Merge remote-tracking branch 'origin/main'

fix

.github/workflows/docs-ci.yaml

@@ -0,0 +1,32 @@
+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: mkdocs gh-deploy -f docs/mkdocs.yml --force

.gitignore

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

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
-
-=======

README.md

@@ -32,100 +32,101 @@ Making pull requests less painful with an AI agent
   
 ## News and Updates
 
+### Jan 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.
+
+### Jan 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 [Installation Guide](https://pr-agent-docs.codium.ai/installation/) 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 [Usage Guide](https://pr-agent-docs.codium.ai/usage-guide/) 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).
+- See the [Tools Guide](https://pr-agent-docs.codium.ai/tools/) for a detailed description of the different tools.
 
 Supported commands per platform:
 
-|       |                                                                                                                                         | GitHub             | Gitlab             | Bitbucket          | Azure DevOps       |
-|-------|-----------------------------------------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:--------------------:|:--------------------:|
-| TOOLS | Review                                                                                                                                  | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | ⮑ Incremental                                                                                                                           | :white_check_mark: |                    |                    |                    |
-|       | ⮑ [SOC2 Compliance](https://github.com/Codium-ai/pr-agent/blob/main/docs/REVIEW.md#soc2-ticket-compliance-) 💎                           | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Describe                                                                                                                                | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | ⮑ [Inline File Summary](https://github.com/Codium-ai/pr-agent/blob/main/docs/DESCRIBE.md#inline-file-summary-) 💎                        | :white_check_mark: |                    |                    |                    |
-|       | Improve                                                                                                                                 | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | ⮑ Extended                                                                                                                              | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Ask                                                                                                                                     | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | ⮑ [Ask on code lines](./docs/ASK.md#ask-lines)                                                                                          | :white_check_mark: | :white_check_mark: |                    |                    |
-|       | [Custom Suggestions](https://github.com/Codium-ai/pr-agent/blob/main/docs/CUSTOM_SUGGESTIONS.md) 💎                                      | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | [Test](https://github.com/Codium-ai/pr-agent/blob/main/docs/TEST.md) 💎                                                                  | :white_check_mark: | :white_check_mark: |                    | :white_check_mark: |
-|       | Reflect and Review                                                                                                                      | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Update CHANGELOG.md                                                                                                                     | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Find Similar Issue                                                                                                                      | :white_check_mark: |                    |                    |                    |
-|       | [Add PR Documentation](https://github.com/Codium-ai/pr-agent/blob/main/docs/ADD_DOCUMENTATION.md) 💎                                     | :white_check_mark: | :white_check_mark: |                   | :white_check_mark: |
-|       | [Custom Labels](https://github.com/Codium-ai/pr-agent/blob/main/docs/DESCRIBE.md#handle-custom-labels-from-the-repos-labels-page-gem) 💎 | :white_check_mark: | :white_check_mark: |                    | :white_check_mark: |
-|       | [Analyze](https://github.com/Codium-ai/pr-agent/blob/main/docs/Analyze.md) 💎                                                            | :white_check_mark: | :white_check_mark: |                    | :white_check_mark: |
-|       | [CI Feedback](https://github.com/Codium-ai/pr-agent/blob/main/docs/CI_FEEDBACK.md) 💎                                                    | :white_check_mark: |                    |                    |                    |
-|       |                                                                                                                                         |                    |                    |                    |                    |
-| USAGE | CLI                                                                                                                                     | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | App / webhook                                                                                                                           | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Tagging bot                                                                                                                             | :white_check_mark: |                    |                    |                    |
-|       | Actions                                                                                                                                 | :white_check_mark: |                    | :white_check_mark: |                    |
-|       |                                                                                                                                         |                    |                    |                    |                    |
-| CORE  | PR compression                                                                                                                          | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Repo language prioritization                                                                                                            | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Adaptive and token-aware file patch fitting                                                                                             | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | Multiple models support                                                                                                                 | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | [Static code analysis](https://github.com/Codium-ai/pr-agent/blob/main/docs/Analyze.md) 💎                                               | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | [Global and wiki configurations](./Usage.md#configuration) 💎                           | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
-|       | [PR Actions](https://www.codium.ai/images/pr_agent/pr-actions.mp4) 💎                                                                    | :white_check_mark: |                    |                    |                    |
+|       |                                                                                                                   | GitHub             | Gitlab             | Bitbucket          | Azure DevOps       |
+|-------|-------------------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:--------------------:|:--------------------:|
+| TOOLS | Review                                                                                                            | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+|       | ⮑ Incremental                                                                                                     | :white_check_mark: |                    |                    |                    |
+|       | ⮑ [SOC2 Compliance](https://pr-agent-docs.codium.ai/tools/review/#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://pr-agent-docs.codium.ai/tools/describe#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](https://pr-agent-docs.codium.ai/tools/ask#ask-lines)                              | :white_check_mark: | :white_check_mark: |                    |                    |
+|       | [Custom Suggestions](https://pr-agent-docs.codium.ai/tools/custom_suggestions/) 💎                      | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+|       | [Test](https://pr-agent-docs.codium.ai/tools/test/) 💎                                                  | :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://pr-agent-docs.codium.ai/tools/documentation/) 💎                         | :white_check_mark: | :white_check_mark: |                   | :white_check_mark: |
+|       | [Custom Labels](https://pr-agent-docs.codium.ai/tools/custom_labels/) 💎                                | :white_check_mark: | :white_check_mark: |                    | :white_check_mark: |
+|       | [Analyze](https://pr-agent-docs.codium.ai/tools/analyze/) 💎                                            | :white_check_mark: | :white_check_mark: |                    | :white_check_mark: |
+|       | [CI Feedback](https://pr-agent-docs.codium.ai/tools/ci_feedback/) 💎                                    | :white_check_mark: |                    |                    |                    |
+|       | [Similar Code](https://pr-agent-docs.codium.ai/tools/similar_code/) 💎                                  | :white_check_mark: |                    |                    |                    |
+|       |                                                                                                                   |                    |                    |                    |                    |
+| USAGE | CLI                                                                                                               | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+|       | App / webhook                                                                                                     | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+|       | Tagging bot                                                                                                       | :white_check_mark: |                    |                    |                    |
+|       | Actions                                                                                                           | :white_check_mark: |                    | :white_check_mark: |                    |
+|       |                                                                                                                   |                    |                    |                    |                    |
+| CORE  | PR compression                                                                                                    | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+|       | Repo language prioritization                                                                                      | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+|       | Adaptive and token-aware file patch fitting                                                                       | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+|       | Multiple models support                                                                                           | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+|       | [Static code analysis](https://pr-agent-docs.codium.ai/core-abilities/#static-code-analysis) 💎         | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+|       | [Global and wiki configurations](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/) 💎 | :white_check_mark: | :white_check_mark: | :white_check_mark: | :white_check_mark: |
+|       | [PR interactive actions](https://www.codium.ai/images/pr_agent/pr-actions.mp4) 💎                                 | :white_check_mark: |                    |                    |                    |
 - 💎 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
@@ -219,7 +220,7 @@ 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 ...`.
 
 ---
@@ -233,32 +234,26 @@ To use your own version of PR-Agent, you first need to acquire two tokens:
 There are several ways to use PR-Agent:
 
 **Locally**
-- [Use Docker image (no installation required)](./INSTALL.md#use-docker-image-no-installation-required)
-- [Run from source](./INSTALL.md#run-from-source)
+- [Use Docker image (no installation required)](https://pr-agent-docs.codium.ai/installation/locally/#use-docker-image-no-installation-required)
+- [Run from source](https://pr-agent-docs.codium.ai/installation/locally/#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)
+- [Run as a GitHub Action](https://pr-agent-docs.codium.ai/installation/github/#run-as-a-github-action)
+- [Run as a GitHub App](https://pr-agent-docs.codium.ai/installation/github/#run-as-a-github-app)
 
 **GitLab specific methods**
-- [Run a GitLab webhook server](./INSTALL.md#run-a-gitlab-webhook-server)
+- [Run a GitLab webhook server](https://pr-agent-docs.codium.ai/installation/gitlab/)
 
 **BitBucket specific methods**
-- [Run as a Bitbucket Pipeline](./INSTALL.md#run-as-a-bitbucket-pipeline)
+- [Run as a Bitbucket Pipeline](https://pr-agent-docs.codium.ai/installation/bitbucket/)
 
 ## 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.
 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 +263,7 @@ 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 +272,7 @@ 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).

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/README.md

@@ -0,0 +1,15 @@
+# To install:
+pip install mkdocs
+pip install mkdocs-material
+pip install mkdocs-material-extensions
+pip install "mkdocs-material[imaging]"
+
+# docs
+To run localy: `mkdocs serve`
+
+To expand and customize the theme: [Material MKDocs](https://squidfunk.github.io/mkdocs-material/)
+
+The deployment is managed on the gh-pages branches.
+After each merge to main the deplloyment will be taken care of by GH action automatically and the new version will be available at: [Docs](https://codium-ai.github.io/docs/)
+
+Github action is located in `.github/workflows/ci.yml` file.

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/docs/CNAME

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

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
+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
+
 <kbd><img src=https://codium.ai/images/git_patch_logic.png width="768"></kbd>
+
+## YAML Prompting
+TBD
+
+## Static Code Analysis 💎
+TBD

docs/docs/css/custom.css

@@ -0,0 +1,98 @@
+
+
+:root {
+    --md-primary-fg-color: #765bfa;
+    --md-accent-fg-color: #AEA1F1;
+  }
+.md-nav__title, .md-nav__link  {
+    font-size: 16px; /* Adjust the font size as needed */
+}
+
+.md-tabs__link  {
+    font-size: 16px; /* Adjust the font size as needed */
+}
+
+.md-header__title {
+    font-size: 20px; /* Adjust the font size as needed */
+}
+
+/* 
+@media (prefers-color-scheme: light) {
+    body {
+        --md-primary-fg-color: #00ffee !important;
+        --md-primary-bg-color: #ff0000 !important;
+    }
+
+    body, .md-main, .md-content {
+        background-color: #4312f5 !important;
+    }
+}
+
+@media (prefers-color-scheme: dark) {
+    body {
+        --md-primary-fg-color: #171518 !important;
+        --md-primary-bg-color: #171518 !important;
+    }
+
+    body, .md-main, .md-content {
+        background-color: #171518 !important;
+    }
+
+    .md-header__title {
+        color: #ffffff !important;
+    }
+
+    .md-tabs .md-tabs__link {
+        color: #ffffff !important;
+    }
+
+    .md-tabs .md-tabs__link:hover,
+    .md-tabs .md-tabs__link:focus {
+        color: #ffffff !important; 
+    }
+
+    .md-header__button {
+        color: #ffffff !important; 
+    }
+
+    .md-header__button svg {
+        fill: currentColor !important; 
+    }
+
+    .md-header__button:hover,
+    .md-header__button:focus {
+        color: #ffffff !important; 
+    }
+
+    .md-header__button:hover svg,
+    .md-header__button:focus svg {
+        fill: currentColor !important;
+    }
+
+    .md-search__icon svg {
+        fill: #ffffff !important;
+    }
+
+    .md-search__input {
+        color: #ffffff !important;
+    }
+
+    .md-nav__item--active > .md-nav__link--active,
+    .md-nav__link--active {
+        color: #AEA1F1 !important;
+    }
+
+    .md-nav--secondary .md-nav__title {
+        background: #171518;
+        box-shadow: 0 0 0.4rem 0.4rem #171518;
+    }
+
+    .md-nav--lifted>.md-nav__list>.md-nav__item--active>.md-nav__link {
+        background: #171518;
+        box-shadow: 0 0 0.4rem 0.4rem #171518;
+    }
+
+    .md-content a {
+        color: #AEA1F1 !important;
+    }
+} */

docs/docs/index.md

@@ -0,0 +1,162 @@
+# 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                                                                                                       |   ✔️    |   ✔️    |            |      ✔️      |
+|       | Tagging bot                                                                                                         |   ✔️    |        |            |      ✔️      |
+|       | 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>
+<h4><a href="https://github.com/Codium-ai/pr-agent/pull/530">/describe</a></h4>
+<div align="center">
+<p float="center">
+<img src="https://www.codium.ai/images/pr_agent/describe_new_short_main.png" width="512">
+</p>
+</div>
+<hr>
+
+<h4><a href="https://github.com/Codium-ai/pr-agent/pull/732#issuecomment-1975099151">/review</a></h4>
+<div align="center">
+<p float="center">
+<kbd>
+<img src="https://www.codium.ai/images/pr_agent/review_new_short_main.png" width="512">
+</kbd>
+</p>
+</div>
+<hr>
+
+<h4><a href="https://github.com/Codium-ai/pr-agent/pull/732#issuecomment-1975099159">/improve</a></h4>
+<div align="center">
+<p float="center">
+<kbd>
+<img src="https://www.codium.ai/images/pr_agent/improve_new_short_main.png" width="512">
+</kbd>
+</p>
+</div>
+<hr>
+
+<h4><a href="https://github.com/Codium-ai/pr-agent/pull/530">/generate_labels</a></h4>
+<div align="center">
+<p float="center">
+<kbd><img src="https://www.codium.ai/images/pr_agent/geneare_custom_labels_main_short.png" width="300"></kbd>
+</p>
+</div>
+
+[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/78#issuecomment-1639739496">/reflect_and_review:</a></h4>)
+
+[//]: # (<div align="center">)
+
+[//]: # (<p float="center">)
+
+[//]: # (<img src="https://www.codium.ai/images/reflect_and_review.gif" width="800">)
+
+[//]: # (</p>)
+
+[//]: # (</div>)
+
+[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695020538">/ask:</a></h4>)
+
+[//]: # (<div align="center">)
+
+[//]: # (<p float="center">)
+
+[//]: # (<img src="https://www.codium.ai/images/ask-2.gif" width="800">)
+
+[//]: # (</p>)
+
+[//]: # (</div>)
+
+[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695024952">/improve:</a></h4>)
+
+[//]: # (<div align="center">)
+
+[//]: # (<p float="center">)
+
+[//]: # (<img src="https://www.codium.ai/images/improve-2.gif" width="800">)
+
+[//]: # (</p>)
+
+[//]: # (</div>)
+<div align="left">
+
+
+</div>
+<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\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**](./tools/analyze.md/)
+    - [**Custom Code Suggestions**](./tools/custom_suggestions.md/)
+    - [**Tests**](./tools/test.md/)
+    - [**PR documentation**](./tools/documentation.md/)
+    - [**CI feedback**](./tools/ci_feedback.md/)
+    - [**SOC2 compliance check**](./tools/review.md/#soc2-ticket-compliance)
+    - [**Custom labels**](./tools/describe.md/#handle-custom-labels-from-the-repos-labels-page)
+    - [**Global and wiki configuration**](./usage-guide/configuration_options.md/#wiki-configuration-file)
+
+   
+## 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 +1,36 @@
+## 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.
+
+
+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 +1,249 @@
+## 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:
+  issue_comment:
+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:
+  issue_comment:
+
+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: ${{ secrets.GITHUB_TOKEN }}
+```
+2) Add the following secret to your repository under `Settings > Secrets and variables > Actions > New repository secret > Add secret`:
+
+```
+Name = OPENAI_KEY
+Secret = <your key>
+```
+
+The GITHUB_TOKEN secret is automatically created by GitHub.
+
+3) Merge this change to your main branch.
+When you open your next PR, you should see a comment from `github-actions` bot with a review of your PR, and instructions on how to use the rest of the tools.
+
+4) You may configure PR-Agent by adding environment variables under the env section corresponding to any configurable property in the [configuration](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) file. Some examples:
+```yaml
+      env:
+        # ... previous environment values
+        OPENAI.ORG: "<Your organization name under your OpenAI account>"
+        PR_REVIEWER.REQUIRE_TESTS_REVIEW: "false" # Disable tests review
+        PR_CODE_SUGGESTIONS.NUM_CODE_SUGGESTIONS: 6 # Increase number of code suggestions
+```
+
+---
+
+## Run as a GitHub App
+Allowing you to automate the review process on your private or public repositories.
+
+1) Create a GitHub App from the [Github Developer Portal](https://docs.github.com/en/developers/apps/creating-a-github-app).
+
+   - Set the following permissions:
+     - Pull requests: Read & write
+     - Issue comment: Read & write
+     - Metadata: Read-only
+     - Contents: Read-only
+   - Set the following events:
+     - Issue comment
+     - Pull request
+     - Push (if you need to enable triggering on PR update)
+
+2) Generate a random secret for your app, and save it for later. For example, you can use:
+
+```
+WEBHOOK_SECRET=$(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
+
+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 +1,19 @@
+# Installation
+
+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)
+
+___
+Note that [PR-Agent Pro 💎](https://app.codium.ai/), 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.

docs/docs/installation/locally.md

@@ -0,0 +1,84 @@
+## Use Docker image (no installation required)
+
+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/tools/analyze.md

@@ -1,4 +1,4 @@
-# Analyze Tool 💎
+## Overview
 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.
@@ -8,14 +8,17 @@ It can be invoked manually by commenting on any PR:
 /analyze
 ```
 
+## Example usage
 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 
+
+**Notes**
+
 - Language that are currently supported: Python, Java, C++, JavaScript, TypeScript.

docs/docs/tools/ask.md

@@ -1,4 +1,4 @@
-# ASK Tool
+## 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:
@@ -6,13 +6,13 @@ 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. 
@@ -20,5 +20,4 @@ You can run `/ask` on specific lines of code in the PR from the PR's diff view.
 
 <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.
+Note that the tool does not have "memory" of previous questions, and answers each question independently.

docs/docs/tools/ci_feedback.md

@@ -1,7 +1,8 @@
-# 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
@@ -10,7 +11,6 @@ The tool analyzes the failed checks and provides several feedbacks:
 <kbd>
 <img src="https://www.codium.ai/images/pr_agent/failed_check1.png" width="768">
 </kbd>
-
 &rarr;
 <kbd>
 <img src="https://www.codium.ai/images/pr_agent/failed_check2.png" width="768">
@@ -24,8 +24,9 @@ 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
+## 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

@@ -1,4 +1,4 @@
-# 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:
@@ -12,6 +12,7 @@ If we wish to add detect changes to SQL queries in a given PR, we can add the fo
 <kbd><img src=https://codium.ai/images/pr_agent/custom_labels_list.png width="768"></kbd>
 
 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>
 
 Note that in addition to the dedicated tool `generate_labels`, the custom labels will also be used by the `describe` tool.
@@ -20,13 +21,14 @@ 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.
 
@@ -38,9 +40,9 @@ The description should be comprehensive and detailed, indicating when to add the
 
 c. Now the custom labels will be included in the `generate_labels` tool.
 
-*This feature is supported in GitHub and GitLab.
+> This feature is supported in GitHub and GitLab.
 
-#### Configuration changes
+## Configuration options
  - Change `enable_custom_labels` to True: This will turn off the default labels and enable the custom labels provided in the custom_labels.toml file.
  - Add the custom labels. It should be formatted as follows:
 
@@ -53,5 +55,4 @@ description = "Description of when AI should suggest this label"
 
 [custom_labels."Custom Label 2"]
 description = "Description of when AI should suggest this label 2"
-```
-
+```

docs/docs/tools/custom_suggestions.md

@@ -1,16 +1,8 @@
-# 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.
+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:
 
@@ -18,7 +10,7 @@ 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:
+With a [configuration file](../usage-guide/automations_and_usage.md#github-app), use the following template:
 
 ```
 [pr_custom_suggestions]
@@ -50,11 +42,11 @@ The suggestions should focus only on the following:
 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
 
@@ -62,4 +54,4 @@ ___
 
 `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.
+`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

@@ -1,35 +1,26 @@
-# 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:
+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
 ```
 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:
+## Configuration options
+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=...
 ```
 
-**Possible configurations:**
+### 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.
@@ -40,7 +31,7 @@ To edit [configurations](./../pr_agent/settings/configuration.toml#L46) related
 
 - `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)
+- 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.
 
@@ -68,10 +59,10 @@ If you prefer to have the file summaries appear in the "Files changed" tab on ev
 
 - `false` (`default`): File changes walkthrough will be added only to the "Conversation" tab.
 
-Note that this feature is currently available only for GitHub.
+**Note** that this feature is currently available only for GitHub.
 
 
-### Handle custom labels from the Repo's labels page :gem:
+### Handle custom labels from the Repo's labels page 💎
 > 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:
@@ -88,6 +79,7 @@ The description should be comprehensive and detailed, indicating when to add the
 
 
 ### 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.
 
@@ -107,22 +99,19 @@ 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>
-
-==>
-
+&rarr;
 <kbd><img src=https://codium.ai/images/pr_agent/describe_markers_after.png width="768"></kbd>
 
-**Configuration params:**
+### 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:
+- When you first install the app, the [default mode](../usage-guide/automations_and_usage.md#github-app) for the describe tool is:
 ```
 pr_commands = ["/describe --pr_description.add_original_user_description=true" 
                          "--pr_description.keep_original_user_title=true", ...]
@@ -148,9 +137,10 @@ the tool will replace every marker of the form `pr_agent:marker_name` in the PR
 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.
+If you specify [custom labels](#handle-custom-labels-from-the-repos-labels-page) 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
@@ -160,4 +150,4 @@ Examples for custom labels:
 
 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.
+<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/docs/tools/documentation.md

@@ -1,4 +1,4 @@
-# Add Documentation Tool 💎
+## 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:
@@ -8,17 +8,17 @@ It can be invoked manually by commenting on any PR:
 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
+## 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 
+**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.
-
+- A previous version of the tool, that offered support only for new components, was deprecated.

docs/docs/tools/improve.md

@@ -1,16 +1,6 @@
-# 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:
+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
 ```
@@ -18,15 +8,14 @@ The tool can be triggered automatically every time a new PR is [opened](https://
 ### 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.
 
@@ -49,18 +38,21 @@ Hence, the total number of suggestions is proportional to the number of chunks,
 
 ### Configuration options
 
-To edit [configurations](./../pr_agent/settings/configuration.toml#L66) related to the improve tool (`pr_code_suggestions` section), use the following template:
+To edit [configurations](https://github.com/Codium-ai/pr-agent/blob/main/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
+### 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
+
+### 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.
@@ -71,6 +63,7 @@ To edit [configurations](./../pr_agent/settings/configuration.toml#L66) related
 ## 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.
@@ -91,7 +84,6 @@ Use triple quotes to write multi-line instructions. Use bullet points to make th
 ### 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.
+- Suggestions are not meant to be [simplistic](https://github.com/Codium-ai/pr-agent/blob/main/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.
-
+- 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/index.md

@@ -0,0 +1,20 @@
+# 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                                                                                         |
+| **💎 [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                                                   |
+| **💎 [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

@@ -1,34 +1,19 @@
-# 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:
+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
 ```
 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:
+## Configuration options
+
+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:
 ```
 /review --pr_reviewer.some_config1=... --pr_reviewer.some_config2=...
 ```
@@ -38,23 +23,29 @@ To edit [configurations](./../pr_agent/settings/configuration.toml#L19)  related
 - `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 feature is available only in PR-Agent Pro 
+
 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 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:
 ```
@@ -64,7 +55,7 @@ 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.  
+Under the section 'pr_reviewer', the [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/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.
@@ -78,7 +69,8 @@ When `require_all_thresholds_for_incremental_review=true` the incremental review
 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
+#### PR Reflection
+
 By invoking:
 ```
 /reflect_and_review
@@ -86,22 +78,17 @@ By invoking:
 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.
 
@@ -111,13 +98,14 @@ Some of the features that are disabled by default are quite useful, and should b
 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.
+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:
+- When you first install the 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", ...]
 ```
@@ -125,13 +113,16 @@ Meaning the `review` tool will run automatically on every PR, with the default c
 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.
 
@@ -152,6 +143,7 @@ Use triple quotes to write multi-line instructions. Use bullet points to make th
 
 
 ### 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:
@@ -173,4 +165,4 @@ You can also enable auto-approval only if the PR meets certain requirements, suc
 ```
 [pr_reviewer]
 maximal_review_effort = 5
-```
+```

docs/docs/tools/similar_code.md

@@ -0,0 +1,61 @@
+## 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`:
+
+<kbd><img src=https://codium.ai/images/pr_agent/similar_code_global2.png width="768"></kbd>
+
+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:
+
+<kbd><img src=https://codium.ai/images/pr_agent/code_search_result_single.png width="768"></kbd>
+
+`Organization Search`:
+
+<kbd><img src=https://codium.ai/images/pr_agent/similar_code_org.png width="768"></kbd>
+
+
+## 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.
+<kbd><img src=https://codium.ai/images/pr_agent/analyze_similar.png width="768"></kbd>
+
+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. 
+
+<kbd><img src=https://codium.ai/images/pr_agent/similar_code_global.png width="768"></kbd>
+
+
+## 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

@@ -1,4 +1,4 @@
-# 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:
 ```
@@ -7,7 +7,9 @@ It can be invoked manually by commenting on any PR:
 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>
 
 Note that to perform retrieval, the `similar_issue` tool indexes all the repo previous issues (once).
@@ -29,11 +31,11 @@ environment = "..."
 These parameters can be obtained by registering to [Pinecone](https://app.pinecone.io/?sessionType=signup/).
 
 
-### How to use:
+## How to use:
 - To invoke the 'similar issue' tool from **CLI**, run:
 `python3 cli.py --issue_url=... similar_issue`
 
 - To invoke the 'similar' issue tool via online usage, [comment](https://github.com/Codium-ai/pr-agent/issues/178#issuecomment-1716934893) on a PR:
 `/similar_issue`
 
-- You can also enable the 'similar issue' tool to run automatically when a new issue is opened, by adding it to the [pr_commands list in the github_app section](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L66)
+- You can also enable the 'similar issue' tool to run automatically when a new issue is opened, by adding it to the [pr_commands list in the github_app section](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L66)

docs/docs/tools/test.md

@@ -1,26 +1,26 @@
-# 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, use 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.
+**Notes**
+- 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

@@ -1,5 +1,4 @@
-# Update Changelog Tool
-
+## 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:
 ```
@@ -8,12 +7,13 @@ It can be invoked manually by commenting on any PR:
 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
+## 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:
+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 +1,218 @@
+## 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 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](../core-abilities/index.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](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 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](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"
+
+[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](https://github.com/Codium-ai/pr-agent/blob/main/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.
+
+### 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 = "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](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 +1,200 @@
+## 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: [#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
+
+### 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.add_original_user_description=true --pr_description.keep_original_user_title=true --pr_description.final_update_message=false",
+    "/review --pr_reviewer.num_code_suggestions=0 --pr_reviewer.final_update_message=false",
+    "/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](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]
+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.
+
+## 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
+```
+
+## 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",
+]
+```
+
+## 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.summarize=false",
+]
+```
+
+## 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 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",
+]
+```

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**.
+
+<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:
+
+```
+[pr_description] # /describe #
+keep_original_user_title=false
+```
+
+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 +1,20 @@
+# Usage guide
+
+- [Introduction](./introduction.md)
+- [Configuration Options](./configuration_options.md)
+- [Managing Mail Notifications](./mail_notifications.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)
+- [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 +1,9 @@
+
+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, [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).
+
+<kbd><img src="https://codium.ai/images/pr_agent/filter_mail_notifications.png" width="512"></kbd>

docs/mkdocs.yml

@@ -0,0 +1,121 @@
+site_name: 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'
+  - Usage Guide: 
+    - 'usage-guide/index.md'
+    - Introduction: 'usage-guide/introduction.md'
+    - Configuration Options: 'usage-guide/configuration_options.md'
+    - Managing email 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'
+    - 💎 Analyze: 'tools/analyze.md'
+    - 💎 Test: 'tools/test.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.png
+  favicon: assets/favicon.ico
+  name: material
+  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
+
+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/
+
+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
+  - attr_list
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:materialx.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/partials/footer.html

@@ -0,0 +1,100 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+<meta charset="UTF-8">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<title>Footer Customization</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 {
+    display: flex;
+    justify-content: center;
+    gap: 20px;
+    margin: 10px 0;
+    
+  }
+  .footer-links, .social-icons {
+    padding: 0;
+    list-style-type: none;
+    display: flex;
+    justify-content: center;
+    gap: 20px;
+    align-items: center;
+  }
+  .footer-links a:hover {
+    color: #AEA1F1;
+  }
+  .social-icons {
+    display: flex;
+    gap: 20px;
+    align-items: center;
+  }
+  .social-icons a:hover {
+    color: #AEA1F1;
+  }
+  .social-icons svg {
+    width: 24px; 
+    height: auto;
+    fill: white;
+  }
+  .footer-text {
+    width: 240px;
+  }
+</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>

pr_agent/algo/__init__.py

@@ -19,7 +19,8 @@ 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,
 }

pr_agent/algo/ai_handlers/litellm_ai_handler.py

@@ -4,8 +4,7 @@ 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
@@ -56,8 +56,11 @@ class LiteLLMAIHandler(BaseAiHandler):
             litellm.replicate_key = get_settings().replicate.key
         if get_settings().get("HUGGINGFACE.KEY", None):
             litellm.huggingface_key = get_settings().huggingface.key
-            if get_settings().get("HUGGINGFACE.API_BASE", None):
-                litellm.api_base = get_settings().huggingface.api_base
+        if get_settings().get("HUGGINGFACE.API_BASE", None) and 'huggingface' in get_settings().config.model:
+            litellm.api_base = get_settings().huggingface.api_base
+            self.api_base = get_settings().huggingface.api_base
+        if get_settings().get("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(
@@ -77,28 +80,11 @@ 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))
+    @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):
-        """
-        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.
-        """
         try:
             resp, finish_reason = None, None
             deployment_id = self.deployment_id
@@ -111,23 +97,31 @@ class LiteLLMAIHandler(BaseAiHandler):
                 "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"]
@@ -135,4 +129,7 @@ class LiteLLMAIHandler(BaseAiHandler):
             get_logger().debug(f"\nAI response:\n{resp}")
             get_logger().debug("Full_response", artifact=response)
 
+            if get_settings().config.verbosity_level >= 2:
+                get_logger().info(f"\nAI response:\n{resp}")
+
         return resp, finish_reason

pr_agent/algo/utils.py

@@ -47,7 +47,20 @@ 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:
@@ -67,7 +80,11 @@ 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>"""
@@ -89,12 +106,16 @@ def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
             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:

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
@@ -175,8 +179,9 @@ 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))
-                    self.publish_comment(
-                        f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
+                    if final_update_message:
+                        self.publish_comment(
+                            f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
                     return
         except Exception as e:
             get_logger().exception(f"Failed to update persistent review, error: {e}")
@@ -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 ""
 

pr_agent/git_providers/git_provider.py

@@ -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

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:
@@ -145,10 +147,10 @@ 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 +199,11 @@ 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
@@ -211,8 +217,9 @@ 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)
-                self.publish_comment(
-                    f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
+                if final_update_message:
+                    self.publish_comment(
+                        f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
                 return
         self.publish_comment(pr_comment)
 
@@ -598,13 +605,36 @@ 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",

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):
@@ -164,8 +166,9 @@ 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})
-                    self.publish_comment(
-                        f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
+                    if final_update_message:
+                        self.publish_comment(
+                            f"**[Persistent {name}]({comment_url})** updated to latest commit {latest_commit_url}")
                     return
         except Exception as e:
             get_logger().exception(f"Failed to update persistent review, error: {e}")

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"}
@@ -118,18 +137,19 @@ async def handle_github_webhooks(background_tasks: BackgroundTasks, request: Req
                     with get_logger().contextualize(**log_context):
                         apply_repo_settings(pr_url)
                         if get_identity_provider().verify_eligibility("bitbucket",
-                                                                         sender_id, pr_url) is not Eligibility.NOT_ELIGIBLE:
-                            auto_review = get_setting_or_env("BITBUCKET_APP.AUTO_REVIEW", None)
-                            if auto_review is None or is_true(auto_review):  # by default, auto review is enabled
-                                await PRReviewer(pr_url).run()
-                            auto_improve = get_setting_or_env("BITBUCKET_APP.AUTO_IMPROVE", None)
-                            if is_true(auto_improve):  # by default, auto improve is disabled
-                                await PRCodeSuggestions(pr_url).run()
-                            auto_describe = get_setting_or_env("BITBUCKET_APP.AUTO_DESCRIBE", None)
-                            if is_true(auto_describe):  # by default, auto describe is disabled
-                                await PRDescription(pr_url).run()
-                # with get_logger().contextualize(**log_context):
-                #     await agent.handle_request(pr_url, "review")
+                                                        sender_id, pr_url) is not Eligibility.NOT_ELIGIBLE:
+                            if get_settings().get("bitbucket_app.pr_commands"):
+                                await _perform_commands_bitbucket("pr_commands", PRAgent(), pr_url, log_context)
+                            else: # backwards compatibility
+                                auto_review = get_setting_or_env("BITBUCKET_APP.AUTO_REVIEW", None)
+                                if is_true(auto_review):  # by default, auto review is disabled
+                                    await PRReviewer(pr_url).run()
+                                auto_improve = get_setting_or_env("BITBUCKET_APP.AUTO_IMPROVE", None)
+                                if is_true(auto_improve):  # by default, auto improve is disabled
+                                    await PRCodeSuggestions(pr_url).run()
+                                auto_describe = get_setting_or_env("BITBUCKET_APP.AUTO_DESCRIBE", None)
+                                if is_true(auto_describe):  # by default, auto describe is disabled
+                                    await PRDescription(pr_url).run()
             elif event == "pullrequest:comment_created":
                 pr_url = data["data"]["pullrequest"]["links"]["html"]["href"]
                 log_context["api_url"] = pr_url

pr_agent/servers/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)
@@ -66,46 +69,57 @@ 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 line_range_['start']['type'] == 'new':
-                start_line = line_range_['start']['new_line']
-                end_line = line_range_['end']['new_line']
-                # else:
-                #     start_line = line_range_['start']['old_line']
-                #     end_line = line_range_['end']['old_line']
-
-                question = body.replace('/ask', '').strip()
-                path = data['object_attributes']['position']['new_path']
-                side = 'RIGHT'# if line_range_['start']['type'] == 'new' else 'LEFT'
-                comment_id = data['object_attributes']["discussion_id"]
-                get_logger().info(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}"
+            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'
+        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}"
+    except Exception as e:
+        get_logger().error(f"Failed to handle ask line comment: {e}")
+    return body
+
+
 @router.get("/")
 async def root():
     return {"status": "ok"}

pr_agent/settings/configuration.toml

@@ -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
@@ -164,9 +165,10 @@ pr_commands = [
 ]
 
 [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.summarize=false",
+]
 
 
 [local]

pr_agent/settings/pr_reviewer_prompts.toml

@@ -49,7 +49,7 @@ 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)
+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 %}
@@ -69,7 +69,7 @@ class Review(BaseModel)
     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 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 +77,12 @@ 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 %}
 =====
@@ -138,15 +138,8 @@ 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_code_suggestions.py

@@ -87,9 +87,14 @@ 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 \
@@ -317,7 +322,7 @@ 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:

pr_agent/tools/pr_reviewer.py

@@ -107,6 +107,17 @@ 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 +132,11 @@ 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)
+                                                                 update_header=True,
+                                                                 final_update_message=final_update_message, )
                 else:
                     self.git_provider.publish_comment(pr_review)
 
@@ -173,7 +186,9 @@ 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:"])
 
         if 'code_feedback' in data:
             code_feedback = data['code_feedback']
@@ -203,21 +218,15 @@ 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:
@@ -244,7 +253,7 @@ 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 +324,10 @@ 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

pr_agent/tools/pr_update_changelog.py

@@ -53,11 +53,16 @@ class PRUpdateChangelog:
         get_logger().debug("Relevant configs", artifacts=relevant_configs)
 
         # currently only GitHub is supported for pushing changelog changes
-        if get_settings().pr_update_changelog.push_changelog_changes and type(self.git_provider) != GithubProvider:
-            get_logger().error("Pushing changelog changes is not currently supported for this code platform")
+        if get_settings().pr_update_changelog.push_changelog_changes and not hasattr(
+            self.git_provider, "create_or_update_pr_file"
+        ):
+            get_logger().error(
+                "Pushing changelog changes is not currently supported for this code platform"
+            )
             if get_settings().config.publish_output:
                 self.git_provider.publish_comment(
-                    "Pushing changelog changes is not currently supported for this code platform")
+                    "Pushing changelog changes is not currently supported for this code platform"
+                )
             return
 
         if get_settings().config.publish_output:
@@ -98,11 +103,11 @@ class PRUpdateChangelog:
     def _prepare_changelog_update(self) -> Tuple[str, str]:
         answer = self.prediction.strip().strip("```").strip()  # noqa B005
         if hasattr(self, "changelog_file"):
-            existing_content = self.changelog_file.decoded_content.decode()
+            existing_content = self.changelog_file
         else:
             existing_content = ""
         if existing_content:
-            new_file_content = answer + "\n\n" + self.changelog_file.decoded_content.decode()
+            new_file_content = answer + "\n\n" + self.changelog_file
         else:
             new_file_content = answer
 
@@ -113,25 +118,28 @@ class PRUpdateChangelog:
         return new_file_content, answer
 
     def _push_changelog_update(self, new_file_content, answer):
-        self.git_provider.repo_obj.update_file(path=self.changelog_file.path,
-                                               message="Update CHANGELOG.md",
-                                               content=new_file_content,
-                                               sha=self.changelog_file.sha,
-                                               branch=self.git_provider.get_pr_branch())
-        d = dict(body="CHANGELOG.md update",
-                 path=self.changelog_file.path,
-                 line=max(2, len(answer.splitlines())),
-                 start_line=1)
+        self.git_provider.create_or_update_pr_file(
+            file_path="CHANGELOG.md",
+            branch=self.git_provider.get_pr_branch(),
+            contents=new_file_content,
+            message="Update CHANGELOG.md",
+        )
 
         sleep(5)  # wait for the file to be updated
-        last_commit_id = list(self.git_provider.pr.get_commits())[-1]
         try:
-            self.git_provider.pr.create_review(commit=last_commit_id, comments=[d])
+            if get_settings().config.git_provider == "github":
+                last_commit_id = list(self.git_provider.pr.get_commits())[-1]
+                d = dict(
+                    body="CHANGELOG.md update",
+                    path="CHANGELOG.md",
+                    line=max(2, len(answer.splitlines())),
+                    start_line=1,
+                )
+                self.git_provider.pr.create_review(commit=last_commit_id, comments=[d])
         except Exception:
             # we can't create a review for some reason, let's just publish a comment
             self.git_provider.publish_comment(f"**Changelog updates:**\n\n{answer}")
 
-
     def _get_default_changelog(self):
         example_changelog = \
 """
@@ -149,20 +157,15 @@ Example:
 
     def _get_changlog_file(self):
         try:
-            self.changelog_file = self.git_provider.repo_obj.get_contents("CHANGELOG.md",
-                                                                          ref=self.git_provider.get_pr_branch())
-            changelog_file_lines = self.changelog_file.decoded_content.decode().splitlines()
+            self.changelog_file = self.git_provider.get_pr_file_content(
+                "CHANGELOG.md", self.git_provider.get_pr_branch()
+            )
+            changelog_file_lines = self.changelog_file.splitlines()
             changelog_file_lines = changelog_file_lines[:CHANGELOG_LINES]
             self.changelog_file_str = "\n".join(changelog_file_lines)
         except Exception:
             self.changelog_file_str = ""
-            if self.commit_changelog:
-                get_logger().info("No CHANGELOG.md file found in the repository. Creating one...")
-                changelog_file = self.git_provider.repo_obj.create_file(path="CHANGELOG.md",
-                                                                             message='add CHANGELOG.md',
-                                                                             content="",
-                                                                             branch=self.git_provider.get_pr_branch())
-                self.changelog_file = changelog_file['content']
+            self.changelog_file = ""
 
         if not self.changelog_file_str:
             self.changelog_file_str = self._get_default_changelog()

requirements.txt

@@ -9,10 +9,10 @@ GitPython==3.1.32
 google-cloud-aiplatform==1.35.0
 google-cloud-storage==2.10.0
 Jinja2==3.1.2
-litellm==0.12.5
+litellm==1.29.1
 loguru==0.7.2
 msrest==0.7.1
-openai==0.27.8
+openai==1.13.3
 pinecone-client
 pinecone-datasets @ git+https://github.com/mrT23/pinecone-datasets.git@main
 lancedb==0.5.1
@@ -25,4 +25,5 @@ starlette-context==0.3.6
 tiktoken==0.5.2
 ujson==5.8.0
 uvicorn==0.22.0
+tenacity==8.2.3
 # langchain==0.0.349 # uncomment this to support language LangChainOpenAIHandler