Merge pull request #404 from Codium-ai/tr/final_fixes

final fixes

Dockerfile.github_action_dockerhub

@@ -1 +1 @@
-FROM codiumai/pr-agent:0.7-github_action
+FROM codiumai/pr-agent:github_action

INSTALL.md

@@ -4,65 +4,69 @@
 To get started with PR-Agent quickly, you first need to acquire two tokens:
 
 1. An OpenAI key from [here](https://platform.openai.com/), with access to GPT-4.
-2. A GitHub personal access token (classic) with the repo scope.
+2. A GitHub\GitLab\BitBucket personal access token (classic) with the repo scope.
 
 There are several ways to use PR-Agent:
 
-- [Method 1: Use Docker image (no installation required)](INSTALL.md#method-1-use-docker-image-no-installation-required)
-- [Method 2: Run from source](INSTALL.md#method-2-run-from-source)
-- [Method 3: Run as a GitHub Action](INSTALL.md#method-3-run-as-a-github-action)
-- [Method 4: Run as a polling server](INSTALL.md#method-4-run-as-a-polling-server)
-- [Method 5: Run as a GitHub App](INSTALL.md#method-5-run-as-a-github-app)
-- [Method 6: Deploy as a Lambda Function](INSTALL.md#method-6---deploy-as-a-lambda-function)
-- [Method 7: AWS CodeCommit](INSTALL.md#method-7---aws-codecommit-setup)
-- [Method 8: Run a GitLab webhook server](INSTALL.md#method-8---run-a-gitlab-webhook-server)
+**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 polling server](INSTALL.md#run-as-a-polling-server)
+- [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)
 ---
 
-### Method 1: Use Docker image (no installation required)
+### Use Docker image (no installation required)
 
 To request a review for a PR, or ask a question about a PR, you can run directly from the Docker image. Here's how:
 
-1. To request a review for a PR, run the following command:
-
 For GitHub:
 ```
-docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent --pr_url <pr_url> review
+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 --pr_url <pr_url> review
+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
 ```
+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.
 
-2. To ask a question about a PR, run the following command:
 
+Similarly, to ask a question about a PR, run the following command:
 ```
 docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent --pr_url <pr_url> ask "<your question>"
 ```
-Note: If you want to ensure you're running a specific version of the Docker image, consider using the image's digest. 
-The digest is a unique identifier for a specific version of an image. You can pull and run an image using its digest by referencing it like so: repository@sha256:digest. Always ensure you're using the correct and trusted digest for your operations.
 
-1. To request a review for a PR using a specific digest, run the following command:
+A list of the relevant tools can be found in the [tools guide](./docs/TOOLS_GUIDE.md).
+
+
+Note: 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
 ```
-
-2. To ask a question about a PR using the same digest, run the following command:
-```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> ask "<your question>"
+in addition, you can run a [specific released versions](./RELEASE_NOTES.md) of pr-agent, for example:
+```
+codiumai/pr-agent@v0.8
 ```
-
-Possible questions you can ask include:
-
-- What is the main theme of this PR?
-- Is the PR ready for merge?
-- What are the main changes in this PR?
-- Should this PR be split into smaller parts?
-- Can you compose a rhymed song about this PR?
 
 ---
 
-### Method 2: Run from source
+### Run from source
 
 1. Clone this repository:
 
@@ -88,17 +92,20 @@ chmod 600 pr_agent/settings/.secrets.toml
 
 ```
 export PYTHONPATH=[$PYTHONPATH:]<PATH to pr_agent folder>
-python pr_agent/cli.py --pr_url <pr_url> /review
-python pr_agent/cli.py --pr_url <pr_url> /ask <your question>
-python pr_agent/cli.py --pr_url <pr_url> /describe
-python pr_agent/cli.py --pr_url <pr_url> /improve
+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 --issue_url <issue_url> similar_issue
+...
 ```
 
 ---
 
-### Method 3: Run as a GitHub Action
+### Run as a GitHub Action
 
-You can use our pre-built Github Action Docker image to run PR-Agent 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`:
 
@@ -122,7 +129,7 @@ jobs:
           OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 ```
-** if you want to pin your action to a specific commit for stability reasons
+** if you want to pin your action to a specific release (v0.7 for example) for stability reasons, use:
 ```yaml
 on:
   pull_request:
@@ -139,7 +146,7 @@ jobs:
     steps:
       - name: PR Agent action step
         id: pragent
-        uses: Codium-ai/pr-agent@<commit_sha>
+        uses: Codium-ai/pr-agent@v0.7
         env:
           OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -152,10 +159,10 @@ OPENAI_KEY: <your key>
 
 The GITHUB_TOKEN secret is automatically created by GitHub.
 
-3. Merge this change to your main branch. 
+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](./Usage.md) file. Some examples:
+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
@@ -166,10 +173,11 @@ When you open your next PR, you should see a comment from `github-actions` bot w
 
 ---
 
-### Method 4: Run as a polling server
-Request reviews by tagging your Github user on a PR
+### Run as a polling server
+Request reviews by tagging your GitHub user on a PR
+
+Follow [steps 1-3](#run-as-a-github-action) of the GitHub Action setup.
 
-Follow steps 1-3 of method 2.
 Run the following command to start the server:
 
 ```
@@ -178,7 +186,7 @@ python pr_agent/servers/github_polling.py
 
 ---
 
-### Method 5: Run as a GitHub App
+### 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).
@@ -220,12 +228,12 @@ git clone https://github.com/Codium-ai/pr-agent.git
    - 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. 
+> 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. 
+> 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:
@@ -259,13 +267,13 @@ docker push codiumai/pr-agent:github_app  # Push to your Docker repository
 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<br>
-> For more information please check out [CONFIGURATION.md](Usage.md#working-from-github-app-pre-built-repo)
+> 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)
 ---
 
-### Method 6 - Deploy as a Lambda Function
+### Deploy as a Lambda Function
 
-1. Follow steps 1-5 of [Method 5](#method-5-run-as-a-github-app).
+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
@@ -277,12 +285,12 @@ docker push codiumai/pr-agent:github_app  # Push to your Docker repository
     ```
 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. Go back to steps 8-9 of [Method 5](#method-5-run-as-a-github-app) with the function url as your Webhook URL.
+6. 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`
 
 ---
 
-### Method 7 - AWS CodeCommit Setup
+### 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:
 
@@ -321,7 +329,7 @@ Example IAM permissions to that user to allow access to CodeCommit:
                 "codecommit:PostComment*",
                 "codecommit:PutCommentReaction",
                 "codecommit:UpdatePullRequestDescription",
-                "codecommit:UpdatePullRequestTitle"                
+                "codecommit:UpdatePullRequestTitle"
             ],
             "Resource": "*"
         }
@@ -352,7 +360,7 @@ PYTHONPATH="/PATH/TO/PROJECTS/pr-agent" python pr_agent/cli.py \
 
 ---
 
-### Method 8 - Run a GitLab webhook server
+### 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:
@@ -365,9 +373,42 @@ WEBHOOK_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
     - 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. Set the secret token to the generated secret from step 2. 
-In the "Trigger" section, check the ‘comments’ and ‘merge request events’ boxes. 
+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.
 
 
+
+### 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.
+
+
+### Run on a hosted Bitbucket app
+
+Please contact <support@codium.ai> 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) implmentation.
+
+
 =======

PR_COMPRESSION.md

@@ -1,4 +1,4 @@
-# Git Patch Logic
+# 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)
@@ -16,7 +16,7 @@ We prioritize the languages of the repo based on the following criteria:
 ## 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 6 lines above and below the patch
+2. We Expand the surrounding context of each patch to 3 lines above and below the patch
 ## Large PR
 
 ### Motivation
@@ -25,7 +25,7 @@ We want to be able to pack as much information as possible in a single LMM promp
 
 
 
-#### PR compression strategy
+#### 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

README.md

@@ -9,6 +9,7 @@ Making pull requests less painful with an AI agent
 
 [![GitHub license](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://github.com/Codium-ai/pr-agent/blob/main/LICENSE)
 [![Discord](https://badgen.net/badge/icon/discord?icon=discord&label&color=purple)](https://discord.com/channels/1057273017547378788/1126104260430528613)
+[![Twitter](https://img.shields.io/twitter/follow/codiumai)](https://twitter.com/codiumai)
     <a href="https://github.com/Codium-ai/pr-agent/commits/main">
     <img alt="GitHub" src="https://img.shields.io/github/last-commit/Codium-ai/pr-agent/main?style=for-the-badge" height="20">
     </a>
@@ -17,20 +18,25 @@ Making pull requests less painful with an AI agent
 
 CodiumAI `PR-Agent` is an open-source tool aiming to help developers review pull requests faster and more efficiently. It automatically analyzes the pull request and can provide several types of commands:
 
-‣ **Auto Description (`/describe`)**: Automatically generating [PR description](https://github.com/Codium-ai/pr-agent/pull/229#issue-1860711415) - title, type, summary, code walkthrough and labels.
+‣ **Auto Description ([`/describe`](./docs/DESCRIBE.md))**: Automatically generating PR description - title, type, summary, code walkthrough and labels.
 \
-‣ **Auto Review (`/review`)**: [Adjustable feedback](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695022908) about the PR main theme, type, relevant tests, security issues, score, and various suggestions for the PR content.
+‣ **Auto Review ([`/review`](./docs/REVIEW.md))**: Adjustable feedback about the PR main theme, type, relevant tests, security issues, score, and various suggestions for the PR content.
 \
-‣ **Question Answering (`/ask ...`)**: Answering [free-text questions](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021332) about the PR.
+‣ **Question Answering ([`/ask ...`](./docs/ASK.md))**: Answering free-text questions about the PR.
 \
-‣ **Code Suggestions (`/improve`)**: [Committable code suggestions](https://github.com/Codium-ai/pr-agent/pull/229#discussion_r1306919276) for improving the PR.
+‣ **Code Suggestions ([`/improve`](./docs/IMPROVE.md))**: Committable code suggestions for improving the PR.
 \
-‣ **Update Changelog (`/update_changelog`)**: Automatically updating the CHANGELOG.md file with the [PR changes](https://github.com/Codium-ai/pr-agent/pull/168#discussion_r1282077645).
+‣ **Update Changelog ([`/update_changelog`](./docs/UPDATE_CHANGELOG.md))**: Automatically updating the CHANGELOG.md file with the PR changes.
 \
-‣ **Find similar issue (`/similar_issue`)**: Automatically retrieves and presents [similar issues](https://github.com/Alibaba-MIIL/ASL/issues/107).
+‣ **Find Similar Issue ([`/similar_issue`](./docs/SIMILAR_ISSUE.md))**: Automatically retrieves and presents similar issues
+\
+‣ **Add Documentation ([`/add_docs`](./docs/ADD_DOCUMENTATION.md))**: Automatically adds documentation to un-documented functions/classes in the PR.
 
+See the [Installation Guide](./INSTALL.md) for instructions how to install and run the tool on different platforms.
 
-See the [usage guide](./Usage.md) for instructions how to run the different tools from [CLI](./Usage.md#working-from-a-local-repo-cli), or by [online usage](./Usage.md#online-usage), as well as additional details on optional commands and configurations.
+See the [Usage Guide](./Usage.md) for instructions how to run the different tools from _CLI_, _online usage_, or by _automatically triggering_ them when a new PR is opened.
+
+See the [Tools Guide](./docs/TOOLS_GUIDE.md) for detailed description of the different tools.
 
 <h3>Example results:</h3>
 </div>
@@ -100,13 +106,15 @@ See the [usage guide](./Usage.md) for instructions how to run the different tool
 |       |                                             | 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:        |          |          |       |
+|       | 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:    |
 |       |                                             |        |        |      |      |      |
 | 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:    |           |          |          |
@@ -120,7 +128,7 @@ See the [usage guide](./Usage.md) for instructions how to run the different tool
 |       | 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:    |      |      |      |      |      |
 
-Review the **[usage guide](./Usage.md)** section for detailed instructions how to use the different tools, select the relevant git provider (GitHub, Gitlab, Bitbucket,...), and adjust the configuration file to your needs.
+Review the [usage guide](./Usage.md) section for detailed instructions how to use the different tools, select the relevant git provider (GitHub, Gitlab, Bitbucket,...), and adjust the configuration file to your needs.
 
 ## Try it now
 
@@ -157,12 +165,13 @@ There are several ways to use PR-Agent:
 - [Method 6: Deploy as a Lambda Function](INSTALL.md#method-6---deploy-as-a-lambda-function)
 - [Method 7: AWS CodeCommit](INSTALL.md#method-7---aws-codecommit-setup)
 - [Method 8: Run a GitLab webhook server](INSTALL.md#method-8---run-a-gitlab-webhook-server)
+- [Method 9: Run as a Bitbucket Pipeline](INSTALL.md#method-9-run-as-a-bitbucket-pipeline)
 
 ## How it works
 
 The following diagram illustrates PR-Agent tools and their flow:
 
-![PR-Agent Tools](https://www.codium.ai/wp-content/uploads/2023/07/codiumai-diagram-v4.jpg)
+![PR-Agent Tools](https://www.codium.ai/wp-content/uploads/2023/10/codiumai-diagram-v5.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
 
@@ -192,9 +201,12 @@ Here are some advantages of PR-Agent:
   - [x] Rank the PR (see [here](https://github.com/Codium-ai/pr-agent/pull/89))   
   - [ ] Enforcing CONTRIBUTING.md guidelines
   - [ ] Performance (are there any performance issues)
-  - [ ] Documentation (is the PR properly documented)
+  - [x] Documentation (is the PR properly documented)
   - [ ] ...
 
+See the [Release notes](./RELEASE_NOTES.md) for updates on the latest changes.
+
+
 ## Similar Projects
 
 - [CodiumAI - Meaningful tests for busy devs](https://github.com/Codium-ai/codiumai-vscode-release) (although various capabilities are much more advanced in the CodiumAI IDE plugins)
@@ -202,7 +214,12 @@ Here are some advantages of PR-Agent:
 - [openai-pr-reviewer](https://github.com/coderabbitai/openai-pr-reviewer)
 - [CodeReview BOT](https://github.com/anc95/ChatGPT-CodeReview)
 - [AI-Maintainer](https://github.com/merwanehamadi/AI-Maintainer)
-  
+
+## Data Privacy
+
+If you use self-host PR-Agent, e.g. via CLI running on your computer, 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
+
 ## Links
 
 [![Join our Discord community](https://raw.githubusercontent.com/Codium-ai/codiumai-vscode-release/main/media/docs/Joincommunity.png)](https://discord.gg/kG35uSHDBc)

RELEASE_NOTES.md

@@ -1,3 +1,19 @@
+## [Version 0.8] - 2023-09-27
+- codiumai/pr-agent:0.8
+- codiumai/pr-agent:0.8-github_app
+- codiumai/pr-agent:0.8-bitbucket-app
+- codiumai/pr-agent:0.8-gitlab_webhook
+- codiumai/pr-agent:0.8-github_polling
+- codiumai/pr-agent:0.8-github_action
+
+### Added::Algo
+- GitHub Action: Can control which tools will run automatically when a new PR is created. (see usage guide: https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-action)
+- Code suggestion tool: Will try to avoid an 'add comments' suggestion  (see https://github.com/Codium-ai/pr-agent/pull/327)
+
+### Fixed
+- Gitlab: Fixed a bug of improper usage of pr_id
+
+
 ## [Version 0.7] - 2023-09-20
 
 ### Docker Tags
@@ -20,6 +36,3 @@
 ### Fixed
 - Protection against no code suggestions generated.
 - Resilience to repositories where the languages cannot be automatically detected.
-
-
-

Usage.md

@@ -1,4 +1,4 @@
-## Usage guide
+## Usage Guide
 
 ### Table of Contents
 - [Introduction](#introduction)
@@ -6,19 +6,19 @@
 - [Online usage](#online-usage)
 - [Working with GitHub App](#working-with-github-app)
 - [Working with GitHub Action](#working-with-github-action)
+- [Changing a model](#changing-a-model)
+- [Working with large PRs](#working-with-large-prs)
 - [Appendix - additional configurations walkthrough](#appendix---additional-configurations-walkthrough)
 
 ### Introduction
 
-There are 3 basic ways to invoke CodiumAI PR-Agent:
+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
 
-See the [installation guide](/INSTALL.md) for instructions on how to setup your own PR-Agent.
 
 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.
 
@@ -27,10 +27,22 @@ GitHub App and GitHub Action also enable to run PR-Agent specific tool automatic
 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.
 
-**git provider:**
+The [Tools Guide](./docs/TOOLS_GUIDE.md) provides a detailed description of the different tools and their configurations.
+
+#### 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 is also exposed the following environment variables:
+
+ - `IGNORE.GLOB`
+ - `IGNORE.REGEX`
+
+See [dynaconf envvars documentation](https://www.dynaconf.com/envvars/).
+
+#### 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", "azure", "codecommit", "local"
+"github", "gitlab", "azure", "codecommit", "local", "gerrit"
 `
 
 [//]: # (** online usage:**)
@@ -47,15 +59,14 @@ The [git_provider](pr_agent/settings/configuration.toml#L4) field in the configu
 
 ### Working from a local repo (CLI)
 When running from your local repo (CLI), your local configuration file will be used.
-
 Examples for invoking the different tools via the CLI:
 
-- **Review**:       `python cli.py --pr_url=<pr_url>  review`
-- **Describe**:     `python cli.py --pr_url=<pr_url>  describe`
-- **Improve**:      `python cli.py --pr_url=<pr_url>  improve`
-- **Ask**:          `python cli.py --pr_url=<pr_url>  ask "Write me a poem about this PR"`
-- **Reflect**:      `python cli.py --pr_url=<pr_url>  reflect`
-- **Update Changelog**:      `python cli.py --pr_url=<pr_url>  update_changelog`
+- **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).
 
@@ -63,7 +74,7 @@ Examples for invoking the different tools via the CLI:
 
 (1) in addition to editing your local configuration file, you can also change any configuration value by adding it to the command line:
 ```
-python cli.py --pr_url=<pr_url>  /review --pr_reviewer.extra_instructions="focus on the file: ..."
+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`:
@@ -93,15 +104,15 @@ 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.
+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
-When running PR-Agent from [GitHub App](INSTALL.md#method-5-run-as-a-github-app), the default configurations from a pre-built repo will be initially loaded.
+When running PR-Agent from [GitHub App](INSTALL.md#method-5-run-as-a-github-app), the default configurations from a pre-built docker will be initially loaded.
 
 #### GitHub app automatic tools
-The [github_app](pr_agent/settings/configuration.toml#L56) section defines GitHub app specific configurations. 
-An important parameter is `pr_commands`, which is a list of tools that will be **run automatically when a new PR is opened**:
+The [github_app](pr_agent/settings/configuration.toml#L56) section defines GitHub app specific configurations.
+An important parameter is `pr_commands`, which is a list of tools that will be **run automatically** when a new PR is opened:
 ```
 [github_app]
 pr_commands = [
@@ -112,7 +123,7 @@ pr_commands = [
 This means that when a new PR is opened, PR-Agent will run the `describe` and `auto_review` tools.
 For the describe tool, the `add_original_user_description` and `keep_original_user_title` parameters will be set to true.
 
-However, you can override the default tool parameters by uploading a local configuration file called `.pr_agent.toml` to the root of your repo.
+You can override the default tool parameters by uploading a local configuration file called `.pr_agent.toml` to the root of your repo.
 For example, if your local `.pr_agent.toml` file contains:
 ```
 [pr_description]
@@ -121,12 +132,18 @@ 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]
+pr_commands = ""
+```
+
+
 Note that a local `.pr_agent.toml` file enables you to edit and customize the default parameters of any tool, not just the ones that are run automatically.
 
 #### 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. 
+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:
@@ -142,34 +159,47 @@ 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).
 
 ### Working with GitHub Action
-TBD
+You can configure settings in GitHub action by adding environment variables under the env section in `.github/workflows/pr_agent.yml` 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
+        github_action.auto_review: "true" # Enable auto review
+        github_action.auto_describe: "true" # Enable auto describe
+        github_action.auto_improve: "false" # Disable auto improve
+```
+specifically, `github_action.auto_review`, `github_action.auto_describe` and `github_action.auto_improve` are used to enable/disable automatic tools that run when a new PR is opened.
 
-### Appendix - additional configurations walkthrough
+If not set, the default option is that only the `review` tool will run automatically when a new PR is opened.
+
+### Changing a model
 
-#### 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: 
+To use Azure, set in your .secrets.toml:
 ```
 api_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
+openai.deployment_id = ""  # The deployment name you chose when you deployed the engine
 ```
-in your .secrets.toml
 
-and 
+and
 ```
 [config]
 model="" # the OpenAI model you've deployed on Azure (e.g. gpt-3.5-turbo)
 ```
-in the configuration.toml 
+in the configuration.toml
 
 #### Huggingface
 
-**Local**  
+**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:
@@ -189,7 +219,7 @@ MAX_TOKENS={
 model = "ollama/llama2"
 
 [ollama] # in .secrets.toml
-api_base = ... # the base url for your huggingface inference endpoint 
+api_base = ... # the base url for your huggingface inference endpoint
 ```
 
 **Inference Endpoints**
@@ -210,7 +240,7 @@ 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 
+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))
 
@@ -228,12 +258,50 @@ key = ...
 
 Also review the [AiHandler](pr_agent/algo/ai_handler.py) file for instruction how to set keys for other models.
 
+### 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)
+
+### Appendix - additional configurations walkthrough
+
+
 #### 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 ..."
 ```
 
+#### 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.
+
+
 #### Azure DevOps provider
 To use Azure DevOps provider use the following settings in configuration.toml:
 ```
@@ -248,25 +316,3 @@ And use the following settings (you have to replace the values) in .secrets.toml
 org = "https://dev.azure.com/YOUR_ORGANIZATION/"
 pat = "YOUR_PAT_TOKEN"
 ```
-
-#### Similar issue tool
-
-[Example usage](https://github.com/Alibaba-MIIL/ASL/issues/107)
-
-<img src=./pics/similar_issue_tool.png width="768">
-
-To enable usage of the '**similar issue**' tool, you need to set the following keys in `.secrets.toml` (or in the relevant environment variables):
-```
-[pinecone]
-api_key = "..."
-environment = "..."
-```
-These parameters can be obtained by registering to [Pinecone](https://app.pinecone.io/?sessionType=signup/).
-
-- 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)

docs/ADD_DOCUMENTATION.md

@@ -0,0 +1,15 @@
+# Add Documentation Tool
+The `add_docs` tool scans the PR code changes, and automatically suggests documentation for the undocumented code components (functions, classes, etc.).
+
+It can be invoked manually by commenting on any PR:
+```
+/add_docs
+```
+For example:
+
+<kbd><img src=./../pics/add_docs_comment.png width="768"></kbd>
+<kbd><img src=./../pics/add_docs.png width="768"></kbd>
+
+### Configuration options
+ - `docs_style`: The exact style of the documentation (for python docstring). you can choose between: `google`, `numpy`, `sphinx`, `restructuredtext`, `plain`. Default is `sphinx`.
+ - `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".

docs/ASK.md

@@ -0,0 +1,11 @@
+# ASK Tool
+
+The `ask` tool answers questions about the PR, based on the PR code changes.
+It can be invoked manually by commenting on any PR:
+```
+/ask "..."
+```
+For example:
+
+<kbd><img src=./../pics/ask_comment.png width="768"></kbd>
+<kbd><img src=./../pics/ask.png width="768"></kbd>

docs/DESCRIBE.md

@@ -0,0 +1,62 @@
+# Describe Tool
+
+The `describe` tool scans the PR code changes, and automatically generates PR description - title, type, summary, code walkthrough and labels.
+It can be invoked manually by commenting on any PR:
+```
+/describe
+```
+For example:
+
+<kbd><img src=./../pics/describe_comment.png width="768"></kbd>
+
+<kbd><img src=./../pics/describe.png width="768"></kbd>
+
+The `describe` tool can also be triggered automatically every time a new PR is opened. See examples for automatic triggers for [GitHub App](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools) and [GitHub Action](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-action)
+
+### Configuration options
+
+Under the section 'pr_description', the [configuration file](./../pr_agent/settings/configuration.toml#L28) contains options to customize the 'describe' tool:
+
+- `publish_labels`: if set to true, the tool will publish the labels to the PR. Default is true.
+
+- `publish_description_as_comment`: if set to true, the tool will publish the description as a comment to the PR. If false, it will overwrite the origianl description. Default is false.
+
+- `add_original_user_description`: if set to true, the tool will add the original user description to the generated description. Default is false.
+
+- `keep_original_user_title`: if set to true, the tool will keep the original PR title, and won't change it. Default is false.
+
+- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
+
+### Markers template
+
+markers enable to easily integrate user's content and auto-generated content, with a template-like mechanism.
+
+For example, if the PR original description was:
+```
+User content...
+
+
+## PR Description:
+pr_agent:summary
+
+## PR Walkthrough:
+pr_agent:walkthrough
+```
+The marker `pr_agent:summary` will be replaced with the PR summary, and `pr_agent:walkthrough` will be replaced with the PR walkthrough.
+
+##### Example:
+```
+        env:
+          pr_description.use_description_markers: 'true'
+```          
+
+<kbd><img src=./../pics/describe_markers_before.png width="768"></kbd>
+
+==>
+
+<kbd><img src=./../pics/describe_markers_after.png width="768"></kbd>
+
+##### Configuration params:
+
+- `use_description_markers`: if set to true, the tool will use markers template. It replaces every marker of the form `pr_agent:marker_name` with the relevant content. Default is false.
+- `include_generated_by_header`: if set to true, the tool will add a dedicated header: 'Generated by PR Agent at ...' to any automatic content. Default is true.

docs/GENERATE_CUSTOM_LABELS.md

@@ -0,0 +1,35 @@
+# Generate Custom Labels
+The `generte_labels` tool scans the PR code changes, and given a list of labels and their descriptions, it automatically suggests labels that match the PR code changes.
+
+It can be invoked manually by commenting on any PR:
+```
+/generate_labels
+```
+For example:
+
+If we wish to add detect changes to SQL queries in a given PR, we can add the following custom label along with its description:
+
+<kbd><img src=./../pics/custom_labels_list.png width="768"></kbd>
+When running the `generte_labels` tool on a PR that includes changes in SQL queries, it will automatically suggest the custom label:
+<kbd><img src=./../pics/custom_label_published.png width="768"></kbd>
+
+### Configuration options
+To enable custom labels, you need to add the following configuration to the [custom_labels file](./../pr_agent/settings/custom_labels.toml):
+ - 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 to the custom_labels.toml file. It should be formatted as follows:
+ ```
+[custom_labels."Custom Label Name"]
+description = "Description of when AI should suggest this label"
+```
+ - You can add modify the list to include all the custom labels you wish to use in your repository.
+
+#### Github Action
+To use the `generte_labels` tool with Github Action:
+
+- Add the following file to your repository under `env` section in `.github/workflows/pr_agent.yml`
+- Comma separated list of custom labels and their descriptions
+- The number of labels and descriptions should be the same and in the same order (empty descriptions are allowed):
+```
+CUSTOM_LABELS: "label1, label2, ..."
+CUSTOM_LABELS_DESCRIPTION: "label1 description, label2 description, ..."
+```

docs/IMPROVE.md

@@ -0,0 +1,45 @@
+# Improve Tool
+
+The `improve` tool scans the PR code changes, and automatically generate committable suggestions for improving the PR code.
+It can be invoked manually by commenting on any PR:
+```
+/improve
+```
+For example:
+
+<kbd><img src=./../pics/improve_comment.png width="768"></kbd>
+<kbd><img src=./../pics/improve.png width="768"></kbd>
+
+The `improve` tool can also be triggered automatically every time a new PR is opened. See examples for automatic triggers for [GitHub App](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools) and [GitHub Action](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-action)
+
+An extended mode, which does not involve PR Compression and provides more comprehensive suggestions, can be invoked by commenting on any PR:
+```
+/improve --extended
+```
+Note that the extended mode divides the PR code changes into chunks, up to the token limits, where each chunk is handled separately (multiple calls to GPT-4).
+Hence, the total number of suggestions is proportional to the number of chunks, i.e. the size of the PR.
+
+### Configuration options
+
+Under the section 'pr_code_suggestions', the [configuration file](./../pr_agent/settings/configuration.toml#L40) contains options to customize the 'improve' tool:
+
+- `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.
+
+#### params for '/improve --extended' mode
+- `num_code_suggestions_per_chunk`: number of code suggestions provided by the 'improve' tool, per chunk. Default is 8.
+- `rank_extended_suggestions`: if set to true, the tool will rank the suggestions, based on importance. Default is true.
+- `max_number_of_calls`: maximum number of chunks. Default is 5.
+- `final_clip_factor`: factor to remove suggestions with low confidence. Default is 0.9.
+
+
+#### A note on code suggestions quality
+
+- With current level of AI for code (GPT-4), mistakes can happen. Not all the suggestions will be perfect, and a user should not accept all of them automatically.
+
+- Suggestions are not meant to be [simplistic](./../pr_agent/settings/pr_code_suggestions_prompts.toml#L34). Instead, they aim to give deep feedback and raise questions, ideas and thoughts to the user, who can then use his judgment, experience, and understanding of the code base.
+
+- Recommended to use the 'extra_instructions' field to guide the model to suggestions that are more relevant to the specific needs of the project.
+
+- Best quality will be obtained by using 'improve --extended' mode.

docs/REVIEW.md

@@ -0,0 +1,57 @@
+# Review Tool
+
+The `review` tool scans the PR code changes, and automatically generates a PR review.
+It can be invoked manually by commenting on any PR:
+```
+/review
+```
+For example:
+
+<kbd><img src=./../pics/review_comment.png width="768"></kbd>
+<kbd><img src=./../pics/describe.png width="768"></kbd>
+
+The `review` tool can also be triggered automatically every time a new PR is opened. See examples for automatic triggers for [GitHub App](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools) and [GitHub Action](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-action)
+
+### Configuration options
+
+Under the section 'pr_reviewer', the [configuration file](./../pr_agent/settings/configuration.toml#L16) contains options to customize the 'review' tool:
+
+- `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_security_review`: if set to true, the tool will add a section that checks if the PR contains security issues. Default is true.
+- `require_estimate_effort_to_review`: if set to true, the tool will add a section that estimates thed effort needed to review the PR. Default is true.
+- `num_code_suggestions`: number of code suggestions provided by the 'review' tool. Default is 4.
+- `inline_code_comments`: if set to true, the tool will publish the code suggestions as comments on the code diff. Default is false.
+- `automatic_review`: if set to false, no automatic reviews will be done. Default is true.
+- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
+####  Incremental Mode
+For an incremental review, which 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, the following command can be used:
+```
+/improve -i
+```
+Note that the incremental mode is only available for GitHub.
+
+<kbd><img src=./../pics/incremental_review.png width="768"></kbd>
+
+#### PR Reflection
+By invoking:
+```
+/reflect_and_review
+```
+The tool will first ask the author questions about the PR, and will guide the review based on his answers.
+
+<kbd><img src=./../pics/reflection_questions.png width="768"></kbd>
+<kbd><img src=./../pics/reflection_answers.png width="768"></kbd>
+<kbd><img src=./../pics/reflection_insights.png width="768"></kbd>
+
+
+#### A note on code suggestions quality
+
+- With current level of AI for code (GPT-4), mistakes can happen. 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_reviewer_prompts.toml#L29). Instead, they aim to give deep feedback and raise questions, ideas and thoughts to the user, who can then use his judgment, experience, and understanding of the code base.
+
+- Recommended to use the 'extra_instructions' field to guide the model to suggestions that are more relevant to the specific needs of the project.
+
+- Unlike the 'review' feature, which does a lot of things, the ['improve --extended'](./IMPROVE.md) feature is dedicated only to suggestions, and usually gives better results.

docs/SIMILAR_ISSUE.md

@@ -0,0 +1,31 @@
+# Similar Issue Tool
+The similar issue tool retrieves the most similar issues to the current issue.
+It can be invoked manually by commenting on any PR:
+```
+/similar_issue
+```
+For example:
+
+<kbd><img src=./../pics/similar_issue_original_issue.png width="768"></kbd>
+<kbd><img src=./../pics/similar_issue_comment.png width="768"></kbd>
+<kbd><img src=./../pics/similar_issue.png width="768"></kbd>
+
+Note that to perform retrieval, the `similar_issue` tool indexes all the repo previous issues (once).
+
+To enable usage of the '**similar issue**' tool, you need to set the following keys in `.secrets.toml` (or in the relevant environment variables):
+```
+[pinecone]
+api_key = "..."
+environment = "..."
+```
+These parameters can be obtained by registering to [Pinecone](https://app.pinecone.io/?sessionType=signup/).
+
+
+### 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)

docs/TOOLS_GUIDE.md

@@ -0,0 +1,10 @@
+## Tools Guide
+- [DESCRIBE](./DESCRIBE.md)
+- [REVIEW](./REVIEW.md)
+- [IMPROVE](./IMPROVE.md)
+- [ASK](./ASK.md)
+- [SIMILAR_ISSUE](./SIMILAR_ISSUE.md)
+- [UPDATE CHANGELOG](./UPDATE_CHANGELOG.md)
+- [ADD DOCUMENTATION](./ADD_DOCUMENTATION.md)
+
+See the **[installation guide](/INSTALL.md)** for instructions on how to setup PR-Agent.

docs/UPDATE_CHANGELOG.md

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

pr_agent/agent/pr_agent.py

@@ -1,19 +1,18 @@
-import logging
-import os
 import shlex
-import tempfile
 
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider
+from pr_agent.git_providers.utils import apply_repo_settings
+from pr_agent.tools.pr_add_docs import PRAddDocs
 from pr_agent.tools.pr_code_suggestions import PRCodeSuggestions
+from pr_agent.tools.pr_config import PRConfig
 from pr_agent.tools.pr_description import PRDescription
+from pr_agent.tools.pr_generate_labels import PRGenerateLabels
 from pr_agent.tools.pr_information_from_user import PRInformationFromUser
-from pr_agent.tools.pr_similar_issue import PRSimilarIssue
 from pr_agent.tools.pr_questions import PRQuestions
 from pr_agent.tools.pr_reviewer import PRReviewer
+from pr_agent.tools.pr_similar_issue import PRSimilarIssue
 from pr_agent.tools.pr_update_changelog import PRUpdateChangelog
-from pr_agent.tools.pr_config import PRConfig
 
 command2class = {
     "auto_review": PRReviewer,
@@ -32,6 +31,8 @@ command2class = {
     "config": PRConfig,
     "settings": PRConfig,
     "similar_issue": PRSimilarIssue,
+    "add_docs": PRAddDocs,
+    "generate_labels": PRGenerateLabels,
 }
 
 commands = list(command2class.keys())
@@ -42,22 +43,7 @@ class PRAgent:
 
     async def handle_request(self, pr_url, request, notify=None) -> bool:
         # First, apply repo specific settings if exists
-        if get_settings().config.use_repo_settings_file:
-            repo_settings_file = None
-            try:
-                git_provider = get_git_provider()(pr_url)
-                repo_settings = git_provider.get_repo_settings()
-                if repo_settings:
-                    repo_settings_file = None
-                    fd, repo_settings_file = tempfile.mkstemp(suffix='.toml')
-                    os.write(fd, repo_settings)
-                    get_settings().load_file(repo_settings_file)
-            finally:
-                if repo_settings_file:
-                    try:
-                        os.remove(repo_settings_file)
-                    except Exception as e:
-                        logging.error(f"Failed to remove temporary settings file {repo_settings_file}", e)
+        apply_repo_settings(pr_url)
 
         # Then, apply user specific settings if exists
         request = request.replace("'", "\\'")
@@ -67,8 +53,8 @@ class PRAgent:
         args = update_settings_from_args(args)
 
         action = action.lstrip("/").lower()
-        if action == "reflect_and_review" and not get_settings().pr_reviewer.ask_and_reflect:
-            action = "review"
+        if action == "reflect_and_review":
+            get_settings().pr_reviewer.ask_and_reflect = True
         if action == "answer":
             if notify:
                 notify()
@@ -82,3 +68,4 @@ class PRAgent:
         else:
             return False
         return True
+

pr_agent/algo/ai_handler.py

@@ -1,4 +1,3 @@
-import logging
 import os
 
 import litellm
@@ -7,6 +6,8 @@ from litellm import acompletion
 from openai.error import APIError, RateLimitError, Timeout, TryAgain
 from retry import retry
 from pr_agent.config_loader import get_settings
+from pr_agent.log import get_logger
+
 OPENAI_RETRIES = 5
 
 
@@ -88,33 +89,34 @@ class AiHandler:
         try:
             deployment_id = self.deployment_id
             if get_settings().config.verbosity_level >= 2:
-                logging.debug(
+                get_logger().debug(
                     f"Generating completion with {model}"
                     f"{(' from deployment ' + deployment_id) if deployment_id else ''}"
                 )
+            if self.azure:
+                model = 'azure/' + model
+            messages = [{"role": "system", "content": system}, {"role": "user", "content": user}]
             response = await acompletion(
                 model=model,
                 deployment_id=deployment_id,
-                messages=[
-                    {"role": "system", "content": system},
-                    {"role": "user", "content": user}
-                ],
+                messages=messages,
                 temperature=temperature,
-                azure=self.azure,
                 force_timeout=get_settings().config.ai_timeout
             )
         except (APIError, Timeout, TryAgain) as e:
-            logging.error("Error during OpenAI inference: ", e)
+            get_logger().error("Error during OpenAI inference: ", e)
             raise
         except (RateLimitError) as e:
-            logging.error("Rate limit error during OpenAI inference: ", e)
+            get_logger().error("Rate limit error during OpenAI inference: ", e)
             raise
         except (Exception) as e:
-            logging.error("Unknown error during OpenAI inference: ", e)
+            get_logger().error("Unknown error during OpenAI inference: ", e)
             raise TryAgain from e
         if response is None or len(response["choices"]) == 0:
             raise TryAgain
         resp = response["choices"][0]['message']['content']
         finish_reason = response["choices"][0]["finish_reason"]
-        print(resp, finish_reason)
+        usage = response.get("usage")
+        get_logger().info("AI response", response=resp, messages=messages, finish_reason=finish_reason,
+                          model=model, usage=usage)
         return resp, finish_reason

pr_agent/algo/file_filter.py

@@ -0,0 +1,31 @@
+import fnmatch
+import re
+
+from pr_agent.config_loader import get_settings
+
+def filter_ignored(files):
+    """
+    Filter out files that match the ignore patterns.
+    """
+
+    try:
+        # load regex patterns, and translate glob patterns to regex
+        patterns = get_settings().ignore.regex
+        patterns += [fnmatch.translate(glob) for glob in get_settings().ignore.glob]
+
+        # compile all valid patterns
+        compiled_patterns = []
+        for r in patterns:
+            try:
+                compiled_patterns.append(re.compile(r))
+            except re.error:
+                pass
+
+        # keep filenames that _don't_ match the ignore regex
+        for r in compiled_patterns:
+            files = [f for f in files if not r.match(f.filename)]
+
+    except Exception as e:
+        print(f"Could not filter file list: {e}")
+
+    return files

pr_agent/algo/git_patch_processing.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
-import logging
+
 import re
 
 from pr_agent.config_loader import get_settings
+from pr_agent.log import get_logger
 
 
 def extend_patch(original_file_str, patch_str, num_lines) -> str:
@@ -40,12 +41,16 @@ def extend_patch(original_file_str, patch_str, num_lines) -> str:
                         extended_patch_lines.extend(
                             original_lines[start1 + size1 - 1:start1 + size1 - 1 + num_lines])
 
+                    res = list(match.groups())
+                    for i in range(len(res)):
+                        if res[i] is None:
+                            res[i] = 0
                     try:
-                        start1, size1, start2, size2 = map(int, match.groups()[:4])
+                        start1, size1, start2, size2 = map(int, res[:4])
                     except:  # '@@ -0,0 +1 @@' case
-                        start1, size1, size2 = map(int, match.groups()[:3])
+                        start1, size1, size2 = map(int, res[:3])
                         start2 = 0
-                    section_header = match.groups()[4]
+                    section_header = res[4]
                     extended_start1 = max(1, start1 - num_lines)
                     extended_size1 = size1 + (start1 - extended_start1) + num_lines
                     extended_start2 = max(1, start2 - num_lines)
@@ -59,7 +64,7 @@ def extend_patch(original_file_str, patch_str, num_lines) -> str:
             extended_patch_lines.append(line)
     except Exception as e:
         if get_settings().config.verbosity_level >= 2:
-            logging.error(f"Failed to extend patch: {e}")
+            get_logger().error(f"Failed to extend patch: {e}")
         return patch_str
 
     # finish previous hunk
@@ -130,14 +135,14 @@ def handle_patch_deletions(patch: str, original_file_content_str: str,
     if not new_file_content_str:
         # logic for handling deleted files - don't show patch, just show that the file was deleted
         if get_settings().config.verbosity_level > 0:
-            logging.info(f"Processing file: {file_name}, minimizing deletion file")
+            get_logger().info(f"Processing file: {file_name}, minimizing deletion file")
         patch = None # file was deleted
     else:
         patch_lines = patch.splitlines()
         patch_new = omit_deletion_hunks(patch_lines)
         if patch != patch_new:
             if get_settings().config.verbosity_level > 0:
-                logging.info(f"Processing file: {file_name}, hunks were deleted")
+                get_logger().info(f"Processing file: {file_name}, hunks were deleted")
             patch = patch_new
     return patch
 
@@ -207,10 +212,15 @@ __old hunk__
                 old_content_lines = []
             if match:
                 prev_header_line = header_line
+
+            res = list(match.groups())
+            for i in range(len(res)):
+                if res[i] is None:
+                    res[i] = 0
             try:
-                start1, size1, start2, size2 = map(int, match.groups()[:4])
+                start1, size1, start2, size2 = map(int, res[:4])
             except: # '@@ -0,0 +1 @@' case
-                start1, size1, size2 = map(int, match.groups()[:3])
+                start1, size1, size2 = map(int, res[:3])
                 start2 = 0
 
         elif line.startswith('+'):

pr_agent/algo/pr_processing.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import difflib
-import logging
 import re
 import traceback
 from typing import Any, Callable, List, Tuple
@@ -11,9 +10,11 @@ from github import RateLimitExceededException
 from pr_agent.algo import MAX_TOKENS
 from pr_agent.algo.git_patch_processing import convert_to_hunks_with_lines_numbers, extend_patch, handle_patch_deletions
 from pr_agent.algo.language_handler import sort_files_by_main_languages
+from pr_agent.algo.file_filter import filter_ignored
 from pr_agent.algo.token_handler import TokenHandler, get_token_encoder
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.git_provider import FilePatchInfo, GitProvider
+from pr_agent.log import get_logger
 
 DELETED_FILES_ = "Deleted files:\n"
 
@@ -21,7 +22,6 @@ MORE_MODIFIED_FILES_ = "More modified files:\n"
 
 OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD = 1000
 OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD = 600
-PATCH_EXTRA_LINES = 3
 
 def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler, model: str,
                 add_line_numbers_to_hunks: bool = False, disable_extra_lines: bool = False) -> str:
@@ -44,21 +44,24 @@ def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler, model: s
     """
 
     if disable_extra_lines:
-        global PATCH_EXTRA_LINES
         PATCH_EXTRA_LINES = 0
+    else:
+        PATCH_EXTRA_LINES = get_settings().config.patch_extra_lines
 
     try:
         diff_files = git_provider.get_diff_files()
     except RateLimitExceededException as e:
-        logging.error(f"Rate limit exceeded for git provider API. original message {e}")
+        get_logger().error(f"Rate limit exceeded for git provider API. original message {e}")
         raise
 
+    diff_files = filter_ignored(diff_files)
+
     # get pr languages
     pr_languages = sort_files_by_main_languages(git_provider.get_languages(), diff_files)
 
     # generate a standard diff string, with patch extension
-    patches_extended, total_tokens, patches_extended_tokens = pr_generate_extended_diff(pr_languages, token_handler,
-                                                               add_line_numbers_to_hunks)
+    patches_extended, total_tokens, patches_extended_tokens = pr_generate_extended_diff(
+        pr_languages, token_handler, add_line_numbers_to_hunks, patch_extra_lines=PATCH_EXTRA_LINES)
 
     # if we are under the limit, return the full diff
     if total_tokens + OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD < MAX_TOKENS[model]:
@@ -80,7 +83,8 @@ def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler, model: s
 
 def pr_generate_extended_diff(pr_languages: list,
                               token_handler: TokenHandler,
-                              add_line_numbers_to_hunks: bool) -> Tuple[list, int, list]:
+                              add_line_numbers_to_hunks: bool,
+                              patch_extra_lines: int = 0) -> Tuple[list, int, list]:
     """
     Generate a standard diff string with patch extension, while counting the number of tokens used and applying diff
     minimization techniques if needed.
@@ -102,7 +106,7 @@ def pr_generate_extended_diff(pr_languages: list,
                 continue
 
             # extend each patch with extra lines of context
-            extended_patch = extend_patch(original_file_content_str, patch, num_lines=PATCH_EXTRA_LINES)
+            extended_patch = extend_patch(original_file_content_str, patch, num_lines=patch_extra_lines)
             full_extended_patch = f"\n\n## {file.filename}\n\n{extended_patch}\n"
 
             if add_line_numbers_to_hunks:
@@ -176,7 +180,7 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
 
         # Hard Stop, no more tokens
         if total_tokens > MAX_TOKENS[model] - OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD:
-            logging.warning(f"File was fully skipped, no more tokens: {file.filename}.")
+            get_logger().warning(f"File was fully skipped, no more tokens: {file.filename}.")
             continue
 
         # If the patch is too large, just show the file name
@@ -185,7 +189,7 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
             # TODO: Option for alternative logic to remove hunks from the patch to reduce the number of tokens
             #  until we meet the requirements
             if get_settings().config.verbosity_level >= 2:
-                logging.warning(f"Patch too large, minimizing it, {file.filename}")
+                get_logger().warning(f"Patch too large, minimizing it, {file.filename}")
             if not modified_files_list:
                 total_tokens += token_handler.count_tokens(MORE_MODIFIED_FILES_)
             modified_files_list.append(file.filename)
@@ -200,7 +204,7 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
             patches.append(patch_final)
             total_tokens += token_handler.count_tokens(patch_final)
             if get_settings().config.verbosity_level >= 2:
-                logging.info(f"Tokens: {total_tokens}, last filename: {file.filename}")
+                get_logger().info(f"Tokens: {total_tokens}, last filename: {file.filename}")
 
     return patches, modified_files_list, deleted_files_list
 
@@ -214,7 +218,7 @@ async def retry_with_fallback_models(f: Callable):
             get_settings().set("openai.deployment_id", deployment_id)
             return await f(model)
         except Exception as e:
-            logging.warning(
+            get_logger().warning(
                 f"Failed to generate prediction with {model}"
                 f"{(' from deployment ' + deployment_id) if deployment_id else ''}: "
                 f"{traceback.format_exc()}"
@@ -336,7 +340,7 @@ def clip_tokens(text: str, max_tokens: int) -> str:
         clipped_text = text[:num_output_chars]
         return clipped_text
     except Exception as e:
-        logging.warning(f"Failed to clip tokens: {e}")
+        get_logger().warning(f"Failed to clip tokens: {e}")
         return text
 
 
@@ -347,25 +351,27 @@ def get_pr_multi_diffs(git_provider: GitProvider,
     """
     Retrieves the diff files from a Git provider, sorts them by main language, and generates patches for each file.
     The patches are split into multiple groups based on the maximum number of tokens allowed for the given model.
-    
+
     Args:
         git_provider (GitProvider): An object that provides access to Git provider APIs.
         token_handler (TokenHandler): An object that handles tokens in the context of a pull request.
         model (str): The name of the model.
         max_calls (int, optional): The maximum number of calls to retrieve diff files. Defaults to 5.
-    
+
     Returns:
         List[str]: A list of final diff strings, split into multiple groups based on the maximum number of tokens allowed for the given model.
-    
+
     Raises:
         RateLimitExceededException: If the rate limit for the Git provider API is exceeded.
     """
     try:
         diff_files = git_provider.get_diff_files()
     except RateLimitExceededException as e:
-        logging.error(f"Rate limit exceeded for git provider API. original message {e}")
+        get_logger().error(f"Rate limit exceeded for git provider API. original message {e}")
         raise
 
+    diff_files = filter_ignored(diff_files)
+
     # Sort files by main language
     pr_languages = sort_files_by_main_languages(git_provider.get_languages(), diff_files)
 
@@ -381,7 +387,7 @@ def get_pr_multi_diffs(git_provider: GitProvider,
     for file in sorted_files:
         if call_number > max_calls:
             if get_settings().config.verbosity_level >= 2:
-                logging.info(f"Reached max calls ({max_calls})")
+                get_logger().info(f"Reached max calls ({max_calls})")
             break
 
         original_file_content_str = file.base_file
@@ -404,13 +410,13 @@ def get_pr_multi_diffs(git_provider: GitProvider,
             total_tokens = token_handler.prompt_tokens
             call_number += 1
             if get_settings().config.verbosity_level >= 2:
-                logging.info(f"Call number: {call_number}")
+                get_logger().info(f"Call number: {call_number}")
 
         if patch:
             patches.append(patch)
             total_tokens += new_patch_tokens
             if get_settings().config.verbosity_level >= 2:
-                logging.info(f"Tokens: {total_tokens}, last filename: {file.filename}")
+                get_logger().info(f"Tokens: {total_tokens}, last filename: {file.filename}")
 
     # Add the last chunk
     if patches:

pr_agent/algo/utils.py

@@ -2,7 +2,6 @@ from __future__ import annotations
 
 import difflib
 import json
-import logging
 import re
 import textwrap
 from datetime import datetime
@@ -11,6 +10,7 @@ from typing import Any, List
 import yaml
 from starlette_context import context
 from pr_agent.config_loader import get_settings, global_settings
+from pr_agent.log import get_logger
 
 
 def get_setting(key: str) -> Any:
@@ -62,7 +62,7 @@ def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
                 markdown_text += f"- {emoji} **{key}:**\n\n"
             for item in value:
                 if isinstance(item, dict) and key.lower() == 'code feedback':
-                    markdown_text += parse_code_suggestion(item)
+                    markdown_text += parse_code_suggestion(item, gfm_supported)
                 elif item:
                     markdown_text += f"  - {item}\n"
             if key.lower() == 'code feedback':
@@ -76,7 +76,7 @@ def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
     return markdown_text
 
 
-def parse_code_suggestion(code_suggestions: dict) -> str:
+def parse_code_suggestion(code_suggestions: dict, gfm_supported: bool=True) -> str:
     """
     Convert a dictionary of data into markdown format.
 
@@ -99,6 +99,9 @@ def parse_code_suggestion(code_suggestions: dict) -> str:
                 markdown_text += f"\n  - **{sub_key}:** {sub_value}\n"
             else:
                 markdown_text += f"   **{sub_key}:** {sub_value}\n"
+            if not gfm_supported:
+                if "relevant line" not in sub_key.lower(): # nicer presentation
+                        markdown_text = markdown_text.rstrip('\n') + "\\\n"
 
     markdown_text += "\n"
     return markdown_text
@@ -156,7 +159,7 @@ def try_fix_json(review, max_iter=10, code_suggestions=False):
                 iter_count += 1
 
         if not valid_json:
-            logging.error("Unable to decode JSON response from AI")
+            get_logger().error("Unable to decode JSON response from AI")
             data = {}
 
     return data
@@ -227,7 +230,7 @@ def load_large_diff(filename, new_file_content_str: str, original_file_content_s
         diff = difflib.unified_diff(original_file_content_str.splitlines(keepends=True),
                                     new_file_content_str.splitlines(keepends=True))
         if get_settings().config.verbosity_level >= 2:
-            logging.warning(f"File was modified, but no patch was found. Manually creating patch: {filename}.")
+            get_logger().warning(f"File was modified, but no patch was found. Manually creating patch: {filename}.")
         patch = ''.join(diff)
     except Exception:
         pass
@@ -259,12 +262,12 @@ def update_settings_from_args(args: List[str]) -> List[str]:
                 vals = arg.split('=', 1)
                 if len(vals) != 2:
                     if len(vals) > 2: # --extended is a valid argument
-                        logging.error(f'Invalid argument format: {arg}')
+                        get_logger().error(f'Invalid argument format: {arg}')
                     other_args.append(arg)
                     continue
                 key, value = _fix_key_value(*vals)
                 get_settings().set(key, value)
-                logging.info(f'Updated setting {key} to: "{value}"')
+                get_logger().info(f'Updated setting {key} to: "{value}"')
             else:
                 other_args.append(arg)
     return other_args
@@ -276,7 +279,7 @@ def _fix_key_value(key: str, value: str):
     try:
         value = yaml.safe_load(value)
     except Exception as e:
-        logging.error(f"Failed to parse YAML for config override {key}={value}", exc_info=e)
+        get_logger().error(f"Failed to parse YAML for config override {key}={value}", exc_info=e)
     return key, value
 
 
@@ -285,7 +288,7 @@ def load_yaml(review_text: str) -> dict:
     try:
         data = yaml.safe_load(review_text)
     except Exception as e:
-        logging.error(f"Failed to parse AI prediction: {e}")
+        get_logger().error(f"Failed to parse AI prediction: {e}")
         data = try_fix_yaml(review_text)
     return data
 
@@ -296,8 +299,24 @@ def try_fix_yaml(review_text: str) -> dict:
         review_text_lines_tmp = '\n'.join(review_text_lines[:-i])
         try:
             data = yaml.load(review_text_lines_tmp, Loader=yaml.SafeLoader)
-            logging.info(f"Successfully parsed AI prediction after removing {i} lines")
+            get_logger().info(f"Successfully parsed AI prediction after removing {i} lines")
             break
         except:
             pass
     return data
+
+
+def set_custom_labels(variables):
+    labels = get_settings().custom_labels
+    if not labels:
+        # set default labels
+        labels = ['Bug fix', 'Tests', 'Bug fix with tests', 'Refactoring', 'Enhancement', 'Documentation', 'Other']
+        labels_list = "\n      - ".join(labels) if labels else ""
+        labels_list = f"      - {labels_list}" if labels_list else ""
+        variables["custom_labels"] = labels_list
+        return
+    final_labels = ""
+    for k, v in labels.items():
+        final_labels += f"      - {k} ({v['description']})\n"
+    variables["custom_labels"] = final_labels
+    variables["custom_labels_examples"] = f"      - {list(labels.keys())[0]}"

pr_agent/cli.py

@@ -1,11 +1,12 @@
 import argparse
 import asyncio
-import logging
 import os
 
 from pr_agent.agent.pr_agent import PRAgent, commands
 from pr_agent.config_loader import get_settings
+from pr_agent.log import setup_logger
 
+setup_logger()
 
 def run(inargs=None):
     parser = argparse.ArgumentParser(description='AI based pull request analyzer', usage=
@@ -47,7 +48,6 @@ For example: 'python cli.py --pr_url=... review --pr_reviewer.extra_instructions
         parser.print_help()
         return
 
-    logging.basicConfig(level=os.environ.get("LOGLEVEL", "INFO"))
     command = args.command.lower()
     get_settings().set("CONFIG.CLI_MODE", True)
     if args.issue_url:

pr_agent/config_loader.py

@@ -14,6 +14,7 @@ global_settings = Dynaconf(
     settings_files=[join(current_dir, f) for f in [
         "settings/.secrets.toml",
         "settings/configuration.toml",
+        "settings/ignore.toml",
         "settings/language_extensions.toml",
         "settings/pr_reviewer_prompts.toml",
         "settings/pr_questions_prompts.toml",
@@ -22,7 +23,10 @@ global_settings = Dynaconf(
         "settings/pr_sort_code_suggestions_prompts.toml",
         "settings/pr_information_from_user_prompts.toml",
         "settings/pr_update_changelog_prompts.toml",
-        "settings_prod/.secrets.toml"
+        "settings/pr_custom_labels.toml",
+        "settings/pr_add_docs.toml",
+        "settings_prod/.secrets.toml",
+        "settings/custom_labels.toml"
     ]]
 )
 

pr_agent/git_providers/azuredevops_provider.py

@@ -1,10 +1,11 @@
 import json
-import logging
 from typing import Optional, Tuple
 from urllib.parse import urlparse
 
 import os
 
+from ..log import get_logger
+
 AZURE_DEVOPS_AVAILABLE = True
 try:
     from msrest.authentication import BasicAuthentication
@@ -55,7 +56,7 @@ class AzureDevopsProvider:
                                                                  path=".pr_agent.toml")
             return contents
         except Exception as e:
-            logging.exception("get repo settings error")
+            get_logger().exception("get repo settings error")
             return ""
 
     def get_files(self):
@@ -88,6 +89,8 @@ class AzureDevopsProvider:
                 changes_obj = self.azure_devops_client.get_changes(project=self.workspace_slug,
                                                                    repository_id=self.repo_slug, commit_id=c.commit_id)
                 for i in changes_obj.changes:
+                    if(i['item']['gitObjectType'] == 'tree'):
+                        continue
                     diffs.append(i['item']['path'])
                     diff_types[i['item']['path']] = i['changeType']
 
@@ -98,14 +101,18 @@ class AzureDevopsProvider:
                     continue
 
                 version = GitVersionDescriptor(version=head_sha.commit_id, version_type='commit')
-                new_file_content_str = self.azure_devops_client.get_item(repository_id=self.repo_slug,
-                                                                         path=file,
-                                                                         project=self.workspace_slug,
-                                                                         version_descriptor=version,
-                                                                         download=False,
-                                                                         include_content=True)
+                try:
+                    new_file_content_str = self.azure_devops_client.get_item(repository_id=self.repo_slug,
+                                                                            path=file,
+                                                                            project=self.workspace_slug,
+                                                                            version_descriptor=version,
+                                                                            download=False,
+                                                                            include_content=True)
 
-                new_file_content_str = new_file_content_str.content
+                    new_file_content_str = new_file_content_str.content
+                except Exception as error:
+                    get_logger().error("Failed to retrieve new file content of %s at version %s. Error: %s", file, version, str(error))
+                    new_file_content_str = ""
 
                 edit_type = EDIT_TYPE.MODIFIED
                 if diff_types[file] == 'add':
@@ -116,13 +123,17 @@ class AzureDevopsProvider:
                     edit_type = EDIT_TYPE.RENAMED
 
                 version = GitVersionDescriptor(version=base_sha.commit_id, version_type='commit')
-                original_file_content_str = self.azure_devops_client.get_item(repository_id=self.repo_slug,
+                try:
+                    original_file_content_str = self.azure_devops_client.get_item(repository_id=self.repo_slug,
                                                                               path=file,
                                                                               project=self.workspace_slug,
                                                                               version_descriptor=version,
                                                                               download=False,
                                                                               include_content=True)
-                original_file_content_str = original_file_content_str.content
+                    original_file_content_str = original_file_content_str.content
+                except Exception as error:
+                    get_logger().error("Failed to retrieve original file content of %s at version %s. Error: %s", file, version, str(error))
+                    original_file_content_str = ""
 
                 patch = load_large_diff(file, new_file_content_str, original_file_content_str)
 
@@ -156,7 +167,7 @@ class AzureDevopsProvider:
                                                          pull_request_id=self.pr_num,
                                                          git_pull_request_to_update=updated_pr)
         except Exception as e:
-            logging.exception(f"Could not update pull request {self.pr_num} description: {e}")
+            get_logger().exception(f"Could not update pull request {self.pr_num} description: {e}")
 
     def remove_initial_comment(self):
         return ""  # not implemented yet
@@ -225,9 +236,6 @@ class AzureDevopsProvider:
     def _parse_pr_url(pr_url: str) -> Tuple[str, int]:
         parsed_url = urlparse(pr_url)
 
-        if 'azure.com' not in parsed_url.netloc:
-            raise ValueError("The provided URL is not a valid Azure DevOps URL")
-
         path_parts = parsed_url.path.strip('/').split('/')
 
         if len(path_parts) < 6 or path_parts[4] != 'pullrequest':

pr_agent/git_providers/bitbucket_provider.py

@@ -1,5 +1,4 @@
 import json
-import logging
 from typing import Optional, Tuple
 from urllib.parse import urlparse
 
@@ -7,8 +6,9 @@ import requests
 from atlassian.bitbucket import Cloud
 from starlette_context import context
 
-from ..algo.pr_processing import clip_tokens, find_line_number_of_relevant_line_in_file
+from ..algo.pr_processing import find_line_number_of_relevant_line_in_file
 from ..config_loader import get_settings
+from ..log import get_logger
 from .git_provider import FilePatchInfo, GitProvider
 
 
@@ -61,14 +61,14 @@ class BitbucketProvider(GitProvider):
 
             if not relevant_lines_start or relevant_lines_start == -1:
                 if get_settings().config.verbosity_level >= 2:
-                    logging.exception(
+                    get_logger().exception(
                         f"Failed to publish code suggestion, relevant_lines_start is {relevant_lines_start}"
                     )
                 continue
 
             if relevant_lines_end < relevant_lines_start:
                 if get_settings().config.verbosity_level >= 2:
-                    logging.exception(
+                    get_logger().exception(
                         f"Failed to publish code suggestion, "
                         f"relevant_lines_end is {relevant_lines_end} and "
                         f"relevant_lines_start is {relevant_lines_start}"
@@ -97,7 +97,7 @@ class BitbucketProvider(GitProvider):
             return True
         except Exception as e:
             if get_settings().config.verbosity_level >= 2:
-                logging.error(f"Failed to publish code suggestion, error: {e}")
+                get_logger().error(f"Failed to publish code suggestion, error: {e}")
             return False
 
     def is_supported(self, capability: str) -> bool:
@@ -144,7 +144,7 @@ class BitbucketProvider(GitProvider):
             for comment in self.temp_comments:
                 self.pr.delete(f"comments/{comment}")
         except Exception as e:
-            logging.exception(f"Failed to remove temp comments, error: {e}")
+            get_logger().exception(f"Failed to remove temp comments, error: {e}")
 
 
     # funtion to create_inline_comment
@@ -152,7 +152,7 @@ class BitbucketProvider(GitProvider):
         position, absolute_position = find_line_number_of_relevant_line_in_file(self.get_diff_files(), relevant_file.strip('`'), relevant_line_in_file)
         if position == -1:
             if get_settings().config.verbosity_level >= 2:
-                logging.info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
+                get_logger().info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
             subject_type = "FILE"
         else:
             subject_type = "LINE"

pr_agent/git_providers/codecommit_provider.py

@@ -1,17 +1,16 @@
-import logging
 import os
 import re
 from collections import Counter
 from typing import List, Optional, Tuple
 from urllib.parse import urlparse
 
-from ..algo.language_handler import is_valid_file, language_extension_map
-from ..algo.pr_processing import clip_tokens
-from ..algo.utils import load_large_diff
-from ..config_loader import get_settings
-from .git_provider import EDIT_TYPE, FilePatchInfo, GitProvider, IncrementalPR
 from pr_agent.git_providers.codecommit_client import CodeCommitClient
 
+from ..algo.language_handler import is_valid_file, language_extension_map
+from ..algo.utils import load_large_diff
+from .git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
+from ..log import get_logger
+
 
 class PullRequestCCMimic:
     """
@@ -166,7 +165,7 @@ class CodeCommitProvider(GitProvider):
 
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
         if is_temporary:
-            logging.info(pr_comment)
+            get_logger().info(pr_comment)
             return
 
         pr_comment = CodeCommitProvider._remove_markdown_html(pr_comment)
@@ -188,12 +187,12 @@ class CodeCommitProvider(GitProvider):
         for suggestion in code_suggestions:
             # Verify that each suggestion has the required keys
             if not all(key in suggestion for key in ["body", "relevant_file", "relevant_lines_start"]):
-                logging.warning(f"Skipping code suggestion #{counter}: Each suggestion must have 'body', 'relevant_file', 'relevant_lines_start' keys")
+                get_logger().warning(f"Skipping code suggestion #{counter}: Each suggestion must have 'body', 'relevant_file', 'relevant_lines_start' keys")
                 continue
        
             # Publish the code suggestion to CodeCommit
             try:
-                logging.debug(f"Code Suggestion #{counter} in file: {suggestion['relevant_file']}: {suggestion['relevant_lines_start']}")
+                get_logger().debug(f"Code Suggestion #{counter} in file: {suggestion['relevant_file']}: {suggestion['relevant_lines_start']}")
                 self.codecommit_client.publish_comment(
                     repo_name=self.repo_name,
                     pr_number=self.pr_num,
@@ -233,8 +232,20 @@ class CodeCommitProvider(GitProvider):
         raise NotImplementedError("CodeCommit provider does not support publishing inline comments yet")
 
     def get_title(self):
-        return self.pr.get("title", "")
+        return self.pr.title
 
+    def get_pr_id(self):
+        """
+        Returns the PR ID in the format: "repo_name/pr_number".
+        Note: This is an internal identifier for PR-Agent, 
+        and is not the same as the CodeCommit PR identifier.
+        """
+        try:
+            pr_id = f"{self.repo_name}/{self.pr_num}"
+            return pr_id
+        except:
+            return ""
+        
     def get_languages(self):
         """
         Returns a dictionary of languages, containing the percentage of each language used in the PR.
@@ -284,11 +295,11 @@ class CodeCommitProvider(GitProvider):
         return self.codecommit_client.get_file(self.repo_name, settings_filename, self.pr.source_commit, optional=True)
 
     def add_eyes_reaction(self, issue_comment_id: int) -> Optional[int]:
-        logging.info("CodeCommit provider does not support eyes reaction yet")
+        get_logger().info("CodeCommit provider does not support eyes reaction yet")
         return True
 
     def remove_reaction(self, issue_comment_id: int, reaction_id: int) -> bool:
-        logging.info("CodeCommit provider does not support removing reactions yet")
+        get_logger().info("CodeCommit provider does not support removing reactions yet")
         return True
 
     @staticmethod
@@ -354,7 +365,7 @@ class CodeCommitProvider(GitProvider):
         # TODO: implement support for multiple targets in one CodeCommit PR
         #       for now, we are only using the first target in the PR
         if len(response.targets) > 1:
-            logging.warning(
+            get_logger().warning(
                 "Multiple targets in one PR is not supported for CodeCommit yet. Continuing, using the first target only..."
             )
 

pr_agent/git_providers/gerrit_provider.py

@@ -1,5 +1,4 @@
 import json
-import logging
 import os
 import pathlib
 import shutil
@@ -7,18 +6,16 @@ import subprocess
 import uuid
 from collections import Counter, namedtuple
 from pathlib import Path
-from tempfile import mkdtemp, NamedTemporaryFile
+from tempfile import NamedTemporaryFile, mkdtemp
 
 import requests
 import urllib3.util
 from git import Repo
 
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers.git_provider import GitProvider, FilePatchInfo, \
-    EDIT_TYPE
+from pr_agent.git_providers.git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
 from pr_agent.git_providers.local_git_provider import PullRequestMimic
-
-logger = logging.getLogger(__name__)
+from pr_agent.log import get_logger
 
 
 def _call(*command, **kwargs) -> (int, str, str):
@@ -33,42 +30,42 @@ def _call(*command, **kwargs) -> (int, str, str):
 
 
 def clone(url, directory):
-    logger.info("Cloning %s to %s", url, directory)
+    get_logger().info("Cloning %s to %s", url, directory)
     stdout = _call('git', 'clone', "--depth", "1", url, directory)
-    logger.info(stdout)
+    get_logger().info(stdout)
 
 
 def fetch(url, refspec, cwd):
-    logger.info("Fetching %s %s", url, refspec)
+    get_logger().info("Fetching %s %s", url, refspec)
     stdout = _call(
         'git', 'fetch', '--depth', '2', url, refspec,
         cwd=cwd
     )
-    logger.info(stdout)
+    get_logger().info(stdout)
 
 
 def checkout(cwd):
-    logger.info("Checking out")
+    get_logger().info("Checking out")
     stdout = _call('git', 'checkout', "FETCH_HEAD", cwd=cwd)
-    logger.info(stdout)
+    get_logger().info(stdout)
 
 
 def show(*args, cwd=None):
-    logger.info("Show")
+    get_logger().info("Show")
     return _call('git', 'show', *args, cwd=cwd)
 
 
 def diff(*args, cwd=None):
-    logger.info("Diff")
+    get_logger().info("Diff")
     patch = _call('git', 'diff', *args, cwd=cwd)
     if not patch:
-        logger.warning("No changes found")
+        get_logger().warning("No changes found")
         return
     return patch
 
 
 def reset_local_changes(cwd):
-    logger.info("Reset local changes")
+    get_logger().info("Reset local changes")
     _call('git', 'checkout', "--force", cwd=cwd)
 
 

pr_agent/git_providers/git_provider.py

@@ -1,4 +1,3 @@
-import logging
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
 
@@ -6,6 +5,8 @@ from dataclasses import dataclass
 from enum import Enum
 from typing import Optional
 
+from pr_agent.log import get_logger
+
 
 class EDIT_TYPE(Enum):
     ADDED = 1
@@ -127,13 +128,16 @@ class GitProvider(ABC):
     def get_commit_messages(self):
         pass
 
+    def get_pr_id(self):
+        return ""
+
 def get_main_pr_language(languages, files) -> str:
     """
     Get the main language of the commit. Return an empty string if cannot determine.
     """
     main_language_str = ""
     if not languages:
-        logging.info("No languages detected")
+        get_logger().info("No languages detected")
         return main_language_str
 
     try:
@@ -169,7 +173,7 @@ def get_main_pr_language(languages, files) -> str:
             main_language_str = top_language
 
     except Exception as e:
-        logging.exception(e)
+        get_logger().exception(e)
         pass
 
     return main_language_str

pr_agent/git_providers/github_provider.py

@@ -1,20 +1,19 @@
-import logging
 import hashlib
-
 from datetime import datetime
-from typing import Optional, Tuple, Any
+from typing import Optional, Tuple
 from urllib.parse import urlparse
 
-from github import AppAuthentication, Auth, Github, GithubException, Reaction
+from github import AppAuthentication, Auth, Github, GithubException
 from retry import retry
 from starlette_context import context
 
-from .git_provider import FilePatchInfo, GitProvider, IncrementalPR
 from ..algo.language_handler import is_valid_file
+from ..algo.pr_processing import clip_tokens, find_line_number_of_relevant_line_in_file
 from ..algo.utils import load_large_diff
-from ..algo.pr_processing import find_line_number_of_relevant_line_in_file, clip_tokens
 from ..config_loader import get_settings
+from ..log import get_logger
 from ..servers.utils import RateLimitExceeded
+from .git_provider import FilePatchInfo, GitProvider, IncrementalPR
 
 
 class GithubProvider(GitProvider):
@@ -58,7 +57,7 @@ class GithubProvider(GitProvider):
             self.file_set = dict()
             for commit in self.incremental.commits_range:
                 if commit.commit.message.startswith(f"Merge branch '{self._get_repo().default_branch}'"):
-                    logging.info(f"Skipping merge commit {commit.commit.message}")
+                    get_logger().info(f"Skipping merge commit {commit.commit.message}")
                     continue
                 self.file_set.update({file.filename: file for file in commit.files})
 
@@ -78,7 +77,7 @@ class GithubProvider(GitProvider):
         self.previous_review = None
         self.comments = list(self.pr.get_issue_comments())
         for index in range(len(self.comments) - 1, -1, -1):
-            if self.comments[index].body.startswith("## PR Analysis"):
+            if self.comments[index].body.startswith("## PR Analysis") or self.comments[index].body.startswith("## Incremental PR Review"):
                 self.previous_review = self.comments[index]
                 break
 
@@ -130,7 +129,7 @@ class GithubProvider(GitProvider):
             return diff_files
 
         except GithubException.RateLimitExceededException as e:
-            logging.error(f"Rate limit exceeded for GitHub API. Original message: {e}")
+            get_logger().error(f"Rate limit exceeded for GitHub API. Original message: {e}")
             raise RateLimitExceeded("Rate limit exceeded for GitHub API.") from e
 
     def publish_description(self, pr_title: str, pr_body: str):
@@ -138,7 +137,7 @@ class GithubProvider(GitProvider):
 
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
         if is_temporary and not get_settings().config.publish_output_progress:
-            logging.debug(f"Skipping publish_comment for temporary comment: {pr_comment}")
+            get_logger().debug(f"Skipping publish_comment for temporary comment: {pr_comment}")
             return
         response = self.pr.create_issue_comment(pr_comment)
         if hasattr(response, "user") and hasattr(response.user, "login"):
@@ -156,7 +155,7 @@ class GithubProvider(GitProvider):
         position, absolute_position = find_line_number_of_relevant_line_in_file(self.diff_files, relevant_file.strip('`'), relevant_line_in_file)
         if position == -1:
             if get_settings().config.verbosity_level >= 2:
-                logging.info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
+                get_logger().info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
             subject_type = "FILE"
         else:
             subject_type = "LINE"
@@ -179,13 +178,13 @@ class GithubProvider(GitProvider):
 
             if not relevant_lines_start or relevant_lines_start == -1:
                 if get_settings().config.verbosity_level >= 2:
-                    logging.exception(
+                    get_logger().exception(
                         f"Failed to publish code suggestion, relevant_lines_start is {relevant_lines_start}")
                 continue
 
             if relevant_lines_end < relevant_lines_start:
                 if get_settings().config.verbosity_level >= 2:
-                    logging.exception(f"Failed to publish code suggestion, "
+                    get_logger().exception(f"Failed to publish code suggestion, "
                                       f"relevant_lines_end is {relevant_lines_end} and "
                                       f"relevant_lines_start is {relevant_lines_start}")
                 continue
@@ -212,7 +211,7 @@ class GithubProvider(GitProvider):
             return True
         except Exception as e:
             if get_settings().config.verbosity_level >= 2:
-                logging.error(f"Failed to publish code suggestion, error: {e}")
+                get_logger().error(f"Failed to publish code suggestion, error: {e}")
             return False
 
     def remove_initial_comment(self):
@@ -221,7 +220,7 @@ class GithubProvider(GitProvider):
                 if comment.is_temporary:
                     comment.delete()
         except Exception as e:
-            logging.exception(f"Failed to remove initial comment, error: {e}")
+            get_logger().exception(f"Failed to remove initial comment, error: {e}")
 
     def get_title(self):
         return self.pr.title
@@ -239,9 +238,10 @@ class GithubProvider(GitProvider):
     def get_user_id(self):
         if not self.github_user_id:
             try:
-                self.github_user_id = self.github_client.get_user().login
+                self.github_user_id = self.github_client.get_user().raw_data['login']
             except Exception as e:
-                logging.exception(f"Failed to get user id, error: {e}")
+                self.github_user_id = ""
+                # logging.exception(f"Failed to get user id, error: {e}")
         return self.github_user_id
 
     def get_notifications(self, since: datetime):
@@ -258,7 +258,10 @@ class GithubProvider(GitProvider):
 
     def get_repo_settings(self):
         try:
-            contents = self.repo_obj.get_contents(".pr_agent.toml", ref=self.pr.head.sha).decoded_content
+            # contents = self.repo_obj.get_contents(".pr_agent.toml", ref=self.pr.head.sha).decoded_content
+
+            # more logical to take 'pr_agent.toml' from the default branch
+            contents = self.repo_obj.get_contents(".pr_agent.toml").decoded_content
             return contents
         except Exception:
             return ""
@@ -268,7 +271,7 @@ class GithubProvider(GitProvider):
             reaction = self.pr.get_issue_comment(issue_comment_id).create_reaction("eyes")
             return reaction.id
         except Exception as e:
-            logging.exception(f"Failed to add eyes reaction, error: {e}")
+            get_logger().exception(f"Failed to add eyes reaction, error: {e}")
             return None
 
     def remove_reaction(self, issue_comment_id: int, reaction_id: int) -> bool:
@@ -276,7 +279,7 @@ class GithubProvider(GitProvider):
             self.pr.get_issue_comment(issue_comment_id).delete_reaction(reaction_id)
             return True
         except Exception as e:
-            logging.exception(f"Failed to remove eyes reaction, error: {e}")
+            get_logger().exception(f"Failed to remove eyes reaction, error: {e}")
             return False
 
 
@@ -395,13 +398,13 @@ class GithubProvider(GitProvider):
                 "PUT", f"{self.pr.issue_url}/labels", input=post_parameters
             )
         except Exception as e:
-            logging.exception(f"Failed to publish labels, error: {e}")
+            get_logger().exception(f"Failed to publish labels, error: {e}")
 
     def get_labels(self):
         try:
             return [label.name for label in self.pr.labels]
         except Exception as e:
-            logging.exception(f"Failed to get labels, error: {e}")
+            get_logger().exception(f"Failed to get labels, error: {e}")
             return []
 
     def get_commit_messages(self):
@@ -443,6 +446,13 @@ class GithubProvider(GitProvider):
                 return link
         except Exception as e:
             if get_settings().config.verbosity_level >= 2:
-                logging.info(f"Failed adding line link, error: {e}")
+                get_logger().info(f"Failed adding line link, error: {e}")
 
         return ""
+
+    def get_pr_id(self):
+        try:
+            pr_id = f"{self.repo}/{self.pr_num}"
+            return pr_id
+        except:
+            return ""

pr_agent/git_providers/gitlab_provider.py

@@ -1,4 +1,4 @@
-import logging
+import hashlib
 import re
 from typing import Optional, Tuple
 from urllib.parse import urlparse
@@ -7,12 +7,12 @@ import gitlab
 from gitlab import GitlabGetError
 
 from ..algo.language_handler import is_valid_file
-from ..algo.pr_processing import clip_tokens
+from ..algo.pr_processing import clip_tokens, find_line_number_of_relevant_line_in_file
 from ..algo.utils import load_large_diff
 from ..config_loader import get_settings
 from .git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
+from ..log import get_logger
 
-logger = logging.getLogger()
 
 class DiffNotFoundError(Exception):
     """Raised when the diff for a merge request cannot be found."""
@@ -58,7 +58,7 @@ class GitLabProvider(GitProvider):
         try:
             self.last_diff = self.mr.diffs.list(get_all=True)[-1]
         except IndexError as e:
-            logger.error(f"Could not get diff for merge request {self.id_mr}")
+            get_logger().error(f"Could not get diff for merge request {self.id_mr}")
             raise DiffNotFoundError(f"Could not get diff for merge request {self.id_mr}") from e
 
 
@@ -98,7 +98,7 @@ class GitLabProvider(GitProvider):
                     if isinstance(new_file_content_str, bytes):
                         new_file_content_str = bytes.decode(new_file_content_str, 'utf-8')
                 except UnicodeDecodeError:
-                    logging.warning(
+                    get_logger().warning(
                         f"Cannot decode file {diff['old_path']} or {diff['new_path']} in merge request {self.id_mr}")
 
                 edit_type = EDIT_TYPE.MODIFIED
@@ -134,7 +134,7 @@ class GitLabProvider(GitProvider):
             self.mr.description = pr_body
             self.mr.save()
         except Exception as e:
-            logging.exception(f"Could not update merge request {self.id_mr} description: {e}")
+            get_logger().exception(f"Could not update merge request {self.id_mr} description: {e}")
 
     def publish_comment(self, mr_comment: str, is_temporary: bool = False):
         comment = self.mr.notes.create({'body': mr_comment})
@@ -156,12 +156,12 @@ class GitLabProvider(GitProvider):
     def send_inline_comment(self,body: str,edit_type: str,found: bool,relevant_file: str,relevant_line_in_file: int,
                             source_line_no: int, target_file: str,target_line_no: int) -> None:
         if not found:
-            logging.info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
+            get_logger().info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
         else:
             # in order to have exact sha's we have to find correct diff for this change
             diff = self.get_relevant_diff(relevant_file, relevant_line_in_file)
             if diff is None:
-                logger.error(f"Could not get diff for merge request {self.id_mr}")
+                get_logger().error(f"Could not get diff for merge request {self.id_mr}")
                 raise DiffNotFoundError(f"Could not get diff for merge request {self.id_mr}")
             pos_obj = {'position_type': 'text',
                        'new_path': target_file.filename,
@@ -174,24 +174,23 @@ class GitLabProvider(GitProvider):
             else:
                 pos_obj['new_line'] = target_line_no - 1
                 pos_obj['old_line'] = source_line_no - 1
-            logging.debug(f"Creating comment in {self.id_mr} with body {body} and position {pos_obj}")
-            self.mr.discussions.create({'body': body,
-                                        'position': pos_obj})
+            get_logger().debug(f"Creating comment in {self.id_mr} with body {body} and position {pos_obj}")
+            self.mr.discussions.create({'body': body, 'position': pos_obj})
 
     def get_relevant_diff(self, relevant_file: str, relevant_line_in_file: int) -> Optional[dict]:
         changes = self.mr.changes()  # Retrieve the changes for the merge request once
         if not changes:
-            logging.error('No changes found for the merge request.')
+            get_logger().error('No changes found for the merge request.')
             return None
         all_diffs = self.mr.diffs.list(get_all=True)
         if not all_diffs:
-            logging.error('No diffs found for the merge request.')
+            get_logger().error('No diffs found for the merge request.')
             return None
         for diff in all_diffs:
             for change in changes['changes']:
                 if change['new_path'] == relevant_file and relevant_line_in_file in change['diff']:
                     return diff
-            logging.debug(
+            get_logger().debug(
                 f'No relevant diff found for {relevant_file} {relevant_line_in_file}. Falling back to last diff.')
         return self.last_diff  # fallback to last_diff if no relevant diff is found
 
@@ -226,7 +225,10 @@ class GitLabProvider(GitProvider):
                 self.send_inline_comment(body, edit_type, found, relevant_file, relevant_line_in_file, source_line_no,
                                          target_file, target_line_no)
             except Exception as e:
-                logging.exception(f"Could not publish code suggestion:\nsuggestion: {suggestion}\nerror: {e}")
+                get_logger().exception(f"Could not publish code suggestion:\nsuggestion: {suggestion}\nerror: {e}")
+
+        # note that we publish suggestions one-by-one. so, if one fails, the rest will still be published
+        return True
 
     def search_line(self, relevant_file, relevant_line_in_file):
         target_file = None
@@ -287,7 +289,7 @@ class GitLabProvider(GitProvider):
             for comment in self.temp_comments:
                 comment.delete()
         except Exception as e:
-            logging.exception(f"Failed to remove temp comments, error: {e}")
+            get_logger().exception(f"Failed to remove temp comments, error: {e}")
 
     def get_title(self):
         return self.mr.title
@@ -355,7 +357,7 @@ class GitLabProvider(GitProvider):
             self.mr.labels = list(set(pr_types))
             self.mr.save()
         except Exception as e:
-            logging.exception(f"Failed to publish labels, error: {e}")
+            get_logger().exception(f"Failed to publish labels, error: {e}")
 
     def publish_inline_comments(self, comments: list[dict]):
         pass
@@ -378,4 +380,35 @@ class GitLabProvider(GitProvider):
             commit_messages_str = ""
         if max_tokens:
             commit_messages_str = clip_tokens(commit_messages_str, max_tokens)
-        return commit_messages_str
+        return commit_messages_str
+
+    def get_pr_id(self):
+        try:
+            pr_id = self.mr.web_url
+            return pr_id
+        except:
+            return ""
+
+    def generate_link_to_relevant_line_number(self, suggestion) -> str:
+        try:
+            relevant_file = suggestion['relevant file'].strip('`').strip("'")
+            relevant_line_str = suggestion['relevant line']
+            if not relevant_line_str:
+                return ""
+
+            position, absolute_position = find_line_number_of_relevant_line_in_file \
+                (self.diff_files, relevant_file, relevant_line_str)
+
+            if absolute_position != -1:
+                # link to right file only
+                link = f"https://gitlab.com/codiumai/pr-agent/-/blob/{self.mr.source_branch}/{relevant_file}?ref_type=heads#L{absolute_position}"
+
+                # # link to diff
+                # sha_file = hashlib.sha1(relevant_file.encode('utf-8')).hexdigest()
+                # link = f"{self.pr.web_url}/diffs#{sha_file}_{absolute_position}_{absolute_position}"
+                return link
+        except Exception as e:
+            if get_settings().config.verbosity_level >= 2:
+                get_logger().info(f"Failed adding line link, error: {e}")
+
+        return ""

pr_agent/git_providers/local_git_provider.py

@@ -1,4 +1,3 @@
-import logging
 from collections import Counter
 from pathlib import Path
 from typing import List
@@ -7,6 +6,7 @@ from git import Repo
 
 from pr_agent.config_loader import _find_repository_root, get_settings
 from pr_agent.git_providers.git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
+from pr_agent.log import get_logger
 
 
 class PullRequestMimic:
@@ -49,7 +49,7 @@ class LocalGitProvider(GitProvider):
         """
         Prepare the repository for PR-mimic generation.
         """
-        logging.debug('Preparing repository for PR-mimic generation...')
+        get_logger().debug('Preparing repository for PR-mimic generation...')
         if self.repo.is_dirty():
             raise ValueError('The repository is not in a clean state. Please commit or stash pending changes.')
         if self.target_branch_name not in self.repo.heads:

pr_agent/git_providers/utils.py

@@ -0,0 +1,36 @@
+import copy
+import os
+import tempfile
+
+from dynaconf import Dynaconf
+
+from pr_agent.config_loader import get_settings
+from pr_agent.git_providers import get_git_provider
+from pr_agent.log import get_logger
+
+
+def apply_repo_settings(pr_url):
+    if get_settings().config.use_repo_settings_file:
+        repo_settings_file = None
+        try:
+            git_provider = get_git_provider()(pr_url)
+            repo_settings = git_provider.get_repo_settings()
+            if repo_settings:
+                repo_settings_file = None
+                fd, repo_settings_file = tempfile.mkstemp(suffix='.toml')
+                os.write(fd, repo_settings)
+                new_settings = Dynaconf(settings_files=[repo_settings_file])
+                for section, contents in new_settings.as_dict().items():
+                    section_dict = copy.deepcopy(get_settings().as_dict().get(section, {}))
+                    for key, value in contents.items():
+                        section_dict[key] = value
+                    get_settings().unset(section)
+                    get_settings().set(section, section_dict, merge=False)
+                    get_logger().info(f"Applying repo settings for section {section}, contents: {contents}")
+
+        finally:
+            if repo_settings_file:
+                try:
+                    os.remove(repo_settings_file)
+                except Exception as e:
+                    get_logger().error(f"Failed to remove temporary settings file {repo_settings_file}", e)

pr_agent/log/__init__.py

@@ -0,0 +1,40 @@
+import json
+import logging
+import sys
+from enum import Enum
+
+from loguru import logger
+
+
+class LoggingFormat(str, Enum):
+    CONSOLE = "CONSOLE"
+    JSON = "JSON"
+
+
+def json_format(record: dict) -> str:
+    return record["message"]
+
+
+def setup_logger(level: str = "INFO", fmt: LoggingFormat = LoggingFormat.CONSOLE):
+    level: int = logging.getLevelName(level.upper())
+    if type(level) is not int:
+        level = logging.INFO
+
+    if fmt == LoggingFormat.JSON:
+        logger.remove(None)
+        logger.add(
+            sys.stdout,
+            level=level,
+            format="{message}",
+            colorize=False,
+            serialize=True,
+        )
+    elif fmt == LoggingFormat.CONSOLE:
+        logger.remove(None)
+        logger.add(sys.stdout, level=level, colorize=True)
+
+    return logger
+
+
+def get_logger(*args, **kwargs):
+    return logger

pr_agent/secret_providers/google_cloud_storage_secret_provider.py

@@ -1,9 +1,8 @@
 import ujson
-
 from google.cloud import storage
 
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers.gitlab_provider import logger
+from pr_agent.log import get_logger
 from pr_agent.secret_providers.secret_provider import SecretProvider
 
 
@@ -15,7 +14,7 @@ class GoogleCloudStorageSecretProvider(SecretProvider):
             self.bucket_name = get_settings().google_cloud_storage.bucket_name
             self.bucket = self.client.bucket(self.bucket_name)
         except Exception as e:
-            logger.error(f"Failed to initialize Google Cloud Storage Secret Provider: {e}")
+            get_logger().error(f"Failed to initialize Google Cloud Storage Secret Provider: {e}")
             raise e
 
     def get_secret(self, secret_name: str) -> str:
@@ -23,7 +22,7 @@ class GoogleCloudStorageSecretProvider(SecretProvider):
             blob = self.bucket.blob(secret_name)
             return blob.download_as_string()
         except Exception as e:
-            logger.error(f"Failed to get secret {secret_name} from Google Cloud Storage: {e}")
+            get_logger().error(f"Failed to get secret {secret_name} from Google Cloud Storage: {e}")
             return ""
 
     def store_secret(self, secret_name: str, secret_value: str):
@@ -31,5 +30,5 @@ class GoogleCloudStorageSecretProvider(SecretProvider):
             blob = self.bucket.blob(secret_name)
             blob.upload_from_string(secret_value)
         except Exception as e:
-            logger.error(f"Failed to store secret {secret_name} in Google Cloud Storage: {e}")
+            get_logger().error(f"Failed to store secret {secret_name} in Google Cloud Storage: {e}")
             raise e

pr_agent/servers/bitbucket_app.py

@@ -1,9 +1,7 @@
 import copy
 import hashlib
 import json
-import logging
 import os
-import sys
 import time
 
 import jwt
@@ -18,9 +16,10 @@ from starlette_context.middleware import RawContextMiddleware
 
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.config_loader import get_settings, global_settings
+from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.secret_providers import get_secret_provider
 
-logging.basicConfig(stream=sys.stdout, level=logging.INFO)
+setup_logger(fmt=LoggingFormat.JSON)
 router = APIRouter()
 secret_provider = get_secret_provider()
 
@@ -49,7 +48,7 @@ async def get_bearer_token(shared_secret: str, client_key: str):
         bearer_token = response.json()["access_token"]
         return bearer_token
     except Exception as e:
-        logging.error(f"Failed to get bearer token: {e}")
+        get_logger().error(f"Failed to get bearer token: {e}")
         raise e
 
 @router.get("/")
@@ -60,21 +59,23 @@ async def handle_manifest(request: Request, response: Response):
         manifest = manifest.replace("app_key", get_settings().bitbucket.app_key)
         manifest = manifest.replace("base_url", get_settings().bitbucket.base_url)
     except:
-        logging.error("Failed to replace api_key in Bitbucket manifest, trying to continue")
+        get_logger().error("Failed to replace api_key in Bitbucket manifest, trying to continue")
     manifest_obj = json.loads(manifest)
     return JSONResponse(manifest_obj)
 
 @router.post("/webhook")
 async def handle_github_webhooks(background_tasks: BackgroundTasks, request: Request):
-    print(request.headers)
+    log_context = {"server_type": "bitbucket_app"}
+    get_logger().debug(request.headers)
     jwt_header = request.headers.get("authorization", None)
     if jwt_header:
         input_jwt = jwt_header.split(" ")[1]
     data = await request.json()
-    print(data)
+    get_logger().debug(data)
     async def inner():
         try:
             owner = data["data"]["repository"]["owner"]["username"]
+            log_context["sender"] = owner
             secrets = json.loads(secret_provider.get_secret(owner))
             shared_secret = secrets["shared_secret"]
             client_key = secrets["client_key"]
@@ -86,13 +87,19 @@ async def handle_github_webhooks(background_tasks: BackgroundTasks, request: Req
             agent = PRAgent()
             if event == "pullrequest:created":
                 pr_url = data["data"]["pullrequest"]["links"]["html"]["href"]
-                await agent.handle_request(pr_url, "review")
+                log_context["api_url"] = pr_url
+                log_context["event"] = "pull_request"
+                with get_logger().contextualize(**log_context):
+                    await agent.handle_request(pr_url, "review")
             elif event == "pullrequest:comment_created":
                 pr_url = data["data"]["pullrequest"]["links"]["html"]["href"]
+                log_context["api_url"] = pr_url
+                log_context["event"] = "comment"
                 comment_body = data["data"]["comment"]["content"]["raw"]
-                await agent.handle_request(pr_url, comment_body)
+                with get_logger().contextualize(**log_context):
+                    await agent.handle_request(pr_url, comment_body)
         except Exception as e:
-            logging.error(f"Failed to handle webhook: {e}")
+            get_logger().error(f"Failed to handle webhook: {e}")
     background_tasks.add_task(inner)
     return "OK"
 
@@ -103,9 +110,10 @@ async def handle_github_webhooks(request: Request, response: Response):
 @router.post("/installed")
 async def handle_installed_webhooks(request: Request, response: Response):
     try:
-        print(request.headers)
+        get_logger().info("handle_installed_webhooks")
+        get_logger().info(request.headers)
         data = await request.json()
-        print(data)
+        get_logger().info(data)
         shared_secret = data["sharedSecret"]
         client_key = data["clientKey"]
         username = data["principal"]["username"]
@@ -115,13 +123,15 @@ async def handle_installed_webhooks(request: Request, response: Response):
         }
         secret_provider.store_secret(username, json.dumps(secrets))
     except Exception as e:
-        logging.error(f"Failed to register user: {e}")
+        get_logger().error(f"Failed to register user: {e}")
         return JSONResponse({"error": "Unable to register user"}, status_code=500)
 
 @router.post("/uninstalled")
 async def handle_uninstalled_webhooks(request: Request, response: Response):
+    get_logger().info("handle_uninstalled_webhooks")
+
     data = await request.json()
-    print(data)
+    get_logger().info(data)
 
 
 def start():

pr_agent/servers/gerrit_server.py

@@ -1,6 +1,4 @@
 import copy
-import logging
-import sys
 from enum import Enum
 from json import JSONDecodeError
 
@@ -12,9 +10,10 @@ from starlette_context import context
 from starlette_context.middleware import RawContextMiddleware
 
 from pr_agent.agent.pr_agent import PRAgent
-from pr_agent.config_loader import global_settings, get_settings
+from pr_agent.config_loader import get_settings, global_settings
+from pr_agent.log import get_logger, setup_logger
 
-logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
+setup_logger()
 router = APIRouter()
 
 
@@ -35,7 +34,7 @@ class Item(BaseModel):
 
 @router.post("/api/v1/gerrit/{action}")
 async def handle_gerrit_request(action: Action, item: Item):
-    logging.debug("Received a Gerrit request")
+    get_logger().debug("Received a Gerrit request")
     context["settings"] = copy.deepcopy(global_settings)
 
     if action == Action.ask:
@@ -54,7 +53,7 @@ async def get_body(request):
     try:
         body = await request.json()
     except JSONDecodeError as e:
-        logging.error("Error parsing request body", e)
+        get_logger().error("Error parsing request body", e)
         return {}
     return body
 

pr_agent/servers/github_action_runner.py

@@ -5,6 +5,10 @@ import os
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
+from pr_agent.git_providers.utils import apply_repo_settings
+from pr_agent.log import get_logger
+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
 
 
@@ -15,8 +19,11 @@ async def run_action():
     OPENAI_KEY = os.environ.get('OPENAI_KEY') or os.environ.get('OPENAI.KEY')
     OPENAI_ORG = os.environ.get('OPENAI_ORG') or os.environ.get('OPENAI.ORG')
     GITHUB_TOKEN = os.environ.get('GITHUB_TOKEN')
-    get_settings().set("CONFIG.PUBLISH_OUTPUT_PROGRESS", False)
+    CUSTOM_LABELS = os.environ.get('CUSTOM_LABELS')
+    CUSTOM_LABELS_DESCRIPTIONS = os.environ.get('CUSTOM_LABELS_DESCRIPTIONS')
+    # CUSTOM_LABELS is a comma separated list of labels (string), convert to list and strip spaces
 
+    get_settings().set("CONFIG.PUBLISH_OUTPUT_PROGRESS", False)
 
     # Check if required environment variables are set
     if not GITHUB_EVENT_NAME:
@@ -31,6 +38,7 @@ async def run_action():
     if not GITHUB_TOKEN:
         print("GITHUB_TOKEN not set")
         return
+    # CUSTOM_LABELS_DICT = handle_custom_labels(CUSTOM_LABELS, CUSTOM_LABELS_DESCRIPTIONS)
 
     # Set the environment variables in the settings
     get_settings().set("OPENAI.KEY", OPENAI_KEY)
@@ -38,6 +46,7 @@ async def run_action():
         get_settings().set("OPENAI.ORG", OPENAI_ORG)
     get_settings().set("GITHUB.USER_TOKEN", GITHUB_TOKEN)
     get_settings().set("GITHUB.DEPLOYMENT_TYPE", "user")
+    # get_settings().set("CUSTOM_LABELS", CUSTOM_LABELS_DICT)
 
     # Load the event payload
     try:
@@ -47,13 +56,30 @@ async def run_action():
         print(f"Failed to parse JSON: {e}")
         return
 
+    try:
+        get_logger().info("Applying repo settings")
+        pr_url = event_payload.get("pull_request", {}).get("html_url")
+        if pr_url:
+            apply_repo_settings(pr_url)
+            get_logger().info(f"enable_custom_labels: {get_settings().config.enable_custom_labels}")
+    except Exception as e:
+        get_logger().info(f"github action: failed to apply repo settings: {e}")
+
     # Handle pull request event
     if GITHUB_EVENT_NAME == "pull_request":
         action = event_payload.get("action")
         if action in ["opened", "reopened"]:
             pr_url = event_payload.get("pull_request", {}).get("url")
             if pr_url:
-                await PRReviewer(pr_url).run()
+                auto_review = os.environ.get('github_action.auto_review', None)
+                if auto_review is None or (isinstance(auto_review, str) and auto_review.lower() == 'true'):
+                    await PRReviewer(pr_url).run()
+                auto_describe = os.environ.get('github_action.auto_describe', None)
+                if isinstance(auto_describe, str) and auto_describe.lower() == 'true':
+                    await PRDescription(pr_url).run()
+                auto_improve = os.environ.get('github_action.auto_improve', None)
+                if isinstance(auto_improve, str) and auto_improve.lower() == 'true':
+                    await PRCodeSuggestions(pr_url).run()
 
     # Handle issue comment event
     elif GITHUB_EVENT_NAME == "issue_comment":
@@ -78,5 +104,31 @@ async def run_action():
                         await PRAgent().handle_request(url, body)
 
 
+def handle_custom_labels(CUSTOM_LABELS, CUSTOM_LABELS_DESCRIPTIONS):
+    if CUSTOM_LABELS:
+        CUSTOM_LABELS = [x.strip() for x in CUSTOM_LABELS.split(',')]
+    else:
+        # Set default labels
+        CUSTOM_LABELS = ['Bug fix', 'Tests', 'Bug fix with tests', 'Refactoring', 'Enhancement', 'Documentation',
+                         'Other']
+        print(f"Using default labels: {CUSTOM_LABELS}")
+    if CUSTOM_LABELS_DESCRIPTIONS:
+        CUSTOM_LABELS_DESCRIPTIONS = [x.strip() for x in CUSTOM_LABELS_DESCRIPTIONS.split(',')]
+    else:
+        # Set default labels
+        CUSTOM_LABELS_DESCRIPTIONS = ['Fixes a bug in the code', 'Adds or modifies tests',
+                                     'Fixes a bug in the code and adds or modifies tests',
+                                     'Refactors the code without changing its functionality',
+                                     'Adds new features or functionality',
+                                     'Adds or modifies documentation',
+                                     'Other changes that do not fit in any of the above categories']
+        print(f"Using default labels: {CUSTOM_LABELS_DESCRIPTIONS}")
+    # create a dictionary of labels and descriptions
+    CUSTOM_LABELS_DICT = dict()
+    for i in range(len(CUSTOM_LABELS)):
+        CUSTOM_LABELS_DICT[CUSTOM_LABELS[i]] = {'description': CUSTOM_LABELS_DESCRIPTIONS[i]}
+    return CUSTOM_LABELS_DICT
+
+
 if __name__ == '__main__':
     asyncio.run(run_action())

pr_agent/servers/github_app.py

@@ -1,6 +1,4 @@
 import copy
-import logging
-import sys
 import os
 import time
 from typing import Any, Dict
@@ -15,9 +13,12 @@ from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings, global_settings
 from pr_agent.git_providers import get_git_provider
+from pr_agent.git_providers.utils import apply_repo_settings
+from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.servers.utils import verify_signature
 
-logging.basicConfig(stream=sys.stdout, level=logging.INFO)
+setup_logger(fmt=LoggingFormat.JSON)
+
 router = APIRouter()
 
 
@@ -28,11 +29,11 @@ async def handle_github_webhooks(request: Request, response: Response):
     Verifies the request signature, parses the request body, and passes it to the handle_request function for further
     processing.
     """
-    logging.debug("Received a GitHub webhook")
+    get_logger().debug("Received a GitHub webhook")
 
     body = await get_body(request)
 
-    logging.debug(f'Request body:\n{body}')
+    get_logger().debug(f'Request body:\n{body}')
     installation_id = body.get("installation", {}).get("id")
     context["installation_id"] = installation_id
     context["settings"] = copy.deepcopy(global_settings)
@@ -44,13 +45,13 @@ async def handle_github_webhooks(request: Request, response: Response):
 @router.post("/api/v1/marketplace_webhooks")
 async def handle_marketplace_webhooks(request: Request, response: Response):
     body = await get_body(request)
-    logging.info(f'Request body:\n{body}')
+    get_logger().info(f'Request body:\n{body}')
 
 async def get_body(request):
     try:
         body = await request.json()
     except Exception as e:
-        logging.error("Error parsing request body", e)
+        get_logger().error("Error parsing request body", e)
         raise HTTPException(status_code=400, detail="Error parsing request body") from e
     webhook_secret = getattr(get_settings().github, 'webhook_secret', None)
     if webhook_secret:
@@ -76,8 +77,8 @@ async def handle_request(body: Dict[str, Any], event: str):
         return {}
     agent = PRAgent()
     bot_user = get_settings().github_app.bot_user
-    logging.info(f"action: '{action}'")
-    logging.info(f"event: '{event}'")
+    sender = body.get("sender", {}).get("login")
+    log_context = {"action": action, "event": event, "sender": sender, "server_type": "github_app"}
 
     if get_settings().github_app.duplicate_requests_cache and _is_duplicate_request(body):
         return {}
@@ -87,22 +88,23 @@ async def handle_request(body: Dict[str, Any], event: str):
         if "comment" not in body:
             return {}
         comment_body = body.get("comment", {}).get("body")
-        sender = body.get("sender", {}).get("login")
         if sender and bot_user in sender:
-            logging.info(f"Ignoring comment from {bot_user} user")
+            get_logger().info(f"Ignoring comment from {bot_user} user")
             return {}
-        logging.info(f"Processing comment from {sender} user")
+        get_logger().info(f"Processing comment from {sender} user")
         if "issue" in body and "pull_request" in body["issue"] and "url" in body["issue"]["pull_request"]:
             api_url = body["issue"]["pull_request"]["url"]
         elif "comment" in body and "pull_request_url" in body["comment"]:
             api_url = body["comment"]["pull_request_url"]
         else:
             return {}
-        logging.info(body)
-        logging.info(f"Handling comment because of event={event} and action={action}")
+        log_context["api_url"] = api_url
+        get_logger().info(body)
+        get_logger().info(f"Handling comment because of event={event} and action={action}")
         comment_id = body.get("comment", {}).get("id")
         provider = get_git_provider()(pr_url=api_url)
-        await agent.handle_request(api_url, comment_body, notify=lambda: provider.add_eyes_reaction(comment_id))
+        with get_logger().contextualize(**log_context):
+            await agent.handle_request(api_url, comment_body, notify=lambda: provider.add_eyes_reaction(comment_id))
 
     # handle pull_request event:
     #   automatically review opened/reopened/ready_for_review PRs as long as they're not in draft,
@@ -114,6 +116,7 @@ async def handle_request(body: Dict[str, Any], event: str):
         api_url = pull_request.get("url")
         if not api_url:
             return {}
+        log_context["api_url"] = api_url
         if pull_request.get("draft", True) or pull_request.get("state") != "open" or pull_request.get("user", {}).get("login", "") == bot_user:
             return {}
         if action in get_settings().github_app.handle_pr_actions:
@@ -123,18 +126,20 @@ async def handle_request(body: Dict[str, Any], event: str):
                 if pull_request.get("created_at") == pull_request.get("updated_at"):
                     # avoid double reviews when opening a PR for the first time
                     return {}
-            logging.info(f"Performing review because of event={event} and action={action}")
+            get_logger().info(f"Performing review because of event={event} and action={action}")
+            apply_repo_settings(api_url)
             for command in get_settings().github_app.pr_commands:
                 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)
-                logging.info(body)
-                logging.info(f"Performing command: {new_command}")
-                await agent.handle_request(api_url, new_command)
+                get_logger().info(body)
+                get_logger().info(f"Performing command: {new_command}")
+                with get_logger().contextualize(**log_context):
+                    await agent.handle_request(api_url, new_command)
 
-    logging.info("event or action does not require handling")
+    get_logger().info("event or action does not require handling")
     return {}
 
 
@@ -144,7 +149,7 @@ def _is_duplicate_request(body: Dict[str, Any]) -> bool:
     This function checks if the request is duplicate and if so - ignores it.
     """
     request_hash = hash(str(body))
-    logging.info(f"request_hash: {request_hash}")
+    get_logger().info(f"request_hash: {request_hash}")
     request_time = time.monotonic()
     ttl = get_settings().github_app.duplicate_requests_cache_ttl  # in seconds
     to_delete = [key for key, key_time in _duplicate_requests_cache.items() if request_time - key_time > ttl]
@@ -153,7 +158,7 @@ def _is_duplicate_request(body: Dict[str, Any]) -> bool:
     is_duplicate = request_hash in _duplicate_requests_cache
     _duplicate_requests_cache[request_hash] = request_time
     if is_duplicate:
-        logging.info(f"Ignoring duplicate request {request_hash}")
+        get_logger().info(f"Ignoring duplicate request {request_hash}")
     return is_duplicate
 
 

pr_agent/servers/github_polling.py

@@ -1,6 +1,4 @@
 import asyncio
-import logging
-import sys
 from datetime import datetime, timezone
 
 import aiohttp
@@ -8,9 +6,10 @@ import aiohttp
 from pr_agent.agent.pr_agent import PRAgent
 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
 from pr_agent.servers.help import bot_help_text
 
-logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
+setup_logger(fmt=LoggingFormat.JSON)
 NOTIFICATION_URL = "https://api.github.com/notifications"
 
 
@@ -94,7 +93,7 @@ async def polling_loop():
                                             comment_body = comment['body'] if 'body' in comment else ''
                                             commenter_github_user = comment['user']['login'] \
                                                 if 'user' in comment else ''
-                                            logging.info(f"Commenter: {commenter_github_user}\nComment: {comment_body}")
+                                            get_logger().info(f"Commenter: {commenter_github_user}\nComment: {comment_body}")
                                             user_tag = "@" + user_id
                                             if user_tag not in comment_body:
                                                 continue
@@ -112,7 +111,7 @@ async def polling_loop():
                         print(f"Failed to fetch notifications. Status code: {response.status}")
 
             except Exception as e:
-                logging.error(f"Exception during processing of a notification: {e}")
+                get_logger().error(f"Exception during processing of a notification: {e}")
 
 
 if __name__ == '__main__':

pr_agent/servers/gitlab_webhook.py

@@ -1,7 +1,5 @@
 import copy
 import json
-import logging
-import sys
 
 import uvicorn
 from fastapi import APIRouter, FastAPI, Request, status
@@ -14,26 +12,37 @@ from starlette_context.middleware import RawContextMiddleware
 
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.config_loader import get_settings, global_settings
+from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.secret_providers import get_secret_provider
 
-logging.basicConfig(stream=sys.stdout, level=logging.INFO)
+setup_logger(fmt=LoggingFormat.JSON)
 router = APIRouter()
 
 secret_provider = get_secret_provider() if get_settings().get("CONFIG.SECRET_PROVIDER") else None
 
 
+def handle_request(background_tasks: BackgroundTasks, url: str, body: str, log_context: dict):
+    log_context["action"] = body
+    log_context["event"] = "pull_request" if body == "/review" else "comment"
+    log_context["api_url"] = url
+    with get_logger().contextualize(**log_context):
+        background_tasks.add_task(PRAgent().handle_request, url, body)
+
+
 @router.post("/webhook")
 async def gitlab_webhook(background_tasks: BackgroundTasks, request: Request):
+    log_context = {"server_type": "gitlab_app"}
     if request.headers.get("X-Gitlab-Token") and secret_provider:
         request_token = request.headers.get("X-Gitlab-Token")
         secret = secret_provider.get_secret(request_token)
         try:
             secret_dict = json.loads(secret)
             gitlab_token = secret_dict["gitlab_token"]
+            log_context["sender"] = secret_dict["id"]
             context["settings"] = copy.deepcopy(global_settings)
             context["settings"].gitlab.personal_access_token = gitlab_token
         except Exception as e:
-            logging.error(f"Failed to validate secret {request_token}: {e}")
+            get_logger().error(f"Failed to validate secret {request_token}: {e}")
             return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
     elif get_settings().get("GITLAB.SHARED_SECRET"):
         secret = get_settings().get("GITLAB.SHARED_SECRET")
@@ -45,17 +54,17 @@ async def gitlab_webhook(background_tasks: BackgroundTasks, request: Request):
     if not gitlab_token:
         return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
     data = await request.json()
-    logging.info(json.dumps(data))
+    get_logger().info(json.dumps(data))
     if data.get('object_kind') == 'merge_request' and data['object_attributes'].get('action') in ['open', 'reopen']:
-        logging.info(f"A merge request has been opened: {data['object_attributes'].get('title')}")
+        get_logger().info(f"A merge request has been opened: {data['object_attributes'].get('title')}")
         url = data['object_attributes'].get('url')
-        background_tasks.add_task(PRAgent().handle_request, url, "/review")
+        handle_request(background_tasks, url, "/review")
     elif data.get('object_kind') == 'note' and data['event_type'] == 'note':
         if 'merge_request' in data:
             mr = data['merge_request']
             url = mr.get('url')
             body = data.get('object_attributes', {}).get('note')
-            background_tasks.add_task(PRAgent().handle_request, url, body)
+            handle_request(background_tasks, url, body)
     return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
 
 

pr_agent/servers/serverless.py

@@ -1,12 +1,10 @@
-import logging
-
 from fastapi import FastAPI
 from mangum import Mangum
 
+from pr_agent.log import setup_logger
 from pr_agent.servers.github_app import router
 
-logger = logging.getLogger()
-logger.setLevel(logging.DEBUG)
+setup_logger()
 
 app = FastAPI()
 app.include_router(router)

pr_agent/settings/configuration.toml

@@ -10,6 +10,7 @@ use_repo_settings_file=true
 ai_timeout=180
 max_description_tokens = 500
 max_commits_tokens = 500
+patch_extra_lines = 3
 secret_provider="google_cloud_storage"
 cli_mode=false
 
@@ -30,11 +31,15 @@ publish_labels=true
 publish_description_as_comment=false
 add_original_user_description=false
 keep_original_user_title=false
+use_bullet_points=true
 extra_instructions = ""
+
 # markers
 use_description_markers=false
 include_generated_by_header=true
 
+#custom_labels = ['Bug fix', 'Tests', 'Bug fix with tests', 'Refactoring', 'Enhancement', 'Documentation', 'Other']
+
 [pr_questions] # /ask #
 
 [pr_code_suggestions] # /improve #
@@ -47,6 +52,10 @@ rank_extended_suggestions = true
 max_number_of_calls = 5
 final_clip_factor = 0.9
 
+[pr_add_docs] # /add_docs #
+extra_instructions = ""
+docs_style = "Sphinx Style" # "Google Style with Args, Returns, Attributes...etc", "Numpy Style", "Sphinx Style", "PEP257", "reStructuredText"
+
 [pr_update_changelog] # /update_changelog #
 push_changelog_changes=false
 extra_instructions = ""
@@ -58,6 +67,11 @@ extra_instructions = ""
 deployment_type = "user"
 ratelimit_retries = 5
 
+[github_action]
+# auto_review = true    # set as env var in .github/workflows/pr-agent.yaml
+# auto_describe = true  # set as env var in .github/workflows/pr-agent.yaml
+# auto_improve = true   # set as env var in .github/workflows/pr-agent.yaml
+
 [github_app]
 # these toggles allows running the github app from custom deployments
 bot_user = "github-actions[bot]"
@@ -112,4 +126,4 @@ max_issues_to_scan = 500
 [pinecone]
 # fill and place in .secrets.toml
 #api_key = ...
-# environment = "gcp-starter"
+# environment = "gcp-starter"

pr_agent/settings/custom_labels.toml

@@ -0,0 +1,18 @@
+[config]
+enable_custom_labels=false
+
+## template for custom labels
+#[custom_labels."Bug fix"]
+#description = "Fixes a bug in the code"
+#[custom_labels."Tests"]
+#description = "Adds or modifies tests"
+#[custom_labels."Bug fix with tests"]
+#description = "Fixes a bug in the code and adds or modifies tests"
+#[custom_labels."Refactoring"]
+#description = "Code refactoring without changing functionality"
+#[custom_labels."Enhancement"]
+#description = "Adds new features or functionality"
+#[custom_labels."Documentation"]
+#description = "Adds or modifies documentation"
+#[custom_labels."Other"]
+#description = "Other changes that do not fit in any of the above categories"

pr_agent/settings/ignore.toml

@@ -0,0 +1,11 @@
+[ignore]
+
+glob = [
+    # Ignore files and directories matching these glob patterns.
+    # See https://docs.python.org/3/library/glob.html
+    'vendor/**',
+]
+regex = [
+    # Ignore files and directories matching these regex patterns.
+    # See https://learnbyexample.github.io/python-regex-cheatsheet/
+]

pr_agent/settings/language_extensions.toml

@@ -53,7 +53,8 @@ default = [
     'xz',
     'zip',
     'zst',
-    'snap'
+    'snap',
+    'lockb'
 ]
 extra = [
     'md',
@@ -432,3 +433,6 @@ reStructuredText = [".rst", ".rest", ".rest.txt", ".rst.txt", ]
 wisp = [".wisp", ]
 xBase = [".prg", ".prw", ]
 
+[docs_blacklist_extensions]
+# Disable docs for these extensions of text files and scripts that are not programming languages of function, classes and methods
+docs_blacklist = ['sql', 'txt', 'yaml', 'json', 'xml', 'md', 'rst', 'rest', 'rest.txt', 'rst.txt', 'mdpolicy', 'mdown', 'markdown', 'mdwn', 'mkd', 'mkdn', 'mkdown', 'sh']

pr_agent/settings/pr_add_docs.toml

@@ -0,0 +1,117 @@
+[pr_add_docs_prompt]
+system="""You are a language model called PR-Code-Documentation Agent, that specializes in generating documentation for code.
+Your task is to generate meaningfull {{ docs_for_language }} to a PR (the '+' lines).
+
+Example for a PR Diff input:
+'
+## src/file1.py
+
+@@ -12,3 +12,5 @@ def func1():
+__new hunk__
+12  code line that already existed in the file...
+13  code line that already existed in the file....
+14 +new code line1 added in the PR
+15 +new code line2 added in the PR
+16  code line that already existed in the file...
+__old hunk__
+ code line that already existed in the file...
+-code line that was removed in the PR
+ code line that already existed in the file...
+
+
+@@ ... @@ def func2():
+__new hunk__
+...
+__old hunk__
+...
+
+
+## src/file2.py
+...
+'
+
+Specific instructions:
+- Try to identify edited/added code components (classes/functions/methods...) that are undocumented. and generate {{ docs_for_language }} for each one.
+- If there are documented (any type of {{ language }} documentation) code components in the PR, Don't generate {{ docs_for_language }} for them.
+- Ignore code components that don't appear fully in the '__new hunk__' section. For example. you must see the component header and body,
+- Make sure the {{ docs_for_language }} starts and ends with standart {{ language }} {{ docs_for_language }} signs.
+- The {{ docs_for_language }} should be in standard format.
+- Provide the exact line number (inclusive) where the {{ docs_for_language }} should be added.
+
+
+{%- if extra_instructions %}
+
+Extra instructions from the user:
+'
+{{ extra_instructions }}
+'
+{%- endif %}
+
+You must use the following YAML schema to format your answer:
+```yaml
+Code Documentation:
+  type: array
+  uniqueItems: true
+  items:
+    relevant file:
+      type: string
+      description: the relevant file full path
+    relevant line:
+      type: integer
+      description: |-
+        The relevant line number from a '__new hunk__' section where the {{ docs_for_language }} should be added.
+    doc placement:
+      type: string
+      enum:
+        - before
+        - after
+      description: |-
+        The {{ docs_for_language }} placement relative to the relevant line (code component).
+    documentation:
+      type: string
+      description: |-
+        The {{ docs_for_language }} content. It should be complete, correctly formatted and indented, and without line numbers.
+```
+
+Example output:
+```yaml
+Code Documentation:
+-   relevant file: |-
+        src/file1.py
+    relevant lines: 12
+    doc placement: after
+    documentation: |-
+        \"\"\"
+        This is a python docstring for func1.
+        \"\"\"
+- ...
+...
+```
+
+
+Each YAML output MUST be after a newline, indented, with block scalar indicator ('|-').
+Don't repeat the prompt in the answer, and avoid outputting the 'type' and 'description' fields.
+"""
+
+user="""PR Info:
+
+Title: '{{ title }}'
+
+Branch: '{{ branch }}'
+
+Description: '{{description}}'
+
+{%- if language %}
+
+Main language: {{language}}
+{%- endif %}
+
+
+The PR Diff:
+```
+{{- diff|trim }}
+```
+
+Response (should be a valid YAML, and nothing else):
+```yaml
+"""

pr_agent/settings/pr_code_suggestions_prompts.toml

@@ -1,6 +1,6 @@
 [pr_code_suggestions_prompt]
 system="""You are a language model called PR-Code-Reviewer, that specializes in suggesting code improvements for Pull Request (PR).
-Your task is to provide meaningful and actionable code suggestions, to improve the new code presented in a PR.
+Your task is to provide meaningful and actionable code suggestions, to improve the new code presented in a PR (the '+' lines in the diff).
 
 Example for a PR Diff input:
 '
@@ -31,14 +31,13 @@ __old hunk__
 '
 
 Specific instructions:
-- Provide up to {{ num_code_suggestions }} code suggestions.
+- Provide up to {{ num_code_suggestions }} code suggestions. Try to provide diverse and insightful suggestions.
 - Prioritize suggestions that address major problems, issues and bugs in the code.
   As a second priority, suggestions should focus on best practices, code readability, maintainability, enhancments, performance, and other aspects.
-  Don't suggest to add docstring or type hints.
-  Try to provide diverse and insightful suggestions.
+- Don't suggest to add docstring, type hints, or comments.
 - Suggestions should refer only to code from the '__new hunk__' sections, and focus on new lines of code (lines starting with '+').
-  Avoid making suggestions that have already been implemented in the PR code. For example, if you want to add logs, or change a variable to const, or anything else, make sure it isn't already in the '__new hunk__' code.
-  For each suggestion, make sure to take into consideration also the context, meaning the lines before and after the relevant code.
+- Avoid making suggestions that have already been implemented in the PR code. For example, if you want to add logs, or change a variable to const, or anything else, make sure it isn't already in the '__new hunk__' code.
+- For each suggestion, make sure to take into consideration also the context, meaning the lines before and after the relevant code.
 - Provide the exact line numbers range (inclusive) for each issue.
 - Assume there is additional relevant code, that is not included in the diff.
 
@@ -46,7 +45,9 @@ Specific instructions:
 {%- if extra_instructions %}
 
 Extra instructions from the user:
+'
 {{ extra_instructions }}
+'
 {%- endif %}
 
 You must use the following YAML schema to format your answer:

pr_agent/settings/pr_custom_labels.toml

@@ -0,0 +1,72 @@
+[pr_custom_labels_prompt]
+system="""You are CodiumAI-PR-Reviewer, a language model designed to review git pull requests.
+Your task is to label the type of the PR content.
+- Make sure not to focus the new PR code (the '+' lines).
+- If needed, each YAML output should be in block scalar format ('|-')
+{%- if extra_instructions %}
+
+Extra instructions from the user:
+'
+{{ extra_instructions }}
+'
+{% endif %}
+
+You must use the following YAML schema to format your answer:
+```yaml
+PR Type:
+  type: array
+{%- if enable_custom_labels %}
+  description: One or more labels that describe the PR type. Don't output the description in the parentheses.
+{%- endif %}
+  items:
+    type: string
+    enum:
+{%- if enable_custom_labels %}
+{{ custom_labels }}
+{%- else %}
+      - Bug fix
+      - Tests
+      - Refactoring
+      - Enhancement
+      - Documentation
+      - Other
+{%- endif %}
+
+Example output:
+```yaml
+PR Type:
+{%- if enable_custom_labels %}
+{{ custom_labels_examples }}
+{%- else %}
+  - Bug fix
+  - Tests
+{%- endif %}
+```
+
+Make sure to output a valid YAML. Don't repeat the prompt in the answer, and avoid outputting the 'type' and 'description' fields.
+"""
+
+user="""PR Info:
+Previous title: '{{title}}'
+Previous description: '{{description}}'
+Branch: '{{branch}}'
+{%- if language %}
+
+Main language: {{language}}
+{%- endif %}
+{%- if commit_messages_str %}
+
+Commit messages:
+{{commit_messages_str}}
+{%- endif %}
+
+
+The PR Git Diff:
+```
+{{diff}}
+```
+Note that lines in the diff body are prefixed with a symbol that represents the type of change: '-' for deletions, '+' for additions, and ' ' (a space) for unchanged lines.
+
+Response (should be a valid YAML, and nothing else):
+```yaml
+"""

pr_agent/settings/pr_description_prompts.toml

@@ -7,7 +7,9 @@ Your task is to provide full description of the PR content.
 {%- if extra_instructions %}
 
 Extra instructions from the user:
+'
 {{ extra_instructions }}
+'
 {% endif %}
 
 You must use the following YAML schema to format your answer:
@@ -17,19 +19,26 @@ PR Title:
   description: an informative title for the PR, describing its main theme
 PR Type:
   type: array
+{%- if enable_custom_labels %}
+  description: One or more labels that describe the PR type. Don't output the description in the parentheses.
+{%- endif %}
   items:
     type: string
     enum:
+{%- if enable_custom_labels %}
+{{ custom_labels }}
+{%- else %}
       - Bug fix
       - Tests
-      - Bug fix with tests
       - Refactoring
       - Enhancement
       - Documentation
       - Other
+{%- endif %}
 PR Description:
   type: string
-  description: an informative and concise description of the PR
+  description: an informative and concise description of the PR.
+  {%- if use_bullet_points %} Use bullet points. {% endif %}
 PR Main Files Walkthrough:
   type: array
   maxItems: 10
@@ -49,7 +58,11 @@ Example output:
 PR Title: |-
   ...
 PR Type:
+{%- if enable_custom_labels %}
+{{ custom_labels_examples }}
+{%- else %}
   - Bug fix
+{%- endif %}
 PR Description: |-
   ...
 PR Main Files Walkthrough:

pr_agent/settings/pr_reviewer_prompts.toml

@@ -22,20 +22,22 @@ code line that already existed in the file....
 ...
 '
 
-Thre review should focus on new code added in the PR (lines starting with '+'), and not on code that already existed in the file (lines starting with '-', or without prefix).
+The review should focus on new code added in the PR (lines starting with '+'), and not on code that already existed in the file (lines starting with '-', or without prefix).
 
 {%- if num_code_suggestions > 0 %}
-- Provide up to {{ num_code_suggestions }} code suggestions.
+- Provide up to {{ num_code_suggestions }} code suggestions. Try to provide diverse and insightful suggestions.
 - Focus on important suggestions like fixing code problems, issues and bugs. As a second priority, provide suggestions for meaningful code improvements, like performance, vulnerability, modularity, and best practices.
 - Avoid making suggestions that have already been implemented in the PR code. For example, if you want to add logs, or change a variable to const, or anything else, make sure it isn't already in the PR code.
-- Don't suggest to add docstring or type hints.
+- Don't suggest to add docstring, type hints, or comments.
 - Suggestions should focus on improving the new code added in the PR (lines starting with '+')
 {%- endif %}
 
 {%- if extra_instructions %}
 
 Extra instructions from the user:
+'
 {{ extra_instructions }}
+'
 {% endif %}
 
 You must use the following YAML schema to format your answer:
@@ -49,13 +51,22 @@ PR Analysis:
     description: summary of the PR in 2-3 sentences.
   Type of PR:
     type: string
+{%- if enable_custom_labels %}
+  description: One or more labels that describe the PR type. Don't output the description in the parentheses.
+{%- endif %}
+  items:
+    type: string
     enum:
+{%- if enable_custom_labels %}
+{{ custom_labels }}
+{%- else %}
       - Bug fix
       - Tests
       - Refactoring
       - Enhancement
       - Documentation
       - Other
+{%- endif %}
 {%- if require_score %}
   Score:
     type: int
@@ -97,10 +108,10 @@ PR Feedback:
   General suggestions:
     type: string
     description: |-
-      General suggestions and feedback for the contributors and maintainers of
-      this PR. May include important suggestions for the overall structure,
-      primary purpose, best practices, critical bugs, and other aspects of the
-      PR. Don't address PR title and description, or lack of tests. Explain your suggestions.
+      General suggestions and feedback for the contributors and maintainers of this PR.
+      May include important suggestions for the overall structure,
+      primary purpose, best practices, critical bugs, and other aspects of the PR.
+      Don't address PR title and description, or lack of tests. Explain your suggestions.
 {%- if num_code_suggestions > 0 %}
   Code feedback:
     type: array
@@ -113,11 +124,10 @@ PR Feedback:
       suggestion:
         type: string
         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.
+          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.
       relevant line:
         type: string
         description: |-
@@ -129,8 +139,7 @@ PR Feedback:
   Security concerns:
     type: string
     description: >-
-      yes\\no question: does this PR code introduce possible security concerns or
-      issues, like SQL injection, XSS, CSRF, and others ? If answered 'yes',explain your answer shortly
+      yes\\no question: 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 ? If answered 'yes', explain your answer briefly.
 {%- endif %}
 ```
 
@@ -151,6 +160,9 @@ PR Analysis:
 {%- if require_focused %}
   Focused PR: no, because ...
 {%- endif %}
+{%- if require_estimate_effort_to_review %}
+  Estimated effort to review [1-5]: 3, because ...
+{%- endif %}
 PR Feedback:
   General PR suggestions: |-
     ...
@@ -193,7 +205,9 @@ Here are questions to better understand the PR. Use the answers to provide bette
 {{question_str|trim}}
 
 User answers:
+'
 {{answer_str|trim}}
+'
 ######
 {%- endif %}
 

pr_agent/settings/pr_update_changelog_prompts.toml

@@ -8,7 +8,9 @@ Your task is to update the CHANGELOG.md file of the project, to shortly summariz
 {%- if extra_instructions %}
 
 Extra instructions from the user:
+'
 {{ extra_instructions }}
+'
 {%- endif %}
 """
 

pr_agent/tools/pr_add_docs.py

@@ -0,0 +1,179 @@
+import copy
+import textwrap
+from typing import Dict
+
+from jinja2 import Environment, StrictUndefined
+
+from pr_agent.algo.ai_handler import AiHandler
+from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
+from pr_agent.algo.token_handler import TokenHandler
+from pr_agent.algo.utils import load_yaml
+from pr_agent.config_loader import get_settings
+from pr_agent.git_providers import get_git_provider
+from pr_agent.git_providers.git_provider import get_main_pr_language
+from pr_agent.log import get_logger
+
+
+class PRAddDocs:
+    def __init__(self, pr_url: str, cli_mode=False, args: list = None):
+
+        self.git_provider = get_git_provider()(pr_url)
+        self.main_language = get_main_pr_language(
+            self.git_provider.get_languages(), self.git_provider.get_files()
+        )
+
+        self.ai_handler = AiHandler()
+        self.patches_diff = None
+        self.prediction = None
+        self.cli_mode = cli_mode
+        self.vars = {
+            "title": self.git_provider.pr.title,
+            "branch": self.git_provider.get_pr_branch(),
+            "description": self.git_provider.get_pr_description(),
+            "language": self.main_language,
+            "diff": "",  # empty diff for initial calculation
+            "extra_instructions": get_settings().pr_add_docs.extra_instructions,
+            "commit_messages_str": self.git_provider.get_commit_messages(),
+            'docs_for_language': get_docs_for_language(self.main_language,
+                                                       get_settings().pr_add_docs.docs_style),
+        }
+        self.token_handler = TokenHandler(self.git_provider.pr,
+                                          self.vars,
+                                          get_settings().pr_add_docs_prompt.system,
+                                          get_settings().pr_add_docs_prompt.user)
+
+    async def run(self):
+        try:
+            get_logger().info('Generating code Docs for PR...')
+            if get_settings().config.publish_output:
+                self.git_provider.publish_comment("Generating Documentation...", is_temporary=True)
+
+            get_logger().info('Preparing PR documentation...')
+            await retry_with_fallback_models(self._prepare_prediction)
+            data = self._prepare_pr_code_docs()
+            if (not data) or (not 'Code Documentation' in data):
+                get_logger().info('No code documentation found for PR.')
+                return
+
+            if get_settings().config.publish_output:
+                get_logger().info('Pushing PR documentation...')
+                self.git_provider.remove_initial_comment()
+                get_logger().info('Pushing inline code documentation...')
+                self.push_inline_docs(data)
+        except Exception as e:
+            get_logger().error(f"Failed to generate code documentation for PR, error: {e}")
+
+    async def _prepare_prediction(self, model: str):
+        get_logger().info('Getting PR diff...')
+
+        # Disable adding docs to scripts and other non-relevant text files
+        from pr_agent.algo.language_handler import bad_extensions
+        bad_extensions += get_settings().docs_blacklist_extensions.docs_blacklist
+
+        self.patches_diff = get_pr_diff(self.git_provider,
+                                        self.token_handler,
+                                        model,
+                                        add_line_numbers_to_hunks=True,
+                                        disable_extra_lines=False)
+
+        get_logger().info('Getting AI prediction...')
+        self.prediction = await self._get_prediction(model)
+
+    async def _get_prediction(self, model: str):
+        variables = copy.deepcopy(self.vars)
+        variables["diff"] = self.patches_diff  # update diff
+        environment = Environment(undefined=StrictUndefined)
+        system_prompt = environment.from_string(get_settings().pr_add_docs_prompt.system).render(variables)
+        user_prompt = environment.from_string(get_settings().pr_add_docs_prompt.user).render(variables)
+        if get_settings().config.verbosity_level >= 2:
+            get_logger().info(f"\nSystem prompt:\n{system_prompt}")
+            get_logger().info(f"\nUser prompt:\n{user_prompt}")
+        response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
+                                                                        system=system_prompt, user=user_prompt)
+
+        return response
+
+    def _prepare_pr_code_docs(self) -> Dict:
+        docs = self.prediction.strip()
+        data = load_yaml(docs)
+        if isinstance(data, list):
+            data = {'Code Documentation': data}
+        return data
+
+    def push_inline_docs(self, data):
+        docs = []
+
+        if not data['Code Documentation']:
+            return self.git_provider.publish_comment('No code documentation found to improve this PR.')
+
+        for d in data['Code Documentation']:
+            try:
+                if get_settings().config.verbosity_level >= 2:
+                    get_logger().info(f"add_docs: {d}")
+                relevant_file = d['relevant file'].strip()
+                relevant_line = int(d['relevant line'])  # absolute position
+                documentation = d['documentation']
+                doc_placement = d['doc placement'].strip()
+                if documentation:
+                    new_code_snippet = self.dedent_code(relevant_file, relevant_line, documentation, doc_placement,
+                                                        add_original_line=True)
+
+                    body = f"**Suggestion:** Proposed documentation\n```suggestion\n" + new_code_snippet + "\n```"
+                    docs.append({'body': body, 'relevant_file': relevant_file,
+                                             'relevant_lines_start': relevant_line,
+                                             'relevant_lines_end': relevant_line})
+            except Exception:
+                if get_settings().config.verbosity_level >= 2:
+                    get_logger().info(f"Could not parse code docs: {d}")
+
+        is_successful = self.git_provider.publish_code_suggestions(docs)
+        if not is_successful:
+            get_logger().info("Failed to publish code docs, trying to publish each docs separately")
+            for doc_suggestion in docs:
+                self.git_provider.publish_code_suggestions([doc_suggestion])
+
+    def dedent_code(self, relevant_file, relevant_lines_start, new_code_snippet, doc_placement='after',
+                    add_original_line=False):
+        try:  # dedent code snippet
+            self.diff_files = self.git_provider.diff_files if self.git_provider.diff_files \
+                else self.git_provider.get_diff_files()
+            original_initial_line = None
+            for file in self.diff_files:
+                if file.filename.strip() == relevant_file:
+                    original_initial_line = file.head_file.splitlines()[relevant_lines_start - 1]
+                    break
+            if original_initial_line:
+                if doc_placement == 'after':
+                    line = file.head_file.splitlines()[relevant_lines_start]
+                else:
+                    line = original_initial_line
+                suggested_initial_line = new_code_snippet.splitlines()[0]
+                original_initial_spaces = len(line) - len(line.lstrip())
+                suggested_initial_spaces = len(suggested_initial_line) - len(suggested_initial_line.lstrip())
+                delta_spaces = original_initial_spaces - suggested_initial_spaces
+                if delta_spaces > 0:
+                    new_code_snippet = textwrap.indent(new_code_snippet, delta_spaces * " ").rstrip('\n')
+                if add_original_line:
+                    if doc_placement == 'after':
+                        new_code_snippet = original_initial_line + "\n" + new_code_snippet
+                    else:
+                        new_code_snippet = new_code_snippet.rstrip() + "\n" + original_initial_line
+        except Exception as e:
+            if get_settings().config.verbosity_level >= 2:
+                get_logger().info(f"Could not dedent code snippet for file {relevant_file}, error: {e}")
+
+        return new_code_snippet
+
+
+def get_docs_for_language(language, style):
+    language = language.lower()
+    if language == 'java':
+        return "Javadocs"
+    elif language in ['python', 'lisp', 'clojure']:
+        return f"Docstring ({style})"
+    elif language in ['javascript', 'typescript']:
+        return "JSdocs"
+    elif language == 'c++':
+        return "Doxygen"
+    else:
+        return "Docs"

pr_agent/tools/pr_code_suggestions.py

@@ -1,16 +1,17 @@
 import copy
-import logging
 import textwrap
-from typing import List, Dict
+from typing import Dict, List
+
 from jinja2 import Environment, StrictUndefined
 
 from pr_agent.algo.ai_handler import AiHandler
-from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models, get_pr_multi_diffs
+from pr_agent.algo.pr_processing import get_pr_diff, get_pr_multi_diffs, retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
 from pr_agent.algo.utils import load_yaml
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import BitbucketProvider, get_git_provider
+from pr_agent.git_providers import get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language
+from pr_agent.log import get_logger
 
 
 class PRCodeSuggestions:
@@ -22,7 +23,10 @@ class PRCodeSuggestions:
         )
 
         # extended mode
-        self.is_extended = any(["extended" in arg for arg in args])
+        try:
+            self.is_extended = any(["extended" in arg for arg in args])
+        except:
+            self.is_extended = False
         if self.is_extended:
             num_code_suggestions = get_settings().pr_code_suggestions.num_code_suggestions_per_chunk
         else:
@@ -49,42 +53,42 @@ class PRCodeSuggestions:
 
     async def run(self):
         try:
-            logging.info('Generating code suggestions for PR...')
+            get_logger().info('Generating code suggestions for PR...')
             if get_settings().config.publish_output:
                 self.git_provider.publish_comment("Preparing review...", is_temporary=True)
 
-            logging.info('Preparing PR review...')
+            get_logger().info('Preparing PR review...')
             if not self.is_extended:
                 await retry_with_fallback_models(self._prepare_prediction)
                 data = self._prepare_pr_code_suggestions()
             else:
                 data = await retry_with_fallback_models(self._prepare_prediction_extended)
             if (not data) or (not 'Code suggestions' in data):
-                logging.info('No code suggestions found for PR.')
+                get_logger().info('No code suggestions found for PR.')
                 return
 
             if (not self.is_extended and get_settings().pr_code_suggestions.rank_suggestions) or \
                     (self.is_extended and get_settings().pr_code_suggestions.rank_extended_suggestions):
-                logging.info('Ranking Suggestions...')
+                get_logger().info('Ranking Suggestions...')
                 data['Code suggestions'] = await self.rank_suggestions(data['Code suggestions'])
 
             if get_settings().config.publish_output:
-                logging.info('Pushing PR review...')
+                get_logger().info('Pushing PR review...')
                 self.git_provider.remove_initial_comment()
-                logging.info('Pushing inline code suggestions...')
+                get_logger().info('Pushing inline code suggestions...')
                 self.push_inline_code_suggestions(data)
         except Exception as e:
-            logging.error(f"Failed to generate code suggestions for PR, error: {e}")
+            get_logger().error(f"Failed to generate code suggestions for PR, error: {e}")
 
     async def _prepare_prediction(self, model: str):
-        logging.info('Getting PR diff...')
+        get_logger().info('Getting PR diff...')
         self.patches_diff = get_pr_diff(self.git_provider,
                                         self.token_handler,
                                         model,
                                         add_line_numbers_to_hunks=True,
                                         disable_extra_lines=True)
 
-        logging.info('Getting AI prediction...')
+        get_logger().info('Getting AI prediction...')
         self.prediction = await self._get_prediction(model)
 
     async def _get_prediction(self, model: str):
@@ -94,8 +98,8 @@ class PRCodeSuggestions:
         system_prompt = environment.from_string(get_settings().pr_code_suggestions_prompt.system).render(variables)
         user_prompt = environment.from_string(get_settings().pr_code_suggestions_prompt.user).render(variables)
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"\nSystem prompt:\n{system_prompt}")
-            logging.info(f"\nUser prompt:\n{user_prompt}")
+            get_logger().info(f"\nSystem prompt:\n{system_prompt}")
+            get_logger().info(f"\nUser prompt:\n{user_prompt}")
         response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
                                                                         system=system_prompt, user=user_prompt)
 
@@ -117,7 +121,7 @@ class PRCodeSuggestions:
         for d in data['Code suggestions']:
             try:
                 if get_settings().config.verbosity_level >= 2:
-                    logging.info(f"suggestion: {d}")
+                    get_logger().info(f"suggestion: {d}")
                 relevant_file = d['relevant file'].strip()
                 relevant_lines_start = int(d['relevant lines start'])  # absolute position
                 relevant_lines_end = int(d['relevant lines end'])
@@ -133,11 +137,11 @@ class PRCodeSuggestions:
                                          'relevant_lines_end': relevant_lines_end})
             except Exception:
                 if get_settings().config.verbosity_level >= 2:
-                    logging.info(f"Could not parse suggestion: {d}")
+                    get_logger().info(f"Could not parse suggestion: {d}")
 
         is_successful = self.git_provider.publish_code_suggestions(code_suggestions)
         if not is_successful:
-            logging.info("Failed to publish code suggestions, trying to publish each suggestion separately")
+            get_logger().info("Failed to publish code suggestions, trying to publish each suggestion separately")
             for code_suggestion in code_suggestions:
                 self.git_provider.publish_code_suggestions([code_suggestion])
 
@@ -159,19 +163,19 @@ class PRCodeSuggestions:
                     new_code_snippet = textwrap.indent(new_code_snippet, delta_spaces * " ").rstrip('\n')
         except Exception as e:
             if get_settings().config.verbosity_level >= 2:
-                logging.info(f"Could not dedent code snippet for file {relevant_file}, error: {e}")
+                get_logger().info(f"Could not dedent code snippet for file {relevant_file}, error: {e}")
 
         return new_code_snippet
 
     async def _prepare_prediction_extended(self, model: str) -> dict:
-        logging.info('Getting PR diff...')
+        get_logger().info('Getting PR diff...')
         patches_diff_list = get_pr_multi_diffs(self.git_provider, self.token_handler, model,
                                                max_calls=get_settings().pr_code_suggestions.max_number_of_calls)
 
-        logging.info('Getting multi AI predictions...')
+        get_logger().info('Getting multi AI predictions...')
         prediction_list = []
         for i, patches_diff in enumerate(patches_diff_list):
-            logging.info(f"Processing chunk {i + 1} of {len(patches_diff_list)}")
+            get_logger().info(f"Processing chunk {i + 1} of {len(patches_diff_list)}")
             self.patches_diff = patches_diff
             prediction = await self._get_prediction(model)
             prediction_list.append(prediction)
@@ -219,8 +223,8 @@ class PRCodeSuggestions:
                 variables)
             user_prompt = environment.from_string(get_settings().pr_sort_code_suggestions_prompt.user).render(variables)
             if get_settings().config.verbosity_level >= 2:
-                logging.info(f"\nSystem prompt:\n{system_prompt}")
-                logging.info(f"\nUser prompt:\n{user_prompt}")
+                get_logger().info(f"\nSystem prompt:\n{system_prompt}")
+                get_logger().info(f"\nUser prompt:\n{user_prompt}")
             response, finish_reason = await self.ai_handler.chat_completion(model=model, system=system_prompt,
                                                                             user=user_prompt)
 
@@ -235,7 +239,7 @@ class PRCodeSuggestions:
                 data_sorted = data_sorted[:new_len]
         except Exception as e:
             if get_settings().config.verbosity_level >= 1:
-                logging.info(f"Could not sort suggestions, error: {e}")
+                get_logger().info(f"Could not sort suggestions, error: {e}")
             data_sorted = suggestion_list
 
         return data_sorted

pr_agent/tools/pr_config.py

@@ -1,7 +1,6 @@
-import logging
-
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
+from pr_agent.log import get_logger
 
 
 class PRConfig:
@@ -19,11 +18,11 @@ class PRConfig:
         self.git_provider = get_git_provider()(pr_url)
 
     async def run(self):
-        logging.info('Getting configuration settings...')
-        logging.info('Preparing configs...')
+        get_logger().info('Getting configuration settings...')
+        get_logger().info('Preparing configs...')
         pr_comment = self._prepare_pr_configs()
         if get_settings().config.publish_output:
-            logging.info('Pushing configs...')
+            get_logger().info('Pushing configs...')
             self.git_provider.publish_comment(pr_comment)
             self.git_provider.remove_initial_comment()
         return ""
@@ -44,5 +43,5 @@ class PRConfig:
                 comment_str += f"\n{header.lower()}.{key.lower()} = {repr(value) if isinstance(value, str) else value}"
                 comment_str += "  "
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"comment_str:\n{comment_str}")
+            get_logger().info(f"comment_str:\n{comment_str}")
         return comment_str

pr_agent/tools/pr_description.py

@@ -1,7 +1,5 @@
 import copy
-import json
 import re
-import logging
 from typing import List, Tuple
 
 from jinja2 import Environment, StrictUndefined
@@ -9,10 +7,11 @@ from jinja2 import Environment, StrictUndefined
 from pr_agent.algo.ai_handler import AiHandler
 from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import load_yaml
+from pr_agent.algo.utils import load_yaml, set_custom_labels
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language
+from pr_agent.log import get_logger
 
 
 class PRDescription:
@@ -29,7 +28,7 @@ class PRDescription:
         self.main_pr_language = get_main_pr_language(
             self.git_provider.get_languages(), self.git_provider.get_files()
         )
-        self.pr_id = f"{self.git_provider.repo}/{self.git_provider.pr_num}"
+        self.pr_id = self.git_provider.get_pr_id()
 
         # Initialize the AI handler
         self.ai_handler = AiHandler()
@@ -41,8 +40,12 @@ class PRDescription:
             "description": self.git_provider.get_pr_description(full=False),
             "language": self.main_pr_language,
             "diff": "",  # empty diff for initial calculation
+            "use_bullet_points": get_settings().pr_description.use_bullet_points,
             "extra_instructions": get_settings().pr_description.extra_instructions,
-            "commit_messages_str": self.git_provider.get_commit_messages()
+            "commit_messages_str": self.git_provider.get_commit_messages(),
+            "enable_custom_labels": get_settings().config.enable_custom_labels,
+            "custom_labels": "",
+            "custom_labels_examples": "",
         }
 
         self.user_description = self.git_provider.get_user_description()
@@ -65,13 +68,13 @@ class PRDescription:
         """
 
         try:
-            logging.info(f"Generating a PR description {self.pr_id}")
+            get_logger().info(f"Generating a PR description {self.pr_id}")
             if get_settings().config.publish_output:
-                self.git_provider.publish_comment("Preparing pr description...", is_temporary=True)
+                self.git_provider.publish_comment("Preparing PR description...", is_temporary=True)
 
             await retry_with_fallback_models(self._prepare_prediction)
 
-            logging.info(f"Preparing answer {self.pr_id}")
+            get_logger().info(f"Preparing answer {self.pr_id}")
             if self.prediction:
                 self._prepare_data()
             else:
@@ -88,7 +91,7 @@ class PRDescription:
             full_markdown_description = f"## Title\n\n{pr_title}\n\n___\n{pr_body}"
 
             if get_settings().config.publish_output:
-                logging.info(f"Pushing answer {self.pr_id}")
+                get_logger().info(f"Pushing answer {self.pr_id}")
                 if get_settings().pr_description.publish_description_as_comment:
                     self.git_provider.publish_comment(full_markdown_description)
                 else:
@@ -100,7 +103,7 @@ class PRDescription:
                         self.git_provider.publish_labels(pr_labels + current_labels)
                 self.git_provider.remove_initial_comment()
         except Exception as e:
-            logging.error(f"Error generating PR description {self.pr_id}: {e}")
+            get_logger().error(f"Error generating PR description {self.pr_id}: {e}")
         
         return ""
 
@@ -121,9 +124,9 @@ class PRDescription:
         if get_settings().pr_description.use_description_markers and 'pr_agent:' not in self.user_description:
             return None
 
-        logging.info(f"Getting PR diff {self.pr_id}")
+        get_logger().info(f"Getting PR diff {self.pr_id}")
         self.patches_diff = get_pr_diff(self.git_provider, self.token_handler, model)
-        logging.info(f"Getting AI prediction {self.pr_id}")
+        get_logger().info(f"Getting AI prediction {self.pr_id}")
         self.prediction = await self._get_prediction(model)
 
     async def _get_prediction(self, model: str) -> str:
@@ -140,12 +143,13 @@ class PRDescription:
         variables["diff"] = self.patches_diff  # update diff
 
         environment = Environment(undefined=StrictUndefined)
+        set_custom_labels(variables)
         system_prompt = environment.from_string(get_settings().pr_description_prompt.system).render(variables)
         user_prompt = environment.from_string(get_settings().pr_description_prompt.user).render(variables)
 
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"\nSystem prompt:\n{system_prompt}")
-            logging.info(f"\nUser prompt:\n{user_prompt}")
+            get_logger().info(f"\nSystem prompt:\n{system_prompt}")
+            get_logger().info(f"\nUser prompt:\n{user_prompt}")
 
         response, finish_reason = await self.ai_handler.chat_completion(
             model=model,
@@ -156,7 +160,6 @@ class PRDescription:
 
         return response
 
-
     def _prepare_data(self):
         # Load the AI prediction data into a dictionary
         self.data = load_yaml(self.prediction.strip())
@@ -178,7 +181,7 @@ class PRDescription:
         return pr_types
 
     def _prepare_pr_answer_with_markers(self) -> Tuple[str, str]:
-        logging.info(f"Using description marker replacements {self.pr_id}")
+        get_logger().info(f"Using description marker replacements {self.pr_id}")
         title = self.vars["title"]
         body = self.user_description
         if get_settings().pr_description.include_generated_by_header:
@@ -186,6 +189,11 @@ class PRDescription:
         else:
             ai_header = ""
 
+        ai_type = self.data.get('PR Type')
+        if ai_type and not re.search(r'<!--\s*pr_agent:type\s*-->', body):
+            pr_type = f"{ai_header}{ai_type}"
+            body = body.replace('pr_agent:type', pr_type)
+
         ai_summary = self.data.get('PR Description')
         if ai_summary and not re.search(r'<!--\s*pr_agent:summary\s*-->', body):
             summary = f"{ai_header}{ai_summary}"
@@ -252,6 +260,6 @@ class PRDescription:
                 pr_body += "\n___\n"
 
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"title:\n{title}\n{pr_body}")
+            get_logger().info(f"title:\n{title}\n{pr_body}")
 
         return title, pr_body

pr_agent/tools/pr_generate_labels.py

@@ -0,0 +1,163 @@
+import copy
+import re
+from typing import List, Tuple
+
+from jinja2 import Environment, StrictUndefined
+
+from pr_agent.algo.ai_handler import AiHandler
+from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
+from pr_agent.algo.token_handler import TokenHandler
+from pr_agent.algo.utils import load_yaml, set_custom_labels
+from pr_agent.config_loader import get_settings
+from pr_agent.git_providers import get_git_provider
+from pr_agent.git_providers.git_provider import get_main_pr_language
+from pr_agent.log import get_logger
+
+
+class PRGenerateLabels:
+    def __init__(self, pr_url: str, args: list = None):
+        """
+        Initialize the PRGenerateLabels object with the necessary attributes and objects for generating labels
+        corresponding to the PR using an AI model.
+        Args:
+            pr_url (str): The URL of the pull request.
+            args (list, optional): List of arguments passed to the PRGenerateLabels class. Defaults to None.
+        """
+        # Initialize the git provider and main PR language
+        self.git_provider = get_git_provider()(pr_url)
+        self.main_pr_language = get_main_pr_language(
+            self.git_provider.get_languages(), self.git_provider.get_files()
+        )
+        self.pr_id = self.git_provider.get_pr_id()
+
+        # Initialize the AI handler
+        self.ai_handler = AiHandler()
+    
+        # Initialize the variables dictionary
+        self.vars = {
+            "title": self.git_provider.pr.title,
+            "branch": self.git_provider.get_pr_branch(),
+            "description": self.git_provider.get_pr_description(full=False),
+            "language": self.main_pr_language,
+            "diff": "",  # empty diff for initial calculation
+            "use_bullet_points": get_settings().pr_description.use_bullet_points,
+            "extra_instructions": get_settings().pr_description.extra_instructions,
+            "commit_messages_str": self.git_provider.get_commit_messages(),
+            "custom_labels": "",
+            "custom_labels_examples": "",
+            "enable_custom_labels": get_settings().config.enable_custom_labels,
+        }
+
+        # Initialize the token handler
+        self.token_handler = TokenHandler(
+            self.git_provider.pr,
+            self.vars,
+            get_settings().pr_custom_labels_prompt.system,
+            get_settings().pr_custom_labels_prompt.user,
+        )
+    
+        # Initialize patches_diff and prediction attributes
+        self.patches_diff = None
+        self.prediction = None
+
+    async def run(self):
+        """
+        Generates a PR labels using an AI model and publishes it to the PR.
+        """
+
+        try:
+            get_logger().info(f"Generating a PR labels {self.pr_id}")
+            if get_settings().config.publish_output:
+                self.git_provider.publish_comment("Preparing PR labels...", is_temporary=True)
+
+            await retry_with_fallback_models(self._prepare_prediction)
+
+            get_logger().info(f"Preparing answer {self.pr_id}")
+            if self.prediction:
+                self._prepare_data()
+            else:
+                return None
+
+            pr_labels = self._prepare_labels()
+
+            if get_settings().config.publish_output:
+                get_logger().info(f"Pushing labels {self.pr_id}")
+                if self.git_provider.is_supported("get_labels"):
+                    current_labels = self.git_provider.get_labels()
+                    if current_labels is None:
+                        current_labels = []
+                    self.git_provider.publish_labels(pr_labels + current_labels)
+                self.git_provider.remove_initial_comment()
+        except Exception as e:
+            get_logger().error(f"Error generating PR labels {self.pr_id}: {e}")
+        
+        return ""
+
+    async def _prepare_prediction(self, model: str) -> None:
+        """
+        Prepare the AI prediction for the PR labels based on the provided model.
+
+        Args:
+            model (str): The name of the model to be used for generating the prediction.
+
+        Returns:
+            None
+
+        Raises:
+            Any exceptions raised by the 'get_pr_diff' and '_get_prediction' functions.
+
+        """
+
+        get_logger().info(f"Getting PR diff {self.pr_id}")
+        self.patches_diff = get_pr_diff(self.git_provider, self.token_handler, model)
+        get_logger().info(f"Getting AI prediction {self.pr_id}")
+        self.prediction = await self._get_prediction(model)
+
+    async def _get_prediction(self, model: str) -> str:
+        """
+        Generate an AI prediction for the PR labels based on the provided model.
+
+        Args:
+            model (str): The name of the model to be used for generating the prediction.
+
+        Returns:
+            str: The generated AI prediction.
+        """
+        variables = copy.deepcopy(self.vars)
+        variables["diff"] = self.patches_diff  # update diff
+
+        environment = Environment(undefined=StrictUndefined)
+        set_custom_labels(variables)
+        system_prompt = environment.from_string(get_settings().pr_custom_labels_prompt.system).render(variables)
+        user_prompt = environment.from_string(get_settings().pr_custom_labels_prompt.user).render(variables)
+
+        if get_settings().config.verbosity_level >= 2:
+            get_logger().info(f"\nSystem prompt:\n{system_prompt}")
+            get_logger().info(f"\nUser prompt:\n{user_prompt}")
+
+        response, finish_reason = await self.ai_handler.chat_completion(
+            model=model,
+            temperature=0.2,
+            system=system_prompt,
+            user=user_prompt
+        )
+
+        return response
+
+    def _prepare_data(self):
+        # Load the AI prediction data into a dictionary
+        self.data = load_yaml(self.prediction.strip())
+
+
+
+    def _prepare_labels(self) -> List[str]:
+        pr_types = []
+
+        # If the 'PR Type' key is present in the dictionary, split its value by comma and assign it to 'pr_types'
+        if 'PR Type' in self.data:
+            if type(self.data['PR Type']) == list:
+                pr_types = self.data['PR Type']
+            elif type(self.data['PR Type']) == str:
+                pr_types = self.data['PR Type'].split(',')
+
+        return pr_types

pr_agent/tools/pr_information_from_user.py

@@ -1,5 +1,4 @@
 import copy
-import logging
 
 from jinja2 import Environment, StrictUndefined
 
@@ -9,6 +8,7 @@ from pr_agent.algo.token_handler import TokenHandler
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language
+from pr_agent.log import get_logger
 
 
 class PRInformationFromUser:
@@ -34,22 +34,22 @@ class PRInformationFromUser:
         self.prediction = None
 
     async def run(self):
-        logging.info('Generating question to the user...')
+        get_logger().info('Generating question to the user...')
         if get_settings().config.publish_output:
             self.git_provider.publish_comment("Preparing questions...", is_temporary=True)
         await retry_with_fallback_models(self._prepare_prediction)
-        logging.info('Preparing questions...')
+        get_logger().info('Preparing questions...')
         pr_comment = self._prepare_pr_answer()
         if get_settings().config.publish_output:
-            logging.info('Pushing questions...')
+            get_logger().info('Pushing questions...')
             self.git_provider.publish_comment(pr_comment)
             self.git_provider.remove_initial_comment()
         return ""
 
     async def _prepare_prediction(self, model):
-        logging.info('Getting PR diff...')
+        get_logger().info('Getting PR diff...')
         self.patches_diff = get_pr_diff(self.git_provider, self.token_handler, model)
-        logging.info('Getting AI prediction...')
+        get_logger().info('Getting AI prediction...')
         self.prediction = await self._get_prediction(model)
 
     async def _get_prediction(self, model: str):
@@ -59,8 +59,8 @@ class PRInformationFromUser:
         system_prompt = environment.from_string(get_settings().pr_information_from_user_prompt.system).render(variables)
         user_prompt = environment.from_string(get_settings().pr_information_from_user_prompt.user).render(variables)
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"\nSystem prompt:\n{system_prompt}")
-            logging.info(f"\nUser prompt:\n{user_prompt}")
+            get_logger().info(f"\nSystem prompt:\n{system_prompt}")
+            get_logger().info(f"\nUser prompt:\n{user_prompt}")
         response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
                                                                         system=system_prompt, user=user_prompt)
         return response
@@ -68,7 +68,7 @@ class PRInformationFromUser:
     def _prepare_pr_answer(self) -> str:
         model_output = self.prediction.strip()
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"answer_str:\n{model_output}")
+            get_logger().info(f"answer_str:\n{model_output}")
         answer_str = f"{model_output}\n\n Please respond to the questions above in the following format:\n\n" +\
                      "\n>/answer\n>1) ...\n>2) ...\n>...\n"
         return answer_str

pr_agent/tools/pr_questions.py

@@ -1,5 +1,4 @@
 import copy
-import logging
 
 from jinja2 import Environment, StrictUndefined
 
@@ -9,6 +8,7 @@ from pr_agent.algo.token_handler import TokenHandler
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language
+from pr_agent.log import get_logger
 
 
 class PRQuestions:
@@ -44,22 +44,22 @@ class PRQuestions:
         return question_str
 
     async def run(self):
-        logging.info('Answering a PR question...')
+        get_logger().info('Answering a PR question...')
         if get_settings().config.publish_output:
             self.git_provider.publish_comment("Preparing answer...", is_temporary=True)
         await retry_with_fallback_models(self._prepare_prediction)
-        logging.info('Preparing answer...')
+        get_logger().info('Preparing answer...')
         pr_comment = self._prepare_pr_answer()
         if get_settings().config.publish_output:
-            logging.info('Pushing answer...')
+            get_logger().info('Pushing answer...')
             self.git_provider.publish_comment(pr_comment)
             self.git_provider.remove_initial_comment()
         return ""
 
     async def _prepare_prediction(self, model: str):
-        logging.info('Getting PR diff...')
+        get_logger().info('Getting PR diff...')
         self.patches_diff = get_pr_diff(self.git_provider, self.token_handler, model)
-        logging.info('Getting AI prediction...')
+        get_logger().info('Getting AI prediction...')
         self.prediction = await self._get_prediction(model)
 
     async def _get_prediction(self, model: str):
@@ -69,8 +69,8 @@ class PRQuestions:
         system_prompt = environment.from_string(get_settings().pr_questions_prompt.system).render(variables)
         user_prompt = environment.from_string(get_settings().pr_questions_prompt.user).render(variables)
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"\nSystem prompt:\n{system_prompt}")
-            logging.info(f"\nUser prompt:\n{user_prompt}")
+            get_logger().info(f"\nSystem prompt:\n{system_prompt}")
+            get_logger().info(f"\nUser prompt:\n{user_prompt}")
         response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
                                                                         system=system_prompt, user=user_prompt)
         return response
@@ -79,5 +79,5 @@ class PRQuestions:
         answer_str = f"Question: {self.question_str}\n\n"
         answer_str += f"Answer:\n{self.prediction.strip()}\n\n"
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"answer_str:\n{answer_str}")
+            get_logger().info(f"answer_str:\n{answer_str}")
         return answer_str

pr_agent/tools/pr_reviewer.py

@@ -1,6 +1,4 @@
 import copy
-import json
-import logging
 from collections import OrderedDict
 from typing import List, Tuple
 
@@ -9,13 +7,13 @@ from jinja2 import Environment, StrictUndefined
 from yaml import SafeLoader
 
 from pr_agent.algo.ai_handler import AiHandler
-from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models, \
-    find_line_number_of_relevant_line_in_file, clip_tokens
+from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import convert_to_markdown, try_fix_json, try_fix_yaml, load_yaml
+from pr_agent.algo.utils import convert_to_markdown, load_yaml, try_fix_yaml, set_custom_labels
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
 from pr_agent.git_providers.git_provider import IncrementalPR, get_main_pr_language
+from pr_agent.log import get_logger
 from pr_agent.servers.help import actions_help_text, bot_help_text
 
 
@@ -65,6 +63,8 @@ class PRReviewer:
             'answer_str': answer_str,
             "extra_instructions": get_settings().pr_reviewer.extra_instructions,
             "commit_messages_str": self.git_provider.get_commit_messages(),
+            "custom_labels": "",
+            "enable_custom_labels": get_settings().config.enable_custom_labels,
         }
 
         self.token_handler = TokenHandler(
@@ -98,29 +98,29 @@ class PRReviewer:
 
         try:
             if self.is_auto and not get_settings().pr_reviewer.automatic_review:
-                logging.info(f'Automatic review is disabled {self.pr_url}')
+                get_logger().info(f'Automatic review is disabled {self.pr_url}')
                 return None
 
-            logging.info(f'Reviewing PR: {self.pr_url} ...')
+            get_logger().info(f'Reviewing PR: {self.pr_url} ...')
 
             if get_settings().config.publish_output:
                 self.git_provider.publish_comment("Preparing review...", is_temporary=True)
 
             await retry_with_fallback_models(self._prepare_prediction)
 
-            logging.info('Preparing PR review...')
+            get_logger().info('Preparing PR review...')
             pr_comment = self._prepare_pr_review()
 
             if get_settings().config.publish_output:
-                logging.info('Pushing PR review...')
+                get_logger().info('Pushing PR review...')
                 self.git_provider.publish_comment(pr_comment)
                 self.git_provider.remove_initial_comment()
 
                 if get_settings().pr_reviewer.inline_code_comments:
-                    logging.info('Pushing inline code comments...')
+                    get_logger().info('Pushing inline code comments...')
                     self._publish_inline_code_comments()
         except Exception as e:
-            logging.error(f"Failed to review PR: {e}")
+            get_logger().error(f"Failed to review PR: {e}")
 
     async def _prepare_prediction(self, model: str) -> None:
         """
@@ -132,9 +132,9 @@ class PRReviewer:
         Returns:
             None
         """
-        logging.info('Getting PR diff...')
+        get_logger().info('Getting PR diff...')
         self.patches_diff = get_pr_diff(self.git_provider, self.token_handler, model)
-        logging.info('Getting AI prediction...')
+        get_logger().info('Getting AI prediction...')
         self.prediction = await self._get_prediction(model)
 
     async def _get_prediction(self, model: str) -> str:
@@ -151,12 +151,13 @@ class PRReviewer:
         variables["diff"] = self.patches_diff  # update diff
 
         environment = Environment(undefined=StrictUndefined)
+        set_custom_labels(variables)
         system_prompt = environment.from_string(get_settings().pr_review_prompt.system).render(variables)
         user_prompt = environment.from_string(get_settings().pr_review_prompt.user).render(variables)
 
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"\nSystem prompt:\n{system_prompt}")
-            logging.info(f"\nUser prompt:\n{user_prompt}")
+            get_logger().info(f"\nSystem prompt:\n{system_prompt}")
+            get_logger().info(f"\nUser prompt:\n{user_prompt}")
 
         response, finish_reason = await self.ai_handler.chat_completion(
             model=model,
@@ -209,6 +210,22 @@ class PRReviewer:
                         link = self.git_provider.generate_link_to_relevant_line_number(suggestion)
                         if link:
                             suggestion['relevant line'] = f"[{suggestion['relevant line']}]({link})"
+                    else:
+                        pass
+                        # try:
+                        #     relevant_file = suggestion['relevant file'].strip('`').strip("'")
+                        #     relevant_line_str = suggestion['relevant line']
+                        #     if not relevant_line_str:
+                        #         return ""
+                        #
+                        #     position, absolute_position = find_line_number_of_relevant_line_in_file(
+                        #         self.git_provider.diff_files, relevant_file, relevant_line_str)
+                        #     if absolute_position != -1:
+                        #         suggestion[
+                        #             'relevant line'] = f"{suggestion['relevant line']} (line {absolute_position})"
+                        # except:
+                        #     pass
+
 
         # Add incremental review section
         if self.incremental.is_incremental:
@@ -225,14 +242,15 @@ class PRReviewer:
         # Add help text if not in CLI mode
         if not get_settings().get("CONFIG.CLI_MODE", False):
             markdown_text += "\n### How to use\n"
-            if user and '[bot]' not in user:
+            bot_user = "[bot]" if get_settings().github_app.override_deployment_type else get_settings().github_app.bot_user
+            if user and bot_user not in user:
                 markdown_text += bot_help_text(user)
             else:
                 markdown_text += actions_help_text
 
         # Log markdown response if verbosity level is high
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"Markdown response:\n{markdown_text}")
+            get_logger().info(f"Markdown response:\n{markdown_text}")
 
         if markdown_text == None or len(markdown_text) == 0:
             markdown_text = ""
@@ -251,7 +269,7 @@ class PRReviewer:
         try:
             data = yaml.load(review_text, Loader=SafeLoader)
         except Exception as e:
-            logging.error(f"Failed to parse AI prediction: {e}")
+            get_logger().error(f"Failed to parse AI prediction: {e}")
             data = try_fix_yaml(review_text)
 
         comments: List[str] = []
@@ -260,7 +278,7 @@ class PRReviewer:
             relevant_line_in_file = suggestion.get('relevant line', '').strip()
             content = suggestion.get('suggestion', '')
             if not relevant_file or not relevant_line_in_file or not content:
-                logging.info("Skipping inline comment with missing file/line/content")
+                get_logger().info("Skipping inline comment with missing file/line/content")
                 continue
 
             if self.git_provider.is_supported("create_inline_comment"):

pr_agent/tools/pr_similar_issue.py

@@ -1,18 +1,18 @@
-import copy
-import json
-import logging
+import time
 from enum import Enum
-from typing import List, Tuple
-import pinecone
+from typing import List
+
 import openai
 import pandas as pd
+import pinecone
+from pinecone_datasets import Dataset, DatasetMetadata
 from pydantic import BaseModel, Field
 
 from pr_agent.algo import MAX_TOKENS
 from pr_agent.algo.token_handler import TokenHandler
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
-from pinecone_datasets import Dataset, DatasetMetadata
+from pr_agent.log import get_logger
 
 MODEL = "text-embedding-ada-002"
 
@@ -47,6 +47,13 @@ class PRSimilarIssue:
 
         # check if index exists, and if repo is already indexed
         run_from_scratch = False
+        if run_from_scratch:  # for debugging
+            pinecone.init(api_key=api_key, environment=environment)
+            if index_name in pinecone.list_indexes():
+                get_logger().info('Removing index...')
+                pinecone.delete_index(index_name)
+                get_logger().info('Done')
+
         upsert = True
         pinecone.init(api_key=api_key, environment=environment)
         if not index_name in pinecone.list_indexes():
@@ -62,11 +69,11 @@ class PRSimilarIssue:
                     upsert = False
 
         if run_from_scratch or upsert:  # index the entire repo
-            logging.info('Indexing the entire repo...')
+            get_logger().info('Indexing the entire repo...')
 
-            logging.info('Getting issues...')
+            get_logger().info('Getting issues...')
             issues = list(repo_obj.get_issues(state='all'))
-            logging.info('Done')
+            get_logger().info('Done')
             self._update_index_with_issues(issues, repo_name_for_index, upsert=upsert)
         else:  # update index if needed
             pinecone_index = pinecone.Index(index_name=index_name)
@@ -92,20 +99,20 @@ class PRSimilarIssue:
                     break
 
             if issues_to_update:
-                logging.info(f'Updating index with {counter} new issues...')
+                get_logger().info(f'Updating index with {counter} new issues...')
                 self._update_index_with_issues(issues_to_update, repo_name_for_index, upsert=True)
             else:
-                logging.info('No new issues to update')
+                get_logger().info('No new issues to update')
 
     async def run(self):
-        logging.info('Getting issue...')
+        get_logger().info('Getting issue...')
         repo_name, original_issue_number = self.git_provider._parse_issue_url(self.issue_url.split('=')[-1])
         issue_main = self.git_provider.repo_obj.get_issue(original_issue_number)
         issue_str, comments, number = self._process_issue(issue_main)
         openai.api_key = get_settings().openai.key
-        logging.info('Done')
+        get_logger().info('Done')
 
-        logging.info('Querying...')
+        get_logger().info('Querying...')
         res = openai.Embedding.create(input=[issue_str], engine=MODEL)
         embeds = [record['embedding'] for record in res['data']]
         pinecone_index = pinecone.Index(index_name=self.index_name)
@@ -117,7 +124,16 @@ class PRSimilarIssue:
         relevant_comment_number_list = []
         score_list = []
         for r in res['matches']:
-            issue_number = int(r["id"].split('.')[0].split('_')[-1])
+            # skip example issue
+            if 'example_issue_' in r["id"]:
+                continue
+
+            try:
+                issue_number = int(r["id"].split('.')[0].split('_')[-1])
+            except:
+                get_logger().debug(f"Failed to parse issue number from {r['id']}")
+                continue
+
             if original_issue_number == issue_number:
                 continue
             if issue_number not in relevant_issues_number_list:
@@ -127,9 +143,9 @@ class PRSimilarIssue:
             else:
                 relevant_comment_number_list.append(-1)
             score_list.append(str("{:.2f}".format(r['score'])))
-        logging.info('Done')
+        get_logger().info('Done')
 
-        logging.info('Publishing response...')
+        get_logger().info('Publishing response...')
         similar_issues_str = "### Similar Issues\n___\n\n"
         for i, issue_number_similar in enumerate(relevant_issues_number_list):
             issue = self.git_provider.repo_obj.get_issue(issue_number_similar)
@@ -140,8 +156,8 @@ class PRSimilarIssue:
             similar_issues_str += f"{i + 1}. **[{title}]({url})** (score={score_list[i]})\n\n"
         if get_settings().config.publish_output:
             response = issue_main.create_comment(similar_issues_str)
-        logging.info(similar_issues_str)
-        logging.info('Done')
+        get_logger().info(similar_issues_str)
+        get_logger().info('Done')
 
     def _process_issue(self, issue):
         header = issue.title
@@ -155,7 +171,7 @@ class PRSimilarIssue:
         return issue_str, comments, number
 
     def _update_index_with_issues(self, issues_list, repo_name_for_index, upsert=False):
-        logging.info('Processing issues...')
+        get_logger().info('Processing issues...')
         corpus = Corpus()
         example_issue_record = Record(
             id=f"example_issue_{repo_name_for_index}",
@@ -171,9 +187,9 @@ class PRSimilarIssue:
 
             counter += 1
             if counter % 100 == 0:
-                logging.info(f"Scanned {counter} issues")
+                get_logger().info(f"Scanned {counter} issues")
             if counter >= self.max_issues_to_scan:
-                logging.info(f"Scanned {self.max_issues_to_scan} issues, stopping")
+                get_logger().info(f"Scanned {self.max_issues_to_scan} issues, stopping")
                 break
 
             issue_str, comments, number = self._process_issue(issue)
@@ -210,9 +226,9 @@ class PRSimilarIssue:
                             )
                             corpus.append(comment_record)
         df = pd.DataFrame(corpus.dict()["documents"])
-        logging.info('Done')
+        get_logger().info('Done')
 
-        logging.info('Embedding...')
+        get_logger().info('Embedding...')
         openai.api_key = get_settings().openai.key
         list_to_encode = list(df["text"].values)
         try:
@@ -220,7 +236,7 @@ class PRSimilarIssue:
             embeds = [record['embedding'] for record in res['data']]
         except:
             embeds = []
-            logging.error('Failed to embed entire list, embedding one by one...')
+            get_logger().error('Failed to embed entire list, embedding one by one...')
             for i, text in enumerate(list_to_encode):
                 try:
                     res = openai.Embedding.create(input=[text], engine=MODEL)
@@ -231,21 +247,23 @@ class PRSimilarIssue:
         meta = DatasetMetadata.empty()
         meta.dense_model.dimension = len(embeds[0])
         ds = Dataset.from_pandas(df, meta)
-        logging.info('Done')
+        get_logger().info('Done')
 
         api_key = get_settings().pinecone.api_key
         environment = get_settings().pinecone.environment
         if not upsert:
-            logging.info('Creating index from scratch...')
+            get_logger().info('Creating index from scratch...')
             ds.to_pinecone_index(self.index_name, api_key=api_key, environment=environment)
+            time.sleep(15)  # wait for pinecone to finalize indexing before querying
         else:
-            logging.info('Upserting index...')
+            get_logger().info('Upserting index...')
             namespace = ""
             batch_size: int = 100
             concurrency: int = 10
             pinecone.init(api_key=api_key, environment=environment)
             ds._upsert_to_index(self.index_name, namespace, batch_size, concurrency)
-        logging.info('Done')
+            time.sleep(5)  # wait for pinecone to finalize upserting before querying
+        get_logger().info('Done')
 
 
 class IssueLevel(str, Enum):

pr_agent/tools/pr_update_changelog.py

@@ -1,5 +1,4 @@
 import copy
-import logging
 from datetime import date
 from time import sleep
 from typing import Tuple
@@ -10,8 +9,9 @@ from pr_agent.algo.ai_handler import AiHandler
 from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import GithubProvider, get_git_provider
+from pr_agent.git_providers import get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language
+from pr_agent.log import get_logger
 
 CHANGELOG_LINES = 50
 
@@ -48,26 +48,26 @@ class PRUpdateChangelog:
     async def run(self):
         # assert type(self.git_provider) == GithubProvider, "Currently only Github is supported"
 
-        logging.info('Updating the changelog...')
+        get_logger().info('Updating the changelog...')
         if get_settings().config.publish_output:
             self.git_provider.publish_comment("Preparing changelog updates...", is_temporary=True)
         await retry_with_fallback_models(self._prepare_prediction)
-        logging.info('Preparing PR changelog updates...')
+        get_logger().info('Preparing PR changelog updates...')
         new_file_content, answer = self._prepare_changelog_update()
         if get_settings().config.publish_output:
             self.git_provider.remove_initial_comment()
-            logging.info('Publishing changelog updates...')
+            get_logger().info('Publishing changelog updates...')
             if self.commit_changelog:
-                logging.info('Pushing PR changelog updates to repo...')
+                get_logger().info('Pushing PR changelog updates to repo...')
                 self._push_changelog_update(new_file_content, answer)
             else:
-                logging.info('Publishing PR changelog as comment...')
+                get_logger().info('Publishing PR changelog as comment...')
                 self.git_provider.publish_comment(f"**Changelog updates:**\n\n{answer}")
 
     async def _prepare_prediction(self, model: str):
-        logging.info('Getting PR diff...')
+        get_logger().info('Getting PR diff...')
         self.patches_diff = get_pr_diff(self.git_provider, self.token_handler, model)
-        logging.info('Getting AI prediction...')
+        get_logger().info('Getting AI prediction...')
         self.prediction = await self._get_prediction(model)
 
     async def _get_prediction(self, model: str):
@@ -77,8 +77,8 @@ class PRUpdateChangelog:
         system_prompt = environment.from_string(get_settings().pr_update_changelog_prompt.system).render(variables)
         user_prompt = environment.from_string(get_settings().pr_update_changelog_prompt.user).render(variables)
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"\nSystem prompt:\n{system_prompt}")
-            logging.info(f"\nUser prompt:\n{user_prompt}")
+            get_logger().info(f"\nSystem prompt:\n{system_prompt}")
+            get_logger().info(f"\nUser prompt:\n{user_prompt}")
         response, finish_reason = await self.ai_handler.chat_completion(model=model, temperature=0.2,
                                                                         system=system_prompt, user=user_prompt)
 
@@ -100,7 +100,7 @@ class PRUpdateChangelog:
                       "\n>'/update_changelog --pr_update_changelog.push_changelog_changes=true'\n"
 
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"answer:\n{answer}")
+            get_logger().info(f"answer:\n{answer}")
 
         return new_file_content, answer
 
@@ -149,7 +149,7 @@ Example:
         except Exception:
             self.changelog_file_str = ""
             if self.commit_changelog:
-                logging.info("No CHANGELOG.md file found in the repository. Creating one...")
+                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="",

requirements.txt

@@ -20,4 +20,5 @@ ujson==5.8.0
 azure-devops==7.1.0b3
 msrest==0.7.1
 pinecone-client
-pinecone-datasets @ git+https://github.com/mrT23/pinecone-datasets.git@main
+pinecone-datasets @ git+https://github.com/mrT23/pinecone-datasets.git@main
+loguru==0.7.2

tests/unittest/test_codecommit_client.py

@@ -110,7 +110,7 @@ class TestCodeCommitProvider:
         # Mock the response from the AWS client for get_pull_request method
         api.boto_client.get_pull_request.return_value = {
             "pullRequest": {
-                "pullRequestId": "3",
+                "pullRequestId": "321",
                 "title": "My PR",
                 "description": "My PR description",
                 "pullRequestTargets": [

tests/unittest/test_codecommit_provider.py

@@ -1,6 +1,8 @@
 import pytest
+from unittest.mock import patch
 from pr_agent.git_providers.codecommit_provider import CodeCommitFile
 from pr_agent.git_providers.codecommit_provider import CodeCommitProvider
+from pr_agent.git_providers.codecommit_provider import PullRequestCCMimic
 from pr_agent.git_providers.git_provider import EDIT_TYPE
 
 
@@ -25,6 +27,21 @@ class TestCodeCommitFile:
 
 
 class TestCodeCommitProvider:
+    def test_get_title(self):
+        # Test that the get_title() function returns the PR title
+        with patch.object(CodeCommitProvider, "__init__", lambda x, y: None):
+            provider = CodeCommitProvider(None)
+            provider.pr = PullRequestCCMimic("My Test PR Title", [])
+            assert provider.get_title() == "My Test PR Title"
+
+    def test_get_pr_id(self):
+        # Test that the get_pr_id() function returns the correct ID
+        with patch.object(CodeCommitProvider, "__init__", lambda x, y: None):
+            provider = CodeCommitProvider(None)
+            provider.repo_name = "my_test_repo"
+            provider.pr_num = 321
+            assert provider.get_pr_id() == "my_test_repo/321"
+
     def test_parse_pr_url(self):
         # Test that the _parse_pr_url() function can extract the repo name and PR number from a CodeCommit URL
         url = "https://us-east-1.console.aws.amazon.com/codesuite/codecommit/repositories/my_test_repo/pull-requests/321"
@@ -169,4 +186,4 @@ class TestCodeCommitProvider:
     def test_remove_markdown_html(self):
         input = "## PR Feedback\n<details><summary>Code feedback:</summary>\nfile foo\n</summary>\n"
         expect = "## PR Feedback\nCode feedback:\nfile foo\n\n"
-        assert CodeCommitProvider._remove_markdown_html(input) == expect
+        assert CodeCommitProvider._remove_markdown_html(input) == expect

tests/unittest/test_file_filter.py

@@ -0,0 +1,80 @@
+import pytest
+from pr_agent.algo.file_filter import filter_ignored
+from pr_agent.config_loader import global_settings
+
+class TestIgnoreFilter:
+    def test_no_ignores(self):
+        """
+        Test no files are ignored when no patterns are specified.
+        """
+        files = [
+            type('', (object,), {'filename': 'file1.py'})(),
+            type('', (object,), {'filename': 'file2.java'})(),
+            type('', (object,), {'filename': 'file3.cpp'})(),
+            type('', (object,), {'filename': 'file4.py'})(),
+            type('', (object,), {'filename': 'file5.py'})()
+        ]
+        assert filter_ignored(files) == files, "Expected all files to be returned when no ignore patterns are given."
+
+    def test_glob_ignores(self, monkeypatch):
+        """
+        Test files are ignored when glob patterns are specified.
+        """
+        monkeypatch.setattr(global_settings.ignore, 'glob', ['*.py'])
+
+        files = [
+            type('', (object,), {'filename': 'file1.py'})(),
+            type('', (object,), {'filename': 'file2.java'})(),
+            type('', (object,), {'filename': 'file3.cpp'})(),
+            type('', (object,), {'filename': 'file4.py'})(),
+            type('', (object,), {'filename': 'file5.py'})()
+        ]
+        expected = [
+            files[1],
+            files[2]
+        ]
+
+        filtered_files = filter_ignored(files)
+        assert filtered_files == expected, f"Expected {[file.filename for file in expected]}, but got {[file.filename for file in filtered_files]}."
+
+    def test_regex_ignores(self, monkeypatch):
+        """
+        Test files are ignored when regex patterns are specified.
+        """
+        monkeypatch.setattr(global_settings.ignore, 'regex', ['^file[2-4]\..*$'])
+
+        files = [
+            type('', (object,), {'filename': 'file1.py'})(),
+            type('', (object,), {'filename': 'file2.java'})(),
+            type('', (object,), {'filename': 'file3.cpp'})(),
+            type('', (object,), {'filename': 'file4.py'})(),
+            type('', (object,), {'filename': 'file5.py'})()
+        ]
+        expected = [
+            files[0],
+            files[4]
+        ]
+
+        filtered_files = filter_ignored(files)
+        assert filtered_files == expected, f"Expected {[file.filename for file in expected]}, but got {[file.filename for file in filtered_files]}."
+
+    def test_invalid_regex(self, monkeypatch):
+        """
+        Test invalid patterns are quietly ignored.
+        """
+        monkeypatch.setattr(global_settings.ignore, 'regex', ['(((||', '^file[2-4]\..*$'])
+
+        files = [
+            type('', (object,), {'filename': 'file1.py'})(),
+            type('', (object,), {'filename': 'file2.java'})(),
+            type('', (object,), {'filename': 'file3.cpp'})(),
+            type('', (object,), {'filename': 'file4.py'})(),
+            type('', (object,), {'filename': 'file5.py'})()
+        ]
+        expected = [
+            files[0],
+            files[4]
+        ]
+
+        filtered_files = filter_ignored(files)
+        assert filtered_files == expected, f"Expected {[file.filename for file in expected]}, but got {[file.filename for file in filtered_files]}."

tests/unittest/test_handle_patch_deletions.py

@@ -43,18 +43,6 @@ class TestHandlePatchDeletions:
         assert handle_patch_deletions(patch, original_file_content_str, new_file_content_str,
                                       file_name) == patch.rstrip()
 
-    # Tests that handle_patch_deletions logs a message when verbosity_level is greater than 0
-    def test_handle_patch_deletions_happy_path_verbosity_level_greater_than_0(self, caplog):
-        patch = '--- a/file.py\n+++ b/file.py\n@@ -1,2 +1,2 @@\n-foo\n-bar\n+baz\n'
-        original_file_content_str = 'foo\nbar\n'
-        new_file_content_str = ''
-        file_name = 'file.py'
-        get_settings().config.verbosity_level = 1
-
-        with caplog.at_level(logging.INFO):
-            handle_patch_deletions(patch, original_file_content_str, new_file_content_str, file_name)
-            assert any("Processing file" in message for message in caplog.messages)
-
     # Tests that handle_patch_deletions returns 'File was deleted' when new_file_content_str is empty
     def test_handle_patch_deletions_edge_case_new_file_content_empty(self):
         patch = '--- a/file.py\n+++ b/file.py\n@@ -1,2 +1,2 @@\n-foo\n-bar\n'