the
-        pull request.
-        model (str): The model used for tokenization.
-        convert_hunks_to_line_numbers (bool): A boolean indicating whether to convert hunks to line numbers in the diff.
-    Returns:
-        Tuple[list, list, list]: A tuple containing the following lists:
-            - patches: A list of compressed diff patches for each file in the pull request.
-            - modified_files_list: A list of file names that were skipped due to large patch size.
-            - deleted_files_list: A list of file names that were deleted in the pull request.
-
-    Minimization techniques to reduce the number of tokens:
-    0. Start from the largest diff patch to smaller ones
-    1. Don't use extend context lines around diff
-    2. Minimize deleted files
-    3. Minimize deleted hunks
-    4. Minimize all remaining files when you reach token limit
-    """
-
-    patches = []
-    added_files_list = []
-    modified_files_list = []
+                                convert_hunks_to_line_numbers: bool,
+                                large_pr_handling: bool) -> Tuple[list, list, list, list, dict, list]:
     deleted_files_list = []
+
     # sort each one of the languages in top_langs by the number of tokens in the diff
     sorted_files = []
     for lang in top_langs:
         sorted_files.extend(sorted(lang['files'], key=lambda x: x.tokens, reverse=True))
 
-    total_tokens = token_handler.prompt_tokens
+    # generate patches for each file, and count tokens
+    file_dict = {}
     for file in sorted_files:
         original_file_content_str = file.base_file
         new_file_content_str = file.head_file
@@ -195,51 +237,87 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
         patch = handle_patch_deletions(patch, original_file_content_str,
                                        new_file_content_str, file.filename, file.edit_type)
         if patch is None:
-            if not deleted_files_list:
-                total_tokens += token_handler.count_tokens(DELETED_FILES_)
-            deleted_files_list.append(file.filename)
-            total_tokens += token_handler.count_tokens(file.filename) + 1
+            if file.filename not in deleted_files_list:
+                deleted_files_list.append(file.filename)
             continue
 
         if convert_hunks_to_line_numbers:
             patch = convert_to_hunks_with_lines_numbers(patch, file)
 
         new_patch_tokens = token_handler.count_tokens(patch)
+        file_dict[file.filename] = {'patch': patch, 'tokens': new_patch_tokens, 'edit_type': file.edit_type}
+
+    max_tokens_model = get_max_tokens(model)
+
+    # first iteration
+    files_in_patches_list = []
+    remaining_files_list =  [file.filename for file in sorted_files]
+    patches_list =[]
+    total_tokens_list = []
+    total_tokens, patches, remaining_files_list, files_in_patch_list = generate_full_patch(convert_hunks_to_line_numbers, file_dict,
+                                       max_tokens_model, remaining_files_list, token_handler)
+    patches_list.append(patches)
+    total_tokens_list.append(total_tokens)
+    files_in_patches_list.append(files_in_patch_list)
+
+    # additional iterations (if needed)
+    if large_pr_handling:
+        NUMBER_OF_ALLOWED_ITERATIONS = get_settings().pr_description.max_ai_calls - 1 # one more call is to summarize
+        for i in range(NUMBER_OF_ALLOWED_ITERATIONS-1):
+            if remaining_files_list:
+                total_tokens, patches, remaining_files_list, files_in_patch_list = generate_full_patch(convert_hunks_to_line_numbers,
+                                                                                 file_dict,
+                                                                                  max_tokens_model,
+                                                                                  remaining_files_list, token_handler)
+                if patches:
+                    patches_list.append(patches)
+                    total_tokens_list.append(total_tokens)
+                    files_in_patches_list.append(files_in_patch_list)
+            else:
+                break
+
+    return patches_list, total_tokens_list, deleted_files_list, remaining_files_list, file_dict, files_in_patches_list
+
+
+def generate_full_patch(convert_hunks_to_line_numbers, file_dict, max_tokens_model,remaining_files_list_prev, token_handler):
+    total_tokens = token_handler.prompt_tokens # initial tokens
+    patches = []
+    remaining_files_list_new = []
+    files_in_patch_list = []
+    for filename, data in file_dict.items():
+        if filename not in remaining_files_list_prev:
+            continue
+
+        patch = data['patch']
+        new_patch_tokens = data['tokens']
+        edit_type = data['edit_type']
 
         # Hard Stop, no more tokens
-        if total_tokens > get_max_tokens(model) - OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD:
-            get_logger().warning(f"File was fully skipped, no more tokens: {file.filename}.")
+        if total_tokens > max_tokens_model - OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD:
+            get_logger().warning(f"File was fully skipped, no more tokens: {filename}.")
             continue
 
         # If the patch is too large, just show the file name
-        if total_tokens + new_patch_tokens > get_max_tokens(model) - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD:
+        if total_tokens + new_patch_tokens > max_tokens_model - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD:
             # Current logic is to skip the patch if it's too large
             # TODO: Option for alternative logic to remove hunks from the patch to reduce the number of tokens
             #  until we meet the requirements
             if get_settings().config.verbosity_level >= 2:
-                get_logger().warning(f"Patch too large, minimizing it, {file.filename}")
-            if file.edit_type == EDIT_TYPE.ADDED:
-                if not added_files_list:
-                    total_tokens += token_handler.count_tokens(ADDED_FILES_)
-                added_files_list.append(file.filename)
-            else:
-                if not modified_files_list:
-                    total_tokens += token_handler.count_tokens(MORE_MODIFIED_FILES_)
-                modified_files_list.append(file.filename)
-                total_tokens += token_handler.count_tokens(file.filename) + 1
+                get_logger().warning(f"Patch too large, skipping it, {filename}")
+            remaining_files_list_new.append(filename)
             continue
 
         if patch:
             if not convert_hunks_to_line_numbers:
-                patch_final = f"\n\n## file: '{file.filename.strip()}\n\n{patch.strip()}\n'"
+                patch_final = f"\n\n## file: '{filename.strip()}\n\n{patch.strip()}\n'"
             else:
                 patch_final = "\n\n" + patch.strip()
             patches.append(patch_final)
             total_tokens += token_handler.count_tokens(patch_final)
+            files_in_patch_list.append(filename)
             if get_settings().config.verbosity_level >= 2:
-                get_logger().info(f"Tokens: {total_tokens}, last filename: {file.filename}")
-
-    return patches, modified_files_list, deleted_files_list, added_files_list
+                get_logger().info(f"Tokens: {total_tokens}, last filename: {filename}")
+    return total_tokens, patches, remaining_files_list_new, files_in_patch_list
 
 
 async def retry_with_fallback_models(f: Callable, model_type: ModelType = ModelType.REGULAR):
@@ -358,9 +436,25 @@ def get_pr_multi_diffs(git_provider: GitProvider,
         patch = convert_to_hunks_with_lines_numbers(patch, file)
         new_patch_tokens = token_handler.count_tokens(patch)
 
-        if patch and (token_handler.prompt_tokens + new_patch_tokens) > get_max_tokens(model) - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD:
-            get_logger().warning(f"Patch too large, skipping: {file.filename}")
-            continue
+        if patch and (token_handler.prompt_tokens + new_patch_tokens) > get_max_tokens(
+                model) - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD:
+            if get_settings().config.get('large_patch_policy', 'skip') == 'skip':
+                get_logger().warning(f"Patch too large, skipping: {file.filename}")
+                continue
+            elif get_settings().config.get('large_patch_policy') == 'clip':
+                delta_tokens = get_max_tokens(model) - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD - token_handler.prompt_tokens
+                patch_clipped = clip_tokens(patch, delta_tokens, delete_last_line=True, num_input_tokens=new_patch_tokens)
+                new_patch_tokens = token_handler.count_tokens(patch_clipped)
+                if patch_clipped and (token_handler.prompt_tokens + new_patch_tokens) > get_max_tokens(
+                        model) - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD:
+                    get_logger().warning(f"Patch too large, skipping: {file.filename}")
+                    continue
+                else:
+                    get_logger().info(f"Clipped large patch for file: {file.filename}")
+                    patch = patch_clipped
+            else:
+                get_logger().warning(f"Patch too large, skipping: {file.filename}")
+                continue
 
         if patch and (total_tokens + new_patch_tokens > get_max_tokens(model) - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD):
             final_diff = "\n".join(patches)

pr_agent/algo/token_handler.py

@@ -1,12 +1,25 @@
 from jinja2 import Environment, StrictUndefined
 from tiktoken import encoding_for_model, get_encoding
-
 from pr_agent.config_loader import get_settings
+from threading import Lock
 
 
-def get_token_encoder():
-    return encoding_for_model(get_settings().config.model) if "gpt" in get_settings().config.model else get_encoding(
-        "cl100k_base")
+class TokenEncoder:
+    _encoder_instance = None
+    _model = None
+    _lock = Lock()  # Create a lock object
+
+    @classmethod
+    def get_token_encoder(cls):
+        model = get_settings().config.model
+        if cls._encoder_instance is None or model != cls._model:  # Check without acquiring the lock for performance
+            with cls._lock:  # Lock acquisition to ensure thread safety
+                if cls._encoder_instance is None or model != cls._model:
+                    cls._model = model
+                    cls._encoder_instance = encoding_for_model(cls._model) if "gpt" in cls._model else get_encoding(
+                        "cl100k_base")
+        return cls._encoder_instance
+
 
 class TokenHandler:
     """
@@ -31,7 +44,7 @@ class TokenHandler:
         - system: The system string.
         - user: The user string.
         """
-        self.encoder = get_token_encoder()
+        self.encoder = TokenEncoder.get_token_encoder()
         if pr is not None:
             self.prompt_tokens = self._get_system_user_tokens(pr, self.encoder, vars, system, user)
 

pr_agent/algo/utils.py

@@ -2,8 +2,10 @@ from __future__ import annotations
 
 import difflib
 import json
+import os
 import re
 import textwrap
+import time
 from datetime import datetime
 from enum import Enum
 from typing import Any, List, Tuple
@@ -12,7 +14,7 @@ import yaml
 from starlette_context import context
 
 from pr_agent.algo import MAX_TOKENS
-from pr_agent.algo.token_handler import get_token_encoder
+from pr_agent.algo.token_handler import TokenEncoder
 from pr_agent.config_loader import get_settings, global_settings
 from pr_agent.algo.types import FilePatchInfo
 from pr_agent.log import get_logger
@@ -21,6 +23,12 @@ class ModelType(str, Enum):
     REGULAR = "regular"
     TURBO = "turbo"
 
+
+class PRReviewHeader(str, Enum):
+    REGULAR = "## PR Reviewer Guide"
+    INCREMENTAL = "## Incremental PR Reviewer Guide"
+
+
 def get_setting(key: str) -> Any:
     try:
         key = key.upper()
@@ -29,7 +37,7 @@ def get_setting(key: str) -> Any:
         return global_settings.get(key, None)
 
 
-def emphasize_header(text: str) -> str:
+def emphasize_header(text: str, only_markdown=False) -> str:
     try:
         # Finding the position of the first occurrence of ": "
         colon_position = text.find(": ")
@@ -37,7 +45,10 @@ def emphasize_header(text: str) -> str:
         # Splitting the string and wrapping the first part in <strong> tags
         if colon_position != -1:
             # Everything before the colon (inclusive) is wrapped in <strong> tags
-            transformed_string = "<strong>" + text[:colon_position + 1] + "</strong>" + text[colon_position + 1:]
+            if only_markdown:
+                transformed_string = f"**{text[:colon_position + 1]}**\n" + text[colon_position + 1:]
+            else:
+                transformed_string = "<strong>" + text[:colon_position + 1] + "</strong>" +'<br>' + text[colon_position + 1:]
         else:
             # If there's no ": ", return the original string
             transformed_string = text
@@ -47,68 +58,153 @@ def emphasize_header(text: str) -> str:
         get_logger().exception(f"Failed to emphasize header: {e}")
         return text
 
-def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
+
+def unique_strings(input_list: List[str]) -> List[str]:
+    if not input_list or not isinstance(input_list, list):
+        return input_list
+    seen = set()
+    unique_list = []
+    for item in input_list:
+        if item not in seen:
+            unique_list.append(item)
+            seen.add(item)
+    return unique_list
+
+def convert_to_markdown_v2(output_data: dict, gfm_supported: bool = True, incremental_review=None) -> str:
     """
     Convert a dictionary of data into markdown format.
     Args:
         output_data (dict): A dictionary containing data to be converted to markdown format.
     Returns:
         str: The markdown formatted text generated from the input dictionary.
-    """    
+    """
 
     emojis = {
-        "Possible issues": "🔍",
+        "Can be split": "🔀",
+        "Possible issues": "⚡",
+        "Key issues to review": "⚡",
         "Score": "🏅",
         "Relevant tests": "🧪",
         "Focused PR": "✨",
+        "Relevant ticket": "🎫",
         "Security concerns": "🔒",
         "Insights from user's answers": "📝",
         "Code feedback": "🤖",
         "Estimated effort to review [1-5]": "⏱️",
     }
     markdown_text = ""
-    markdown_text += f"## PR Review\n\n"
-    if gfm_supported:
-        markdown_text += "<table>\n<tr>\n"
-        # markdown_text += """<td> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Feedback&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</td> <td></td></tr>"""
-
+    if not incremental_review:
+        markdown_text += f"{PRReviewHeader.REGULAR.value} 🔍\n\n"
+    else:
+        markdown_text += f"{PRReviewHeader.INCREMENTAL.value} 🔍\n\n"
+        markdown_text += f"⏮️ Review for commits since previous PR-Agent review {incremental_review}.\n\n"
     if not output_data or not output_data.get('review', {}):
         return ""
 
+    if gfm_supported:
+        markdown_text += "<table>\n"
+
     for key, value in output_data['review'].items():
         if value is None or value == '' or value == {} or value == []:
-            continue
+            if key.lower() != 'can_be_split':
+                continue
         key_nice = key.replace('_', ' ').capitalize()
         emoji = emojis.get(key_nice, "")
-        if gfm_supported:
-            if 'Estimated effort to review' in key_nice:
-                key_nice = 'Estimated&nbsp;effort&nbsp;to&nbsp;review [1-5]'
-            if 'security concerns' in key_nice.lower():
-                value = emphasize_header(value.strip())
-                markdown_text += f"<tr><td> {emoji}&nbsp;<strong>{key_nice}</strong></td><td>\n\n{value}\n\n</td></tr>\n"
-            elif 'possible issues' in key_nice.lower():
-                value = value.strip()
-                issues = value.split('\n- ')
-                number_of_issues = len(issues)
-                if number_of_issues > 1:
-                    markdown_text += f"<tr><td rowspan={number_of_issues}> {emoji}&nbsp;<strong>{key_nice}</strong></td>\n"
-                    for i, issue in enumerate(issues):
-                        issue = issue.strip('-').strip()
-                        issue = emphasize_header(issue.strip())
-                        if i == 0:
-                            markdown_text += f"<td>\n\n{issue}</td></tr>\n"
-                        else:
-                            markdown_text += f"<tr>\n<td>\n\n{issue}</td></tr>\n"
+        if 'Estimated effort to review' in key_nice:
+            key_nice = 'Estimated effort to review'
+            if value.isnumeric():
+                value_int = int(value)
+            else:
+                try:
+                    value_int = int(value.split(',')[0])
+                except ValueError:
+                    continue
+            blue_bars = '🔵' * value_int
+            white_bars = '⚪' * (5 - value_int)
+            value = f"{value_int} {blue_bars}{white_bars}"
+            if gfm_supported:
+                markdown_text += f"<tr><td>"
+                markdown_text += f"{emoji}&nbsp;<strong>{key_nice}</strong>: {value}"
+                markdown_text += f"</td></tr>\n"
+            else:
+                markdown_text += f"### {emoji} {key_nice}: {value}\n\n"
+        elif 'relevant tests' in key_nice.lower():
+            value = value.strip().lower()
+            if gfm_supported:
+                markdown_text += f"<tr><td>"
+                if is_value_no(value):
+                    markdown_text += f"{emoji}&nbsp;<strong>No relevant tests</strong>"
                 else:
-                    value = emphasize_header(value.strip('-').strip())
-                    markdown_text += f"<tr><td> {emoji}&nbsp;<strong>{key_nice}</strong></td><td>\n\n{value}\n\n</td></tr>\n"
+                    markdown_text += f"{emoji}&nbsp;<strong>PR contains tests</strong>"
+                markdown_text += f"</td></tr>\n"
             else:
-                markdown_text += f"<tr><td> {emoji}&nbsp;<strong>{key_nice}</strong></td><td>\n\n{value}\n\n</td></tr>\n"
+                if gfm_supported:
+                    markdown_text += f"<tr><td>"
+                    if is_value_no(value):
+                        markdown_text += f"{emoji}&nbsp;<strong>No relevant tests</strong>"
+                    else:
+                        markdown_text += f"{emoji}&nbsp;<strong>PR contains tests</strong>"
+                else:
+                    if is_value_no(value):
+                        markdown_text += f'### {emoji} No relevant tests\n\n'
+                    else:
+                        markdown_text += f"### PR contains tests\n\n"
+        elif 'security concerns' in key_nice.lower():
+            if gfm_supported:
+                markdown_text += f"<tr><td>"
+                if is_value_no(value):
+                    markdown_text += f"{emoji}&nbsp;<strong>No security concerns identified</strong>"
+                else:
+                    markdown_text += f"{emoji}&nbsp;<strong>Security concerns</strong><br><br>\n\n"
+                    value = emphasize_header(value.strip())
+                    markdown_text += f"{value}"
+                markdown_text += f"</td></tr>\n"
+            else:
+                if is_value_no(value):
+                    markdown_text += f'### {emoji} No security concerns identified\n\n'
+                else:
+                    markdown_text += f"### {emoji} Security concerns\n\n"
+                    value = emphasize_header(value.strip())
+                    markdown_text += f"{value}\n\n"
+        elif 'can be split' in key_nice.lower():
+            if gfm_supported:
+                markdown_text += f"<tr><td>"
+                markdown_text += process_can_be_split(emoji, value)
+                markdown_text += f"</td></tr>\n"
+        elif 'key issues to review' in key_nice.lower():
+            value = value.strip()
+            if is_value_no(value):
+                if gfm_supported:
+                    markdown_text += f"<tr><td>"
+                    markdown_text += f"{emoji}&nbsp;<strong>No key issues to review</strong>"
+                    markdown_text += f"</td></tr>\n"
+                else:
+                    markdown_text += f"### {emoji} No key issues to review\n\n"
+            else:
+                issues = value.split('\n- ')
+                for i, _ in enumerate(issues):
+                    issues[i] = issues[i].strip().strip('-').strip()
+                issues = unique_strings(issues) # remove duplicates
+                if gfm_supported:
+                    markdown_text += f"<tr><td>"
+                    markdown_text += f"{emoji}&nbsp;<strong>{key_nice}</strong><br><br>\n\n"
+                else:
+                    markdown_text += f"### {emoji} Key issues to review:\n\n"
+                for i, issue in enumerate(issues):
+                    if not issue:
+                        continue
+                    issue = emphasize_header(issue, only_markdown=True)
+                    markdown_text += f"{issue}\n\n"
+                if gfm_supported:
+                    markdown_text += f"</td></tr>\n"
         else:
-            if len(value.split()) > 1:
-                markdown_text += f"{emoji} **{key_nice}:**\n\n {value}\n\n"
+            if gfm_supported:
+                markdown_text += f"<tr><td>"
+                markdown_text += f"{emoji}&nbsp;<strong>{key_nice}</strong>: {value}"
+                markdown_text += f"</td></tr>\n"
             else:
-                markdown_text += f"{emoji} **{key_nice}:** {value}\n\n"
+                markdown_text += f"### {emoji} {key_nice}: {value}\n\n"
+
     if gfm_supported:
         markdown_text += "</table>\n"
 
@@ -118,18 +214,70 @@ def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
             markdown_text += f"<details><summary> <strong>Code feedback:</strong></summary>\n\n"
             markdown_text += "<hr>"
         else:
-            markdown_text += f"\n\n** Code feedback:**\n\n"
+            markdown_text += f"\n\n### Code feedback:\n\n"
         for i, value in enumerate(output_data['code_feedback']):
             if value is None or value == '' or value == {} or value == []:
                 continue
             markdown_text += parse_code_suggestion(value, i, gfm_supported)+"\n\n"
         if markdown_text.endswith('<hr>'):
-            markdown_text = markdown_text[:-4]
+            markdown_text= markdown_text[:-4]
         if gfm_supported:
             markdown_text += f"</details>"
-    #print(markdown_text)
+
+    return markdown_text
 
 
+def process_can_be_split(emoji, value):
+    try:
+        # key_nice = "Can this PR be split?"
+        key_nice = "Multiple PR themes"
+        markdown_text = ""
+        if not value or isinstance(value, list) and len(value) == 1:
+            value = "No"
+            # markdown_text += f"<tr><td> {emoji}&nbsp;<strong>{key_nice}</strong></td><td>\n\n{value}\n\n</td></tr>\n"
+            # markdown_text += f"### {emoji} No multiple PR themes\n\n"
+            markdown_text += f"{emoji} <strong>No multiple PR themes</strong>\n\n"
+        else:
+            markdown_text += f"{emoji} <strong>{key_nice}</strong><br><br>\n\n"
+            for i, split in enumerate(value):
+                title = split.get('title', '')
+                relevant_files = split.get('relevant_files', [])
+                markdown_text += f"<details><summary>\nSub-PR theme: <b>{title}</b></summary>\n\n"
+                markdown_text += f"___\n\nRelevant files:\n\n"
+                for file in relevant_files:
+                    markdown_text += f"- {file}\n"
+                markdown_text += f"___\n\n"
+                markdown_text += f"</details>\n\n"
+
+                # markdown_text += f"#### Sub-PR theme: {title}\n\n"
+                # markdown_text += f"Relevant files:\n\n"
+                # for file in relevant_files:
+                #     markdown_text += f"- {file}\n"
+                # markdown_text += "\n"
+            # number_of_splits = len(value)
+            # markdown_text += f"<tr><td rowspan={number_of_splits}> {emoji}&nbsp;<strong>{key_nice}</strong></td>\n"
+            # for i, split in enumerate(value):
+            #     title = split.get('title', '')
+            #     relevant_files = split.get('relevant_files', [])
+            #     if i == 0:
+            #         markdown_text += f"<td><details><summary>\nSub-PR theme:<br><strong>{title}</strong></summary>\n\n"
+            #         markdown_text += f"<hr>\n"
+            #         markdown_text += f"Relevant files:\n"
+            #         markdown_text += f"<ul>\n"
+            #         for file in relevant_files:
+            #             markdown_text += f"<li>{file}</li>\n"
+            #         markdown_text += f"</ul>\n\n</details></td></tr>\n"
+            #     else:
+            #         markdown_text += f"<tr>\n<td><details><summary>\nSub-PR theme:<br><strong>{title}</strong></summary>\n\n"
+            #         markdown_text += f"<hr>\n"
+            #         markdown_text += f"Relevant files:\n"
+            #         markdown_text += f"<ul>\n"
+            #         for file in relevant_files:
+            #             markdown_text += f"<li>{file}</li>\n"
+            #         markdown_text += f"</ul>\n\n</details></td></tr>\n"
+    except Exception as e:
+        get_logger().exception(f"Failed to process can be split: {e}")
+        return ""
     return markdown_text
 
 
@@ -298,7 +446,7 @@ def convert_str_to_datetime(date_str):
     return datetime.strptime(date_str, datetime_format)
 
 
-def load_large_diff(filename, new_file_content_str: str, original_file_content_str: str) -> str:
+def load_large_diff(filename, new_file_content_str: str, original_file_content_str: str, show_warning: bool = True) -> str:
     """
     Generate a patch for a modified file by comparing the original content of the file with the new content provided as
     input.
@@ -317,7 +465,7 @@ def load_large_diff(filename, new_file_content_str: str, original_file_content_s
     try:
         diff = difflib.unified_diff(original_file_content_str.splitlines(keepends=True),
                                     new_file_content_str.splitlines(keepends=True))
-        if get_settings().config.verbosity_level >= 2:
+        if get_settings().config.verbosity_level >= 2 and show_warning:
             get_logger().warning(f"File was modified, but no patch was found. Manually creating patch: {filename}.")
         patch = ''.join(diff)
     except Exception:
@@ -349,7 +497,7 @@ def update_settings_from_args(args: List[str]) -> List[str]:
                 arg = arg.strip('-').strip()
                 vals = arg.split('=', 1)
                 if len(vals) != 2:
-                    if len(vals) > 2: # --extended is a valid argument
+                    if len(vals) > 2:  # --extended is a valid argument
                         get_logger().error(f'Invalid argument format: {arg}')
                     other_args.append(arg)
                     continue
@@ -371,25 +519,28 @@ def _fix_key_value(key: str, value: str):
     return key, value
 
 
-def load_yaml(response_text: str, keys_fix_yaml: List[str] = []) -> dict:
+def load_yaml(response_text: str, keys_fix_yaml: List[str] = [], first_key="", last_key="") -> dict:
     response_text = response_text.removeprefix('```yaml').rstrip('`')
     try:
         data = yaml.safe_load(response_text)
     except Exception as e:
         get_logger().error(f"Failed to parse AI prediction: {e}")
-        data = try_fix_yaml(response_text, keys_fix_yaml=keys_fix_yaml)
+        data = try_fix_yaml(response_text, keys_fix_yaml=keys_fix_yaml, first_key=first_key, last_key=last_key)
     return data
 
 
-def try_fix_yaml(response_text: str, keys_fix_yaml: List[str] = []) -> dict:
+def try_fix_yaml(response_text: str,
+                 keys_fix_yaml: List[str] = [],
+                 first_key="",
+                 last_key="",) -> dict:
     response_text_lines = response_text.split('\n')
 
-    keys = ['relevant line:', 'suggestion content:', 'relevant file:', 'existing code:', 'improved code:']
-    keys = keys + keys_fix_yaml
+    keys_yaml = ['relevant line:', 'suggestion content:', 'relevant file:', 'existing code:', 'improved code:']
+    keys_yaml = keys_yaml + keys_fix_yaml
     # first fallback - try to convert 'relevant line: ...' to relevant line: |-\n        ...'
     response_text_lines_copy = response_text_lines.copy()
     for i in range(0, len(response_text_lines_copy)):
-        for key in keys:
+        for key in keys_yaml:
             if key in response_text_lines_copy[i] and not '|-' in response_text_lines_copy[i]:
                 response_text_lines_copy[i] = response_text_lines_copy[i].replace(f'{key}',
                                                                                   f'{key} |-\n        ')
@@ -400,19 +551,20 @@ def try_fix_yaml(response_text: str, keys_fix_yaml: List[str] = []) -> dict:
     except:
         get_logger().info(f"Failed to parse AI prediction after adding |-\n")
 
-    # second fallback - try to extract only range from first ```yaml to ````
+    # second fallback - try to extract only range from first ```yaml to ```
     snippet_pattern = r'```(yaml)?[\s\S]*?```'
     snippet = re.search(snippet_pattern, '\n'.join(response_text_lines_copy))
     if snippet:
         snippet_text = snippet.group()
         try:
             data = yaml.safe_load(snippet_text.removeprefix('```yaml').rstrip('`'))
-            get_logger().info(f"Successfully parsed AI prediction after extracting yaml snippet")
+            get_logger().info(f"Successfully parsed AI prediction after extracting yaml snippet with second fallback")
             return data
         except:
             pass
 
-     # third fallback - try to remove leading and trailing curly brackets
+
+    # third fallback - try to remove leading and trailing curly brackets
     response_text_copy = response_text.strip().rstrip().removeprefix('{').removesuffix('}').rstrip(':\n')
     try:
         data = yaml.safe_load(response_text_copy)
@@ -421,7 +573,27 @@ def try_fix_yaml(response_text: str, keys_fix_yaml: List[str] = []) -> dict:
     except:
         pass
 
-    # fourth fallback - try to remove last lines
+    # forth fallback - try to extract yaml snippet by 'first_key' and 'last_key'
+    # note that 'last_key' can be in practice a key that is not the last key in the yaml snippet.
+    # it just needs to be some inner key, so we can look for newlines after it
+    if first_key and last_key:
+        index_start = response_text.find(f"\n{first_key}:")
+        if index_start == -1:
+            index_start = response_text.find(f"{first_key}:")
+        index_last_code = response_text.rfind(f"{last_key}:")
+        index_end = response_text.find("\n\n", index_last_code) # look for newlines after last_key
+        if index_end == -1:
+            index_end = len(response_text)
+        response_text_copy = response_text[index_start:index_end].strip().strip('```yaml').strip('`').strip()
+        try:
+            data = yaml.safe_load(response_text_copy)
+            get_logger().info(f"Successfully parsed AI prediction after extracting yaml snippet")
+            return data
+        except:
+            pass
+
+
+    # fifth fallback - try to remove last lines
     data = {}
     for i in range(1, len(response_text_lines)):
         response_text_lines_tmp = '\n'.join(response_text_lines[:-i])
@@ -437,7 +609,7 @@ def set_custom_labels(variables, git_provider=None):
     if not get_settings().config.enable_custom_labels:
         return
 
-    labels = get_settings().custom_labels
+    labels = get_settings().get('custom_labels', {})
     if not labels:
         # set default labels
         labels = ['Bug fix', 'Tests', 'Bug fix with tests', 'Enhancement', 'Documentation', 'Other']
@@ -494,7 +666,7 @@ def get_max_tokens(model):
     return max_tokens_model
 
 
-def clip_tokens(text: str, max_tokens: int, add_three_dots=True) -> str:
+def clip_tokens(text: str, max_tokens: int, add_three_dots=True, num_input_tokens=None, delete_last_line=False) -> str:
     """
     Clip the number of tokens in a string to a maximum number of tokens.
 
@@ -509,16 +681,30 @@ def clip_tokens(text: str, max_tokens: int, add_three_dots=True) -> str:
         return text
 
     try:
-        encoder = get_token_encoder()
-        num_input_tokens = len(encoder.encode(text))
+        if num_input_tokens is None:
+            encoder = TokenEncoder.get_token_encoder()
+            num_input_tokens = len(encoder.encode(text))
         if num_input_tokens <= max_tokens:
             return text
+        if max_tokens < 0:
+            return ""
+
+        # calculate the number of characters to keep
         num_chars = len(text)
         chars_per_token = num_chars / num_input_tokens
-        num_output_chars = int(chars_per_token * max_tokens)
-        clipped_text = text[:num_output_chars]
-        if add_three_dots:
-            clipped_text += "...(truncated)"
+        factor = 0.9  # reduce by 10% to be safe
+        num_output_chars = int(factor * chars_per_token * max_tokens)
+
+        # clip the text
+        if num_output_chars > 0:
+            clipped_text = text[:num_output_chars]
+            if delete_last_line:
+                clipped_text = clipped_text.rsplit('\n', 1)[0]
+            if add_three_dots:
+                clipped_text += "\n...(truncated)"
+        else: # if the text is empty
+            clipped_text =  ""
+
         return clipped_text
     except Exception as e:
         get_logger().warning(f"Failed to clip tokens: {e}")
@@ -604,3 +790,97 @@ def find_line_number_of_relevant_line_in_file(diff_files: List[FilePatchInfo],
                             absolute_position = start2 + delta - 1
                             break
     return position, absolute_position
+
+def validate_and_await_rate_limit(rate_limit_status=None, git_provider=None, get_rate_limit_status_func=None):
+    if git_provider and not rate_limit_status:
+        rate_limit_status = {'resources': git_provider.github_client.get_rate_limit().raw_data}
+
+    if not rate_limit_status:
+        rate_limit_status = get_rate_limit_status_func()
+    # validate that the rate limit is not exceeded
+    is_rate_limit = False
+    for key, value in rate_limit_status['resources'].items():
+        if value['remaining'] == 0:
+            print(f"key: {key}, value: {value}")
+            is_rate_limit = True
+            sleep_time_sec = value['reset'] - datetime.now().timestamp()
+            sleep_time_hour = sleep_time_sec / 3600.0
+            print(f"Rate limit exceeded. Sleeping for {sleep_time_hour} hours")
+            if sleep_time_sec > 0:
+                time.sleep(sleep_time_sec+1)
+
+            if git_provider:
+                rate_limit_status = {'resources': git_provider.github_client.get_rate_limit().raw_data}
+            else:
+                rate_limit_status = get_rate_limit_status_func()
+
+    return is_rate_limit
+
+
+def get_largest_component(pr_url):
+    from pr_agent.tools.pr_analyzer import PRAnalyzer
+    publish_output = get_settings().config.publish_output
+    get_settings().config.publish_output = False  # disable publish output
+    analyzer = PRAnalyzer(pr_url)
+    methods_dict_files = analyzer.run_sync()
+    get_settings().config.publish_output = publish_output
+    max_lines_changed = 0
+    file_b = ""
+    component_name_b = ""
+    for file in methods_dict_files:
+        for method in methods_dict_files[file]:
+            try:
+                if methods_dict_files[file][method]['num_plus_lines'] > max_lines_changed:
+                    max_lines_changed = methods_dict_files[file][method]['num_plus_lines']
+                    file_b = file
+                    component_name_b = method
+            except:
+                pass
+    if component_name_b:
+        get_logger().info(f"Using the largest changed component: '{component_name_b}'")
+        return component_name_b, file_b
+    else:
+        return None, None
+
+def github_action_output(output_data: dict, key_name: str):
+    try:
+        if not get_settings().get('github_action_config.enable_output', False):
+            return
+
+        key_data = output_data.get(key_name, {})
+        with open(os.environ['GITHUB_OUTPUT'], 'a') as fh:
+            print(f"{key_name}={json.dumps(key_data, indent=None, ensure_ascii=False)}", file=fh)
+    except Exception as e:
+        get_logger().error(f"Failed to write to GitHub Action output: {e}")
+    return
+
+
+def show_relevant_configurations(relevant_section: str) -> str:
+    forbidden_keys = ['ai_disclaimer', 'ai_disclaimer_title', 'ANALYTICS_FOLDER', 'secret_provider',
+                      'trial_prefix_message', 'no_eligible_message', 'identity_provider', 'ALLOWED_REPOS','APP_NAME']
+
+    markdown_text = ""
+    markdown_text += "\n<hr>\n<details> <summary><strong>🛠️ Relevant configurations:</strong></summary> \n\n"
+    markdown_text +="<br>These are the relevant [configurations](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) for this tool:\n\n"
+    markdown_text += f"**[config**]\n```yaml\n\n"
+    for key, value in get_settings().config.items():
+        if key in forbidden_keys:
+            continue
+        markdown_text += f"{key}: {value}\n"
+    markdown_text += "\n```\n"
+    markdown_text += f"\n**[{relevant_section}]**\n```yaml\n\n"
+    for key, value in get_settings().get(relevant_section, {}).items():
+        if key in forbidden_keys:
+            continue
+        markdown_text += f"{key}: {value}\n"
+    markdown_text += "\n```"
+    markdown_text += "\n</details>\n"
+    return markdown_text
+
+def is_value_no(value):
+    if value is None:
+        return True
+    value_str = str(value).strip().lower()
+    if value_str == 'no' or value_str == 'none' or value_str == 'false':
+        return True
+    return False

pr_agent/cli.py

@@ -10,47 +10,61 @@ log_level = os.environ.get("LOG_LEVEL", "INFO")
 setup_logger(log_level)
 
 
-
-def run(inargs=None):
+def set_parser():
     parser = argparse.ArgumentParser(description='AI based pull request analyzer', usage=
-"""\
-Usage: cli.py --pr-url=<URL on supported git hosting service> <command> [<args>].
-For example:
-- cli.py --pr_url=... review
-- cli.py --pr_url=... describe
-- cli.py --pr_url=... improve
-- cli.py --pr_url=... ask "write me a poem about this PR"
-- cli.py --pr_url=... reflect
-- cli.py --issue_url=... similar_issue
+    """\
+    Usage: cli.py --pr-url=<URL on supported git hosting service> <command> [<args>].
+    For example:
+    - cli.py --pr_url=... review
+    - cli.py --pr_url=... describe
+    - cli.py --pr_url=... improve
+    - cli.py --pr_url=... ask "write me a poem about this PR"
+    - cli.py --pr_url=... reflect
+    - cli.py --issue_url=... similar_issue
 
-Supported commands:
-- review / review_pr - Add a review that includes a summary of the PR and specific suggestions for improvement.
+    Supported commands:
+    - review / review_pr - Add a review that includes a summary of the PR and specific suggestions for improvement.
 
-- ask / ask_question [question] - Ask a question about the PR.
+    - ask / ask_question [question] - Ask a question about the PR.
 
-- describe / describe_pr - Modify the PR title and description based on the PR's contents.
+    - describe / describe_pr - Modify the PR title and description based on the PR's contents.
 
-- improve / improve_code - Suggest improvements to the code in the PR as pull request comments ready to commit.
-Extended mode ('improve --extended') employs several calls, and provides a more thorough feedback
+    - improve / improve_code - Suggest improvements to the code in the PR as pull request comments ready to commit.
+    Extended mode ('improve --extended') employs several calls, and provides a more thorough feedback
 
-- reflect - Ask the PR author questions about the PR.
+    - reflect - Ask the PR author questions about the PR.
 
-- update_changelog - Update the changelog based on the PR's contents.
+    - update_changelog - Update the changelog based on the PR's contents.
 
-- add_docs
+    - add_docs
 
-- generate_labels
+    - generate_labels
 
 
-Configuration:
-To edit any configuration parameter from 'configuration.toml', just add -config_path=<value>.
-For example: 'python cli.py --pr_url=... review --pr_reviewer.extra_instructions="focus on the file: ..."'
-""")
+    Configuration:
+    To edit any configuration parameter from 'configuration.toml', just add -config_path=<value>.
+    For example: 'python cli.py --pr_url=... review --pr_reviewer.extra_instructions="focus on the file: ..."'
+    """)
     parser.add_argument('--pr_url', type=str, help='The URL of the PR to review', default=None)
     parser.add_argument('--issue_url', type=str, help='The URL of the Issue to review', default=None)
     parser.add_argument('command', type=str, help='The', choices=commands, default='review')
     parser.add_argument('rest', nargs=argparse.REMAINDER, default=[])
-    args = parser.parse_args(inargs)
+    return parser
+
+
+def run_command(pr_url, command):
+    # Preparing the command
+    run_command_str = f"--pr_url={pr_url} {command.lstrip('/')}"
+    args = set_parser().parse_args(run_command_str.split())
+
+    # Run the command. Feedback will appear in GitHub PR comments
+    run(args=args)
+
+
+def run(inargs=None, args=None):
+    parser = set_parser()
+    if not args:
+        args = parser.parse_args(inargs)
     if not args.pr_url and not args.issue_url:
         parser.print_help()
         return

pr_agent/cli_pip.py

@@ -0,0 +1,23 @@
+from pr_agent import cli
+from pr_agent.config_loader import get_settings
+
+
+def main():
+    # Fill in the following values
+    provider = "github"  # GitHub provider
+    user_token = "..."  # GitHub user token
+    openai_key = "..."  # OpenAI key
+    pr_url = "..."  # PR URL, for example 'https://github.com/Codium-ai/pr-agent/pull/809'
+    command = "/review"  # Command to run (e.g. '/review', '/describe', '/ask="What is the purpose of this PR?"')
+
+    # Setting the configurations
+    get_settings().set("CONFIG.git_provider", provider)
+    get_settings().set("openai.key", openai_key)
+    get_settings().set("github.user_token", user_token)
+
+    # Run the command. Feedback will appear in GitHub PR comments
+    cli.run_command(pr_url, command)
+
+
+if __name__ == '__main__':
+    main()

pr_agent/config_loader.py

@@ -21,6 +21,7 @@ global_settings = Dynaconf(
         "settings/pr_line_questions_prompts.toml",
         "settings/pr_description_prompts.toml",
         "settings/pr_code_suggestions_prompts.toml",
+        "settings/pr_code_suggestions_reflect_prompts.toml",
         "settings/pr_sort_code_suggestions_prompts.toml",
         "settings/pr_information_from_user_prompts.toml",
         "settings/pr_update_changelog_prompts.toml",
@@ -33,6 +34,15 @@ global_settings = Dynaconf(
 
 
 def get_settings():
+    """
+    Retrieves the current settings.
+
+    This function attempts to fetch the settings from the starlette_context's context object. If it fails,
+    it defaults to the global settings defined outside of this function.
+
+    Returns:
+        Dynaconf: The current settings object, either from the context or the global default.
+    """
     try:
         return context["settings"]
     except Exception:
@@ -40,7 +50,7 @@ def get_settings():
 
 
 # Add local configuration from pyproject.toml of the project being reviewed
-def _find_repository_root() -> Path:
+def _find_repository_root() -> Optional[Path]:
     """
     Identify project root directory by recursively searching for the .git directory in the parent directories.
     """
@@ -60,7 +70,7 @@ def _find_pyproject() -> Optional[Path]:
     """
     repo_root = _find_repository_root()
     if repo_root:
-        pyproject = _find_repository_root() / "pyproject.toml"
+        pyproject = repo_root / "pyproject.toml"
         return pyproject if pyproject.is_file() else None
     return None
 

pr_agent/git_providers/__init__.py

@@ -2,12 +2,13 @@ from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.bitbucket_provider import BitbucketProvider
 from pr_agent.git_providers.bitbucket_server_provider import BitbucketServerProvider
 from pr_agent.git_providers.codecommit_provider import CodeCommitProvider
+from pr_agent.git_providers.git_provider import GitProvider
 from pr_agent.git_providers.github_provider import GithubProvider
 from pr_agent.git_providers.gitlab_provider import GitLabProvider
 from pr_agent.git_providers.local_git_provider import LocalGitProvider
 from pr_agent.git_providers.azuredevops_provider import AzureDevopsProvider
 from pr_agent.git_providers.gerrit_provider import GerritProvider
-
+from starlette_context import context
 
 _GIT_PROVIDERS = {
     'github': GithubProvider,
@@ -16,10 +17,11 @@ _GIT_PROVIDERS = {
     'bitbucket_server': BitbucketServerProvider,
     'azure': AzureDevopsProvider,
     'codecommit': CodeCommitProvider,
-    'local' : LocalGitProvider,
+    'local': LocalGitProvider,
     'gerrit': GerritProvider,
 }
 
+
 def get_git_provider():
     try:
         provider_id = get_settings().config.git_provider
@@ -28,3 +30,33 @@ def get_git_provider():
     if provider_id not in _GIT_PROVIDERS:
         raise ValueError(f"Unknown git provider: {provider_id}")
     return _GIT_PROVIDERS[provider_id]
+
+
+def get_git_provider_with_context(pr_url) -> GitProvider:
+    """
+    Get a GitProvider instance for the given PR URL. If the GitProvider instance is already in the context, return it.
+    """
+
+    is_context_env = None
+    try:
+        is_context_env = context.get("settings", None)
+    except Exception:
+        pass  # we are not in a context environment (CLI)
+
+    # check if context["git_provider"]["pr_url"] exists
+    if is_context_env and context.get("git_provider", {}).get("pr_url", {}):
+        git_provider = context["git_provider"]["pr_url"]
+        # possibly check if the git_provider is still valid, or if some reset is needed
+        # ...
+        return git_provider
+    else:
+        try:
+            provider_id = get_settings().config.git_provider
+            if provider_id not in _GIT_PROVIDERS:
+                raise ValueError(f"Unknown git provider: {provider_id}")
+            git_provider = _GIT_PROVIDERS[provider_id](pr_url)
+            if is_context_env:
+                context["git_provider"] = {pr_url: git_provider}
+            return git_provider
+        except Exception as e:
+            raise ValueError(f"Failed to get git provider for {pr_url}") from e

pr_agent/git_providers/azuredevops_provider.py

@@ -2,6 +2,7 @@ import os
 from typing import Optional, Tuple
 from urllib.parse import urlparse
 
+from ..algo.file_filter import filter_ignored
 from ..log import get_logger
 from ..algo.language_handler import is_valid_file
 from ..algo.utils import clip_tokens, find_line_number_of_relevant_line_in_file, load_large_diff
@@ -26,6 +27,7 @@ try:
         CommentThread,
         GitVersionDescriptor,
         GitPullRequest,
+        GitPullRequestIterationChanges,
     )
 except ImportError:
     AZURE_DEVOPS_AVAILABLE = False
@@ -165,7 +167,7 @@ class AzureDevopsProvider(GitProvider):
         except Exception as e:
             get_logger().exception(f"Failed to publish labels, error: {e}")
 
-    def get_pr_labels(self):
+    def get_pr_labels(self, update=False):
         try:
             labels = self.azure_devops_client.get_pull_request_labels(
                 project=self.workspace_slug,
@@ -230,32 +232,73 @@ class AzureDevopsProvider(GitProvider):
             base_sha = self.pr.last_merge_target_commit
             head_sha = self.pr.last_merge_source_commit
 
-            commits = self.azure_devops_client.get_pull_request_commits(
-                project=self.workspace_slug,
+            # Get PR iterations
+            iterations = self.azure_devops_client.get_pull_request_iterations(
                 repository_id=self.repo_slug,
                 pull_request_id=self.pr_num,
+                project=self.workspace_slug
             )
+            changes = None
+            if iterations:
+                iteration_id = iterations[-1].id  # Get the last iteration (most recent changes)
 
+                # Get changes for the iteration
+                changes = self.azure_devops_client.get_pull_request_iteration_changes(
+                    repository_id=self.repo_slug,
+                    pull_request_id=self.pr_num,
+                    iteration_id=iteration_id,
+                    project=self.workspace_slug
+                )
             diff_files = []
             diffs = []
             diff_types = {}
+            if changes:
+                for change in changes.change_entries:
+                    item = change.additional_properties.get('item', {})
+                    path = item.get('path', None)
+                    if path:
+                        diffs.append(path)
+                        diff_types[path] = change.additional_properties.get('changeType', 'Unknown')
 
-            for c in commits:
-                changes_obj = self.azure_devops_client.get_changes(
-                    project=self.workspace_slug,
-                    repository_id=self.repo_slug,
-                    commit_id=c.commit_id,
-                )
-                for i in changes_obj.changes:
-                    if i["item"]["gitObjectType"] == "tree":
-                        continue
-                    diffs.append(i["item"]["path"])
-                    diff_types[i["item"]["path"]] = i["changeType"]
+            # wrong implementation - gets all the files that were changed in any commit in the PR
+            # commits = self.azure_devops_client.get_pull_request_commits(
+            #     project=self.workspace_slug,
+            #     repository_id=self.repo_slug,
+            #     pull_request_id=self.pr_num,
+            # )
+            #
+            # diff_files = []
+            # diffs = []
+            # diff_types = {}
 
-            diffs = list(set(diffs))
+            # for c in commits:
+            #     changes_obj = self.azure_devops_client.get_changes(
+            #         project=self.workspace_slug,
+            #         repository_id=self.repo_slug,
+            #         commit_id=c.commit_id,
+            #     )
+            #     for i in changes_obj.changes:
+            #         if i["item"]["gitObjectType"] == "tree":
+            #             continue
+            #         diffs.append(i["item"]["path"])
+            #         diff_types[i["item"]["path"]] = i["changeType"]
+            #
+            # diffs = list(set(diffs))
 
+            diffs_original = diffs
+            diffs = filter_ignored(diffs_original, 'azure')
+            if diffs_original != diffs:
+                try:
+                    get_logger().info(f"Filtered out [ignore] files for pull request:", extra=
+                    {"files": diffs_original,  # diffs is just a list of names
+                     "filtered_files": diffs})
+                except Exception:
+                    pass
+
+            invalid_files_names = []
             for file in diffs:
                 if not is_valid_file(file):
+                    invalid_files_names.append(file)
                     continue
 
                 version = GitVersionDescriptor(
@@ -273,12 +316,13 @@ class AzureDevopsProvider(GitProvider):
 
                     new_file_content_str = new_file_content_str.content
                 except Exception as error:
-                    get_logger().error(
-                        "Failed to retrieve new file content of %s at version %s. Error: %s",
-                        file,
-                        version,
-                        str(error),
-                    )
+                    get_logger().error(f"Failed to retrieve new file content of {file} at version {version}. Error: {str(error)}")
+                    # get_logger().error(
+                    #     "Failed to retrieve new file content of %s at version %s. Error: %s",
+                    #     file,
+                    #     version,
+                    #     str(error),
+                    # )
                     new_file_content_str = ""
 
                 edit_type = EDIT_TYPE.MODIFIED
@@ -303,17 +347,17 @@ class AzureDevopsProvider(GitProvider):
                     )
                     original_file_content_str = original_file_content_str.content
                 except Exception as error:
-                    get_logger().error(
-                        "Failed to retrieve original file content of %s at version %s. Error: %s",
-                        file,
-                        version,
-                        str(error),
-                    )
+                    get_logger().error(f"Failed to retrieve original file content of {file} at version {version}. Error: {str(error)}")
                     original_file_content_str = ""
 
                 patch = load_large_diff(
-                    file, new_file_content_str, original_file_content_str
-                )
+                    file, new_file_content_str, original_file_content_str, show_warning=False
+                ).rstrip()
+
+                # count number of lines added and removed
+                patch_lines = patch.splitlines(keepends=True)
+                num_plus_lines = len([line for line in patch_lines if line.startswith('+')])
+                num_minus_lines = len([line for line in patch_lines if line.startswith('-')])
 
                 diff_files.append(
                     FilePatchInfo(
@@ -322,8 +366,12 @@ class AzureDevopsProvider(GitProvider):
                         patch=patch,
                         filename=file,
                         edit_type=edit_type,
+                        num_plus_lines=num_plus_lines,
+                        num_minus_lines=num_minus_lines,
                     )
                 )
+            get_logger().info(f"Invalid files: {invalid_files_names}")
+
             self.diff_files = diff_files
             return diff_files
         except Exception as e:
@@ -404,7 +452,7 @@ class AzureDevopsProvider(GitProvider):
         return dict(body=body, path=path, position=position, absolute_position=absolute_position) if subject_type == "LINE" else {}
 
     def publish_inline_comments(self, comments: list[dict], disable_fallback: bool = False):
-            overall_sucess = True
+            overall_success = True
             for comment in comments:
                 try:
                     self.publish_comment(comment["body"],
@@ -426,8 +474,8 @@ class AzureDevopsProvider(GitProvider):
                 except Exception as e:
                     if get_settings().config.verbosity_level >= 2:
                         get_logger().error(f"Failed to publish code suggestion, error: {e}")
-                    overall_sucess = False
-            return overall_sucess
+                    overall_success = False
+            return overall_success
 
     def get_title(self):
         return self.pr.title

pr_agent/git_providers/bitbucket_provider.py

@@ -7,6 +7,8 @@ from atlassian.bitbucket import Cloud
 from starlette_context import context
 
 from pr_agent.algo.types import FilePatchInfo, EDIT_TYPE
+from ..algo.file_filter import filter_ignored
+from ..algo.language_handler import is_valid_file
 from ..algo.utils import find_line_number_of_relevant_line_in_file
 from ..config_loader import get_settings
 from ..log import get_logger
@@ -122,13 +124,30 @@ class BitbucketProvider(GitProvider):
         if self.diff_files:
             return self.diff_files
 
-        diffs = self.pr.diffstat()
+        diffs_original = list(self.pr.diffstat())
+        diffs = filter_ignored(diffs_original, 'bitbucket')
+        if diffs != diffs_original:
+            try:
+                names_original = [d.new.path for d in diffs_original]
+                names_filtered = [d.new.path for d in diffs]
+                get_logger().info(f"Filtered out [ignore] files for PR", extra={
+                    'original_files': names_original,
+                    'filtered_files': names_filtered
+                })
+            except Exception as e:
+                pass
+
         diff_split = [
             "diff --git%s" % x for x in self.pr.diff().split("diff --git") if x.strip()
         ]
 
+        invalid_files_names = []
         diff_files = []
         for index, diff in enumerate(diffs):
+            if not is_valid_file(diff.new.path):
+                invalid_files_names.append(diff.new.path)
+                continue
+
             original_file_content_str = self._get_pr_file_content(
                 diff.old.get_data("links")
             )
@@ -150,6 +169,9 @@ class BitbucketProvider(GitProvider):
                 file_patch_canonic_structure.edit_type = EDIT_TYPE.RENAMED
             diff_files.append(file_patch_canonic_structure)
 
+        if invalid_files_names:
+            get_logger().info(f"Invalid file names: {invalid_files_names}")
+
 
         self.diff_files = diff_files
         return diff_files
@@ -160,7 +182,11 @@ class BitbucketProvider(GitProvider):
     def get_comment_url(self, comment):
         return comment.data['links']['html']['href']
 
-    def publish_persistent_comment(self, pr_comment: str, initial_header: str, update_header: bool = True, name='review'):
+    def publish_persistent_comment(self, pr_comment: str,
+                                   initial_header: str,
+                                   update_header: bool = True,
+                                   name='review',
+                                   final_update_message=True):
         try:
             for comment in self.pr.comments():
                 body = comment.raw
@@ -168,15 +194,16 @@ class BitbucketProvider(GitProvider):
                     latest_commit_url = self.get_latest_commit_url()
                     comment_url = self.get_comment_url(comment)
                     if update_header:
-                        updated_header = f"{initial_header}\n\n### ({name.capitalize()} updated until commit {latest_commit_url})\n"
+                        updated_header = f"{initial_header}\n\n#### ({name.capitalize()} updated until commit {latest_commit_url})\n"
                         pr_comment_updated = pr_comment.replace(initial_header, updated_header)
                     else:
                         pr_comment_updated = pr_comment
                     get_logger().info(f"Persistent mode - updating comment {comment_url} to latest {name} message")
                     d = {"content": {"raw": pr_comment_updated}}
                     response = comment._update_data(comment.put(None, data=d))
-                    self.publish_comment(
-                        f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
+                    if final_update_message:
+                        self.publish_comment(
+                            f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
                     return
         except Exception as e:
             get_logger().exception(f"Failed to update persistent review, error: {e}")
@@ -208,7 +235,7 @@ class BitbucketProvider(GitProvider):
         except Exception as e:
             get_logger().exception(f"Failed to remove comment, error: {e}")
 
-    # funtion to create_inline_comment
+    # function to create_inline_comment
     def create_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str, absolute_position: int = None):
         position, absolute_position = find_line_number_of_relevant_line_in_file(self.get_diff_files(),
                                                                             relevant_file.strip('`'),
@@ -337,12 +364,47 @@ class BitbucketProvider(GitProvider):
     def _get_pr(self):
         return self._get_repo().pullrequests.get(self.pr_num)
 
+    def get_pr_file_content(self, file_path: str, branch: str) -> str:
+        try:
+            if branch == self.pr.source_branch:
+                branch = self.pr.data["source"]["commit"]["hash"]
+            elif branch == self.pr.destination_branch:
+                branch = self.pr.data["destination"]["commit"]["hash"]
+            url = (f"https://api.bitbucket.org/2.0/repositories/{self.workspace_slug}/{self.repo_slug}/src/"
+                   f"{branch}/{file_path}")
+            response = requests.request("GET", url, headers=self.headers)
+            if response.status_code == 404:  # not found
+                return ""
+            contents = response.text
+            return contents
+        except Exception:
+            return ""
+
+
+    def create_or_update_pr_file(self, file_path: str, branch: str, contents="", message="") -> None:
+        url = (f"https://api.bitbucket.org/2.0/repositories/{self.workspace_slug}/{self.repo_slug}/src/")
+        if not message:
+            if contents:
+                message = f"Update {file_path}"
+            else:
+                message = f"Create {file_path}"
+        files={file_path: contents}
+        data={
+            "message": message,
+            "branch": branch
+        }
+        headers = {'Authorization':self.headers['Authorization']} if 'Authorization' in self.headers else {}
+        try:
+            requests.request("POST", url, headers=headers, data=data, files=files)
+        except Exception:
+            get_logger().exception(f"Failed to create empty file {file_path} in branch {branch}")
+
     def _get_pr_file_content(self, remote_link: str):
         return ""
 
     def get_commit_messages(self):
         return ""  # not implemented yet
-    
+
     # bitbucket does not support labels
     def publish_description(self, pr_title: str, description: str):
         payload = json.dumps({
@@ -362,7 +424,7 @@ class BitbucketProvider(GitProvider):
     # bitbucket does not support labels
     def publish_labels(self, pr_types: list):
         pass
-    
+
     # bitbucket does not support labels
-    def get_pr_labels(self):
+    def get_pr_labels(self, update=False):
         pass

pr_agent/git_providers/bitbucket_server_provider.py

@@ -1,13 +1,14 @@
 import json
 from typing import Optional, Tuple
-from urllib.parse import urlparse
+from urllib.parse import quote_plus, urlparse
 
 import requests
 from atlassian.bitbucket import Bitbucket
 from starlette_context import context
 
 from .git_provider import GitProvider
-from pr_agent.algo.types import FilePatchInfo
+from ..algo.types import EDIT_TYPE, FilePatchInfo
+from ..algo.language_handler import is_valid_file
 from ..algo.utils import load_large_diff, find_line_number_of_relevant_line_in_file
 from ..config_loader import get_settings
 from ..log import get_logger
@@ -58,6 +59,9 @@ class BitbucketServerProvider(GitProvider):
             return contents
         except Exception:
             return ""
+        
+    def get_pr_id(self):
+        return self.pr_num
 
     def publish_code_suggestions(self, code_suggestions: list) -> bool:
         """
@@ -140,14 +144,8 @@ class BitbucketServerProvider(GitProvider):
         if self.diff_files:
             return self.diff_files
 
-        commits_in_pr = self.bitbucket_client.get_pull_requests_commits(
-            self.workspace_slug,
-            self.repo_slug,
-            self.pr_num
-        )
-
-        commit_list = list(commits_in_pr)
-        base_sha, head_sha = commit_list[0]['parents'][0]['id'], commit_list[-1]['id']
+        base_sha = self.pr.toRef['latestCommit']
+        head_sha = self.pr.fromRef['latestCommit']
 
         diff_files = []
         original_file_content_str = ""
@@ -156,6 +154,10 @@ class BitbucketServerProvider(GitProvider):
         changes = self.bitbucket_client.get_pull_requests_changes(self.workspace_slug, self.repo_slug, self.pr_num)
         for change in changes:
             file_path = change['path']['toString']
+            if not is_valid_file(file_path.split("/")[-1]):
+                get_logger().info(f"Skipping a non-code file: {file_path}")
+                continue
+
             match change['type']:
                 case 'ADD':
                     edit_type = EDIT_TYPE.ADDED
@@ -209,7 +211,7 @@ class BitbucketServerProvider(GitProvider):
     def remove_comment(self, comment):
         pass
 
-    # funtion to create_inline_comment
+    # function to create_inline_comment
     def create_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str,
                               absolute_position: int = None):
 
@@ -241,8 +243,11 @@ class BitbucketServerProvider(GitProvider):
             }
         }
 
-        response = requests.post(url=self._get_pr_comments_url(), json=payload, headers=self.headers)
-        return response
+        try:
+            requests.post(url=self._get_pr_comments_url(), json=payload, headers=self.headers).raise_for_status()
+        except Exception as e:
+            get_logger().error(f"Failed to publish inline comment to '{file}' at line {from_line}, error: {e}")
+            raise e
 
     def generate_link_to_relevant_line_number(self, suggestion) -> str:
         try:
@@ -255,18 +260,37 @@ class BitbucketServerProvider(GitProvider):
             position, absolute_position = find_line_number_of_relevant_line_in_file \
                 (diff_files, relevant_file, relevant_line_str)
 
+            if absolute_position != -1:
+                if self.pr:
+                    link = f"{self.pr_url}/diff#{quote_plus(relevant_file)}?t={absolute_position}"
+                    return link
+                else:
+                    if get_settings().config.verbosity_level >= 2:
+                        get_logger().info(f"Failed adding line link to '{relevant_file}' since PR not set")
+            else:
+                if get_settings().config.verbosity_level >= 2:
+                    get_logger().info(f"Failed adding line link to '{relevant_file}' since position not found")
+
             if absolute_position != -1 and self.pr_url:
-                link = f"{self.pr_url}/#L{relevant_file}T{absolute_position}"
+                link = f"{self.pr_url}/diff#{quote_plus(relevant_file)}?t={absolute_position}"
                 return link
         except Exception as e:
             if get_settings().config.verbosity_level >= 2:
-                get_logger().info(f"Failed adding line link, error: {e}")
+                get_logger().info(f"Failed adding line link to '{relevant_file}', error: {e}")
 
         return ""
 
     def publish_inline_comments(self, comments: list[dict]):
         for comment in comments:
-            self.publish_inline_comment(comment['body'], comment['position'], comment['path'])
+            if 'position' in comment:
+                self.publish_inline_comment(comment['body'], comment['position'], comment['path'])
+            elif 'start_line' in comment: # multi-line comment
+                # note that bitbucket does not seem to support range - only a comment on a single line - https://community.developer.atlassian.com/t/api-post-endpoint-for-inline-pull-request-comments/60452
+                self.publish_inline_comment(comment['body'], comment['start_line'], comment['path'])
+            elif 'line' in comment: # single-line comment
+                self.publish_inline_comment(comment['body'], comment['line'], comment['path'])
+            else:
+                get_logger().error(f"Could not publish inline comment: {comment}")
 
     def get_title(self):
         return self.pr.title
@@ -278,7 +302,10 @@ class BitbucketServerProvider(GitProvider):
         return self.pr.fromRef['displayId']
 
     def get_pr_description_full(self):
-        return self.pr.description
+        if hasattr(self.pr, "description"):
+            return self.pr.description
+        else:
+            return None
 
     def get_user_id(self):
         return 0
@@ -305,7 +332,7 @@ class BitbucketServerProvider(GitProvider):
         path_parts = parsed_url.path.strip("/").split("/")
         if len(path_parts) < 6 or path_parts[4] != "pull-requests":
             raise ValueError(
-                "The provided URL does not appear to be a Bitbucket PR URL"
+                f"The provided URL '{pr_url}' does not appear to be a Bitbucket PR URL"
             )
 
         workspace_slug = path_parts[1]
@@ -313,7 +340,7 @@ class BitbucketServerProvider(GitProvider):
         try:
             pr_number = int(path_parts[5])
         except ValueError as e:
-            raise ValueError("Unable to convert PR number to integer") from e
+            raise ValueError(f"Unable to convert PR number '{path_parts[5]}' to integer") from e
 
         return workspace_slug, repo_slug, pr_number
 
@@ -334,20 +361,25 @@ class BitbucketServerProvider(GitProvider):
             raise NotImplementedError("Get commit messages function not implemented yet.")
     # bitbucket does not support labels
     def publish_description(self, pr_title: str, description: str):
-        payload = json.dumps({
+        payload = {
+            "version": self.pr.version,
             "description": description,
-            "title": pr_title
-        })
-
-        response = requests.put(url=self.bitbucket_pull_request_api_url, headers=self.headers, data=payload)
-        return response
+            "title": pr_title,
+            "reviewers": self.pr.reviewers # needs to be sent otherwise gets wiped
+        }
+        try:
+            self.bitbucket_client.update_pull_request(self.workspace_slug, self.repo_slug, str(self.pr_num), payload)
+        except Exception as e:
+            get_logger().error(f"Failed to update pull request, error: {e}")
+            raise e
+        
 
     # bitbucket does not support labels
     def publish_labels(self, pr_types: list):
         pass
     
     # bitbucket does not support labels
-    def get_pr_labels(self):
+    def get_pr_labels(self, update=False):
         pass
 
     def _get_pr_comments_url(self):

pr_agent/git_providers/codecommit_provider.py

@@ -10,7 +10,7 @@ from ..algo.utils import load_large_diff
 from .git_provider import GitProvider
 from ..config_loader import get_settings
 from ..log import get_logger
-
+from pr_agent.algo.language_handler import is_valid_file
 
 class PullRequestCCMimic:
     """
@@ -216,7 +216,7 @@ class CodeCommitProvider(GitProvider):
     def publish_labels(self, labels):
         return [""]  # not implemented yet
 
-    def get_pr_labels(self):
+    def get_pr_labels(self, update=False):
         return [""]  # not implemented yet
 
     def remove_initial_comment(self):

pr_agent/git_providers/gerrit_provider.py

@@ -208,7 +208,7 @@ class GerritProvider(GitProvider):
         Comment = namedtuple('Comment', ['body'])
         return Comments([Comment(c['message']) for c in reversed(comments)])
 
-    def get_pr_labels(self):
+    def get_pr_labels(self, update=False):
         raise NotImplementedError(
             'Getting labels is not implemented for the gerrit provider')
 

pr_agent/git_providers/git_provider.py

@@ -13,10 +13,17 @@ class GitProvider(ABC):
     def is_supported(self, capability: str) -> bool:
         pass
 
+    @abstractmethod
+    def get_files(self) -> list:
+        pass
+
     @abstractmethod
     def get_diff_files(self) -> list[FilePatchInfo]:
         pass
 
+    def get_incremental_commits(self, is_incremental):
+        pass
+
     @abstractmethod
     def publish_description(self, pr_title: str, pr_body: str):
         pass
@@ -71,7 +78,7 @@ class GitProvider(ABC):
 
         # if the existing description was generated by the pr-agent, but it doesn't contain a user description,
         # return nothing (empty string) because it means there is no user description
-        user_description_header = "## **user description**"
+        user_description_header = "### **user description**"
         if user_description_header not in description_lowercase:
             get_logger().info(f"Existing description was generated by the pr-agent, but it doesn't contain a user description")
             return ""
@@ -102,8 +109,8 @@ class GitProvider(ABC):
         return original_user_description
 
     def _possible_headers(self):
-        return ("## **user description**", "## **pr type**", "## **pr description**", "## **pr labels**", "## **type**", "## **description**",
-                "## **labels**", "### 🤖 generated by pr agent")
+        return ("### **user description**", "### **pr type**", "### **pr description**", "### **pr labels**", "### **type**", "### **description**",
+                "### **labels**", "### 🤖 generated by pr agent")
 
     def _is_generated_by_pr_agent(self, description_lowercase: str) -> bool:
         possible_headers = self._possible_headers()
@@ -124,7 +131,39 @@ class GitProvider(ABC):
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
         pass
 
-    def publish_persistent_comment(self, pr_comment: str, initial_header: str, update_header: bool, name='review'):
+    def publish_persistent_comment(self, pr_comment: str,
+                                   initial_header: str,
+                                   update_header: bool = True,
+                                   name='review',
+                                   final_update_message=True):
+        self.publish_comment(pr_comment)
+
+    def publish_persistent_comment_full(self, pr_comment: str,
+                                   initial_header: str,
+                                   update_header: bool = True,
+                                   name='review',
+                                   final_update_message=True):
+        try:
+            prev_comments = list(self.get_issue_comments())
+            for comment in prev_comments:
+                if comment.body.startswith(initial_header):
+                    latest_commit_url = self.get_latest_commit_url()
+                    comment_url = self.get_comment_url(comment)
+                    if update_header:
+                        updated_header = f"{initial_header}\n\n#### ({name.capitalize()} updated until commit {latest_commit_url})\n"
+                        pr_comment_updated = pr_comment.replace(initial_header, updated_header)
+                    else:
+                        pr_comment_updated = pr_comment
+                    get_logger().info(f"Persistent mode - updating comment {comment_url} to latest {name} message")
+                    # response = self.mr.notes.update(comment.id, {'body': pr_comment_updated})
+                    self.edit_comment(comment, pr_comment_updated)
+                    if final_update_message:
+                        self.publish_comment(
+                            f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
+                    return
+        except Exception as e:
+            get_logger().exception(f"Failed to update persistent review, error: {e}")
+            pass
         self.publish_comment(pr_comment)
 
     @abstractmethod
@@ -160,7 +199,7 @@ class GitProvider(ABC):
         pass
 
     @abstractmethod
-    def get_pr_labels(self):
+    def get_pr_labels(self, update=False):
         pass
 
     def get_repo_labels(self):
@@ -193,6 +232,12 @@ class GitProvider(ABC):
     def calc_pr_statistics(self, pull_request_data: dict):
         return {}
 
+    def get_num_of_files(self):
+        try:
+            return len(self.get_diff_files())
+        except Exception as e:
+            return -1
+
 
 def get_main_pr_language(languages, files) -> str:
     """
@@ -262,6 +307,7 @@ def get_main_pr_language(languages, files) -> str:
 
     return main_language_str
 
+
 class IncrementalPR:
     def __init__(self, is_incremental: bool = False):
         self.is_incremental = is_incremental

pr_agent/git_providers/github_provider.py

@@ -8,8 +8,9 @@ from github import AppAuthentication, Auth, Github, GithubException
 from retry import retry
 from starlette_context import context
 
+from ..algo.file_filter import filter_ignored
 from ..algo.language_handler import is_valid_file
-from ..algo.utils import load_large_diff, clip_tokens, find_line_number_of_relevant_line_in_file
+from ..algo.utils import PRReviewHeader, load_large_diff, clip_tokens, find_line_number_of_relevant_line_in_file
 from ..config_loader import get_settings
 from ..log import get_logger
 from ..servers.utils import RateLimitExceeded
@@ -18,7 +19,7 @@ from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 
 
 class GithubProvider(GitProvider):
-    def __init__(self, pr_url: Optional[str] = None, incremental=IncrementalPR(False)):
+    def __init__(self, pr_url: Optional[str] = None):
         self.repo_obj = None
         try:
             self.installation_id = context.get("installation_id", None)
@@ -33,17 +34,21 @@ class GithubProvider(GitProvider):
         self.github_user_id = None
         self.diff_files = None
         self.git_files = None
-        self.incremental = incremental
+        self.incremental = IncrementalPR(False)
         if pr_url and 'pull' in pr_url:
             self.set_pr(pr_url)
             self.pr_commits = list(self.pr.get_commits())
-            if self.incremental.is_incremental:
-                self.get_incremental_commits()
             self.last_commit_id = self.pr_commits[-1]
             self.pr_url = self.get_pr_url() # pr_url for github actions can be as api.github.com, so we need to get the url from the pr object
         else:
             self.pr_commits = None
 
+    def get_incremental_commits(self, incremental=IncrementalPR(False)):
+        self.incremental = incremental
+        if self.incremental.is_incremental:
+            self.unreviewed_files_set = dict()
+            self._get_incremental_commits()
+
     def is_supported(self, capability: str) -> bool:
         return True
 
@@ -54,7 +59,7 @@ class GithubProvider(GitProvider):
         self.repo, self.pr_num = self._parse_pr_url(pr_url)
         self.pr = self._get_pr()
 
-    def get_incremental_commits(self):
+    def _get_incremental_commits(self):
         if not self.pr_commits:
             self.pr_commits = list(self.pr.get_commits())
 
@@ -62,14 +67,15 @@ class GithubProvider(GitProvider):
         if self.previous_review:
             self.incremental.commits_range = self.get_commit_range()
             # Get all files changed during the commit range
-            self.file_set = dict()
+
             for commit in self.incremental.commits_range:
                 if commit.commit.message.startswith(f"Merge branch '{self._get_repo().default_branch}'"):
                     get_logger().info(f"Skipping merge commit {commit.commit.message}")
                     continue
-                self.file_set.update({file.filename: file for file in commit.files})
+                self.unreviewed_files_set.update({file.filename: file for file in commit.files})
         else:
-            raise ValueError("No previous review found")
+            get_logger().info("No previous review found, will review the entire PR")
+            self.incremental.is_incremental = False
 
     def get_commit_range(self):
         last_review_time = self.previous_review.created_at
@@ -90,28 +96,36 @@ class GithubProvider(GitProvider):
             self.comments = list(self.pr.get_issue_comments())
         prefixes = []
         if full:
-            prefixes.append("## PR Review")
+            prefixes.append(PRReviewHeader.REGULAR.value)
         if incremental:
-            prefixes.append("## Incremental PR Review")
+            prefixes.append(PRReviewHeader.INCREMENTAL.value)
         for index in range(len(self.comments) - 1, -1, -1):
             if any(self.comments[index].body.startswith(prefix) for prefix in prefixes):
                 return self.comments[index]
 
     def get_files(self):
-        if self.incremental.is_incremental and self.file_set:
-            return self.file_set.values()
+        if self.incremental.is_incremental and self.unreviewed_files_set:
+            return self.unreviewed_files_set.values()
         try:
             git_files = context.get("git_files", None)
             if git_files:
                 return git_files
-            self.git_files = self.pr.get_files()
+            self.git_files = list(self.pr.get_files()) # 'list' to handle pagination
             context["git_files"] = self.git_files
             return self.git_files
         except Exception:
             if not self.git_files:
-                self.git_files = self.pr.get_files()
+                self.git_files = list(self.pr.get_files())
             return self.git_files
 
+    def get_num_of_files(self):
+        if hasattr(self.git_files, "totalCount"):
+            return self.git_files.totalCount
+        else:
+            try:
+                return len(self.git_files)
+            except Exception as e:
+                return -1
 
     @retry(exceptions=RateLimitExceeded,
            tries=get_settings().github.ratelimit_retries, delay=2, backoff=2, jitter=(1, 3))
@@ -135,20 +149,33 @@ class GithubProvider(GitProvider):
             if self.diff_files:
                 return self.diff_files
 
-            files = self.get_files()
-            diff_files = []
+            # filter files using [ignore] patterns
+            files_original = self.get_files()
+            files = filter_ignored(files_original)
+            if files_original != files:
+                try:
+                    names_original = [file.filename for file in files_original]
+                    names_new = [file.filename for file in files]
+                    get_logger().info(f"Filtered out [ignore] files for pull request:", extra=
+                    {"files": names_original,
+                     "filtered_files": names_new})
+                except Exception:
+                    pass
 
+            diff_files = []
+            invalid_files_names = []
             for file in files:
                 if not is_valid_file(file.filename):
+                    invalid_files_names.append(file.filename)
                     continue
 
                 new_file_content_str = self._get_pr_file_content(file, self.pr.head.sha)  # communication with GitHub
                 patch = file.patch
 
-                if self.incremental.is_incremental and self.file_set:
+                if self.incremental.is_incremental and self.unreviewed_files_set:
                     original_file_content_str = self._get_pr_file_content(file, self.incremental.last_seen_commit_sha)
                     patch = load_large_diff(file.filename, new_file_content_str, original_file_content_str)
-                    self.file_set[file.filename] = patch
+                    self.unreviewed_files_set[file.filename] = patch
                 else:
                     original_file_content_str = self._get_pr_file_content(file, self.pr.base.sha)
                     if not patch:
@@ -175,6 +202,8 @@ class GithubProvider(GitProvider):
                                                                num_plus_lines=num_plus_lines,
                                                                num_minus_lines=num_minus_lines,)
                 diff_files.append(file_patch_canonical_structure)
+            if invalid_files_names:
+                get_logger().info(f"Filtered out files with invalid extensions: {invalid_files_names}")
 
             self.diff_files = diff_files
             try:
@@ -197,24 +226,12 @@ class GithubProvider(GitProvider):
     def get_comment_url(self, comment) -> str:
         return comment.html_url
 
-    def publish_persistent_comment(self, pr_comment: str, initial_header: str, update_header: bool = True, name='review'):
-        prev_comments = list(self.pr.get_issue_comments())
-        for comment in prev_comments:
-            body = comment.body
-            if body.startswith(initial_header):
-                latest_commit_url = self.get_latest_commit_url()
-                comment_url = self.get_comment_url(comment)
-                if update_header:
-                    updated_header = f"{initial_header}\n\n### ({name.capitalize()} updated until commit {latest_commit_url})\n"
-                    pr_comment_updated = pr_comment.replace(initial_header, updated_header)
-                else:
-                    pr_comment_updated = pr_comment
-                get_logger().info(f"Persistent mode- updating comment {comment_url} to latest review message")
-                response = comment.edit(pr_comment_updated)
-                self.publish_comment(
-                    f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
-                return
-        self.publish_comment(pr_comment)
+    def publish_persistent_comment(self, pr_comment: str,
+                                   initial_header: str,
+                                   update_header: bool = True,
+                                   name='review',
+                                   final_update_message=True):
+        self.publish_persistent_comment_full(pr_comment, initial_header, update_header, name, final_update_message)
 
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
         if is_temporary and not get_settings().config.publish_output_progress:
@@ -598,13 +615,36 @@ class GithubProvider(GitProvider):
     def _get_pr(self):
         return self._get_repo().get_pull(self.pr_num)
 
-    def _get_pr_file_content(self, file: FilePatchInfo, sha: str) -> str:
+    def get_pr_file_content(self, file_path: str, branch: str) -> str:
         try:
-            file_content_str = str(self._get_repo().get_contents(file.filename, ref=sha).decoded_content.decode())
+            file_content_str = str(
+                self._get_repo()
+                .get_contents(file_path, ref=branch)
+                .decoded_content.decode()
+            )
         except Exception:
             file_content_str = ""
         return file_content_str
 
+    def create_or_update_pr_file(
+        self, file_path: str, branch: str, contents="", message=""
+    ) -> None:
+        try:
+            file_obj = self._get_repo().get_contents(file_path, ref=branch)
+            sha1=file_obj.sha
+        except Exception:
+            sha1=""
+        self.repo_obj.update_file(
+            path=file_path,
+            message=message,
+            content=contents,
+            sha=sha1,
+            branch=branch,
+        )
+
+    def _get_pr_file_content(self, file: FilePatchInfo, sha: str) -> str:
+        return self.get_pr_file_content(file.filename, sha)
+
     def publish_labels(self, pr_types):
         try:
             label_color_map = {"Bug fix": "1d76db", "Tests": "e99695", "Bug fix with tests": "c5def5",
@@ -620,9 +660,16 @@ class GithubProvider(GitProvider):
         except Exception as e:
             get_logger().exception(f"Failed to publish labels, error: {e}")
 
-    def get_pr_labels(self):
+    def get_pr_labels(self, update=False):
         try:
-            return [label.name for label in self.pr.labels]
+            if not update:
+                labels =self.pr.labels
+                return [label.name for label in labels]
+            else: # obtain the latest labels. Maybe they changed while the AI was running
+                headers, labels = self.pr._requester.requestJsonAndCheck(
+                    "GET", f"{self.pr.issue_url}/labels")
+                return [label['name'] for label in labels]
+
         except Exception as e:
             get_logger().exception(f"Failed to get labels, error: {e}")
             return []
@@ -703,22 +750,4 @@ class GithubProvider(GitProvider):
             return False
 
     def calc_pr_statistics(self, pull_request_data: dict):
-        try:
-            out = {}
-            from datetime import datetime
-            created_at = pull_request_data['created_at']
-            closed_at = pull_request_data['closed_at']
-            closed_at_datetime = datetime.strptime(closed_at, "%Y-%m-%dT%H:%M:%SZ")
-            created_at_datetime = datetime.strptime(created_at, "%Y-%m-%dT%H:%M:%SZ")
-            difference = closed_at_datetime - created_at_datetime
-            out['hours'] = difference.total_seconds() / 3600
-            out['commits'] = pull_request_data['commits']
-            out['comments'] = pull_request_data['comments']
-            out['review_comments'] = pull_request_data['review_comments']
-            out['changed_files'] = pull_request_data['changed_files']
-            out['additions'] = pull_request_data['additions']
-            out['deletions'] = pull_request_data['deletions']
-        except Exception as e:
-            get_logger().exception(f"Failed to calculate PR statistics, error: {e}")
-            return {}
-        return out
+        return {}

pr_agent/git_providers/gitlab_provider.py

@@ -6,6 +6,7 @@ from urllib.parse import urlparse
 import gitlab
 from gitlab import GitlabGetError
 
+from ..algo.file_filter import filter_ignored
 from ..algo.language_handler import is_valid_file
 from ..algo.utils import load_large_diff, clip_tokens, find_line_number_of_relevant_line_in_file
 from ..config_loader import get_settings
@@ -63,7 +64,7 @@ class GitLabProvider(GitProvider):
             raise DiffNotFoundError(f"Could not get diff for merge request {self.id_mr}") from e
 
 
-    def _get_pr_file_content(self, file_path: str, branch: str) -> str:
+    def get_pr_file_content(self, file_path: str, branch: str) -> str:
         try:
             return self.gl.projects.get(self.id_project).files.get(file_path, branch).decode()
         except GitlabGetError:
@@ -84,55 +85,71 @@ class GitLabProvider(GitProvider):
         if self.diff_files:
             return self.diff_files
 
-        diffs = self.mr.changes()['changes']
+        # filter files using [ignore] patterns
+        diffs_original = self.mr.changes()['changes']
+        diffs = filter_ignored(diffs_original, 'gitlab')
+        if diffs != diffs_original:
+            try:
+                names_original = [diff['new_path'] for diff in diffs_original]
+                names_filtered = [diff['new_path'] for diff in diffs]
+                get_logger().info(f"Filtered out [ignore] files for merge request {self.id_mr}", extra={
+                    'original_files': names_original,
+                    'filtered_files': names_filtered
+                })
+            except Exception as e:
+                pass
+
         diff_files = []
+        invalid_files_names = []
         for diff in diffs:
-            if is_valid_file(diff['new_path']):
-                # original_file_content_str = self._get_pr_file_content(diff['old_path'], self.mr.target_branch)
-                # new_file_content_str = self._get_pr_file_content(diff['new_path'], self.mr.source_branch)
-                original_file_content_str = self._get_pr_file_content(diff['old_path'], self.mr.diff_refs['base_sha'])
-                new_file_content_str = self._get_pr_file_content(diff['new_path'], self.mr.diff_refs['head_sha'])
+            if not is_valid_file(diff['new_path']):
+                invalid_files_names.append(diff['new_path'])
+                continue
 
-                try:
-                    if isinstance(original_file_content_str, bytes):
-                        original_file_content_str = bytes.decode(original_file_content_str, 'utf-8')
-                    if isinstance(new_file_content_str, bytes):
-                        new_file_content_str = bytes.decode(new_file_content_str, 'utf-8')
-                except UnicodeDecodeError:
-                    get_logger().warning(
-                        f"Cannot decode file {diff['old_path']} or {diff['new_path']} in merge request {self.id_mr}")
+            original_file_content_str = self.get_pr_file_content(diff['old_path'], self.mr.diff_refs['base_sha'])
+            new_file_content_str = self.get_pr_file_content(diff['new_path'], self.mr.diff_refs['head_sha'])
+            try:
+                if isinstance(original_file_content_str, bytes):
+                    original_file_content_str = bytes.decode(original_file_content_str, 'utf-8')
+                if isinstance(new_file_content_str, bytes):
+                    new_file_content_str = bytes.decode(new_file_content_str, 'utf-8')
+            except UnicodeDecodeError:
+                get_logger().warning(
+                    f"Cannot decode file {diff['old_path']} or {diff['new_path']} in merge request {self.id_mr}")
 
-                edit_type = EDIT_TYPE.MODIFIED
-                if diff['new_file']:
-                    edit_type = EDIT_TYPE.ADDED
-                elif diff['deleted_file']:
-                    edit_type = EDIT_TYPE.DELETED
-                elif diff['renamed_file']:
-                    edit_type = EDIT_TYPE.RENAMED
+            edit_type = EDIT_TYPE.MODIFIED
+            if diff['new_file']:
+                edit_type = EDIT_TYPE.ADDED
+            elif diff['deleted_file']:
+                edit_type = EDIT_TYPE.DELETED
+            elif diff['renamed_file']:
+                edit_type = EDIT_TYPE.RENAMED
 
-                filename = diff['new_path']
-                patch = diff['diff']
-                if not patch:
-                    patch = load_large_diff(filename, new_file_content_str, original_file_content_str)
+            filename = diff['new_path']
+            patch = diff['diff']
+            if not patch:
+                patch = load_large_diff(filename, new_file_content_str, original_file_content_str)
 
 
-                # count number of lines added and removed
-                patch_lines = patch.splitlines(keepends=True)
-                num_plus_lines = len([line for line in patch_lines if line.startswith('+')])
-                num_minus_lines = len([line for line in patch_lines if line.startswith('-')])
-                diff_files.append(
-                    FilePatchInfo(original_file_content_str, new_file_content_str,
-                                  patch=patch,
-                                  filename=filename,
-                                  edit_type=edit_type,
-                                  old_filename=None if diff['old_path'] == diff['new_path'] else diff['old_path'],
-                                  num_plus_lines=num_plus_lines,
-                                  num_minus_lines=num_minus_lines, ))
+            # count number of lines added and removed
+            patch_lines = patch.splitlines(keepends=True)
+            num_plus_lines = len([line for line in patch_lines if line.startswith('+')])
+            num_minus_lines = len([line for line in patch_lines if line.startswith('-')])
+            diff_files.append(
+                FilePatchInfo(original_file_content_str, new_file_content_str,
+                              patch=patch,
+                              filename=filename,
+                              edit_type=edit_type,
+                              old_filename=None if diff['old_path'] == diff['new_path'] else diff['old_path'],
+                              num_plus_lines=num_plus_lines,
+                              num_minus_lines=num_minus_lines, ))
+        if invalid_files_names:
+            get_logger().info(f"Filtered out files with invalid extensions: {invalid_files_names}")
 
         self.diff_files = diff_files
         return diff_files
 
-    def get_files(self):
+    def get_files(self) -> list:
         if not self.git_files:
             self.git_files = [change['new_path'] for change in self.mr.changes()['changes']]
         return self.git_files
@@ -151,26 +168,12 @@ class GitLabProvider(GitProvider):
     def get_comment_url(self, comment):
         return f"{self.mr.web_url}#note_{comment.id}"
 
-    def publish_persistent_comment(self, pr_comment: str, initial_header: str, update_header: bool = True, name='review'):
-        try:
-            for comment in self.mr.notes.list(get_all=True)[::-1]:
-                if comment.body.startswith(initial_header):
-                    latest_commit_url = self.get_latest_commit_url()
-                    comment_url = self.get_comment_url(comment)
-                    if update_header:
-                        updated_header = f"{initial_header}\n\n### ({name.capitalize()} updated until commit {latest_commit_url})\n"
-                        pr_comment_updated = pr_comment.replace(initial_header, updated_header)
-                    else:
-                        pr_comment_updated = pr_comment
-                    get_logger().info(f"Persistent mode - updating comment {comment_url} to latest {name} message")
-                    response = self.mr.notes.update(comment.id, {'body': pr_comment_updated})
-                    self.publish_comment(
-                        f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
-                    return
-        except Exception as e:
-            get_logger().exception(f"Failed to update persistent review, error: {e}")
-            pass
-        self.publish_comment(pr_comment)
+    def publish_persistent_comment(self, pr_comment: str,
+                                   initial_header: str,
+                                   update_header: bool = True,
+                                   name='review',
+                                   final_update_message=True):
+        self.publish_persistent_comment_full(pr_comment, initial_header, update_header, name, final_update_message)
 
     def publish_comment(self, mr_comment: str, is_temporary: bool = False):
         comment = self.mr.notes.create({'body': mr_comment})
@@ -181,6 +184,11 @@ class GitLabProvider(GitProvider):
     def edit_comment(self, comment, body: str):
         self.mr.notes.update(comment.id,{'body': body} )
 
+    def edit_comment_from_comment_id(self, comment_id: int, body: str):
+        comment = self.mr.notes.get(comment_id)
+        comment.body = body
+        comment.save()
+
     def reply_to_comment_from_comment_id(self, comment_id: int, body: str):
         discussion = self.mr.discussions.get(comment_id)
         discussion.notes.create({'body': body})
@@ -197,6 +205,10 @@ class GitLabProvider(GitProvider):
     def create_inline_comments(self, comments: list[dict]):
         raise NotImplementedError("Gitlab provider does not support publishing inline comments yet")
 
+    def get_comment_body_from_comment_id(self, comment_id: int):
+        comment = self.mr.notes.get(comment_id)
+        return comment
+
     def send_inline_comment(self,body: str,edit_type: str,found: bool,relevant_file: str,relevant_line_in_file: int,
                             source_line_no: int, target_file: str,target_line_no: int) -> None:
         if not found:
@@ -359,7 +371,7 @@ class GitLabProvider(GitProvider):
         return self.mr.description
 
     def get_issue_comments(self):
-        raise NotImplementedError("GitLab provider does not support issue comments yet")
+        return self.mr.notes.list(get_all=True)[::-1]
 
     def get_repo_settings(self):
         try:
@@ -416,7 +428,7 @@ class GitLabProvider(GitProvider):
     def publish_inline_comments(self, comments: list[dict]):
         pass
 
-    def get_pr_labels(self):
+    def get_pr_labels(self, update=False):
         return self.mr.labels
 
     def get_repo_labels(self):

pr_agent/git_providers/local_git_provider.py

@@ -176,5 +176,5 @@ class LocalGitProvider(GitProvider):
     def get_issue_comments(self):
         raise NotImplementedError('Getting issue comments is not implemented for the local git provider')
 
-    def get_pr_labels(self):
+    def get_pr_labels(self, update=False):
         raise NotImplementedError('Getting labels is not implemented for the local git provider')

pr_agent/git_providers/utils.py

@@ -5,12 +5,13 @@ import tempfile
 from dynaconf import Dynaconf
 
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider
+from pr_agent.git_providers import get_git_provider, get_git_provider_with_context
 from pr_agent.log import get_logger
 from starlette_context import context
 
 
 def apply_repo_settings(pr_url):
+    git_provider = get_git_provider_with_context(pr_url)
     if get_settings().config.use_repo_settings_file:
         repo_settings_file = None
         try:
@@ -20,7 +21,6 @@ def apply_repo_settings(pr_url):
                 repo_settings = None
                 pass
             if repo_settings is None:  # None is different from "", which is a valid value
-                git_provider = get_git_provider()(pr_url)
                 repo_settings = git_provider.get_repo_settings()
                 try:
                     context["repo_settings"] = repo_settings

pr_agent/servers/azuredevops_server_webhook.py

@@ -6,6 +6,8 @@ import json
 import os
 import re
 import secrets
+from urllib.parse import unquote
+
 import uvicorn
 from fastapi import APIRouter, Depends, FastAPI, HTTPException
 from fastapi.security import HTTPBasic, HTTPBasicCredentials
@@ -24,8 +26,9 @@ from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.log import get_logger
 from fastapi import Request, Depends
 from fastapi.security import HTTPBasic, HTTPBasicCredentials
-from pr_agent.log import get_logger
+from pr_agent.log import LoggingFormat, get_logger, setup_logger
 
+setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
 security = HTTPBasic()
 router = APIRouter()
 available_commands_rgx = re.compile(r"^\/(" + "|".join(command2class.keys()) + r")\s*")
@@ -38,8 +41,15 @@ def handle_request(
 ):
     log_context["action"] = body
     log_context["api_url"] = url
-    with get_logger().contextualize(**log_context):
-        background_tasks.add_task(PRAgent().handle_request, url, body)
+
+    async def inner():
+        try:
+            with get_logger().contextualize(**log_context):
+                await PRAgent().handle_request(url, body)
+        except Exception as e:
+            get_logger().error(f"Failed to handle webhook: {e}")
+
+    background_tasks.add_task(inner)
 
 
 # currently only basic auth is supported with azure webhooks
@@ -79,9 +89,9 @@ async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
     get_logger().info(json.dumps(data))
 
     actions = []
-    if data["eventType"] == "git.pullrequest.created": 
+    if data["eventType"] == "git.pullrequest.created":
         # API V1 (latest)
-        pr_url = data["resource"]["_links"]["web"]["href"].replace("_apis/git/repositories", "_git")
+        pr_url = unquote(data["resource"]["_links"]["web"]["href"].replace("_apis/git/repositories", "_git"))
         log_context["event"] = data["eventType"]
         log_context["api_url"] = pr_url
         await _perform_commands_azure("pr_commands", PRAgent(), pr_url, log_context)
@@ -90,9 +100,9 @@ async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
         if available_commands_rgx.match(data["resource"]["comment"]["content"]):
             if(data["resourceVersion"] == "2.0"):
                 repo = data["resource"]["pullRequest"]["repository"]["webUrl"]
-                pr_url = f'{repo}/pullrequest/{data["resource"]["pullRequest"]["pullRequestId"]}'
+                pr_url = unquote(f'{repo}/pullrequest/{data["resource"]["pullRequest"]["pullRequestId"]}')
                 actions = [data["resource"]["comment"]["content"]]
-            else: 
+            else:
                 # API V1 not supported as it does not contain the PR URL
                 return JSONResponse(
                     status_code=status.HTTP_400_BAD_REQUEST,
@@ -110,7 +120,7 @@ async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
 
     log_context["event"] = data["eventType"]
     log_context["api_url"] = pr_url
-    
+
     for action in actions:
         try:
             handle_request(background_tasks, pr_url, action, log_context)
@@ -121,13 +131,13 @@ async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
                 content=json.dumps({"message": "Internal server error"}),
             )
     return JSONResponse(
-        status_code=status.HTTP_202_ACCEPTED, content=jsonable_encoder({"message": "webhook triggerd successfully"})
+        status_code=status.HTTP_202_ACCEPTED, content=jsonable_encoder({"message": "webhook triggered successfully"})
     )
 
 @router.get("/")
 async def root():
     return {"status": "ok"}
-    
+
 def start():
     app = FastAPI(middleware=[Middleware(RawContextMiddleware)])
     app.include_router(router)

pr_agent/servers/bitbucket_app.py

@@ -16,6 +16,7 @@ from starlette_context import context
 from starlette_context.middleware import RawContextMiddleware
 
 from pr_agent.agent.pr_agent import PRAgent
+from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings, global_settings
 from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.identity_providers import get_identity_provider
@@ -27,7 +28,7 @@ from pr_agent.tools.pr_code_suggestions import PRCodeSuggestions
 from pr_agent.tools.pr_description import PRDescription
 from pr_agent.tools.pr_reviewer import PRReviewer
 
-setup_logger(fmt=LoggingFormat.JSON)
+setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
 router = APIRouter()
 secret_provider = get_secret_provider() if get_settings().get("CONFIG.SECRET_PROVIDER") else None
 
@@ -72,6 +73,24 @@ async def handle_manifest(request: Request, response: Response):
     manifest_obj = json.loads(manifest)
     return JSONResponse(manifest_obj)
 
+
+async def _perform_commands_bitbucket(commands_conf: str, agent: PRAgent, api_url: str, log_context: dict):
+    apply_repo_settings(api_url)
+    commands = get_settings().get(f"bitbucket_app.{commands_conf}", {})
+    for command in commands:
+        try:
+            split_command = command.split(" ")
+            command = split_command[0]
+            args = split_command[1:]
+            other_args = update_settings_from_args(args)
+            new_command = ' '.join([command] + other_args)
+            get_logger().info(f"Performing command: {new_command}")
+            with get_logger().contextualize(**log_context):
+                await agent.handle_request(api_url, new_command)
+        except Exception as e:
+            get_logger().error(f"Failed to perform command {command}: {e}")
+
+
 @router.post("/webhook")
 async def handle_github_webhooks(background_tasks: BackgroundTasks, request: Request):
     log_context = {"server_type": "bitbucket_app"}
@@ -118,18 +137,19 @@ async def handle_github_webhooks(background_tasks: BackgroundTasks, request: Req
                     with get_logger().contextualize(**log_context):
                         apply_repo_settings(pr_url)
                         if get_identity_provider().verify_eligibility("bitbucket",
-                                                                         sender_id, pr_url) is not Eligibility.NOT_ELIGIBLE:
-                            auto_review = get_setting_or_env("BITBUCKET_APP.AUTO_REVIEW", None)
-                            if auto_review is None or is_true(auto_review):  # by default, auto review is enabled
-                                await PRReviewer(pr_url).run()
-                            auto_improve = get_setting_or_env("BITBUCKET_APP.AUTO_IMPROVE", None)
-                            if is_true(auto_improve):  # by default, auto improve is disabled
-                                await PRCodeSuggestions(pr_url).run()
-                            auto_describe = get_setting_or_env("BITBUCKET_APP.AUTO_DESCRIBE", None)
-                            if is_true(auto_describe):  # by default, auto describe is disabled
-                                await PRDescription(pr_url).run()
-                # with get_logger().contextualize(**log_context):
-                #     await agent.handle_request(pr_url, "review")
+                                                        sender_id, pr_url) is not Eligibility.NOT_ELIGIBLE:
+                            if get_settings().get("bitbucket_app.pr_commands"):
+                                await _perform_commands_bitbucket("pr_commands", PRAgent(), pr_url, log_context)
+                            else: # backwards compatibility
+                                auto_review = get_setting_or_env("BITBUCKET_APP.AUTO_REVIEW", None)
+                                if is_true(auto_review):  # by default, auto review is disabled
+                                    await PRReviewer(pr_url).run()
+                                auto_improve = get_setting_or_env("BITBUCKET_APP.AUTO_IMPROVE", None)
+                                if is_true(auto_improve):  # by default, auto improve is disabled
+                                    await PRCodeSuggestions(pr_url).run()
+                                auto_describe = get_setting_or_env("BITBUCKET_APP.AUTO_DESCRIBE", None)
+                                if is_true(auto_describe):  # by default, auto describe is disabled
+                                    await PRDescription(pr_url).run()
             elif event == "pullrequest:comment_created":
                 pr_url = data["data"]["pullrequest"]["links"]["html"]["href"]
                 log_context["api_url"] = pr_url

pr_agent/servers/bitbucket_server_webhook.py

@@ -13,9 +13,10 @@ from starlette_context.middleware import RawContextMiddleware
 
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.config_loader import get_settings
-from pr_agent.log import get_logger
+from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.servers.utils import verify_signature
 
+setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
 router = APIRouter()
 
 
@@ -24,8 +25,15 @@ def handle_request(
 ):
     log_context["action"] = body
     log_context["api_url"] = url
-    with get_logger().contextualize(**log_context):
-        background_tasks.add_task(PRAgent().handle_request, url, body)
+    
+    async def inner():
+        try:
+            with get_logger().contextualize(**log_context):
+                await PRAgent().handle_request(url, body)
+        except Exception as e:
+            get_logger().error(f"Failed to handle webhook: {e}")
+
+    background_tasks.add_task(inner)
 
 
 @router.post("/")

pr_agent/servers/github_action_runner.py

@@ -46,19 +46,22 @@ async def run_action():
     if not GITHUB_EVENT_PATH:
         print("GITHUB_EVENT_PATH not set")
         return
-    if not OPENAI_KEY:
-        print("OPENAI_KEY not set")
-        return
     if not GITHUB_TOKEN:
         print("GITHUB_TOKEN not set")
         return
 
     # Set the environment variables in the settings
-    get_settings().set("OPENAI.KEY", OPENAI_KEY)
+    if OPENAI_KEY:
+        get_settings().set("OPENAI.KEY", OPENAI_KEY)
+    else:
+        # Might not be set if the user is using models not from OpenAI
+        print("OPENAI_KEY not set")
     if OPENAI_ORG:
         get_settings().set("OPENAI.ORG", OPENAI_ORG)
     get_settings().set("GITHUB.USER_TOKEN", GITHUB_TOKEN)
     get_settings().set("GITHUB.DEPLOYMENT_TYPE", "user")
+    enable_output = get_setting_or_env("GITHUB_ACTION_CONFIG.ENABLE_OUTPUT", True)
+    get_settings().set("GITHUB_ACTION_CONFIG.ENABLE_OUTPUT", enable_output)
 
     # Load the event payload
     try:
@@ -96,11 +99,14 @@ async def run_action():
 
                 # invoke by default all three tools
                 if auto_describe is None or is_true(auto_describe):
+                    get_settings().pr_description.final_update_message = False  # No final update message when auto_describe is enabled
                     await PRDescription(pr_url).run()
                 if auto_review is None or is_true(auto_review):
                     await PRReviewer(pr_url).run()
                 if auto_improve is None or is_true(auto_improve):
                     await PRCodeSuggestions(pr_url).run()
+        else:
+            get_logger().info(f"Skipping action: {action}")
 
     # Handle issue comment event
     elif GITHUB_EVENT_NAME == "issue_comment" or GITHUB_EVENT_NAME == "pull_request_review_comment":
@@ -121,7 +127,7 @@ async def run_action():
                 if event_payload.get("issue", {}).get("pull_request"):
                     url = event_payload.get("issue", {}).get("pull_request", {}).get("url")
                     is_pr = True
-                elif event_payload.get("comment", {}).get("pull_request_url"): # for 'pull_request_review_comment
+                elif event_payload.get("comment", {}).get("pull_request_url"):  # for 'pull_request_review_comment
                     url = event_payload.get("comment", {}).get("pull_request_url")
                     is_pr = True
                     disable_eyes = True
@@ -133,8 +139,11 @@ async def run_action():
                     comment_id = event_payload.get("comment", {}).get("id")
                     provider = get_git_provider()(pr_url=url)
                     if is_pr:
-                        await PRAgent().handle_request(url, body,
-                                    notify=lambda: provider.add_eyes_reaction(comment_id, disable_eyes=disable_eyes))
+                        await PRAgent().handle_request(
+                            url, body, notify=lambda: provider.add_eyes_reaction(
+                                comment_id, disable_eyes=disable_eyes
+                            )
+                        )
                     else:
                         await PRAgent().handle_request(url, body)
 

pr_agent/servers/github_app.py

@@ -7,6 +7,7 @@ from typing import Any, Dict, Tuple
 
 import uvicorn
 from fastapi import APIRouter, FastAPI, HTTPException, Request, Response
+from starlette.background import BackgroundTasks
 from starlette.middleware import Middleware
 from starlette_context import context
 from starlette_context.middleware import RawContextMiddleware
@@ -14,7 +15,7 @@ from starlette_context.middleware import RawContextMiddleware
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings, global_settings
-from pr_agent.git_providers import get_git_provider
+from pr_agent.git_providers import get_git_provider, get_git_provider_with_context
 from pr_agent.git_providers.git_provider import IncrementalPR
 from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.identity_providers import get_identity_provider
@@ -34,7 +35,7 @@ router = APIRouter()
 
 
 @router.post("/api/v1/github_webhooks")
-async def handle_github_webhooks(request: Request, response: Response):
+async def handle_github_webhooks(background_tasks: BackgroundTasks, request: Request, response: Response):
     """
     Receives and processes incoming GitHub webhook requests.
     Verifies the request signature, parses the request body, and passes it to the handle_request function for further
@@ -47,9 +48,9 @@ async def handle_github_webhooks(request: Request, response: Response):
     installation_id = body.get("installation", {}).get("id")
     context["installation_id"] = installation_id
     context["settings"] = copy.deepcopy(global_settings)
-
-    response = await handle_request(body, event=request.headers.get("X-GitHub-Event", None))
-    return response or {}
+    context["git_provider"] = {}
+    background_tasks.add_task(handle_request, body, event=request.headers.get("X-GitHub-Event", None))
+    return {}
 
 
 @router.post("/api/v1/marketplace_webhooks")
@@ -86,8 +87,13 @@ async def handle_comments_on_pr(body: Dict[str, Any],
         return {}
     comment_body = body.get("comment", {}).get("body")
     if comment_body and isinstance(comment_body, str) and not comment_body.lstrip().startswith("/"):
-        get_logger().info("Ignoring comment not starting with /")
-        return {}
+        if '/ask' in comment_body and comment_body.strip().startswith('> ![image]'):
+            comment_body_split = comment_body.split('/ask')
+            comment_body = '/ask' + comment_body_split[1] +' \n' +comment_body_split[0].strip().lstrip('>')
+            get_logger().info(f"Reformatting comment_body so command is at the beginning: {comment_body}")
+        else:
+            get_logger().info("Ignoring comment not starting with /")
+            return {}
     disable_eyes = False
     if "issue" in body and "pull_request" in body["issue"] and "url" in body["issue"]["pull_request"]:
         api_url = body["issue"]["pull_request"]["url"]
@@ -105,7 +111,7 @@ async def handle_comments_on_pr(body: Dict[str, Any],
         return {}
     log_context["api_url"] = api_url
     comment_id = body.get("comment", {}).get("id")
-    provider = get_git_provider()(pr_url=api_url)
+    provider = get_git_provider_with_context(pr_url=api_url)
     with get_logger().contextualize(**log_context):
         if get_identity_provider().verify_eligibility("github", sender_id, api_url) is not Eligibility.NOT_ELIGIBLE:
             get_logger().info(f"Processing comment on PR {api_url=}, comment_body={comment_body}")
@@ -122,22 +128,25 @@ async def handle_new_pr_opened(body: Dict[str, Any],
                                log_context: Dict[str, Any],
                                agent: PRAgent):
     title = body.get("pull_request", {}).get("title", "")
+    get_settings().config.is_auto_command = True
 
-    # logic to ignore PRs with specific titles (e.g. "[Auto] ...")
-    ignore_pr_title_re = get_settings().get("GITHUB_APP.IGNORE_PR_TITLE", [])
-    if not isinstance(ignore_pr_title_re, list):
-        ignore_pr_title_re = [ignore_pr_title_re]
-    if ignore_pr_title_re and any(re.search(regex, title) for regex in ignore_pr_title_re):
-        get_logger().info(f"Ignoring PR with title '{title}' due to github_app.ignore_pr_title setting")
-        return {}
 
     pull_request, api_url = _check_pull_request_event(action, body, log_context)
     if not (pull_request and api_url):
         get_logger().info(f"Invalid PR event: {action=} {api_url=}")
         return {}
-    if action in get_settings().github_app.handle_pr_actions:  # ['opened', 'reopened', 'ready_for_review', 'review_requested']
+    if action in get_settings().github_app.handle_pr_actions:  # ['opened', 'reopened', 'ready_for_review']
+        # logic to ignore PRs with specific titles (e.g. "[Auto] ...")
+        apply_repo_settings(api_url)
+        ignore_pr_title_re = get_settings().get("GITHUB_APP.IGNORE_PR_TITLE", [])
+        if not isinstance(ignore_pr_title_re, list):
+            ignore_pr_title_re = [ignore_pr_title_re]
+        if ignore_pr_title_re and any(re.search(regex, title) for regex in ignore_pr_title_re):
+            get_logger().info(f"Ignoring PR with title '{title}' due to github_app.ignore_pr_title setting")
+            return {}
+
         if get_identity_provider().verify_eligibility("github", sender_id, api_url) is not Eligibility.NOT_ELIGIBLE:
-            await _perform_auto_commands_github("pr_commands", agent, body, api_url, log_context)
+                await _perform_auto_commands_github("pr_commands", agent, body, api_url, log_context)
         else:
             get_logger().info(f"User {sender=} is not eligible to process PR {api_url=}")
 
@@ -194,14 +203,9 @@ async def handle_push_trigger_for_new_commits(body: Dict[str, Any],
             get_logger().info(f"Finished waiting to process push trigger for {api_url=} - continue with flow")
 
     try:
-        if get_settings().github_app.push_trigger_wait_for_initial_review and not get_git_provider()(api_url,
-                                                                                                     incremental=IncrementalPR(
-                                                                                                             True)).previous_review:
-            get_logger().info(f"Skipping incremental review because there was no initial review for {api_url=} yet")
-            return {}
         if get_identity_provider().verify_eligibility("github", sender_id, api_url) is not Eligibility.NOT_ELIGIBLE:
-            get_logger().info(f"Performing incremental review for {api_url=} because of {event=} and {action=}")
-            await _perform_auto_commands_github("push_commands", agent, body, api_url, log_context)
+                get_logger().info(f"Performing incremental review for {api_url=} because of {event=} and {action=}")
+                await _perform_auto_commands_github("push_commands", agent, body, api_url, log_context)
 
     finally:
         # release the waiting task block
@@ -224,19 +228,22 @@ def handle_closed_pr(body, event, action, log_context):
 def get_log_context(body, event, action, build_number):
     sender = ""
     sender_id = ""
+    sender_type = ""
     try:
         sender = body.get("sender", {}).get("login")
         sender_id = body.get("sender", {}).get("id")
+        sender_type = body.get("sender", {}).get("type")
         repo = body.get("repository", {}).get("full_name", "")
         git_org = body.get("organization", {}).get("login", "")
+        installation_id = body.get("installation", {}).get("id", "")
         app_name = get_settings().get("CONFIG.APP_NAME", "Unknown")
         log_context = {"action": action, "event": event, "sender": sender, "server_type": "github_app",
                        "request_id": uuid.uuid4().hex, "build_number": build_number, "app_name": app_name,
-                       "repo": repo, "git_org": git_org}
+                        "repo": repo, "git_org": git_org, "installation_id": installation_id}
     except Exception as e:
         get_logger().error("Failed to get log context", e)
         log_context = {}
-    return log_context, sender, sender_id
+    return log_context, sender, sender_id, sender_type
 
 
 async def handle_request(body: Dict[str, Any], event: str):
@@ -251,20 +258,31 @@ async def handle_request(body: Dict[str, Any], event: str):
     if not action:
         return {}
     agent = PRAgent()
-    log_context, sender, sender_id = get_log_context(body, event, action, build_number)
+    log_context, sender, sender_id, sender_type = get_log_context(body, event, action, build_number)
 
+    # logic to ignore PRs opened by bot
+    if get_settings().get("GITHUB_APP.IGNORE_BOT_PR", False) and sender_type == "Bot":
+        if 'pr-agent' not in sender:
+            get_logger().info(f"Ignoring PR from '{sender=}' because it is a bot")
+        return {}
+
+    if 'check_run' in body: # handle failed checks
+        # get_logger().debug(f'Request body', artifact=body, event=event) # added inside handle_checks
+        pass
     # handle comments on PRs
-    if action == 'created':
+    elif action == 'created':
         get_logger().debug(f'Request body', artifact=body, event=event)
         await handle_comments_on_pr(body, event, sender, sender_id, action, log_context, agent)
     # handle new PRs
     elif event == 'pull_request' and action != 'synchronize' and action != 'closed':
         get_logger().debug(f'Request body', artifact=body, event=event)
         await handle_new_pr_opened(body, event, sender, sender_id, action, log_context, agent)
+    elif event == "issue_comment" and 'edited' in action:
+        pass # handle_checkbox_clicked
     # handle pull_request event with synchronize action - "push trigger" for new commits
     elif event == 'pull_request' and action == 'synchronize':
-        get_logger().debug(f'Request body', artifact=body, event=event)
-        await handle_push_trigger_for_new_commits(body, event, sender, sender_id, action, log_context, agent)
+        # get_logger().debug(f'Request body', artifact=body, event=event) # added inside handle_push_trigger_for_new_commits
+        await handle_push_trigger_for_new_commits(body, event, sender,sender_id,  action, log_context, agent)
     elif event == 'pull_request' and action == 'closed':
         if get_settings().get("CONFIG.ANALYTICS_FOLDER", ""):
             handle_closed_pr(body, event, action, log_context)
@@ -311,8 +329,7 @@ async def _perform_auto_commands_github(commands_conf: str, agent: PRAgent, body
     apply_repo_settings(api_url)
     commands = get_settings().get(f"github_app.{commands_conf}")
     if not commands:
-        with get_logger().contextualize(**log_context):
-            get_logger().info(f"New PR, but no auto commands configured")
+        get_logger().info(f"New PR, but no auto commands configured")
         return
     for command in commands:
         split_command = command.split(" ")
@@ -320,9 +337,8 @@ async def _perform_auto_commands_github(commands_conf: str, agent: PRAgent, body
         args = split_command[1:]
         other_args = update_settings_from_args(args)
         new_command = ' '.join([command] + other_args)
-        with get_logger().contextualize(**log_context):
-            get_logger().info(f"{commands_conf}. Performing auto command '{new_command}', for {api_url=}")
-            await agent.handle_request(api_url, new_command)
+        get_logger().info(f"{commands_conf}. Performing auto command '{new_command}', for {api_url=}")
+        await agent.handle_request(api_url, new_command)
 
 
 @router.get("/")
@@ -342,5 +358,6 @@ app.include_router(router)
 def start():
     uvicorn.run(app, host="0.0.0.0", port=int(os.environ.get("PORT", "3000")))
 
+
 if __name__ == '__main__':
     start()

pr_agent/servers/github_polling.py

@@ -8,7 +8,7 @@ from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 
-setup_logger(fmt=LoggingFormat.JSON)
+setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
 NOTIFICATION_URL = "https://api.github.com/notifications"
 
 

pr_agent/servers/gitlab_webhook.py

@@ -1,5 +1,6 @@
 import copy
 import json
+from datetime import datetime
 
 import uvicorn
 from fastapi import APIRouter, FastAPI, Request, status
@@ -17,21 +18,46 @@ from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.secret_providers import get_secret_provider
 
-setup_logger(fmt=LoggingFormat.JSON)
+setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
 router = APIRouter()
 
 secret_provider = get_secret_provider() if get_settings().get("CONFIG.SECRET_PROVIDER") else None
 
 
-def handle_request(background_tasks: BackgroundTasks, url: str, body: str, log_context: dict):
+async def get_mr_url_from_commit_sha(commit_sha, gitlab_token, project_id):
+    try:
+        import requests
+        headers = {
+            'Private-Token': f'{gitlab_token}'
+        }
+        # API endpoint to find MRs containing the commit
+        gitlab_url = get_settings().get("GITLAB.URL", 'https://gitlab.com')
+        response = requests.get(
+            f'{gitlab_url}/api/v4/projects/{project_id}/repository/commits/{commit_sha}/merge_requests',
+            headers=headers
+        )
+        merge_requests = response.json()
+        if merge_requests and response.status_code == 200:
+            pr_url = merge_requests[0]['web_url']
+            return pr_url
+        else:
+            get_logger().info(f"No merge requests found for commit: {commit_sha}")
+            return None
+    except Exception as e:
+        get_logger().error(f"Failed to get MR url from commit sha: {e}")
+        return None
+
+async def handle_request(api_url: str, body: str, log_context: dict, sender_id: str):
     log_context["action"] = body
     log_context["event"] = "pull_request" if body == "/review" else "comment"
-    log_context["api_url"] = url
+    log_context["api_url"] = api_url
+
     with get_logger().contextualize(**log_context):
-        background_tasks.add_task(PRAgent().handle_request, url, body)
+        await PRAgent().handle_request(api_url, body)
 
 
-async def _perform_commands_gitlab(commands_conf: str, agent: PRAgent, api_url: str, log_context: dict):
+async def _perform_commands_gitlab(commands_conf: str, agent: PRAgent, api_url: str,
+                                   log_context: dict):
     apply_repo_settings(api_url)
     commands = get_settings().get(f"gitlab.{commands_conf}", {})
     for command in commands:
@@ -48,77 +74,129 @@ async def _perform_commands_gitlab(commands_conf: str, agent: PRAgent, api_url:
             get_logger().error(f"Failed to perform command {command}: {e}")
 
 
+
 @router.post("/webhook")
 async def gitlab_webhook(background_tasks: BackgroundTasks, request: Request):
-    log_context = {"server_type": "gitlab_app"}
-    if request.headers.get("X-Gitlab-Token") and secret_provider:
-        request_token = request.headers.get("X-Gitlab-Token")
-        secret = secret_provider.get_secret(request_token)
-        try:
-            secret_dict = json.loads(secret)
-            gitlab_token = secret_dict["gitlab_token"]
-            log_context["sender"] = secret_dict.get("token_name", secret_dict.get("id", "unknown"))
-            context["settings"] = copy.deepcopy(global_settings)
-            context["settings"].gitlab.personal_access_token = gitlab_token
-        except Exception as e:
-            get_logger().error(f"Failed to validate secret {request_token}: {e}")
+    start_time = datetime.now()
+    request_json = await request.json()
+
+    async def inner(data: dict):
+        log_context = {"server_type": "gitlab_app"}
+        get_logger().debug("Received a GitLab webhook")
+        if request.headers.get("X-Gitlab-Token") and secret_provider:
+            request_token = request.headers.get("X-Gitlab-Token")
+            secret = secret_provider.get_secret(request_token)
+            try:
+                secret_dict = json.loads(secret)
+                gitlab_token = secret_dict["gitlab_token"]
+                log_context["token_id"] = secret_dict.get("token_name", secret_dict.get("id", "unknown"))
+                context["settings"] = copy.deepcopy(global_settings)
+                context["settings"].gitlab.personal_access_token = gitlab_token
+            except Exception as e:
+                get_logger().error(f"Failed to validate secret {request_token}: {e}")
+                return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
+        elif get_settings().get("GITLAB.SHARED_SECRET"):
+            secret = get_settings().get("GITLAB.SHARED_SECRET")
+            if not request.headers.get("X-Gitlab-Token") == secret:
+                get_logger().error("Failed to validate secret")
+                return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
+        else:
+            get_logger().error("Failed to validate secret")
             return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
-    elif get_settings().get("GITLAB.SHARED_SECRET"):
-        secret = get_settings().get("GITLAB.SHARED_SECRET")
-        if not request.headers.get("X-Gitlab-Token") == secret:
+        gitlab_token = get_settings().get("GITLAB.PERSONAL_ACCESS_TOKEN", None)
+        if not gitlab_token:
+            get_logger().error("No gitlab token found")
             return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
-    else:
-        return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
-    gitlab_token = get_settings().get("GITLAB.PERSONAL_ACCESS_TOKEN", None)
-    if not gitlab_token:
-        return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
-    data = await request.json()
-    get_logger().info(json.dumps(data))
-    if data.get('object_kind') == 'merge_request' and data['object_attributes'].get('action') in ['open', 'reopen']:
-        get_logger().info(f"A merge request has been opened: {data['object_attributes'].get('title')}")
-        url = data['object_attributes'].get('url')
-        await _perform_commands_gitlab("pr_commands", PRAgent(), url, log_context)
-        # handle_request(background_tasks, url, "/review", log_context)
-    elif data.get('object_kind') == 'note' and data['event_type'] == 'note':
-        if 'merge_request' in data:
-            mr = data['merge_request']
-            url = mr.get('url')
-            body = data.get('object_attributes', {}).get('note')
-            if data.get('object_attributes', {}).get('type') == 'DiffNote' and '/ask' in body:
-                line_range_ = data['object_attributes']['position']['line_range']
 
-                # if line_range_['start']['type'] == 'new':
-                start_line = line_range_['start']['new_line']
-                end_line = line_range_['end']['new_line']
-                # else:
-                #     start_line = line_range_['start']['old_line']
-                #     end_line = line_range_['end']['old_line']
+        get_logger().info("GitLab data", artifact=data)
+        sender = data.get("user", {}).get("username", "unknown")
+        sender_id = data.get("user", {}).get("id", "unknown")
 
-                question = body.replace('/ask', '').strip()
-                path = data['object_attributes']['position']['new_path']
-                side = 'RIGHT'# if line_range_['start']['type'] == 'new' else 'LEFT'
-                comment_id = data['object_attributes']["discussion_id"]
-                get_logger().info(f"Handling line comment")
-                body = f"/ask_line --line_start={start_line} --line_end={end_line} --side={side} --file_name={path} --comment_id={comment_id} {question}"
+        # logic to ignore bot users (unlike Github, no direct flag for bot users in gitlab)
+        sender_name = data.get("user", {}).get("name", "unknown").lower()
+        if 'codium' in sender_name or 'bot_' in sender_name or 'bot-' in sender_name or '_bot' in sender_name or '-bot' in sender_name:
+            get_logger().info(f"Skipping bot user: {sender_name}")
+            return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
 
-            handle_request(background_tasks, url, body, log_context)
+        log_context["sender"] = sender
+        if data.get('object_kind') == 'merge_request' and data['object_attributes'].get('action') in ['open', 'reopen']:
+            url = data['object_attributes'].get('url')
+            get_logger().info(f"New merge request: {url}")
+            await _perform_commands_gitlab("pr_commands", PRAgent(), url, log_context)
+        elif data.get('object_kind') == 'note' and data.get('event_type') == 'note': # comment on MR
+            if 'merge_request' in data:
+                mr = data['merge_request']
+                url = mr.get('url')
+                get_logger().info(f"A comment has been added to a merge request: {url}")
+                body = data.get('object_attributes', {}).get('note')
+                if data.get('object_attributes', {}).get('type') == 'DiffNote' and '/ask' in body: # /ask_line
+                    body = handle_ask_line(body, data)
 
+                await handle_request(url, body, log_context, sender_id)
+        elif data.get('object_kind') == 'push' and data.get('event_name') == 'push':
+            try:
+                project_id = data['project_id']
+                commit_sha = data['checkout_sha']
+                url = await get_mr_url_from_commit_sha(commit_sha, gitlab_token, project_id)
+                if not url:
+                    get_logger().info(f"No MR found for commit: {commit_sha}")
+                    return JSONResponse(status_code=status.HTTP_200_OK,
+                                        content=jsonable_encoder({"message": "success"}))
+
+                # we need first to apply_repo_settings
+                apply_repo_settings(url)
+                commands_on_push = get_settings().get(f"gitlab.push_commands", {})
+                handle_push_trigger = get_settings().get(f"gitlab.handle_push_trigger", False)
+                if not commands_on_push or not handle_push_trigger:
+                    get_logger().info("Push event, but no push commands found or push trigger is disabled")
+                    return JSONResponse(status_code=status.HTTP_200_OK,
+                                        content=jsonable_encoder({"message": "success"}))
+
+                get_logger().debug(f'A push event has been received: {url}')
+                await _perform_commands_gitlab("push_commands", PRAgent(), url, log_context)
+            except Exception as e:
+                get_logger().error(f"Failed to handle push event: {e}")
+
+    background_tasks.add_task(inner, request_json)
+    end_time = datetime.now()
+    get_logger().info(f"Processing time: {end_time - start_time}", request=request_json)
     return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
 
 
+def handle_ask_line(body, data):
+    try:
+        line_range_ = data['object_attributes']['position']['line_range']
+        # if line_range_['start']['type'] == 'new':
+        start_line = line_range_['start']['new_line']
+        end_line = line_range_['end']['new_line']
+        # else:
+        #     start_line = line_range_['start']['old_line']
+        #     end_line = line_range_['end']['old_line']
+        question = body.replace('/ask', '').strip()
+        path = data['object_attributes']['position']['new_path']
+        side = 'RIGHT'  # if line_range_['start']['type'] == 'new' else 'LEFT'
+        comment_id = data['object_attributes']["discussion_id"]
+        get_logger().info("Handling line comment")
+        body = f"/ask_line --line_start={start_line} --line_end={end_line} --side={side} --file_name={path} --comment_id={comment_id} {question}"
+    except Exception as e:
+        get_logger().error(f"Failed to handle ask line comment: {e}")
+    return body
+
+
 @router.get("/")
 async def root():
     return {"status": "ok"}
 
-def start():
-    gitlab_url = get_settings().get("GITLAB.URL", None)
-    if not gitlab_url:
-        raise ValueError("GITLAB.URL is not set")
-    get_settings().config.git_provider = "gitlab"
-    middleware = [Middleware(RawContextMiddleware)]
-    app = FastAPI(middleware=middleware)
-    app.include_router(router)
+gitlab_url = get_settings().get("GITLAB.URL", None)
+if not gitlab_url:
+    raise ValueError("GITLAB.URL is not set")
+get_settings().config.git_provider = "gitlab"
+middleware = [Middleware(RawContextMiddleware)]
+app = FastAPI(middleware=middleware)
+app.include_router(router)
 
+
+def start():
     uvicorn.run(app, host="0.0.0.0", port=3000)