Update config_loader.py

Tr/branding

.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

@@ -5,5 +5,5 @@ __pycache__
 dist/
 *.egg-info/
 build/
-review.md
 .DS_Store
+docs/.cache/

.pr_agent.toml

@@ -4,4 +4,4 @@ enable_auto_approval = true
 
 
 [pr_code_suggestions]
-summarize=true
+commitable_code_suggestions=false

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

@@ -6,10 +6,11 @@
 <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)
@@ -20,112 +21,138 @@ 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
 
+### May 2, 2024
+Check out the new [PR-Agent Chrome Extension](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl) 🚀🚀🚀
+
+This toolbar integrates seamlessly with your GitHub environment, allowing you to access PR-Agent tools [directly from the GitHub interface](https://www.youtube.com/watch?v=gT5tli7X4H4).
+You can also easily export your chosen configuration, and use it for the automatic commands.
+
+<kbd><img src="https://codium.ai/images/pr_agent/toolbar1.png" width="512"></kbd>
+
+<kbd><img src="https://codium.ai/images/pr_agent/toolbar2.png" width="512"></kbd>
+
+
+### April 14, 2024
+You can now ask questions about images that appear in the comment, where the entire PR is considered as the context.
+see [here](https://pr-agent-docs.codium.ai/tools/ask/#ask-on-images) for more details.
+
+<kbd><img src="https://codium.ai/images/pr_agent/ask_images5.png" width="512"></kbd>
+
+### March 24, 2024
+PR-Agent is now available for easy installation via [pip](https://pr-agent-docs.codium.ai/installation/locally/#using-pip-package).
+
+### March 17, 2024
+- A new feature is now available for the review tool: [`require_can_be_split_review`](https://pr-agent-docs.codium.ai/tools/review/#enabledisable-features). 
+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.
+
+<kbd><img src="https://codium.ai/images/pr_agent/multiple_pr_themes.png" width="512"></kbd>
+
+### March 10, 2024
+- A new [knowledge-base website](https://pr-agent-docs.codium.ai/) for PR-Agent is now available. It includes detailed information about the different tools, usage guides and more, in an accessible and organized format.
+
+### March 8, 2024
+
+- A new tool, [Find Similar Code](https://pr-agent-docs.codium.ai/tools/similar_code/) 💎 is now available. 
+<br>This tool retrieves the most similar code components from inside the organization's codebase, or from open-source code:
+
+<kbd><a href="https://codium.ai/images/pr_agent/similar_code.mp4"><img src="https://codium.ai/images/pr_agent/similar_code_global2.png" width="512"></a></kbd>
+
+(click on the image to see an instructional video)
+
 ### 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 💎
+- You can now use the repo's [wiki page](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/) to set configurations for PR-Agent 💎
 
 <kbd><img src="https://codium.ai/images/pr_agent/wiki_configuration.png" width="512"></kbd>
 
 
-### Feb 21, 2024
-- Added a new command, `/help`, to easily provide a list of available tools and their descriptions, and run them interactively.
-
-<kbd>
-
-<img src="https://www.codium.ai/images/pr_agent/help.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: |                    |                    |                    |
+|-------|-------------------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:--------------------:|:--------------------:|
+| 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 Suggestions](https://pr-agent-docs.codium.ai/tools/custom_suggestions/) 💎                      | ✅ | ✅ | ✅ | ✅ |
+|       | [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                                                                                                                                     | :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: |                    |
+| USAGE | CLI                                                                                                               | ✅ | ✅ | ✅ | ✅ |
+|       | App / webhook                                                                                                     | ✅ | ✅ | ✅ | ✅ |
+|       | Tagging bot                                                                                                       | ✅ |                    |                    |                    |
+|       | Actions                                                                                                           | ✅ |                    | ✅ |                    |
 |       |                                                                                                                   |                    |                    |                    |                    |
-| 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: |                    |                    |                    |
+| 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 Suggestions 💎 ([`/custom_suggestions`](https://pr-agent-docs.codium.ai/tools/custom_suggestions/))**: 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 +246,56 @@ 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 +305,7 @@ 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?
 
@@ -277,7 +314,7 @@ 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).
 

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.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 @@
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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 +1,27 @@
+
+
+:root {
+    --md-primary-fg-color: #765bfa;
+    --md-accent-fg-color: #AEA1F1;
+  }
+.md-nav__title, .md-nav__link  {
+    font-size: 16px; 
+}
+
+.md-tabs__link  {
+    font-size: 16px; 
+}
+
+.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/index.md

@@ -0,0 +1,113 @@
+# 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 Suggestions](./tools/custom_suggestions.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
+
+
+
+## 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\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 Code Suggestions**](./tools/custom_suggestions.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)
+
+   
+## 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:
+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.

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/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:
 
@@ -54,4 +58,3 @@ 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_suggestions.md

@@ -0,0 +1,61 @@
+## Overview
+The `custom_suggestions` 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_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](../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_suggestions --pr_custom_suggestions.prompt="
+The 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_suggestions]
+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_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:
+
+[//]: # (![Custom suggestions prompt](https://codium.ai/images/pr_agent/custom_suggestions_prompt.png){width=512})
+
+[//]: # (→)
+![Custom suggestions 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_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/docs/tools/describe.md

@@ -0,0 +1,185 @@
+## 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
+
+### General configurations
+
+!!! example "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 original description. Default is false.
+
+    - `publish_description_as_comment_persistent`: 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.
+
+    - `add_original_user_description`: if set to true, the tool will add the original user description to the generated description. Default is true.
+
+    - `generate_ai_title`: if set to true, the tool will also generate an AI title for the PR. Default is false.
+
+    - `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](./custom_labels.md#configuration-options)
+
+    - `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".
+    - `enable_help_text`: if set to true, the tool will display a help text in the comment. Default is false.
+
+### 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 collapsable 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}
+
+→
+
+![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).
+
+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.
+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 the Repo's labels page 💎
+
+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:
+![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 +1,129 @@
+## 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 = ...
+...
+```
+
+- 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)
+
+
+
+## Configuration options
+
+!!! example "General options"
+
+    - `num_code_suggestions`: number of code suggestions provided by the 'improve' tool. Default is 4 for CLI, 0 for auto tools.
+    - `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.
+    - `commitable_code_suggestions`: if set to true, the tool will display the suggestions as commitable code comments. Default is false.
+    - `persistent_comment`: if set to true, the improve comment will be persistent, meaning that every new improve request will edit the previous one. Default is false.
+    - `enable_help_text`: if set to true, the tool will display a help text in the comment. Default is true.
+
+!!! example "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 5.
+    - `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.;
+
+## 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.
+
+
+
+## Usage Tips
+
+!!! tip "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.
+
+!!! 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 `exra_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 Suggestions Tool](./custom_suggestions.md) 💎, that will **only** propose 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 Suggestions (`/custom_suggestions`](./custom_suggestions.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 +1,187 @@
+## 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](../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
+```
+
+## 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).
+
+
+## Configuration options
+
+### General configurations
+
+!!! example "General options"
+    - <a name="num_code_suggestions"></a>`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`.
+    - <a name="inline_code_comments"></a>`inline_code_comments`: if set to true, the tool will publish the code suggestions as comments on the code diff. Default is false.
+    - <a name="persistent_comment"></a>`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.
+    - <a name="extra_instructions"></a>`extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
+    - <a name="enable_help_text"></a>`enable_help_text`: if set to true, the tool will display a help text in the comment. Default is true.
+
+!!! example "Enable\\disable sub-sections"
+    You can enable or disable specific sub-sections of the review tool:
+
+    - <a name="require_score_review"></a>`require_score_review`: if set to true, the tool will add a section that scores the PR. Default is false.
+    - <a name="require_tests_review"></a>`require_tests_review`: if set to true, the tool will add a section that checks if the PR contains tests. Default is true.
+    - <a name="require_estimate_effort_to_review"></a>`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.
+    - <a name="require_can_be_split_review"></a>`require_can_be_split_review`: 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.
+
+!!! 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".
+    
+    - <a name="require_soc2_ticket"></a>`require_soc2_ticket`: If set to true, the SOC2 ticket checker sub-tool will be enabled. Default is false.
+    - <a name="soc2_ticket_prompt"></a>`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.
+
+!!! example "Adding PR labels"
+    You can enable the tool to add specific labels to the PR:
+
+    - <a name="enable_review_labels_security"></a>`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.
+    - <a name="enable_review_labels_effort"></a>`enable_review_labels_effort`: if set to true, the tool will publish a 'Review effort [1-5]: x' label. Default is true.
+
+!!! example "Auto-approval"
+    The review tool can approve a PR when a specific comment, `/review auto_approve` is invoked.
+
+    - <a name="enable_auto_approval"></a>`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.
+    - <a name="maximal_review_effort"></a>`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.
+
+![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](https://codium.ai/images/pr_agent/reflection_questions.png){width=512}
+
+![reflection answers](https://codium.ai/images/pr_agent/reflection_answers.png){width=512}
+
+![reflection insights](https://codium.ai/images/pr_agent/reflection_insights.png){width=512}
+
+
+## Usage Tips
+
+!!! tip "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.
+
+!!! 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  "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.
+
+!!! 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
+    ```

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).
 
@@ -29,7 +33,7 @@ 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`
 

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 +1,242 @@
+## 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](https://github.com/Codium-ai/pr-agent/blob/main/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 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)
+```
+
+### 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"
+model_turbo = "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"
+model_turbo = "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"
+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 +1,208 @@
+## 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]
+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",
+    "/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.enable_output: "true" # enable\disable github actions output parameter
+```
+`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 PR 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",
+]
+```
+
+## 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",
+]
+```
+
+## 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 +1,56 @@
+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.
+
+## 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**.
+
+![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://codium-ai.github.io/Docs-PR-Agent/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://codium-ai.github.io/Docs-PR-Agent/installation/#run-from-source), or by invoking a [locally cloned repo](https://codium-ai.github.io/Docs-PR-Agent/installation/#locally).
+For online usage, you will need to setup either a [GitHub App](https://codium-ai.github.io/Docs-PR-Agent/installation/#run-as-a-github-app), or a [GitHub Action](https://codium-ai.github.io/Docs-PR-Agent/installation/#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#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"
+`
+

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 +1,133 @@
+site_name: PR-Agent Documentation 
+repo_url: https://github.com/Codium-ai/pr-agent
+repo_name: Codium-ai/pr-agent
+
+nav: 
+  - Overview: 'index.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 Suggestions: 'tools/custom_suggestions.md'
+    - 💎 CI Feedback: 'tools/ci_feedback.md'
+    - 💎 Similar Code: 'tools/similar_code.md'
+  - Core Abilities: 'core-abilities/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
+    - toc.integrate
+  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: 3
+      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

@@ -73,6 +73,9 @@ class PRAgent:
         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":

pr_agent/algo/__init__.py

@@ -1,8 +1,9 @@
 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,
@@ -10,6 +11,9 @@ MAX_TOKENS = {
     'gpt-4-32k': 32000,
     '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-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,
@@ -19,7 +23,15 @@ MAX_TOKENS = {
     'vertex_ai/codechat-bison-32k': 32000,
     '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,
+    '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,
+    'groq/llama3-8b-8192': 8192,
+    'groq/llama3-70b-8192': 8192,
 }

pr_agent/algo/ai_handlers/base_ai_handler.py

@@ -15,7 +15,7 @@ class BaseAiHandler(ABC):
         pass
 
     @abstractmethod   
-    async def chat_completion(self, model: str, system: str, user: str, temperature: float = 0.2):
+    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:

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
@@ -27,7 +26,8 @@ class LiteLLMAIHandler(BaseAiHandler):
         """
         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
@@ -36,6 +36,8 @@ class LiteLLMAIHandler(BaseAiHandler):
             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):
@@ -50,14 +52,20 @@ 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):
+        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.REPITITION_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(
@@ -65,11 +73,24 @@ class LiteLLMAIHandler(BaseAiHandler):
             )
         if get_settings().get("AWS.BEDROCK_REGION", None):
             litellm.AmazonAnthropicConfig.max_tokens_to_sample = 2000
+            litellm.AmazonAnthropicClaude3Config.max_tokens = 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 +98,73 @@ 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.Timeout)), # 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.Timeout) 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)
+
+            # 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/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
@@ -87,18 +87,30 @@ 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 = \
+    patches_compressed, modified_file_names, deleted_file_names, added_file_names, total_tokens_new = \
         pr_generate_compressed_diff(pr_languages, token_handler, model, add_line_numbers_to_hunks)
 
+    # 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:
+    delta_tokens = 10
+    if added_file_names and (max_tokens - curr_token) > delta_tokens:
         added_list_str = ADDED_FILES_ + "\n".join(added_file_names)
+        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:
+            curr_token += token_handler.count_tokens(added_list_str) + 2
+    if modified_file_names and (max_tokens - curr_token) > delta_tokens:
         modified_list_str = MORE_MODIFIED_FILES_ + "\n".join(modified_file_names)
+        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:
+            curr_token += token_handler.count_tokens(modified_list_str) + 2
+    if deleted_file_names and (max_tokens - curr_token) > delta_tokens:
         deleted_list_str = DELETED_FILES_ + "\n".join(deleted_file_names)
+        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
     try:
         get_logger().debug(f"After pruning, added_list_str: {added_list_str}, modified_list_str: {modified_list_str}, "
@@ -149,7 +161,7 @@ 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]:
+                                convert_hunks_to_line_numbers: bool) -> Tuple[list, list, list, list, int]:
     """
     Generate a compressed diff string for a pull request, using diff minimization techniques to reduce the number of
     tokens used.
@@ -195,10 +207,11 @@ 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_)
+            # if not deleted_files_list:
+            #     total_tokens += token_handler.count_tokens(DELETED_FILES_)
+            if file.filename not in deleted_files_list:
                 deleted_files_list.append(file.filename)
-            total_tokens += token_handler.count_tokens(file.filename) + 1
+            # total_tokens += token_handler.count_tokens(file.filename) + 1
             continue
 
         if convert_hunks_to_line_numbers:
@@ -219,14 +232,17 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
             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_)
+                # if not added_files_list:
+                #     total_tokens += token_handler.count_tokens(ADDED_FILES_)
+                if file.filename not in added_files_list:
                     added_files_list.append(file.filename)
+                # total_tokens += token_handler.count_tokens(file.filename) + 1
             else:
-                if not modified_files_list:
-                    total_tokens += token_handler.count_tokens(MORE_MODIFIED_FILES_)
+                # if not modified_files_list:
+                #     total_tokens += token_handler.count_tokens(MORE_MODIFIED_FILES_)
+                if file.filename not in modified_files_list:
                     modified_files_list.append(file.filename)
-                total_tokens += token_handler.count_tokens(file.filename) + 1
+                # total_tokens += token_handler.count_tokens(file.filename) + 1
             continue
 
         if patch:
@@ -239,7 +255,7 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
             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
+    return patches, modified_files_list, deleted_files_list, added_files_list, total_tokens
 
 
 async def retry_with_fallback_models(f: Callable, model_type: ModelType = ModelType.REGULAR):

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(
+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

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 import difflib
 import json
+import os
 import re
 import textwrap
 from datetime import datetime
@@ -12,7 +13,7 @@ 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
@@ -47,7 +48,20 @@ 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(output_data: dict, gfm_supported: bool = True, incremental_review=None) -> str:
     """
     Convert a dictionary of data into markdown format.
     Args:
@@ -57,7 +71,8 @@ def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
     """
 
     emojis = {
-        "Possible issues": "🔍",
+        "Can be split": "🔀",
+        "Possible issues": "⚡",
         "Score": "🏅",
         "Relevant tests": "🧪",
         "Focused PR": "✨",
@@ -67,7 +82,11 @@ def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
         "Estimated effort to review [1-5]": "⏱️",
     }
     markdown_text = ""
-    markdown_text += f"## PR Review\n\n"
+    if not incremental_review:
+        markdown_text += f"## PR Review 🔍\n\n"
+    else:
+        markdown_text += f"## Incremental PR Review 🔍 \n\n"
+        markdown_text += f"⏮️ Review for commits since previous PR-Agent review {incremental_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>"""
@@ -77,6 +96,7 @@ def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
 
     for key, value in output_data['review'].items():
         if value is None or value == '' or value == {} or value == []:
+            if key.lower() != 'can_be_split':
                 continue
         key_nice = key.replace('_', ' ').capitalize()
         emoji = emojis.get(key_nice, "")
@@ -86,15 +106,21 @@ def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
             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 'can be split' in key_nice.lower():
+                markdown_text += process_can_be_split(emoji, value)
             elif 'possible issues' in key_nice.lower():
                 value = value.strip()
                 issues = value.split('\n- ')
+                for i, _ in enumerate(issues):
+                    issues[i] = issues[i].strip().strip('-').strip()
+                issues = unique_strings(issues) # remove duplicates
                 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 not issue:
+                            continue
+                        issue = emphasize_header(issue)
                         if i == 0:
                             markdown_text += f"<td>\n\n{issue}</td></tr>\n"
                         else:
@@ -133,6 +159,38 @@ def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
     return markdown_text
 
 
+def process_can_be_split(emoji, value):
+    # 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"
+    else:
+        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: <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: <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"
+    return markdown_text
+
+
 def parse_code_suggestion(code_suggestion: dict, i: int = 0, gfm_supported: bool = True) -> str:
     """
     Convert a dictionary of data into markdown format.
@@ -509,7 +567,7 @@ def clip_tokens(text: str, max_tokens: int, add_three_dots=True) -> str:
         return text
 
     try:
-        encoder = get_token_encoder()
+        encoder = TokenEncoder.get_token_encoder()
         num_input_tokens = len(encoder.encode(text))
         if num_input_tokens <= max_tokens:
             return text
@@ -518,7 +576,7 @@ def clip_tokens(text: str, max_tokens: int, add_three_dots=True) -> str:
         num_output_chars = int(chars_per_token * max_tokens)
         clipped_text = text[:num_output_chars]
         if add_three_dots:
-            clipped_text += "...(truncated)"
+            clipped_text += "\n...(truncated)"
         return clipped_text
     except Exception as e:
         get_logger().warning(f"Failed to clip tokens: {e}")
@@ -604,3 +662,15 @@ def find_line_number_of_relevant_line_in_file(diff_files: List[FilePatchInfo],
                             absolute_position = start2 + delta - 1
                             break
     return position, absolute_position
+
+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

pr_agent/cli.py

@@ -9,47 +9,58 @@ from pr_agent.log import setup_logger
 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=[])
+    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()

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

@@ -36,6 +36,7 @@ def get_settings():
     try:
         return context["settings"]
     except Exception:
+        print("error")
         return global_settings
 
 

pr_agent/git_providers/azuredevops_provider.py

@@ -165,7 +165,7 @@ 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,

pr_agent/git_providers/bitbucket_provider.py

@@ -160,7 +160,11 @@ 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
@@ -175,6 +179,7 @@ class BitbucketProvider(GitProvider):
                     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))
+                    if final_update_message:
                         self.publish_comment(
                             f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
                     return
@@ -337,6 +342,41 @@ 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 ""
 
@@ -364,5 +404,5 @@ class BitbucketProvider(GitProvider):
         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

@@ -347,7 +347,7 @@ class BitbucketServerProvider(GitProvider):
         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

@@ -71,7 +71,7 @@ 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 +102,8 @@ 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 +124,11 @@ 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)
 
     @abstractmethod
@@ -160,7 +164,7 @@ 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 +197,12 @@ 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 +272,7 @@ 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

@@ -38,6 +38,7 @@ class GithubProvider(GitProvider):
             self.set_pr(pr_url)
             self.pr_commits = list(self.pr.get_commits())
             if self.incremental.is_incremental:
+                self.unreviewed_files_set = dict()
                 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
@@ -62,14 +63,15 @@ 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
@@ -98,8 +100,8 @@ class GithubProvider(GitProvider):
                 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:
@@ -112,6 +114,11 @@ class GithubProvider(GitProvider):
                 self.git_files = self.pr.get_files()
             return self.git_files
 
+    def get_num_of_files(self):
+        if self.git_files:
+            return self.git_files.totalCount
+        else:
+            return -1
 
     @retry(exceptions=RateLimitExceeded,
            tries=get_settings().github.ratelimit_retries, delay=2, backoff=2, jitter=(1, 3))
@@ -145,10 +152,10 @@ class GithubProvider(GitProvider):
                 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:
@@ -197,7 +204,11 @@ 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'):
+    def publish_persistent_comment(self, pr_comment: str,
+                                   initial_header: str,
+                                   update_header: bool = True,
+                                   name='review',
+                                   final_update_message=True):
         prev_comments = list(self.pr.get_issue_comments())
         for comment in prev_comments:
             body = comment.body
@@ -211,6 +222,7 @@ class GithubProvider(GitProvider):
                     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)
+                if final_update_message:
                     self.publish_comment(
                         f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
                 return
@@ -598,13 +610,36 @@ 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 +655,16 @@ 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 +745,4 @@ 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

pr_agent/git_providers/gitlab_provider.py

@@ -63,7 +63,7 @@ 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:
@@ -88,10 +88,8 @@ class GitLabProvider(GitProvider):
         diff_files = []
         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'])
+                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):
@@ -151,7 +149,11 @@ 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'):
+    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.mr.notes.list(get_all=True)[::-1]:
                 if comment.body.startswith(initial_header):
@@ -164,6 +166,7 @@ class GitLabProvider(GitProvider):
                         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})
+                    if final_update_message:
                         self.publish_comment(
                             f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
                     return
@@ -416,7 +419,7 @@ 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/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
@@ -81,7 +83,7 @@ async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
     actions = []
     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)
@@ -90,7 +92,7 @@ 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: 
                 # API V1 not supported as it does not contain the PR URL

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"}
@@ -119,8 +138,11 @@ async def handle_github_webhooks(background_tasks: BackgroundTasks, request: Req
                         apply_repo_settings(pr_url)
                         if get_identity_provider().verify_eligibility("bitbucket",
                                                         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 auto_review is None or is_true(auto_review):  # by default, auto review is enabled
+                                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
@@ -128,8 +150,6 @@ async def handle_github_webhooks(background_tasks: BackgroundTasks, request: Req
                                 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")
             elif event == "pullrequest:comment_created":
                 pr_url = data["data"]["pullrequest"]["links"]["html"]["href"]
                 log_context["api_url"] = pr_url

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
+    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:
@@ -101,6 +104,8 @@ async def run_action():
                     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":

pr_agent/servers/github_app.py

@@ -86,6 +86,11 @@ 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("/"):
+        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
@@ -135,7 +140,7 @@ async def handle_new_pr_opened(body: Dict[str, Any],
     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']
         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)
         else:
@@ -224,19 +229,22 @@ 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):
@@ -251,7 +259,13 @@ 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 {}
 
     # handle comments on PRs
     if action == 'created':

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

@@ -17,7 +17,7 @@ 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
@@ -51,6 +51,9 @@ async def _perform_commands_gitlab(commands_conf: str, agent: PRAgent, api_url:
 @router.post("/webhook")
 async def gitlab_webhook(background_tasks: BackgroundTasks, request: Request):
     log_context = {"server_type": "gitlab_app"}
+    get_logger().debug("Received a GitLab webhook")
+
+    # Check if the request is authorized
     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)
@@ -66,44 +69,55 @@ async def gitlab_webhook(background_tasks: BackgroundTasks, request: Request):
     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(f"Failed to validate secret")
             return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
     else:
+        get_logger().error(f"Failed to validate secret")
         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:
+        get_logger().error(f"No gitlab token found")
         return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
+
     data = await request.json()
-    get_logger().info(json.dumps(data))
+    get_logger().info("GitLab data", artifact=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')
+        get_logger().info(f"New merge request: {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':
+    elif data.get('object_kind') == 'note' and data['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:
-                line_range_ = data['object_attributes']['position']['line_range']
+            if data.get('object_attributes', {}).get('type') == 'DiffNote' and '/ask' in body: # /ask_line
+                body = handle_ask_line(body, data)
 
+            handle_request(background_tasks, url, body, log_context)
+
+    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'
+        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}"
-
-            handle_request(background_tasks, url, body, log_context)
-
-    return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
+    except Exception as e:
+        get_logger().error(f"Failed to handle ask line comment: {e}")
+    return body
 
 
 @router.get("/")

pr_agent/servers/help.py

@@ -9,7 +9,7 @@ class HelpMessage:
                 "> - **/add_docs** 💎: Generate docstring for new components introduced in the PR.   \n" \
                 "> - **/generate_labels** 💎: Generate labels for the PR based on the PR's contents.   \n" \
                 "> - **/analyze** 💎: Automatically analyzes the PR, and presents changes walkthrough for each component.   \n\n" \
-                ">See the [tools guide](https://github.com/Codium-ai/pr-agent/blob/main/docs/TOOLS_GUIDE.md) for more details.\n" \
+                ">See the [tools guide](https://pr-agent-docs.codium.ai/tools/) for more details.\n" \
                 ">To list the possible configuration parameters, add a **/config** comment.   \n"
        return commands_text
 
@@ -22,116 +22,22 @@ class HelpMessage:
     @staticmethod
     def get_review_usage_guide():
         output ="**Overview:**\n"
-        output +="The `review` tool scans the PR code changes, and generates a PR review. 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 any PR.\n"
+        output +=("The `review` tool scans the PR code changes, and generates a PR review which includes several types of feedbacks, such as possible PR issues, security threats and relevant test in the PR. More feedbacks can be [added](https://pr-agent-docs.codium.ai/tools/review/#general-configurations) by configuring the tool.\n\n"
+                  "The tool can be triggered [automatically](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#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 any PR.\n")
         output +="""\
-When commenting, to edit [configurations](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L19) related to the review tool (`pr_reviewer` section), use the following template:
+- When commenting, to edit [configurations](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L23) related to the review tool (`pr_reviewer` section), use the following template:
 ```
 /review --pr_reviewer.some_config1=... --pr_reviewer.some_config2=...
 ```
-With a [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-app), use the following template:
+- With a [configuration file](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/), use the following template:
 ```
 [pr_reviewer]
 some_config1=...
 some_config2=...
 ```
     """
-        output +="\n\n<table>"
 
-        # extra instructions
-        output += "<tr><td><details> <summary><strong> Utilizing extra instructions</strong></summary><hr>\n\n"
-        output += '''\
-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 'possible issues' 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.
-        '''
-        output += "\n\n</details></td></tr>\n\n"
-
-        # automation
-        output += "<tr><td><details> <summary><strong> How to enable\\disable automation</strong></summary><hr>\n\n"
-        output += """\
-- When you first install PR-Agent 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
-        """
-        output += "\n\n</details></td></tr>\n\n"
-
-#         # code feedback
-#         output += "<tr><td><details> <summary><strong> About the 'Code feedback' section</strong></summary><hr>\n\n"
-#         output+="""\
-# The `review` tool provides several type of feedbacks, one of them is code suggestions.
-# If you are interested **only** in the code suggestions, it is recommended to use the [`improve`](https://github.com/Codium-ai/pr-agent/blob/main/docs/IMPROVE.md) feature instead, since it dedicated only to code suggestions, and usually gives better results.
-# Use the `review` tool if you want to get a more comprehensive feedback, which includes code suggestions as well.
-# """
-#         output += "\n\n</details></td></tr>\n\n"
-
-        # auto-labels
-        output += "<tr><td><details> <summary><strong> Auto-labels</strong></summary><hr>\n\n"
-        output+="""\
-The `review` tool can auto-generate two specific types of labels for a PR:
-- a `possible security issue` label, that detects possible [security issues](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)
-"""
-        output += "\n\n</details></td></tr>\n\n"
-
-        # extra sub-tools
-        output += "<tr><td><details> <summary><strong> Extra sub-tools</strong></summary><hr>\n\n"
-        output += """\
-The `review` tool provides a collection of possible feedbacks about a PR.
-It is recommended to review the [possible options](https://github.com/Codium-ai/pr-agent/blob/main/docs/REVIEW.md#enabledisable-features), and choose the ones relevant for your use case.
-Some of the feature that are disabled by default are quite useful, and should be considered for enabling. For example: 
-`require_score_review`, `require_soc2_ticket`, and more.
-"""
-        output += "\n\n</details></td></tr>\n\n"
-
-        output += "<tr><td><details> <summary><strong> Auto-approve PRs</strong></summary><hr>\n\n"
-        output += '''\
-By invoking:
-```
-/review auto_approve
-```
-The tool will automatically approve the PR, and add a comment with the approval.
-
-
-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)
-
-
-You can also enable auto-approval only if the PR meets certain requirements, such as that the `estimated_review_effort` is equal or below a certain threshold, by adjusting the flag:
-```
-[pr_reviewer]
-maximal_review_effort = 5
-```
-'''
-        output += "\n\n</details></td></tr>\n\n"
-
-        # general
-        output += "\n\n<tr><td><details> <summary><strong> More PR-Agent commands</strong></summary><hr> \n\n"
-        output += HelpMessage.get_general_bot_help_text()
-        output += "\n\n</details></td></tr>\n\n"
-
-        output += "</table>"
-
-        output += f"\n\nSee the [review usage](https://github.com/Codium-ai/pr-agent/blob/main/docs/REVIEW.md) page for a comprehensive guide on using this tool.\n\n"
+        output += f"\n\nSee the review [usage page](https://pr-agent-docs.codium.ai/tools/review/) for a comprehensive guide on using this tool.\n\n"
 
         return output
 
@@ -141,14 +47,14 @@ maximal_review_effort = 5
     def get_describe_usage_guide():
         output = "**Overview:**\n"
         output += "The `describe` tool scans the PR code changes, and generates a description for the PR - title, type, summary, walkthrough and labels. "
-        output += "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.\n"
+        output += "The tool can be triggered [automatically](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#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.\n"
         output += """\
 
 When commenting, to edit [configurations](https://github.com/Codium-ai/pr-agent/blob/main/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=...
 ```
-With a [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-app), use the following template:
+With a [configuration file](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/), use the following template:
 ```
 [pr_description]
 some_config1=...
@@ -160,12 +66,11 @@ some_config2=...
         # automation
         output += "<tr><td><details> <summary><strong> Enabling\\disabling automation </strong></summary><hr>\n\n"
         output += """\
-- 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:
+- When you first install the app, the [default mode](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#github-app-automatic-tools-when-a-new-pr-is-opened) for the describe tool is:
 ```
-pr_commands = ["/describe --pr_description.add_original_user_description=true" 
-                         "--pr_description.keep_original_user_title=true", ...]
+pr_commands = ["/describe", ...]
 ```
-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. 
+meaning the `describe` tool will run automatically on every PR.
 
 - Markers are an alternative way to control the generated description, to give maximal control to the user. If you set:
 ```
@@ -186,7 +91,7 @@ Note that when markers are enabled, if the original PR description does not cont
         output += """\
 The default labels of the `describe` tool are quite generic: [`Bug fix`, `Tests`, `Enhancement`, `Documentation`, `Other`].
 
-If you specify [custom labels](https://github.com/Codium-ai/pr-agent/blob/main/docs/DESCRIBE.md#handle-custom-labels-from-the-repos-labels-page-gem) in the repo's labels page or via configuration file, you can get tailored labels for your use cases.
+If you specify [custom labels](https://pr-agent-docs.codium.ai/tools/describe/#handle-custom-labels-from-the-repos-labels-page) in the repo's labels page or via configuration file, 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
@@ -222,7 +127,7 @@ Be specific, clear, and concise in the instructions. With extra instructions, yo
 Examples for extra instructions:
 ```
 [pr_description] 
-extra_instructions="""
+extra_instructions="""\
 - The PR title should be in the format: '<PR type>: <title>'
 - The title should be short and concise (up to 10 words)
 - ...
@@ -240,7 +145,7 @@ Use triple quotes to write multi-line instructions. Use bullet points to make th
 
         output += "</table>"
 
-        output += f"\n\nSee the [describe usage](https://github.com/Codium-ai/pr-agent/blob/main/docs/DESCRIBE.md) page for a comprehensive guide on using this tool.\n\n"
+        output += f"\n\nSee the [describe usage](https://pr-agent-docs.codium.ai/tools/describe/) page for a comprehensive guide on using this tool.\n\n"
 
         return output
 
@@ -255,17 +160,18 @@ It can be invoked manually by commenting on any PR:
 ```
 
 Note that the tool does not have "memory" of previous questions, and answers each question independently.   
+You can ask questions about the entire PR, about specific code lines, or about an image related to the PR code changes.     
         """
-        output += "\n\n<table>"
+        # output += "\n\n<table>"
+        #
+        # # # general
+        # # output += "\n\n<tr><td><details> <summary><strong> More PR-Agent commands</strong></summary><hr> \n\n"
+        # # output += HelpMessage.get_general_bot_help_text()
+        # # output += "\n\n</details></td></tr>\n\n"
+        #
+        # output += "</table>"
 
-        # general
-        output += "\n\n<tr><td><details> <summary><strong> More PR-Agent commands</strong></summary><hr> \n\n"
-        output += HelpMessage.get_general_bot_help_text()
-        output += "\n\n</details></td></tr>\n\n"
-
-        output += "</table>"
-
-        output += f"\n\nSee the [ask usage](https://github.com/Codium-ai/pr-agent/blob/main/docs/ASK.md) page for a comprehensive guide on using this tool.\n\n"
+        output += f"\n\nSee the [ask usage](https://pr-agent-docs.codium.ai/tools/ask/) page for a comprehensive guide on using this tool.\n\n"
 
         return output
 
@@ -273,16 +179,16 @@ Note that the tool does not have "memory" of previous questions, and answers eac
     @staticmethod
     def get_improve_usage_guide():
         output = "**Overview:**\n"
-        output += "The `improve` tool scans the PR code changes, and automatically generates suggestions for improving the PR code. "
-        output += "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.\n"
+        output += "The code suggestions tool, named `improve`, scans the PR code changes, and automatically generates code suggestions for improving the PR."
+        output += "The tool can be triggered [automatically](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#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.\n"
         output += """\
-When commenting, to edit [configurations](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L69) related to the improve tool (`pr_code_suggestions` section), use the following template:
+- When commenting, to edit [configurations](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L78) related to the improve tool (`pr_code_suggestions` section), use the following template:
 
 ```
 /improve --pr_code_suggestions.some_config1=... --pr_code_suggestions.some_config2=...
 ```
 
-With a [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-app), use the following template:
+- With a [configuration file](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/), use the following template:
 
 ```
 [pr_code_suggestions]
@@ -291,64 +197,7 @@ some_config2=...
 ```
     
 """
-        output += "\n\n<table>"
 
-        # automation
-        output += "<tr><td><details> <summary><strong> Enabling\\disabling automation </strong></summary><hr>\n\n"
-        output += """\
-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 improve tool is:
-
-```
-pr_commands = ["/improve --pr_code_suggestions.summarize=true", ...]
-```
-
-meaning the `improve` tool will run automatically on every PR, with summarization enabled. Delete this line to disable the tool from running automatically.
-"""
-        output += "\n\n</details></td></tr>\n\n"
-
-        # extra instructions
-        output += "<tr><td><details> <summary><strong> Utilizing extra instructions</strong></summary><hr>\n\n"
-        output += '''\
-Extra instructions are very important for the `improve` tool, since they enable 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.
-    '''
-        output += "\n\n</details></td></tr>\n\n"
-
-        # suggestions quality
-        output += "\n\n<tr><td><details> <summary><strong> A note on code suggestions quality</strong></summary><hr> \n\n"
-        output += """\
-- 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. 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 'extra_instructions' field to guide the model to suggestions that are more relevant to the specific needs of the project, or use the [custom suggestions :gem:](https://github.com/Codium-ai/pr-agent/blob/main/docs/CUSTOM_SUGGESTIONS.md) tool
-- With large PRs, best quality will be obtained by using 'improve --extended' mode.
-
-
-"""
-        output += "\n\n</details></td></tr>\n\n"\
-
-        # general
-        output += "\n\n<tr><td><details> <summary><strong> More PR-Agent commands</strong></summary><hr> \n\n"
-        output += HelpMessage.get_general_bot_help_text()
-        output += "\n\n</details></td></tr>\n\n"
-
-        output += "</table>"
-
-        output += f"\n\nSee the [improve usage](https://github.com/Codium-ai/pr-agent/blob/main/docs/IMPROVE.md) page for a more comprehensive guide on using this tool.\n\n"
+        output += f"\n\nSee the improve [usage page](https://pr-agent-docs.codium.ai/tools/improve/) for a comprehensive guide on using this tool.\n\n"
 
         return output

pr_agent/settings/.secrets_template.toml

@@ -29,6 +29,9 @@ key = "" # Optional, uncomment if you want to use Cohere. Acquire through https:
 [replicate]
 key = "" # Optional, uncomment if you want to use Replicate. Acquire through https://replicate.com/
 
+[groq]
+key = "" # Acquire through https://console.groq.com/keys
+
 [huggingface]
 key = "" # Optional, uncomment if you want to use Huggingface Inference API. Acquire through https://huggingface.co/docs/api-inference/quicktour
 api_base = "" # the base url for your huggingface inference endpoint 

pr_agent/settings/configuration.toml

@@ -1,7 +1,7 @@
 [config]
-model="gpt-4" # "gpt-4-0125-preview"
-model_turbo="gpt-4-0125-preview"
-fallback_models=["gpt-3.5-turbo-16k"]
+model="gpt-4-turbo-2024-04-09"
+model_turbo="gpt-4-turbo-2024-04-09"
+fallback_models=["gpt-4-0125-preview"]
 git_provider="github"
 publish_output=true
 publish_output_progress=true
@@ -22,10 +22,10 @@ ai_disclaimer=""  # Pro feature, full text for the AI disclaimer
 
 [pr_reviewer] # /review #
 # enable/disable features
-require_focused_review=false
 require_score_review=false
 require_tests_review=true
 require_estimate_effort_to_review=true
+require_can_be_split_review=false
 # soc2
 require_soc2_ticket=false
 soc2_ticket_prompt="Does the PR description include a link to ticket in a project management system (e.g., Jira, Asana, Trello, etc.) ?"
@@ -36,6 +36,7 @@ ask_and_reflect=false
 #automatic_review=true
 persistent_comment=true
 extra_instructions = ""
+final_update_message = true
 # review labels
 enable_review_labels_security=true
 enable_review_labels_effort=true
@@ -43,7 +44,7 @@ enable_review_labels_effort=true
 require_all_thresholds_for_incremental_review=false
 minimal_commits_for_incremental_review=0
 minimal_minutes_for_incremental_review=0
-enable_help_text=true # Determines whether to include help text in the PR review. Enabled by default.
+enable_help_text=false # Determines whether to include help text in the PR review. Enabled by default.
 # auto approval
 enable_auto_approval=false
 maximal_review_effort=5
@@ -51,15 +52,17 @@ maximal_review_effort=5
 
 [pr_description] # /describe #
 publish_labels=true
-publish_description_as_comment=false
 add_original_user_description=true
-keep_original_user_title=true
+generate_ai_title=false
 use_bullet_points=true
 extra_instructions = ""
 enable_pr_type=true
 final_update_message = true
 enable_help_text=false
 enable_help_comment=true
+# describe as comment
+publish_description_as_comment=false
+publish_description_as_comment_persistent=true
 ## changes walkthrough section
 enable_semantic_files_types=true
 collapsible_file_list='adaptive' # true, false, 'adaptive'
@@ -71,16 +74,17 @@ include_generated_by_header=true
 #custom_labels = ['Bug fix', 'Tests', 'Bug fix with tests', 'Enhancement', 'Documentation', 'Other']
 
 [pr_questions] # /ask #
-enable_help_text=true
+enable_help_text=false
 
 
 [pr_code_suggestions] # /improve #
 max_context_tokens=8000
 num_code_suggestions=4
-summarize = true
+commitable_code_suggestions = false
 extra_instructions = ""
 rank_suggestions = false
-enable_help_text=true
+enable_help_text=false
+persistent_comment=false
 # params for '/improve --extended' mode
 auto_extended_mode=true
 num_code_suggestions_per_chunk=5
@@ -106,8 +110,13 @@ num_tests=3            # number of tests to generate. max 5.
 avoid_mocks=true       # if true, the generated tests will prefer to use real objects instead of mocks
 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
-enable_help_text=true
+enable_help_text=false
 
+[pr_improve_component] # /improve_component #
+num_code_suggestions=4
+extra_instructions = ""
+file = ""              # in case there are several components with the same name, you can specify the relevant file
+class_name = ""
 
 [checks] # /checks (pro feature) #
 enable_auto_checks_feedback=true
@@ -131,6 +140,7 @@ try_fix_invalid_inline_comments = true
 # auto_review = true    # set as env var in .github/workflows/pr-agent.yaml
 # auto_describe = true  # set as env var in .github/workflows/pr-agent.yaml
 # auto_improve = true   # set as env var in .github/workflows/pr-agent.yaml
+# enable_output = true   # set as env var in .github/workflows/pr-agent.yaml
 
 [github_app]
 # these toggles allows running the github app from custom deployments
@@ -138,9 +148,9 @@ override_deployment_type = true
 # settings for "pull_request" event
 handle_pr_actions = ['opened', 'reopened', 'ready_for_review']
 pr_commands = [
-    "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
+    "/describe",
     "/review --pr_reviewer.num_code_suggestions=0",
-    "/improve --pr_code_suggestions.summarize=true",
+    "/improve",
 ]
 # settings for "pull_request" event with "synchronize" action - used to detect and handle push triggers for new commits
 handle_push_trigger = false
@@ -150,23 +160,25 @@ push_trigger_wait_for_initial_review = true
 push_trigger_pending_tasks_backlog = true
 push_trigger_pending_tasks_ttl = 300
 push_commands = [
-    "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
+    "/describe",
     "/review --pr_reviewer.num_code_suggestions=0",
 ]
 ignore_pr_title = []
+ignore_bot_pr = true
 
 [gitlab]
 url = "https://gitlab.com" # URL to the gitlab service
 pr_commands = [
-    "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
+    "/describe",
     "/review --pr_reviewer.num_code_suggestions=0",
-    "/improve --pr_code_suggestions.summarize=true",
+    "/improve",
 ]
 
 [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
+pr_commands = [
+    "/review --pr_reviewer.num_code_suggestions=0",
+    "/improve --pr_code_suggestions.commitable_code_suggestions=true",
+]
 
 
 [local]
@@ -190,7 +202,8 @@ pr_commands = [
 url = ""
 
 [litellm]
-#use_client = false
+# use_client = false
+# drop_params = false
 
 [pr_similar_issue]
 skip_comments = false

pr_agent/settings/pr_code_suggestions_prompts.toml

@@ -54,7 +54,7 @@ class CodeSuggestion(BaseModel):
     relevant_file: str = Field(description="the relevant file full path")
     language: str = Field(description="the code language of the relevant file")
     suggestion_content: str = Field(description="an actionable suggestion for meaningfully improving the new code introduced in the PR")
-{%- if summarize_mode %}
+{%- if not commitable_code_suggestions_mode %}
     existing_code: str = Field(description="a short code snippet from a '__new hunk__' section to illustrate the relevant existing code. Don't show the line numbers.")
     improved_code: str = Field(description="a short code snippet to illustrate the improved code, after applying the suggestion.")
     one_sentence_summary:str = Field(description="a short summary of the suggestion action, in a single sentence. Focus on the 'what'. Be general, and avoid method or variable names.")
@@ -80,7 +80,7 @@ code_suggestions:
     python
   suggestion_content: |
     ...
-{%- if summarize_mode %}
+{%- if not commitable_code_suggestions_mode %}
   existing_code: |
     ...
   improved_code: |

pr_agent/settings/pr_reviewer_prompts.toml

@@ -49,7 +49,13 @@ Extra instructions from the user:
 
 The output must be a YAML object equivalent to type $PRReview, according to the following Pydantic definitions:
 =====
-class Review(BaseModel)
+{%- if require_can_be_split_review %}
+class SubPR(BaseModel):
+    relevant_files: List[str] = Field(description="The relevant files of the sub-PR")
+    title: str = Field(description="Short and concise title for an independent and meaningful sub-PR, composed only from the relevant files")
+{%- endif %}
+
+class Review(BaseModel):
 {%- if require_estimate_effort_to_review %}
     estimated_effort_to_review_[1-5]: str = Field(description="Estimate, on a scale of 1-5 (inclusive), the time and effort required to review this PR by an experienced and knowledgeable developer. 1 means short and easy review , 5 means long and hard review. Take into account the size, complexity, quality, and the needed changes of the PR code diff. Explain your answer in a short and concise manner.")
 {%- endif %}
@@ -61,15 +67,15 @@ class Review(BaseModel)
 {%- endif %}
 {%- if question_str %}
     insights_from_user_answers: str = Field(description="shortly summarize the insights you gained from the user's answers to the questions")
-{%- endif %}
-{%- if require_focused %}
-    focused_pr: str = Field(description="Is this a focused PR, in the sense that all the PR code diff changes are united under a single focused theme ? If the theme is too broad, or the PR code diff changes are too scattered, then the PR is not focused. Explain your answer shortly.")
 {%- endif %}
     possible_issues: str = Field(description="Does this PR code introduce clear issues, bugs, or major performance concerns? If there are no apparent issues, respond with 'No'. If there are any issues, describe them briefly. Use bullet points if more than one issue. Be specific, and provide examples if possible. Start each bullet point with a short specific header, such as: "- Possible Bug: ...", etc.")
     security_concerns: str = Field(description="does this PR code introduce possible vulnerabilities such as exposure of sensitive information (e.g., API keys, secrets, passwords), or security concerns like SQL injection, XSS, CSRF, and others ? Answer 'No' if there are no possible issues. If there are security concerns or issues, start your answer with a short header, such as: 'Sensitive information exposure: ...', 'SQL injection: ...' etc. Explain your answer. Be specific and give examples if possible")
+{%- if require_can_be_split_review %}
+    can_be_split: List[SubPR] = Field(min_items=0, max_items=3, description="Can this PR, which contains {{ num_pr_files }} changed files in total, be divided into smaller sub-PRs with distinct tasks that can be reviewed and merged independently, regardless of the order ? Make sure that the sub-PRs are indeed independent, with no code dependencies between them, and that each sub-PR represent a meaningfull independent task. Output an empty list if the PR code does not needd to be split.")
+{%- endif %}
 {%- if num_code_suggestions > 0 %}
 
-class CodeSuggestion(BaseModel)
+class CodeSuggestion(BaseModel):
     relevant_file: str = Field(description="the relevant file full path")
     language: str = Field(description="the language of the relevant file")
     suggestion: str = Field(description="a concrete suggestion for meaningfully improving the new PR code. Also describe how, specifically, the suggestion can be applied to new PR code. Add tags with importance measure that matches each suggestion ('important' or 'medium'). Do not make suggestions for updating or adding docstrings, renaming PR title and description, or linter like.")
@@ -77,12 +83,12 @@ class CodeSuggestion(BaseModel)
 {%- endif %}
 {%- if num_code_suggestions > 0 %}
 
-class PRReview(BaseModel)
+class PRReview(BaseModel):
     review: Review
     code_feedback: List[CodeSuggestion]
 {%- else %}
 
-class PRReview(BaseModel)
+class PRReview(BaseModel):
     review: Review
 {%- endif %}
 =====
@@ -100,14 +106,18 @@ review:
 {%- endif %}
   relevant_tests: |
     No
-{%- if require_focused %}
-  focused_pr: |
-    no, because ...
-{%- endif %}
   possible_issues: |
     No
   security_concerns: |
     No
+{%- if require_can_be_split_review %}
+    can_be_split: |
+    - relevant_files:
+      - ...
+      - ...
+     title: ...
+    - ...
+{%- endif %}
 {%- if num_code_suggestions > 0 %}
 code_feedback
 - relevant_file: |
@@ -138,15 +148,8 @@ Description:
 ======
 {%- endif %}
 
-{%- if commit_messages_str %}
-
-Commit messages:
-======
-{{commit_messages_str}}
-======
-{%- endif %}
-
 {%- if question_str %}
+
 =====
 Here are questions to better understand the PR. Use the answers to provide better feedback.
 

pr_agent/tools/pr_add_docs.py

@@ -26,6 +26,8 @@ class PRAddDocs:
         )
 
         self.ai_handler = ai_handler()
+        self.ai_handler.main_pr_language = self.main_language
+
         self.patches_diff = None
         self.prediction = None
         self.cli_mode = cli_mode

pr_agent/tools/pr_code_suggestions.py

@@ -46,6 +46,7 @@ class PRCodeSuggestions:
             num_code_suggestions = get_settings().pr_code_suggestions.num_code_suggestions
 
         self.ai_handler = ai_handler()
+        self.ai_handler.main_pr_language = self.main_language
         self.patches_diff = None
         self.prediction = None
         self.cli_mode = cli_mode
@@ -56,7 +57,7 @@ class PRCodeSuggestions:
             "language": self.main_language,
             "diff": "",  # empty diff for initial calculation
             "num_code_suggestions": num_code_suggestions,
-            "summarize_mode": get_settings().pr_code_suggestions.summarize,
+            "commitable_code_suggestions_mode": get_settings().pr_code_suggestions.commitable_code_suggestions,
             "extra_instructions": get_settings().pr_code_suggestions.extra_instructions,
             "commit_messages_str": self.git_provider.get_commit_messages(),
         }
@@ -75,7 +76,7 @@ class PRCodeSuggestions:
             relevant_configs = {'pr_code_suggestions': dict(get_settings().pr_code_suggestions),
                                 'config': dict(get_settings().config)}
             get_logger().debug("Relevant configs", artifacts=relevant_configs)
-            if get_settings().config.publish_output:
+            if get_settings().config.publish_output and get_settings().config.publish_output_progress:
                 if self.git_provider.is_supported("gfm_markdown"):
                     self.progress_response = self.git_provider.publish_comment(self.progress)
                 else:
@@ -87,9 +88,14 @@ class PRCodeSuggestions:
             else:
                 data = await retry_with_fallback_models(self._prepare_prediction_extended, ModelType.TURBO)
 
-
-            if (not data) or (not 'code_suggestions' in data):
-                get_logger().info('No code suggestions found for PR.')
+            if (not data) or (not 'code_suggestions' in data) or (not data['code_suggestions']):
+                get_logger().error('No code suggestions found for PR.')
+                pr_body = "## PR Code Suggestions ✨\n\nNo code suggestions found for PR."
+                get_logger().debug(f"PR output", artifact=pr_body)
+                if self.progress_response:
+                    self.git_provider.edit_comment(self.progress_response, body=pr_body)
+                else:
+                    self.git_provider.publish_comment(pr_body)
                 return
 
             if (not self.is_extended and get_settings().pr_code_suggestions.rank_suggestions) or \
@@ -99,7 +105,7 @@ class PRCodeSuggestions:
 
             if get_settings().config.publish_output:
                 self.git_provider.remove_initial_comment()
-                if get_settings().pr_code_suggestions.summarize and self.git_provider.is_supported("gfm_markdown"):
+                if (not get_settings().pr_code_suggestions.commitable_code_suggestions) and self.git_provider.is_supported("gfm_markdown"):
 
                     # generate summarized suggestions
                     pr_body = self.generate_summarized_suggestions(data)
@@ -107,10 +113,21 @@ class PRCodeSuggestions:
 
                     # add usage guide
                     if get_settings().pr_code_suggestions.enable_help_text:
-                        pr_body += "<hr>\n\n<details> <summary><strong>✨ Improve tool usage guide:</strong></summary><hr> \n\n"
+                        pr_body += "<hr>\n\n<details> <summary><strong>💡 Tool usage guide:</strong></summary><hr> \n\n"
                         pr_body += HelpMessage.get_improve_usage_guide()
                         pr_body += "\n</details>\n"
 
+                    if get_settings().pr_code_suggestions.persistent_comment:
+                        final_update_message = False
+                        self.git_provider.publish_persistent_comment(pr_body,
+                                                                     initial_header="## PR Code Suggestions ✨",
+                                                                     update_header=True,
+                                                                     name="suggestions",
+                                                                     final_update_message=final_update_message, )
+                        if self.progress_response:
+                            self.progress_response.delete()
+                    else:
+
                         if self.progress_response:
                             self.git_provider.edit_comment(self.progress_response, body=pr_body)
                         else:
@@ -179,7 +196,8 @@ class PRCodeSuggestions:
         suggestion_list = []
         one_sentence_summary_list = []
         for i, suggestion in enumerate(data['code_suggestions']):
-            if get_settings().pr_code_suggestions.summarize:
+            try:
+                if not get_settings().pr_code_suggestions.commitable_code_suggestions:
                     if not suggestion or 'one_sentence_summary' not in suggestion or 'label' not in suggestion or 'relevant_file' not in suggestion:
                         get_logger().debug(f"Skipping suggestion {i + 1}, because it is invalid: {suggestion}")
                         continue
@@ -188,15 +206,21 @@ class PRCodeSuggestions:
                         get_logger().debug(f"Skipping suggestion {i + 1}, because it is a duplicate: {suggestion}")
                         continue
 
+                if 'const' in suggestion['suggestion_content'] and 'instead' in suggestion['suggestion_content'] and 'let' in suggestion['suggestion_content']:
+                    get_logger().debug(f"Skipping suggestion {i + 1}, because it uses 'const instead let': {suggestion}")
+                    continue
+
                 if ('existing_code' in suggestion) and ('improved_code' in suggestion) and (
                         suggestion['existing_code'] != suggestion['improved_code']):
                     suggestion = self._truncate_if_needed(suggestion)
-                if get_settings().pr_code_suggestions.summarize:
+                    if not get_settings().pr_code_suggestions.commitable_code_suggestions:
                         one_sentence_summary_list.append(suggestion['one_sentence_summary'])
                     suggestion_list.append(suggestion)
                 else:
                     get_logger().debug(
                         f"Skipping suggestion {i + 1}, because existing code is equal to improved code {suggestion['existing_code']}")
+            except Exception as e:
+                get_logger().error(f"Error processing suggestion {i + 1}: {suggestion}, error: {e}")
         data['code_suggestions'] = suggestion_list
 
         return data
@@ -317,7 +341,7 @@ class PRCodeSuggestions:
             suggestion_list.append(suggestion)
         data_sorted = [[]] * len(suggestion_list)
 
-        if len(suggestion_list ) == 1:
+        if len(suggestion_list) == 1:
             return suggestion_list
 
         try:
@@ -358,7 +382,7 @@ class PRCodeSuggestions:
 
     def generate_summarized_suggestions(self, data: Dict) -> str:
         try:
-            pr_body = "## PR Code Suggestions\n\n"
+            pr_body = "## PR Code Suggestions ✨\n\n"
 
             if len(data.get('code_suggestions', [])) == 0:
                 pr_body += "No suggestions found to improve this PR."
@@ -370,7 +394,7 @@ class PRCodeSuggestions:
                 for ext in extensions:
                     extension_to_language[ext] = language
 
-            pr_body = "## PR Code Suggestions\n\n"
+            pr_body = "## PR Code Suggestions ✨\n\n"
 
             pr_body += "<table>"
             header = f"Suggestions"
@@ -388,11 +412,7 @@ class PRCodeSuggestions:
 
             for label, suggestions in suggestions_labels.items():
                 num_suggestions=len(suggestions)
-                # pr_body += f"""<tr><td><strong>{label}</strong></td>"""
                 pr_body += f"""<tr><td rowspan={num_suggestions}><strong>{label.capitalize()}</strong></td>\n"""
-                # pr_body += f"""<td>"""
-                # pr_body += f"""<details><summary>{len(suggestions)} suggestions</summary>"""
-                # pr_body += f"""<table>"""
                 for i, suggestion in enumerate(suggestions):
 
                     relevant_file = suggestion['relevant_file'].strip()
@@ -439,11 +459,11 @@ class PRCodeSuggestions:
 {example_code}                   
 """
                     pr_body += f"</details>"
-
                     pr_body += f"</td></tr>"
 
+
                 # pr_body += "</details>"
-                pr_body += """</td></tr>"""
+                # pr_body += """</td></tr>"""
             pr_body += """</tr></tbody></table>"""
             return pr_body
         except Exception as e:

pr_agent/tools/pr_description.py

@@ -41,6 +41,7 @@ class PRDescription:
 
         # Initialize the AI handler
         self.ai_handler = ai_handler()
+        self.ai_handler.main_pr_language = self.main_pr_language
 
     
         # Initialize the variables dictionary
@@ -112,21 +113,32 @@ class PRDescription:
                 pr_body += HelpMessage.get_describe_usage_guide()
                 pr_body += "\n</details>\n"
             elif get_settings().pr_description.enable_help_comment:
-                pr_body += "\n\n___\n\n> ✨ **PR-Agent usage**:"
+                pr_body += "\n\n___\n\n> 💡 **PR-Agent usage**:"
                 pr_body += "\n>Comment `/help` on the PR to get a list of all available PR-Agent tools and their descriptions\n\n"
 
             if get_settings().config.publish_output:
                 # publish labels
                 if get_settings().pr_description.publish_labels and self.git_provider.is_supported("get_labels"):
-                    original_labels = self.git_provider.get_pr_labels()
+                    original_labels = self.git_provider.get_pr_labels(update=True)
                     get_logger().debug(f"original labels", artifact=original_labels)
                     user_labels = get_user_labels(original_labels)
-                    get_logger().debug(f"published labels:\n{pr_labels + user_labels}")
-                    self.git_provider.publish_labels(pr_labels + user_labels)
+                    new_labels = pr_labels + user_labels
+                    get_logger().debug(f"published labels", artifact=new_labels)
+                    if sorted(new_labels) != sorted(original_labels):
+                        self.git_provider.publish_labels(new_labels)
+                    else:
+                        get_logger().debug(f"Labels are the same, not updating")
 
                 # publish description
                 if get_settings().pr_description.publish_description_as_comment:
                     full_markdown_description = f"## Title\n\n{pr_title}\n\n___\n{pr_body}"
+                    if get_settings().pr_description.publish_description_as_comment_persistent:
+                        self.git_provider.publish_persistent_comment(full_markdown_description,
+                                                                     initial_header="## Title",
+                                                                     update_header=True,
+                                                                     name="describe",
+                                                                     final_update_message=False, )
+                    else:
                         self.git_provider.publish_comment(full_markdown_description)
                 else:
                     self.git_provider.publish_description(pr_title, pr_body)
@@ -289,7 +301,7 @@ class PRDescription:
 
         # Remove the 'PR Title' key from the dictionary
         ai_title = self.data.pop('title', self.vars["title"])
-        if get_settings().pr_description.keep_original_user_title:
+        if (not get_settings().pr_description.generate_ai_title):
             # Assign the original PR title to the 'title' variable
             title = self.vars["title"]
         else:
@@ -305,7 +317,11 @@ class PRDescription:
                 value = self.file_label_dict
             else:
                 key_publish = key.rstrip(':').replace("_", " ").capitalize()
-                pr_body += f"## **{key_publish}**\n"
+                if key_publish== "Type":
+                    key_publish = "PR Type"
+                # elif key_publish == "Description":
+                #     key_publish = "PR Description"
+                pr_body += f"### **{key_publish}**\n"
             if 'walkthrough' in key.lower():
                 if self.git_provider.is_supported("gfm_markdown"):
                     pr_body += "<details> <summary>files:</summary>\n\n"
@@ -317,7 +333,7 @@ class PRDescription:
                     pr_body += "</details>\n"
             elif 'pr_files' in key.lower():
                 changes_walkthrough, pr_file_changes = self.process_pr_files_prediction(changes_walkthrough, value)
-                changes_walkthrough = f"## **Changes walkthrough**\n{changes_walkthrough}"
+                changes_walkthrough = f"### **Changes walkthrough** 📝\n{changes_walkthrough}"
             else:
                 # if the value is a list, join its items by comma
                 if isinstance(value, list):

pr_agent/tools/pr_generate_labels.py

@@ -35,6 +35,7 @@ class PRGenerateLabels:
 
         # Initialize the AI handler
         self.ai_handler = ai_handler()
+        self.ai_handler.main_pr_language = self.main_pr_language
 
         # Initialize the variables dictionary
         self.vars = {

pr_agent/tools/pr_help_message.py

@@ -18,49 +18,52 @@ class PRHelpMessage:
             relevant_configs = {'pr_help': dict(get_settings().pr_help),
                                 'config': dict(get_settings().config)}
             get_logger().debug("Relevant configs", artifacts=relevant_configs)
-            pr_comment = "## PR Agent Walkthrough\n\n"
-            pr_comment += "🤖 Welcome to the PR Agent, an AI-powered tool for automated pull request analysis, feedback, suggestions and more."""
+            pr_comment = "## PR Agent Walkthrough 🤖\n\n"
+            pr_comment += "Welcome to the PR Agent, an AI-powered tool for automated pull request analysis, feedback, suggestions and more."""
             pr_comment += "\n\nHere is a list of tools you can use to interact with the PR Agent:\n"
-            base_path = "https://github.com/Codium-ai/pr-agent/tree/main/docs"
+            base_path = "https://pr-agent-docs.codium.ai/tools"
 
             tool_names = []
-            tool_names.append(f"[DESCRIBE]({base_path}/DESCRIBE.md)")
-            tool_names.append(f"[REVIEW]({base_path}/REVIEW.md)")
-            tool_names.append(f"[IMPROVE]({base_path}/IMPROVE.md)")
-            tool_names.append(f"[ANALYZE]({base_path}/Analyze.md) 💎")
-            tool_names.append(f"[UPDATE CHANGELOG]({base_path}/UPDATE_CHANGELOG.md)")
-            tool_names.append(f"[ADD DOCUMENTATION]({base_path}/ADD_DOCUMENTATION.md) 💎")
-            tool_names.append(f"[ASK]({base_path}/ASK.md)")
-            tool_names.append(f"[GENERATE CUSTOM LABELS]({base_path}/GENERATE_CUSTOM_LABELS.md)")
-            tool_names.append(f"[TEST]({base_path}/TEST.md) 💎")
-            tool_names.append(f"[CI FEEDBACK]({base_path}/CI_FEEDBACK.md) 💎")
-            tool_names.append(f"[CUSTOM SUGGESTIONS]({base_path}/CUSTOM_SUGGESTIONS.md) 💎")
-            tool_names.append(f"[SIMILAR ISSUE]({base_path}/SIMILAR_ISSUE.md)")
+            tool_names.append(f"[DESCRIBE]({base_path}/describe/)")
+            tool_names.append(f"[REVIEW]({base_path}/review/)")
+            tool_names.append(f"[IMPROVE]({base_path}/improve/)")
+            tool_names.append(f"[UPDATE CHANGELOG]({base_path}/update_changelog/)")
+            tool_names.append(f"[ADD DOCS]({base_path}/documentation/) 💎")
+            tool_names.append(f"[TEST]({base_path}/test/) 💎")
+            tool_names.append(f"[IMPROVE COMPONENT]({base_path}/improve_component/) 💎")
+            tool_names.append(f"[ANALYZE]({base_path}/analyze/) 💎")
+            tool_names.append(f"[ASK]({base_path}/ask/)")
+            tool_names.append(f"[GENERATE CUSTOM LABELS]({base_path}/custom_labels/) 💎")
+            tool_names.append(f"[CI FEEDBACK]({base_path}/ci_feedback/) 💎")
+            tool_names.append(f"[CUSTOM SUGGESTIONS]({base_path}/custom_suggestions/) 💎")
+            tool_names.append(f"[SIMILAR ISSUE]({base_path}/similar_issues/)")
 
             descriptions = []
             descriptions.append("Generates PR description - title, type, summary, code walkthrough and labels")
             descriptions.append("Adjustable feedback about the PR, possible issues, security concerns, review effort and more")
-            descriptions.append("Code suggestions for improving the PR.")
-            descriptions.append("Identifies code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component.")
-            descriptions.append("Automatically updates the changelog.")
-            descriptions.append("Generates documentation to methods/functions/classes that changed in the PR.")
-            descriptions.append("Answering free-text questions about the PR.")
+            descriptions.append("Code suggestions for improving the PR")
+            descriptions.append("Automatically updates the changelog")
+            descriptions.append("Generates documentation to methods/functions/classes that changed in the PR")
+            descriptions.append("Generates unit tests for a specific component, based on the PR code change")
+            descriptions.append("Code suggestions for a specific component that changed in the PR")
+            descriptions.append("Identifies code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component")
+            descriptions.append("Answering free-text questions about the PR")
             descriptions.append("Generates custom labels for the PR, based on specific guidelines defined by the user")
-            descriptions.append("Generates unit tests for a specific component, based on the PR code change.")
-            descriptions.append("Generates feedback and analysis for a failed CI job.")
-            descriptions.append("Generates custom suggestions for improving the PR code, based on specific guidelines defined by the user.")
-            descriptions.append("Automatically retrieves and presents similar issues.")
+            descriptions.append("Generates feedback and analysis for a failed CI job")
+            descriptions.append("Generates custom suggestions for improving the PR code, based only on specific guidelines defined by the user")
+            descriptions.append("Automatically retrieves and presents similar issues")
 
             commands  =[]
             commands.append("`/describe`")
             commands.append("`/review`")
             commands.append("`/improve`")
-            commands.append("`/analyze`")
             commands.append("`/update_changelog`")
             commands.append("`/add_docs`")
+            commands.append("`/test`")
+            commands.append("`/improve_component`")
+            commands.append("`/analyze`")
             commands.append("`/ask`")
             commands.append("`/generate_labels`")
-            commands.append("`/test`")
             commands.append("`/checks`")
             commands.append("`/custom_suggestions`")
             commands.append("`/similar_issue`")
@@ -69,9 +72,13 @@ class PRHelpMessage:
             checkbox_list.append(" - [ ] Run <!-- /describe -->")
             checkbox_list.append(" - [ ] Run <!-- /review -->")
             checkbox_list.append(" - [ ] Run <!-- /improve -->")
-            checkbox_list.append(" - [ ] Run <!-- /analyze -->")
             checkbox_list.append(" - [ ] Run <!-- /update_changelog -->")
             checkbox_list.append(" - [ ] Run <!-- /add_docs -->")
+            checkbox_list.append(" - [ ] Run <!-- /test -->")
+            checkbox_list.append(" - [ ] Run <!-- /improve_component -->")
+            checkbox_list.append(" - [ ] Run <!-- /analyze -->")
+            checkbox_list.append("[*]")
+            checkbox_list.append("[*]")
             checkbox_list.append("[*]")
             checkbox_list.append("[*]")
             checkbox_list.append("[*]")
@@ -80,18 +87,18 @@ class PRHelpMessage:
             checkbox_list.append("[*]")
 
             if isinstance(self.git_provider, GithubProvider):
-                pr_comment += f"<table><tr align='center'><th align='center'>Tool</th><th align='center'>Description</th><th align='center'>Invoke Interactively :gem:</th></tr>"
+                pr_comment += f"<table><tr align='left'><th align='left'>Tool</th><th align='left'>Description</th><th align='left'>Trigger Interactively :gem:</th></tr>"
                 for i in range(len(tool_names)):
-                    pr_comment += f"\n<tr><td align='center'>\n\n<strong>{tool_names[i]}</strong></td>\n<td>{descriptions[i]}</td>\n<td>\n\n{checkbox_list[i]}\n</td></tr>"
+                    pr_comment += f"\n<tr><td align='left'>\n\n<strong>{tool_names[i]}</strong></td>\n<td>{descriptions[i]}</td>\n<td>\n\n{checkbox_list[i]}\n</td></tr>"
                 pr_comment += "</table>\n\n"
                 pr_comment += f"""\n\n(1) Note that each tool be [triggered automatically](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools-for-pr-actions) when a new PR is opened, or called manually by [commenting on a PR](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#online-usage)."""
                 pr_comment += f"""\n\n(2) Tools marked with [*] require additional parameters to be passed. For example, to invoke the `/ask` tool, you need to comment on a PR: `/ask "<question content>"`. See the relevant documentation for each tool for more details."""
             else:
-                pr_comment += f"<table><tr align='center'><th align='center'>Tool</th><th align='left'>Command</th><th align='left'>Description</th></tr>"
+                pr_comment += f"<table><tr align='left'><th align='left'>Tool</th><th align='left'>Command</th><th align='left'>Description</th></tr>"
                 for i in range(len(tool_names)):
-                    pr_comment += f"\n<tr><td align='center'>\n\n<strong>{tool_names[i]}</strong></td><td>{commands[i]}</td><td>{descriptions[i]}</td></tr>"
+                    pr_comment += f"\n<tr><td align='left'>\n\n<strong>{tool_names[i]}</strong></td><td>{commands[i]}</td><td>{descriptions[i]}</td></tr>"
                 pr_comment += "</table>\n\n"
-                pr_comment += f"""\n\nNote that each tool be [invoked automatically](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools-for-pr-actions) when a new PR is opened, or called manually by [commenting on a PR](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#online-usage)."""
+                pr_comment += f"""\n\nNote that each tool be [invoked automatically](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/) when a new PR is opened, or called manually by [commenting on a PR](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#online-usage)."""
             if get_settings().config.publish_output:
                 self.git_provider.publish_comment(pr_comment)
         except Exception as e:

pr_agent/tools/pr_information_from_user.py

@@ -21,6 +21,8 @@ class PRInformationFromUser:
             self.git_provider.get_languages(), self.git_provider.get_files()
         )
         self.ai_handler = ai_handler()
+        self.ai_handler.main_pr_language = self.main_pr_language
+
         self.vars = {
             "title": self.git_provider.pr.title,
             "branch": self.git_provider.get_pr_branch(),

pr_agent/tools/pr_line_questions.py

@@ -22,8 +22,11 @@ class PR_LineQuestions:
     def __init__(self, pr_url: str, args=None, ai_handler: partial[BaseAiHandler,] = LiteLLMAIHandler):
         self.question_str = self.parse_args(args)
         self.git_provider = get_git_provider()(pr_url)
-
+        self.main_pr_language = get_main_pr_language(
+            self.git_provider.get_languages(), self.git_provider.get_files()
+        )
         self.ai_handler = ai_handler()
+        self.ai_handler.main_pr_language = self.main_pr_language
 
         self.vars = {
             "title": self.git_provider.pr.title,

pr_agent/tools/pr_questions.py

@@ -17,11 +17,14 @@ from pr_agent.servers.help import HelpMessage
 class PRQuestions:
     def __init__(self, pr_url: str, args=None, ai_handler: partial[BaseAiHandler,] = LiteLLMAIHandler):
         question_str = self.parse_args(args)
+        self.pr_url = pr_url
         self.git_provider = get_git_provider()(pr_url)
         self.main_pr_language = get_main_pr_language(
             self.git_provider.get_languages(), self.git_provider.get_files()
         )
         self.ai_handler = ai_handler()
+        self.ai_handler.main_pr_language = self.main_pr_language
+
         self.question_str = question_str
         self.vars = {
             "title": self.git_provider.pr.title,
@@ -47,19 +50,25 @@ class PRQuestions:
         return question_str
 
     async def run(self):
-        get_logger().info('Answering a PR question...')
+        get_logger().info(f'Answering a PR question about the PR {self.pr_url} ')
         relevant_configs = {'pr_questions': dict(get_settings().pr_questions),
                             'config': dict(get_settings().config)}
         get_logger().debug("Relevant configs", artifacts=relevant_configs)
         if get_settings().config.publish_output:
             self.git_provider.publish_comment("Preparing answer...", is_temporary=True)
+
+        # identify image
+        img_path = self.idenfity_image_in_comment()
+        if img_path:
+            get_logger().debug(f"Image path identified", artifact=img_path)
+
         await retry_with_fallback_models(self._prepare_prediction)
 
         pr_comment = self._prepare_pr_answer()
         get_logger().debug(f"PR output", artifact=pr_comment)
 
         if self.git_provider.is_supported("gfm_markdown") and get_settings().pr_questions.enable_help_text:
-            pr_comment += "<hr>\n\n<details> <summary><strong>✨ Ask tool usage guide:</strong></summary><hr> \n\n"
+            pr_comment += "<hr>\n\n<details> <summary><strong>💡 Tool usage guide:</strong></summary><hr> \n\n"
             pr_comment += HelpMessage.get_ask_usage_guide()
             pr_comment += "\n</details>\n"
 
@@ -68,6 +77,19 @@ class PRQuestions:
             self.git_provider.remove_initial_comment()
         return ""
 
+    def idenfity_image_in_comment(self):
+        img_path = ''
+        if '![image]' in self.question_str:
+            # assuming structure:
+            # /ask question ...  > ![image](img_path)
+            img_path = self.question_str.split('![image]')[1].strip().strip('()')
+            self.vars['img_path'] = img_path
+        elif 'https://' in self.question_str and ('.png' in self.question_str or 'jpg' in self.question_str): # direct image link
+            # include https:// in the image path
+            img_path = 'https://' + self.question_str.split('https://')[1]
+            self.vars['img_path'] = img_path
+        return img_path
+
     async def _prepare_prediction(self, model: str):
         self.patches_diff = get_pr_diff(self.git_provider, self.token_handler, model)
         if self.patches_diff:
@@ -83,11 +105,17 @@ class PRQuestions:
         environment = Environment(undefined=StrictUndefined)
         system_prompt = environment.from_string(get_settings().pr_questions_prompt.system).render(variables)
         user_prompt = environment.from_string(get_settings().pr_questions_prompt.user).render(variables)
+        if 'img_path' in variables:
+            img_path = self.vars['img_path']
+            response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
+                                                                            system=system_prompt, user=user_prompt,
+                                                                            img_path=img_path)
+        else:
             response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
                                                                             system=system_prompt, user=user_prompt)
         return response
 
     def _prepare_pr_answer(self) -> str:
-        answer_str = f"Question: {self.question_str}\n\n"
-        answer_str += f"Answer:\n{self.prediction.strip()}\n\n"
+        answer_str = f"### **Ask**❓\n{self.question_str}\n\n"
+        answer_str += f"### **Answer:**\n{self.prediction.strip()}\n\n"
         return answer_str

pr_agent/tools/pr_reviewer.py

@@ -8,7 +8,7 @@ from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
 from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import convert_to_markdown, load_yaml, ModelType
+from pr_agent.algo.utils import convert_to_markdown, github_action_output, load_yaml, ModelType
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
 from pr_agent.git_providers.git_provider import IncrementalPR, get_main_pr_language
@@ -46,6 +46,8 @@ class PRReviewer:
         if self.is_answer and not self.git_provider.is_supported("get_issue_comments"):
             raise Exception(f"Answer mode is not supported for {get_settings().config.git_provider} for now")
         self.ai_handler = ai_handler()
+        self.ai_handler.main_pr_language = self.main_language
+
         self.patches_diff = None
         self.prediction = None
 
@@ -56,10 +58,11 @@ class PRReviewer:
             "description": self.git_provider.get_pr_description(),
             "language": self.main_language,
             "diff": "",  # empty diff for initial calculation
+            "num_pr_files": self.git_provider.get_num_of_files(),
             "require_score": get_settings().pr_reviewer.require_score_review,
             "require_tests": get_settings().pr_reviewer.require_tests_review,
-            "require_focused": get_settings().pr_reviewer.require_focused_review,
             "require_estimate_effort_to_review": get_settings().pr_reviewer.require_estimate_effort_to_review,
+            'require_can_be_split_review': get_settings().pr_reviewer.require_can_be_split_review,
             'num_code_suggestions': get_settings().pr_reviewer.num_code_suggestions,
             'question_str': question_str,
             'answer_str': answer_str,
@@ -107,6 +110,17 @@ class PRReviewer:
             relevant_configs = {'pr_reviewer': dict(get_settings().pr_reviewer),
                                 'config': dict(get_settings().config)}
             get_logger().debug("Relevant configs", artifacts=relevant_configs)
+
+            if self.incremental.is_incremental and hasattr(self.git_provider, "unreviewed_files_set") and not self.git_provider.unreviewed_files_set:
+                get_logger().info(f"Incremental review is enabled for {self.pr_url} but there are no new files")
+                previous_review_url = ""
+                if hasattr(self.git_provider, "previous_review"):
+                    previous_review_url = self.git_provider.previous_review.html_url
+                if get_settings().config.publish_output:
+                    self.git_provider.publish_comment(f"Incremental Review Skipped\n"
+                                    f"No files were changed since the [previous PR Review]({previous_review_url})")
+                return None
+
             if get_settings().config.publish_output:
                 self.git_provider.publish_comment("Preparing review...", is_temporary=True)
 
@@ -121,9 +135,11 @@ class PRReviewer:
             if get_settings().config.publish_output:
                 # publish the review
                 if get_settings().pr_reviewer.persistent_comment and not self.incremental.is_incremental:
+                    final_update_message = get_settings().pr_reviewer.final_update_message
                     self.git_provider.publish_persistent_comment(pr_review,
-                                                                 initial_header="## PR Review",
-                                                                 update_header=True)
+                                                                 initial_header="## PR Review 🔍",
+                                                                 update_header=True,
+                                                                 final_update_message=final_update_message, )
                 else:
                     self.git_provider.publish_comment(pr_review)
 
@@ -173,7 +189,10 @@ class PRReviewer:
         Prepare the PR review by processing the AI prediction and generating a markdown-formatted text that summarizes
         the feedback.
         """
-        data = load_yaml(self.prediction.strip())
+        data = load_yaml(self.prediction.strip(),
+                         keys_fix_yaml=["estimated_effort_to_review_[1-5]:", "security_concerns:", "possible_issues:",
+                                        "relevant_file:", "relevant_line:", "suggestion:"])
+        github_action_output(data, 'review')
 
         if 'code_feedback' in data:
             code_feedback = data['code_feedback']
@@ -203,25 +222,19 @@ class PRReviewer:
                         pass
 
 
+        incremental_review_markdown_text = None
         # Add incremental review section
         if self.incremental.is_incremental:
             last_commit_url = f"{self.git_provider.get_pr_url()}/commits/" \
                               f"{self.git_provider.incremental.first_new_commit_sha}"
-            last_commit_msg = self.incremental.commits_range[0].commit.message if self.incremental.commits_range else ""
             incremental_review_markdown_text = f"Starting from commit {last_commit_url}"
-            if last_commit_msg:
-                replacement = last_commit_msg.splitlines(keepends=False)[0].replace('_', r'\_')
-                incremental_review_markdown_text += f"  \n_({replacement})_"
-            data = OrderedDict(data)
-            data.update({'Incremental PR Review': {
-                "⏮️ Review for commits since previous PR-Agent review": incremental_review_markdown_text}})
-            data.move_to_end('Incremental PR Review', last=False)
 
-        markdown_text = convert_to_markdown(data, self.git_provider.is_supported("gfm_markdown"))
+        markdown_text = convert_to_markdown(data, self.git_provider.is_supported("gfm_markdown"),
+                                            incremental_review_markdown_text)
 
         # Add help text if gfm_markdown is supported
         if self.git_provider.is_supported("gfm_markdown") and get_settings().pr_reviewer.enable_help_text:
-            markdown_text += "<hr>\n\n<details> <summary><strong>✨ Review tool usage guide:</strong></summary><hr> \n\n"
+            markdown_text += "<hr>\n\n<details> <summary><strong>💡 Tool usage guide:</strong></summary><hr> \n\n"
             markdown_text += HelpMessage.get_review_usage_guide()
             markdown_text += "\n</details>\n"
 
@@ -244,7 +257,7 @@ class PRReviewer:
                          keys_fix_yaml=["estimated_effort_to_review_[1-5]:", "security_concerns:", "possible_issues:",
                                         "relevant_file:", "relevant_line:", "suggestion:"])
         comments: List[str] = []
-        for suggestion in data.get('PR Feedback', {}).get('Code feedback', []):
+        for suggestion in data.get('code_feedback', []):
             relevant_file = suggestion.get('relevant_file', '').strip()
             relevant_line_in_file = suggestion.get('relevant_line', '').strip()
             content = suggestion.get('suggestion', '')
@@ -315,6 +328,10 @@ class PRReviewer:
         if self.is_auto and not self.incremental.first_new_commit_sha:
             get_logger().info(f"Incremental review is enabled for {self.pr_url} but there are no new commits")
             return False
+
+        if not hasattr(self.git_provider, "get_incremental_commits"):
+            get_logger().info(f"Incremental review is not supported for {get_settings().config.git_provider}")
+            return False
         # checking if there are enough commits to start the review
         num_new_commits = len(self.incremental.commits_range)
         num_commits_threshold = get_settings().pr_reviewer.minimal_commits_for_incremental_review
@@ -341,6 +358,9 @@ class PRReviewer:
         return True
 
     def set_review_labels(self, data):
+        if not get_settings().config.publish_output:
+            return
+
         if (get_settings().pr_reviewer.enable_review_labels_security or
                 get_settings().pr_reviewer.enable_review_labels_effort):
             try:
@@ -356,17 +376,22 @@ class PRReviewer:
                     if security_concerns_bool:
                         review_labels.append('Possible security concern')
 
-                current_labels = self.git_provider.get_pr_labels()
+                current_labels = self.git_provider.get_pr_labels(update=True)
+                if not current_labels:
+                    current_labels = []
+                get_logger().debug(f"Current labels:\n{current_labels}")
                 if current_labels:
                     current_labels_filtered = [label for label in current_labels if
                                                not label.lower().startswith('review effort [1-5]:') and not label.lower().startswith(
                                                    'possible security concern')]
                 else:
                     current_labels_filtered = []
-                if current_labels or review_labels:
-                    get_logger().debug(f"Current labels:\n{current_labels}")
+                new_labels = review_labels + current_labels_filtered
+                if (current_labels or review_labels) and sorted(new_labels) != sorted(current_labels):
                     get_logger().info(f"Setting review labels:\n{review_labels + current_labels_filtered}")
-                    self.git_provider.publish_labels(review_labels + current_labels_filtered)
+                    self.git_provider.publish_labels(new_labels)
+                else:
+                    get_logger().info(f"Review labels are already set:\n{review_labels + current_labels_filtered}")
             except Exception as e:
                 get_logger().error(f"Failed to set review labels, error: {e}")