Merge pull request #512 from Codium-ai/trlabeling_files_extended

Refactoring and Enhancement of PR Description Formatting in 'pr_description.py'

.github/workflows/pr-agent-review.yaml

@@ -24,4 +24,9 @@ jobs:
           OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
           OPENAI_ORG: ${{ secrets.OPENAI_ORG }} # optional
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PINECONE.API_KEY: ${{ secrets.PINECONE_API_KEY }}
+          PINECONE.ENVIRONMENT: ${{ secrets.PINECONE_ENVIRONMENT }}
+          GITHUB_ACTION.AUTO_REVIEW: true
+          GITHUB_ACTION.AUTO_IMPROVE: true
+
 

.pr_agent.toml

@@ -0,0 +1,6 @@
+[pr_reviewer]
+enable_review_labels_effort = true
+
+
+[pr_code_suggestions]
+summarize=true

CONFIGURATION.md

@@ -1,57 +0,0 @@
-## Configuration
-
-The different tools and sub-tools used by CodiumAI PR-Agent are adjustable via the **[configuration file](pr_agent/settings/configuration.toml)**
-
-### Working from CLI
-When running from source (CLI), your local configuration file will be initially used.
-
-Example for invoking the 'review' tools via the CLI: 
-
-```
-python cli.py --pr-url=<pr_url>  review
-```
-In addition to general configurations, the 'review' tool will use parameters from the `[pr_reviewer]` section (every tool has a dedicated section in the configuration file).
-
-Note that you can print results locally, without publishing them, by setting in `configuration.toml`:
-
-```
-[config]
-publish_output=true
-verbosity_level=2
-```
-This is useful for debugging or experimenting with the different tools.
-
-### Working from pre-built repo (GitHub Action/GitHub App/Docker)
-When running PR-Agent from a pre-built repo, the default configuration file will be loaded.
-
-To edit the configuration, you have two options: 
-1. Place a local configuration file in the root of your local repo. The local file will be used instead of the default one.
-2. For online usage, just add `--config_path=<value>` to you command, to edit a specific configuration value.
-For example if you want to edit `pr_reviewer` configurations, you can run:
-```
-/review --pr_reviewer.extra_instructions="..." --pr_reviewer.require_score_review=false ...
-```
-
-Any configuration value in `configuration.toml` file can be similarly edited.
-
-### General configuration parameters
-
-#### Changing a model
-See [here](pr_agent/algo/__init__.py) for the list of available models.
-
-To use Llama2 model, for example, set:
-```
-[config]
-model = "replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"
-[replicate]
-key = ...
-```
-(you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
-
-Also review the [AiHandler](pr_agent/algo/ai_handler.py) file for instruction how to set keys for other models.
-
-#### 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 ..."
-```

Dockerfile.github_action

@@ -2,7 +2,8 @@ FROM python:3.10 as base
 
 WORKDIR /app
 ADD pyproject.toml .
-RUN pip install . && rm pyproject.toml
+ADD requirements.txt .
+RUN pip install . && rm pyproject.toml requirements.txt
 ENV PYTHONPATH=/app
 ADD pr_agent pr_agent
 ADD github_action/entrypoint.sh /

INSTALL.md

@@ -4,128 +4,74 @@
 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 as a GitHub Action](INSTALL.md#method-2-run-as-a-github-action)
-- [Method 3: Run from source](INSTALL.md#method-3-run-from-source)
-- [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)
+**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)
+- [Bitbucket server and data center](INSTALL.md#bitbucket-server-and-data-center)
 ---
 
-### 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:
+A list of the relevant tools can be found in the [tools guide](./docs/TOOLS_GUIDE.md).
 
-1. To request a review for a PR, run the following command:
+To invoke a tool (for example `review`), you can run directly from the Docker image. Here's how:
 
+- For GitHub:
 ```
-docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent --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
 ```
 
-2. To ask a question about a PR, run the following command:
-
+- For GitLab:
 ```
-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>"
+docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
 ```
-Note: If you 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:
+Note: If you have a dedicated GitLab instance, you need to specify the custom url as variable:
+```
+docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> GITLAB.URL=<your gitlab instance url> codiumai/pr-agent:latest --pr_url <pr_url> review
+```
+
+- For BitBucket:
+```
+docker run --rm -it -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$OPENAI_API_KEY -e BITBUCKET.BEARER_TOKEN=$BITBUCKET_BEARER_TOKEN codiumai/pr-agent:latest --pr_url=<pr_url> review
+```
+
+For other git providers, update CONFIG.GIT_PROVIDER accordingly, and check the `pr_agent/settings/.secrets_template.toml` file for the environment variables expected names and values.
+
+---
+
+
+If you want to ensure you're running a specific version of the Docker image, consider using the image's digest:
 ```bash
 docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent@sha256:71b5ee15df59c745d352d84752d01561ba64b6d51327f97d46152f0c58a5f678 --pr_url <pr_url> review
 ```
 
-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>"
+Or you can run a [specific released versions](./RELEASE_NOTES.md) of pr-agent, for example:
 ```
-
-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 as a GitHub Action
-
-You can use our pre-built Github Action Docker image to run PR-Agent as a Github Action. 
-
-1. Add the following file to your repository under `.github/workflows/pr_agent.yml`:
-
-```yaml
-on:
-  pull_request:
-  issue_comment:
-jobs:
-  pr_agent_job:
-    runs-on: ubuntu-latest
-    permissions:
-      issues: write
-      pull-requests: write
-      contents: write
-    name: Run pr agent on every pull request, respond to user comments
-    steps:
-      - name: PR Agent action step
-        id: pragent
-        uses: Codium-ai/pr-agent@main
-        env:
-          OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-```
-** if you want to pin your action to a specific commit for stability reasons
-```yaml
-on:
-  pull_request:
-  issue_comment:
-
-jobs:
-  pr_agent_job:
-    runs-on: ubuntu-latest
-    permissions:
-      issues: write
-      pull-requests: write
-      contents: write
-    name: Run pr agent on every pull request, respond to user comments
-    steps:
-      - name: PR Agent action step
-        id: pragent
-        uses: Codium-ai/pr-agent@<commit_sha>
-        env:
-          OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-```
-2. Add the following secret to your repository under `Settings > Secrets`:
-
-```
-OPENAI_KEY: <your key>
-```
-
-The GITHUB_TOKEN secret is automatically created by GitHub.
-
-3. Merge this change to your main branch. 
-When you open your next PR, you should see a comment from `github-actions` bot with a review of your PR, and instructions on how to use the rest of the tools.
-
-4. You may configure PR-Agent by adding environment variables under the env section corresponding to any configurable property in the [configuration](./CONFIGURATION.md) 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
+codiumai/pr-agent@v0.9
 ```
 
 ---
 
-### Method 3: Run from source
+### Run from source
 
 1. Clone this repository:
 
@@ -151,18 +97,94 @@ 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 --pr_url <pr_url> generate_labels
+python3 -m pr_agent.cli --issue_url <issue_url> similar_issue
+...
 ```
 
 ---
 
-### Method 4: Run as a polling server
-Request reviews by tagging your Github user on a PR
+### Run as a GitHub Action
+
+You can use our pre-built Github Action Docker image to run PR-Agent as a Github Action.
+
+1. Add the following file to your repository under `.github/workflows/pr_agent.yml`:
+
+```yaml
+on:
+  pull_request:
+  issue_comment:
+jobs:
+  pr_agent_job:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+      contents: write
+    name: Run pr agent on every pull request, respond to user comments
+    steps:
+      - name: PR Agent action step
+        id: pragent
+        uses: Codium-ai/pr-agent@main
+        env:
+          OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+```
+** if you want to pin your action to a specific release (v0.7 for example) for stability reasons, use:
+```yaml
+on:
+  pull_request:
+  issue_comment:
+
+jobs:
+  pr_agent_job:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+      contents: write
+    name: Run pr agent on every pull request, respond to user comments
+    steps:
+      - name: PR Agent action step
+        id: pragent
+        uses: Codium-ai/pr-agent@v0.7
+        env:
+          OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+```
+2. Add the following secret to your repository under `Settings > Secrets and variables > Actions > New repository secret > Add secret`:
+
+```
+Name = OPENAI_KEY
+Secret = <your key>
+```
+
+The GITHUB_TOKEN secret is automatically created by GitHub.
+
+3. Merge this change to your main branch.
+When you open your next PR, you should see a comment from `github-actions` bot with a review of your PR, and instructions on how to use the rest of the tools.
+
+4. You may configure PR-Agent by adding environment variables under the env section corresponding to any configurable property in the [configuration](pr_agent/settings/configuration.toml) file. Some examples:
+```yaml
+      env:
+        # ... previous environment values
+        OPENAI.ORG: "<Your organization name under your OpenAI account>"
+        PR_REVIEWER.REQUIRE_TESTS_REVIEW: "false" # Disable tests review
+        PR_CODE_SUGGESTIONS.NUM_CODE_SUGGESTIONS: 6 # Increase number of code suggestions
+```
+
+---
+
+### Run as a 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:
 
 ```
@@ -171,7 +193,7 @@ 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).
@@ -184,6 +206,7 @@ Allowing you to automate the review process on your private or public repositori
    - Set the following events:
      - Issue comment
      - Pull request
+     - Push (if you need to enable triggering on PR update)
 
 2. Generate a random secret for your app, and save it for later. For example, you can use:
 
@@ -213,12 +236,12 @@ 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:
@@ -251,11 +274,14 @@ 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 `.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
@@ -267,12 +293,13 @@ 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. In the environment variables of the Lambda function, specify `AZURE_DEVOPS_CACHE_DIR` to a writable location such as /tmp. (see [link](https://github.com/Codium-ai/pr-agent/pull/450#issuecomment-1840242269))
+7. Go back to steps 8-9 of [Method 5](#run-as-a-github-app) with the function url as your Webhook URL.
     The Webhook URL would look like `https://<LAMBDA_FUNCTION_URL>/api/v1/github_webhooks`
 
 ---
 
-### 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:
 
@@ -309,7 +336,9 @@ Example IAM permissions to that user to allow access to CodeCommit:
                 "codecommit:Get*",
                 "codecommit:List*",
                 "codecommit:PostComment*",
-                "codecommit:PutCommentReaction"
+                "codecommit:PutCommentReaction",
+                "codecommit:UpdatePullRequestDescription",
+                "codecommit:UpdatePullRequestTitle"
             ],
             "Resource": "*"
         }
@@ -338,9 +367,96 @@ PYTHONPATH="/PATH/TO/PROJECTS/pr-agent" python pr_agent/cli.py \
   review
 ```
 
-### Appendix - **Debugging LLM API Calls**  
-If you're testing your codium/pr-agent server, and need to see if calls were made successfully + the exact call logs, you can use the [LiteLLM Debugger tool](https://docs.litellm.ai/docs/debugging/hosted_debugging). 
+---
 
-You can do this by setting `litellm_debugger=true` in configuration.toml. Your Logs will be viewable in real-time @ `admin.litellm.ai/<your_email>`. Set your email in the `.secrets.toml` under 'user_email'.
+### Run a GitLab webhook server
 
-<img src="./pics/debugger.png" width="800"/>
+1. From the GitLab workspace or group, create an access token. Enable the "api" scope only.
+2. Generate a random secret for your app, and save it for later. For example, you can use:
+
+```
+WEBHOOK_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
+```
+3. Follow the instructions to build the Docker image, setup a secrets file and deploy on your own server from [Method 5](#run-as-a-github-app) steps 4-7.
+4. In the secrets file, fill in the following:
+    - Your OpenAI key.
+    - In the [gitlab] section, fill in personal_access_token and shared_secret. The access token can be a personal access token, or a group or project access token.
+    - Set deployment_type to 'gitlab' in [configuration.toml](./pr_agent/settings/configuration.toml)
+5. Create a webhook in GitLab. Set the URL to the URL of your app's server. Set the secret token to the generated secret from step 2.
+In the "Trigger" section, check the ‘comments’ and ‘merge request events’ boxes.
+6. Test your installation by opening a merge request or commenting or a merge request using one of CodiumAI's commands.
+
+
+
+### Run as a Bitbucket Pipeline
+
+
+You can use the Bitbucket Pipeline system to run PR-Agent on every pull request open or update.
+
+1. Add the following file in your repository bitbucket_pipelines.yml
+
+```yaml
+pipelines:
+    pull-requests:
+      '**':
+        - step:
+            name: PR Agent Review
+            image: python:3.10
+            services:
+              - docker
+            script:
+              - docker run -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$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.
+
+Note that comments on a PR are not supported in Bitbucket Pipeline.
+
+
+### Run using CodiumAI-hosted Bitbucket app
+
+Please contact <support@codium.ai> or visit [CodiumAI pricing page](https://www.codium.ai/pricing/) if you're interested in a hosted BitBucket app solution that provides full functionality including PR reviews and comment handling. It's based on the [bitbucket_app.py](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/git_providers/bitbucket_provider.py) implementation.
+
+
+### Bitbucket Server and Data Center
+
+Login into your on-prem instance of Bitbucket with your service account username and password.
+Navigate to `Manage account`, `HTTP Access tokens`, `Create Token`.
+Generate the token and add it to .secret.toml under `bitbucket_server` section
+
+```toml
+[bitbucket_server]
+bearer_token = "<your key>"
+```
+
+#### Run it as CLI
+
+Modify `configuration.toml`:
+
+```toml
+git_provider="bitbucket_server"
+```
+
+and pass the Pull request URL:
+```shell
+python cli.py --pr_url https://git.onpreminstanceofbitbucket.com/projects/PROJECT/repos/REPO/pull-requests/1 review
+```
+
+#### Run it as service
+
+To run pr-agent as webhook, build the docker image:
+```
+docker build . -t codiumai/pr-agent:bitbucket_server_webhook --target bitbucket_server_webhook -f docker/Dockerfile
+docker push codiumai/pr-agent:bitbucket_server_webhook  # Push to your Docker repository
+```
+
+Navigate to `Projects` or `Repositories`, `Settings`, `Webhooks`, `Create Webhook`.
+Fill the name and URL, Authentication None select the Pull Request Opened checkbox to receive that event as webhook.
+
+The URL should end with `/webhook`, for example: https://domain.com/webhook
+
+=======

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
@@ -39,4 +39,4 @@ We use [tiktoken](https://github.com/openai/tiktoken) to tokenize the patches af
 4. If we haven't reached the max token length, add the `deleted files` to the prompt until the prompt reaches the max token length (hard stop), skip the rest of the patches.
 
 ### Example
-![](https://codium.ai/images/git_patch_logic.png)
+<kbd><img src=https://codium.ai/images/git_patch_logic.png width="768"></kbd>

README.md

@@ -2,32 +2,50 @@
 
 <div align="center">
 
-<img src="./pics/logo-dark.png#gh-dark-mode-only" width="330"/>
-<img src="./pics/logo-light.png#gh-light-mode-only" width="330"/><br/>
+
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="https://codium.ai/images/pr_agent/logo-dark.png" width="330">
+  <source media="(prefers-color-scheme: light)" srcset="https://codium.ai/images/pr_agent/logo-light.png" width="330">
+  <img alt="logo">
+</picture>
+<br/>
 Making pull requests less painful with an AI agent
 </div>
 
 [![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>
 </div>
 <div style="text-align:left;">
 
-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 PR feedback:
+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**: 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**: [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**: 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**: [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**: 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`](./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.
+\
+‣ **Generate Custom Labels ([`/generate_labels`](./docs/GENERATE_CUSTOM_LABELS.md))**: Automatically suggests custom labels based on the PR code changes.
 
-<h3>Example results:</h2>
+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_, _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>
 <h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1687561986">/describe:</a></h4>
 <div align="center">
@@ -35,87 +53,104 @@ CodiumAI `PR-Agent` is an open-source tool aiming to help developers review pull
 <img src="https://www.codium.ai/images/describe-2.gif" width="800">
 </p>
 </div>
+
 <h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021901">/review:</a></h4>
 <div align="center">
 <p float="center">
 <img src="https://www.codium.ai/images/review-2.gif" width="800">
 </p>
 </div>
-<h4><a href="https://github.com/Codium-ai/pr-agent/pull/78#issuecomment-1639739496">/reflect_and_review:</a></h4>
-<div align="center">
-<p float="center">
-<img src="https://www.codium.ai/images/reflect_and_review.gif" width="800">
-</p>
-</div>
-<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695020538">/ask:</a></h4>
-<div align="center">
-<p float="center">
-<img src="https://www.codium.ai/images/ask-2.gif" width="800">
-</p>
-</div>
-<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695024952">/improve:</a></h4>
-<div align="center">
-<p float="center">
-<img src="https://www.codium.ai/images/improve-2.gif" width="800">
-</p>
-</div>
+
+[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/78#issuecomment-1639739496">/reflect_and_review:</a></h4>)
+
+[//]: # (<div align="center">)
+
+[//]: # (<p float="center">)
+
+[//]: # (<img src="https://www.codium.ai/images/reflect_and_review.gif" width="800">)
+
+[//]: # (</p>)
+
+[//]: # (</div>)
+
+[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695020538">/ask:</a></h4>)
+
+[//]: # (<div align="center">)
+
+[//]: # (<p float="center">)
+
+[//]: # (<img src="https://www.codium.ai/images/ask-2.gif" width="800">)
+
+[//]: # (</p>)
+
+[//]: # (</div>)
+
+[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695024952">/improve:</a></h4>)
+
+[//]: # (<div align="center">)
+
+[//]: # (<p float="center">)
+
+[//]: # (<img src="https://www.codium.ai/images/improve-2.gif" width="800">)
+
+[//]: # (</p>)
+
+[//]: # (</div>)
 <div align="left">
 
-
+## Table of Contents
 - [Overview](#overview)
 - [Try it now](#try-it-now)
 - [Installation](#installation)
-- [Configuration](./CONFIGURATION.md)
 - [How it works](#how-it-works)
-- [Why use PR-Agent](#why-use-pr-agent)
+- [Why use PR-Agent?](#why-use-pr-agent)
 - [Roadmap](#roadmap)
-- [Similar projects](#similar-projects)
 </div>
 
 
 ## Overview
 `PR-Agent` offers extensive pull request functionalities across various git providers:
-|       |                                             | GitHub | Gitlab | Bitbucket | CodeCommit |
-|-------|---------------------------------------------|:------:|:------:|:---------:|:----------:|
-| TOOLS | Review                                      |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |   :white_check_mark:    |
-|       | ⮑ Inline review                             |   :white_check_mark:    |   :white_check_mark:    |           |          |
-|       | Ask                                         |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:          |
-|       | Auto-Description                            |   :white_check_mark:    |   :white_check_mark:    |           |          |
-|       | Improve Code                                |   :white_check_mark:    |   :white_check_mark:    |           |          |
-|       | ⮑ Extended                             |   :white_check_mark:    |   :white_check_mark:    |           |          |
-|       | Reflect and Review                          |   :white_check_mark:    |                         |           |          |
-|       | Update CHANGELOG.md                         |   :white_check_mark:    |                         |           |          |
-|       |                                             |        |        |      |      |
-| USAGE | CLI                                         |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |   :white_check_mark:    |
-|       | App / webhook                               |   :white_check_mark:    |   :white_check_mark:    |           |          |
-|       | Tagging bot                                 |   :white_check_mark:    |        |           |          |
-|       | Actions                                     |   :white_check_mark:    |        |           |          |
-|       |                                             |        |        |      |      |
-| CORE  | PR compression                              |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |          |
-|       | Repo language prioritization                |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |          |
-|       | Adaptive and token-aware<br />file patch fitting |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |          |
-|       | Multiple models support |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |          |
-|       | Incremental PR Review |   :white_check_mark:    |      |      |      |
+|       |                                             | GitHub | Gitlab | Bitbucket | CodeCommit | Azure DevOps | Gerrit |
+|-------|---------------------------------------------|:------:|:------:|:---------:|:----------:|:----------:|:----------:|
+| TOOLS | Review                                      |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:    |
+|       | ⮑ Incremental                              |   :white_check_mark:    |       |           |       |          |     |
+|       | Ask                                         |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:          |   :white_check_mark:          | :white_check_mark: |  :white_check_mark:    |
+|       | Auto-Description                            |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:        |   :white_check_mark:    |   :white_check_mark:    | :white_check_mark:    |
+|       | Improve Code                                |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:        |   :white_check_mark:    |          |    :white_check_mark:    |
+|       | ⮑ Extended                             |   :white_check_mark:    |   :white_check_mark:    |        :white_check_mark:   |   :white_check_mark:    |          | :white_check_mark:    |
+|       | Reflect and Review                          |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:        |          |   :white_check_mark:    |    :white_check_mark:    |
+|       | Update CHANGELOG.md                         |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:        |   :white_check_mark:    |          |       |
+|       | Find similar issue                          |   :white_check_mark:    |                         |                             |          |          |       |
+|       | Add Documentation                           |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:        |   :white_check_mark:    |          |    :white_check_mark:    |
+|       | Generate Labels                           |   :white_check_mark:    |   :white_check_mark:    |         |     |          |      |
+|       |                                             |        |        |      |      |      |
+| USAGE | CLI                                         |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       |   :white_check_mark:    |   :white_check_mark:    |
+|       | App / webhook                               |   :white_check_mark:    |   :white_check_mark:    |           |          |          |
+|       | Tagging bot                                 |   :white_check_mark:    |        |           |          |          |
+|       | Actions                                     |   :white_check_mark:    |        |           |          |          |
+|       | Web server                                  |       |        |           |          |          |  :white_check_mark:   |
+|       |                                             |        |        |      |      |      |
+| CORE  | PR compression                              |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       | :white_check_mark: |   :white_check_mark:       | :white_check_mark:       |
+|       | Repo language prioritization                |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       | :white_check_mark: |   :white_check_mark:       | :white_check_mark:       |
+|       | Adaptive and token-aware<br />file patch fitting |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       | :white_check_mark: |   :white_check_mark:       | :white_check_mark:       |
+|       | Multiple models support |   :white_check_mark:    |   :white_check_mark:    |   :white_check_mark:       | :white_check_mark: |   :white_check_mark:       | :white_check_mark:       |
+|       | Incremental PR Review |   :white_check_mark:    |      |      |      |      |      |
 
-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
-
-"<pr_url>" is the url of the relevant PR (for example: https://github.com/Codium-ai/pr-agent/pull/50).
-
-In the [configuration](./CONFIGURATION.md) file you can select your git provider (GitHub, Gitlab, Bitbucket), and further configure the different tools.
+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
 
-Try GPT-4 powered PR-Agent on your public GitHub repository for free. Just mention `@CodiumAI-Agent` and add the desired command in any PR comment! The agent will generate a response based on your command.
+You can try GPT-4 powered PR-Agent, on your public GitHub repository, instantly. Just mention `@CodiumAI-Agent` and add the desired command in any PR comment. The agent will generate a response based on your command.
+For example, add a comment to any pull request with the following text:
+```
+@CodiumAI-Agent /review
+```
+and the agent will respond with a review of your PR
 
 ![Review generation process](https://www.codium.ai/images/demo-2.gif)
 
-To set up your own PR-Agent, see the [Installation](#installation) section
+
+To set up your own PR-Agent, see the [Installation](#installation) section below.
 
 ---
 
@@ -129,20 +164,22 @@ To get started with PR-Agent quickly, you first need to acquire two tokens:
 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 as a GitHub Action](INSTALL.md#method-2-run-as-a-github-action)
-- [Method 3: Run from source](INSTALL.md#method-3-run-from-source)
+- [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)
   - Request reviews by tagging your GitHub user on a PR
 - [Method 5: Run as a GitHub App](INSTALL.md#method-5-run-as-a-github-app)
   - Allowing you to automate the review process on your private or public repositories
 - [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://codium.ai/images/pr_agent/diagram-v0.9.png)
 
 Check out the [PR Compression strategy](./PR_COMPRESSION.md) page for more details on how we convert a code diff to a manageable LLM prompt
 
@@ -154,7 +191,7 @@ Here are some advantages of PR-Agent:
 
 - We emphasize **real-life practical usage**. Each tool (review, improve, ask, ...) has a single GPT-4 call, no more. We feel that this is critical for realistic team usage - obtaining an answer quickly (~30 seconds) and affordably.
 - Our [PR Compression strategy](./PR_COMPRESSION.md)  is a core ability that enables to effectively tackle both short and long PRs.
-- Our JSON prompting strategy enables to have **modular, customizable tools**. For example, the '/review' tool categories can be controlled via the [configuration](./CONFIGURATION.md) file. Adding additional categories is easy and accessible.
+- Our JSON prompting strategy enables to have **modular, customizable tools**. For example, the '/review' tool categories can be controlled via the [configuration](pr_agent/settings/configuration.toml) file. Adding additional categories is easy and accessible.
 - We support **multiple git providers** (GitHub, Gitlab, Bitbucket, CodeCommit), **multiple ways** to use the tool (CLI, GitHub Action, GitHub App, Docker, ...), and **multiple models** (GPT-4, GPT-3.5, Anthropic, Cohere, Llama2).
 - We are open-source, and welcome contributions from the community.
 
@@ -164,7 +201,7 @@ Here are some advantages of PR-Agent:
 - [x] Support additional models, as a replacement for OpenAI (see [here](https://github.com/Codium-ai/pr-agent/pull/172))
 - [x] Develop additional logic for handling large PRs (see [here](https://github.com/Codium-ai/pr-agent/pull/229))
 - [ ] Add additional context to the prompt. For example, repo (or relevant files) summarization, with tools such a [ctags](https://github.com/universal-ctags/ctags)
-- [ ] PR-Agent for issues, and just for pull requests
+- [x] PR-Agent for issues
 - [ ] Adding more tools. Possible directions:
   - [x] PR description
   - [x] Inline code suggestions
@@ -172,13 +209,34 @@ 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)
+- [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)
 - [Aider - GPT powered coding in your terminal](https://github.com/paul-gauthier/aider)
 - [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 a self-hosted PR-Agent with your OpenAI API key, it is between you and OpenAI. You can read their API data privacy policy here:
+https://openai.com/enterprise-privacy
+
+When using a PR-Agent app hosted by CodiumAI, we will not store any of your data, nor will we used it for training.
+You will also benefit from an OpenAI account with zero data retention.
+
+## Links
+
+[![Join our Discord community](https://raw.githubusercontent.com/Codium-ai/codiumai-vscode-release/main/media/docs/Joincommunity.png)](https://discord.gg/kG35uSHDBc)
+
+- Discord community: https://discord.gg/kG35uSHDBc
+- CodiumAI site: https://codium.ai
+- Blog: https://www.codium.ai/blog/
+- Troubleshooting: https://www.codium.ai/blog/technical-faq-and-troubleshooting/
+- Support: support@codium.ai

RELEASE_NOTES.md

@@ -0,0 +1,103 @@
+## [Version 0.11] - 2023-12-07
+- codiumai/pr-agent:0.11
+- codiumai/pr-agent:0.11-github_app
+- codiumai/pr-agent:0.11-bitbucket-app
+- codiumai/pr-agent:0.11-gitlab_webhook
+- codiumai/pr-agent:0.11-github_polling
+- codiumai/pr-agent:0.11-github_action
+
+### Added::Algo
+- New section in `/describe` tool - [PR changes walkthrough](https://github.com/Codium-ai/pr-agent/pull/509)
+- Improving PR Agent [prompts](https://github.com/Codium-ai/pr-agent/pull/501)
+- Persistent tools (`/review`, `/describe`) now send an [update message](https://github.com/Codium-ai/pr-agent/pull/499) after finishing
+- Add Amazon Bedrock [support](https://github.com/Codium-ai/pr-agent/pull/483)
+
+### Fixed
+- Update [dependencies](https://github.com/Codium-ai/pr-agent/pull/503) in requirements.txt for Python 3.12
+
+
+## [Version 0.10] - 2023-11-15
+- codiumai/pr-agent:0.10
+- codiumai/pr-agent:0.10-github_app
+- codiumai/pr-agent:0.10-bitbucket-app
+- codiumai/pr-agent:0.10-gitlab_webhook
+- codiumai/pr-agent:0.10-github_polling
+- codiumai/pr-agent:0.10-github_action
+
+### Added::Algo
+- Review tool now works with [persistent comments](https://github.com/Codium-ai/pr-agent/pull/451) by default
+- Bitbucket now publishes review suggestions with [code links](https://github.com/Codium-ai/pr-agent/pull/428)
+- Enabling to limit [max number of tokens](https://github.com/Codium-ai/pr-agent/pull/437/files)
+- Support ['gpt-4-1106-preview'](https://github.com/Codium-ai/pr-agent/pull/437/files) model
+- Support for Google's [Vertex AI](https://github.com/Codium-ai/pr-agent/pull/436)
+- Implementing [thresholds](https://github.com/Codium-ai/pr-agent/pull/423) for incremental PR reviews
+- Decoupled custom labels from [PR type](https://github.com/Codium-ai/pr-agent/pull/431)
+
+### Fixed
+- Fixed bug in [parsing quotes](https://github.com/Codium-ai/pr-agent/pull/446) in CLI
+- Preserve [user-added labels](https://github.com/Codium-ai/pr-agent/pull/433) in pull requests
+- Bug fixes in GitLab and BitBucket
+
+## [Version 0.9] - 2023-10-29
+- codiumai/pr-agent:0.9
+- codiumai/pr-agent:0.9-github_app
+- codiumai/pr-agent:0.9-bitbucket-app
+- codiumai/pr-agent:0.9-gitlab_webhook
+- codiumai/pr-agent:0.9-github_polling
+- codiumai/pr-agent:0.9-github_action
+
+### Added::Algo
+- New tool - [generate_labels](https://github.com/Codium-ai/pr-agent/blob/main/docs/GENERATE_CUSTOM_LABELS.md)
+- New ability to use [customize labels](https://github.com/Codium-ai/pr-agent/blob/main/docs/GENERATE_CUSTOM_LABELS.md#how-to-enable-custom-labels) on the `review` and `describe` tools.
+- New tool - [add_docs](https://github.com/Codium-ai/pr-agent/blob/main/docs/ADD_DOCUMENTATION.md)
+- GitHub Action: Can now use a `.pr_agent.toml` file to control configuration parameters (see [Usage Guide](./Usage.md#working-with-github-action)).
+- GitHub App: Added ability to trigger tools on [push events](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools-for-new-code-pr-push)
+- Support custom domain URLs for Azure devops integration (see [link](https://github.com/Codium-ai/pr-agent/pull/381)).
+- PR Description default mode is now in [bullet points](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L35).
+
+### Added::Documentation
+Significant documentation updates (see [Installation Guide](https://github.com/Codium-ai/pr-agent/blob/main/INSTALL.md), [Usage Guide](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md), and [Tools Guide](https://github.com/Codium-ai/pr-agent/blob/main/docs/TOOLS_GUIDE.md))
+
+### Fixed
+- Fixed support for BitBucket pipeline (see [link](https://github.com/Codium-ai/pr-agent/pull/386))
+- Fixed a bug in `review -i` tool
+- Added blacklist for specific file extensions in `add_docs` tool (see [link](https://github.com/Codium-ai/pr-agent/pull/385/))
+
+## [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
+- codiumai/pr-agent:0.7
+- codiumai/pr-agent:0.7-github_app
+- codiumai/pr-agent:0.7-bitbucket-app
+- codiumai/pr-agent:0.7-gitlab_webhook
+- codiumai/pr-agent:0.7-github_polling
+- codiumai/pr-agent:0.7-github_action
+ 
+### Added::Algo
+- New tool /similar_issue - Currently on GitHub app and CLI: indexes the issues in the repo, find the most similar issues to the target issue.
+- Describe markers: Empower the /describe tool with a templating capability (see more details in https://github.com/Codium-ai/pr-agent/pull/273).
+- New feature in the /review tool - added an estimated effort estimation to the review (https://github.com/Codium-ai/pr-agent/pull/306).
+
+### Added::Infrastructure
+- Implementation of a GitLab webhook.
+- Implementation of a BitBucket app.
+
+### Fixed
+- Protection against no code suggestions generated.
+- Resilience to repositories where the languages cannot be automatically detected.

Usage.md

@@ -0,0 +1,419 @@
+## Usage Guide
+
+### Table of Contents
+- [Introduction](#introduction)
+- [Working from a local repo (CLI)](#working-from-a-local-repo-cli)
+- [Online usage](#online-usage)
+- [Working with GitHub App](#working-with-github-app)
+- [Working with GitHub Action](#working-with-github-action)
+- [Working with BitBucket App](#working-with-bitbucket-self-hosted-app)
+- [Changing a model](#changing-a-model)
+- [Working with large PRs](#working-with-large-prs)
+- [Appendix - additional configurations walkthrough](#appendix---additional-configurations-walkthrough)
+
+### Introduction
+
+After [installation](/INSTALL.md), there are three basic ways to invoke CodiumAI PR-Agent:
+1. Locally running a CLI command
+2. Online usage - by [commenting](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021901) on a PR
+3. Enabling PR-Agent tools to run automatically when a new PR is opened
+
+
+Specifically, CLI commands can be issued by invoking a pre-built [docker image](/INSTALL.md#running-from-source), or by invoking a [locally cloned repo](INSTALL.md#method-2-run-from-source).
+For online usage, you will need to setup either a [GitHub App](INSTALL.md#method-5-run-as-a-github-app), or a [GitHub Action](INSTALL.md#method-3-run-as-a-github-action).
+GitHub App and GitHub Action also enable to run PR-Agent specific tool automatically when a new PR is opened.
+
+
+#### The configuration file
+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.
+
+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 also exposes the following environment variables:
+
+ - `IGNORE.GLOB`
+ - `IGNORE.REGEX`
+
+For example, to ignore python files in a PR with online usage, comment on a PR:
+`/review --ignore.glob=['*.py']`
+
+To ignore python files in all PRs, set in a configuration file:
+```
+[ignore]
+glob = ['*.py']
+```
+
+#### 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", "gerrit"
+`
+
+[//]: # (** online usage:**)
+
+[//]: # (Options that are available in the configuration file can be specified at run time when calling actions. Two examples:)
+
+[//]: # (```)
+
+[//]: # (- /review --pr_reviewer.extra_instructions="focus on the file: ...")
+
+[//]: # (- /describe --pr_description.add_original_user_description=false -pr_description.extra_instructions="make sure to mention: ...")
+
+[//]: # (```)
+
+### Working from a local repo (CLI)
+When running from your local repo (CLI), your local configuration file will be used.
+Examples of invoking the different tools via the CLI:
+
+- **Review**:       `python -m pr_agent.cli --pr_url=<pr_url>  review`
+- **Describe**:     `python -m pr_agent.cli --pr_url=<pr_url>  describe`
+- **Improve**:      `python -m pr_agent.cli --pr_url=<pr_url>  improve`
+- **Ask**:          `python -m pr_agent.cli --pr_url=<pr_url>  ask "Write me a poem about this PR"`
+- **Reflect**:      `python -m pr_agent.cli --pr_url=<pr_url>  reflect`
+- **Update Changelog**:      `python -m pr_agent.cli --pr_url=<pr_url>  update_changelog`
+
+`<pr_url>` is the url of the relevant PR (for example: https://github.com/Codium-ai/pr-agent/pull/50).
+
+**Notes:**
+
+(1) in addition to editing your local configuration file, you can also change any configuration value by adding it to the command line:
+```
+python -m pr_agent.cli --pr_url=<pr_url>  /review --pr_reviewer.extra_instructions="focus on the file: ..."
+```
+
+(2) You can print results locally, without publishing them, by setting in `configuration.toml`:
+```
+[config]
+publish_output=true
+verbosity_level=2
+```
+This is useful for debugging or experimenting with different tools.
+
+
+### Online usage
+
+Online usage means invoking PR-Agent tools by [comments](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021901) on a PR.
+Commands for invoking the different tools via comments:
+
+- **Review**:       `/review`
+- **Describe**:     `/describe`
+- **Improve**:      `/improve`
+- **Ask**:          `/ask "..."`
+- **Reflect**:      `/reflect`
+- **Update Changelog**:      `/update_changelog`
+
+
+To edit a specific configuration value, just add `--config_path=<value>` to any command.
+For example, if you want to edit the `review` tool configurations, you can run:
+```
+/review --pr_reviewer.extra_instructions="..." --pr_reviewer.require_score_review=false
+```
+Any configuration value in [configuration file](pr_agent/settings/configuration.toml) file can be similarly edited. Comment `/config` to see the list of available configurations.
+
+
+### Working with GitHub App
+When running PR-Agent from GitHub App, the default [configuration file](pr_agent/settings/configuration.toml) from a pre-built docker will be initially loaded.
+
+By uploading a local `.pr_agent.toml` file to the root of the repo's main branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
+
+For example, if you set in `.pr_agent.toml`:
+
+```
+[pr_reviewer]
+num_code_suggestions=1
+```
+
+Then you will overwrite the default number of code suggestions to 1.
+
+#### GitHub app automatic tools
+The [github_app](pr_agent/settings/configuration.toml#L76) section defines GitHub app-specific configurations.  
+In this section you can define configurations to control the conditions for which tools will **run automatically**.  
+
+##### GitHub app automatic tools for PR actions
+The GitHub app can respond to the following actions on a PR:
+1. `opened` - Opening a new PR
+2. `reopened` - Reopening a closed PR
+3. `ready_for_review` - Moving a PR from Draft to Open
+4. `review_requested` - Specifically requesting review (in the PR reviewers list) from the `github-actions[bot]` user
+
+The configuration parameter `handle_pr_actions` defines the list of actions for which the GitHub app will trigger the PR-Agent.  
+The configuration parameter `pr_commands` defines the list of tools that will be **run automatically** when one of the above actions happens (e.g., a new PR is opened):
+```
+[github_app]
+handle_pr_actions = ['opened', 'reopened', 'ready_for_review', 'review_requested']
+pr_commands = [
+    "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
+    "/auto_review",
+]
+```
+This means that when a new PR is opened/reopened or marked as ready for review, 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.
+
+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]
+add_original_user_description = false
+keep_original_user_title = false
+```
+When a new PR is opened, PR-Agent will run the `describe` tool with the above parameters.
+
+To cancel the automatic run of all the tools, set:
+```
+[github_app]
+handle_pr_actions = []
+```
+
+##### GitHub app automatic tools for new code (PR push)
+In addition to running automatic tools when a PR is opened, the GitHub app can also respond to new code that is pushed to an open PR.
+
+The configuration toggle `handle_push_trigger` can be used to enable this feature.  
+The configuration parameter `push_commands` defines the list of tools that will be **run automatically** when new code is pushed to the PR.
+```
+[github_app]
+handle_push_trigger = true
+push_commands = [
+    "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
+    "/auto_review -i --pr_reviewer.remove_previous_review_comment=true",
+]
+```
+This means that when new code is pushed to the PR, the PR-Agent will run the `describe` and incremental `auto_review` tools.  
+For the describe tool, the `add_original_user_description` and `keep_original_user_title` parameters will be set to true.  
+For the `auto_review` tool, it will run in incremental mode, and the `remove_previous_review_comment` parameter will be set to true.
+
+Much like the configurations for `pr_commands`, you can override the default tool parameters by uploading a local configuration file to the root of your repo.
+
+#### Editing the prompts
+The prompts for the various PR-Agent tools are defined in the `pr_agent/settings` folder.
+In practice, the prompts are loaded and stored as a standard setting object.
+Hence, editing them is similar to editing any other configuration value - just place the relevant key in `.pr_agent.toml`file, and override the default value.
+
+For example, if you want to edit the prompts of the [describe](./pr_agent/settings/pr_description_prompts.toml) tool, you can add the following to your `.pr_agent.toml` file:
+```
+[pr_description_prompt]
+system="""
+...
+"""
+user="""
+...
+"""
+```
+Note that the new prompt will need to generate an output compatible with the relevant [post-process function](./pr_agent/tools/pr_description.py#L137).
+
+### Working with GitHub Action
+You can configure settings in GitHub action by adding environment variables under the env section in `.github/workflows/pr_agent.yml` file. 
+Specifically, start by setting the following environment variables:
+```yaml
+      env:
+        OPENAI_KEY: ${{ secrets.OPENAI_KEY }} # Make sure to add your OpenAI key to your repo secrets
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Make sure to add your GitHub token to your repo secrets
+        github_action.auto_review: "true" # enable\disable auto review
+        github_action.auto_describe: "true" # enable\disable auto describe
+        github_action.auto_improve: "false" # enable\disable auto improve
+```
+`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.
+If not set, the default option is that only the `review` tool will run automatically when a new PR is opened.
+
+Note that you can give additional config parameters by adding environment variables to `.github/workflows/pr_agent.yml`, or by using a `.pr_agent.toml` file in the root of your repo, similar to the GitHub App usage.
+
+For example, you can set an environment variable: `pr_description.add_original_user_description=false`, or add a `.pr_agent.toml` file with the following content:
+```
+[pr_description]
+add_original_user_description = false
+```
+
+### Working with BitBucket Self-Hosted App
+Similar to GitHub app, when running PR-Agent from BitBucket App, the default [configuration file](pr_agent/settings/configuration.toml) from a pre-built docker will be initially loaded.
+
+By uploading a local `.pr_agent.toml` file to the root of the repo's main branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
+
+For example, if your local `.pr_agent.toml` file contains:
+```
+[pr_reviewer]
+inline_code_comments = true
+```
+
+Each time you invoke a `/review` tool, it will use inline code comments.
+
+### Changing a model
+
+See [here](pr_agent/algo/__init__.py) for the list of available models.
+To use a different model than the default (GPT-4), you need to edit [configuration file](pr_agent/settings/configuration.toml#L2).
+For models and environments not from OPENAI, you might need to provide additional keys and other parameters. See below for instructions.
+
+#### Azure
+To use Azure, set in your `.secrets.toml` (working from CLI), or in the GitHub `Settings > Secrets and variables` (working from GitHub App or GitHub Action):
+```
+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"
+openai.deployment_id = ""  # The deployment name you chose when you deployed the engine
+```
+
+and set in your configuration file:
+```
+[config]
+model="" # the OpenAI model you've deployed on Azure (e.g. gpt-3.5-turbo)
+```
+
+#### Huggingface
+
+**Local**
+You can run Huggingface models locally through either [VLLM](https://docs.litellm.ai/docs/providers/vllm) or [Ollama](https://docs.litellm.ai/docs/providers/ollama)
+
+E.g. to use a new Huggingface model locally via Ollama, set:
+```
+[__init__.py]
+MAX_TOKENS = {
+    "model-name-on-ollama": <max_tokens>
+}
+e.g.
+MAX_TOKENS={
+    ...,
+    "ollama/llama2": 4096
+}
+
+
+[config] # in configuration.toml
+model = "ollama/llama2"
+
+[ollama] # in .secrets.toml
+api_base = ... # the base url for your huggingface inference endpoint
+# e.g. if running Ollama locally, you may use:
+api_base = "http://localhost:11434/"
+```
+
+**Inference Endpoints**
+
+To use a new model with Huggingface Inference Endpoints, for example, set:
+```
+[__init__.py]
+MAX_TOKENS = {
+    "model-name-on-huggingface": <max_tokens>
+}
+e.g.
+MAX_TOKENS={
+    ...,
+    "meta-llama/Llama-2-7b-chat-hf": 4096
+}
+[config] # in configuration.toml
+model = "huggingface/meta-llama/Llama-2-7b-chat-hf"
+
+[huggingface] # in .secrets.toml
+key = ... # your huggingface api key
+api_base = ... # the base url for your huggingface inference endpoint
+```
+(you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
+
+#### Replicate
+
+To use Llama2 model with Replicate, for example, set:
+```
+[config] # in configuration.toml
+model = "replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"
+[replicate] # in .secrets.toml
+key = ...
+```
+(you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
+
+
+Also review the [AiHandler](pr_agent/algo/ai_handler.py) file for instruction how to set keys for other models.
+
+#### Vertex AI
+
+To use Google's Vertex AI platform and its associated models (chat-bison/codechat-bison) set:
+
+``` 
+[config] # in configuration.toml
+model = "vertex_ai/codechat-bison"
+fallback_models="vertex_ai/codechat-bison"
+
+[vertexai] # in .secrets.toml
+vertex_project = "my-google-cloud-project"
+vertex_location = ""
+```
+
+Your [application default credentials](https://cloud.google.com/docs/authentication/application-default-credentials) will be used for authentication so there is no need to set explicit credentials in most environments.
+
+If you do want to set explicit credentials then you can use the `GOOGLE_APPLICATION_CREDENTIALS` environment variable set to a path to a json credentials file.
+
+#### Amazon Bedrock
+
+To use Amazon Bedrock and its foundational models, add the below configuration:
+
+``` 
+[config] # in configuration.toml
+model = "anthropic.claude-v2"
+fallback_models="anthropic.claude-instant-v1"
+
+[aws] # in .secrets.toml
+bedrock_region = "us-east-1"
+```
+
+Note that you have to add access to foundational models before using them. Please refer to [this document](https://docs.aws.amazon.com/bedrock/latest/userguide/setting-up.html) for more details.
+
+AWS session is automatically authenticated from your environment, but you can also explicitly set `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY` environment variables.
+
+### 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:
+```
+[config]
+git_provider="azure"
+use_repo_settings_file=false
+```
+
+And use the following settings (you have to replace the values) in .secrets.toml:
+```
+[azure_devops]
+org = "https://dev.azure.com/YOUR_ORGANIZATION/"
+pat = "YOUR_PAT_TOKEN"
+```

docker/Dockerfile

@@ -14,10 +14,18 @@ FROM base as bitbucket_app
 ADD pr_agent pr_agent
 CMD ["python", "pr_agent/servers/bitbucket_app.py"]
 
+FROM base as bitbucket_server_webhook
+ADD pr_agent pr_agent
+CMD ["python", "pr_agent/servers/bitbucket_server_webhook.py"]
+
 FROM base as github_polling
 ADD pr_agent pr_agent
 CMD ["python", "pr_agent/servers/github_polling.py"]
 
+FROM base as gitlab_webhook
+ADD pr_agent pr_agent
+CMD ["python", "pr_agent/servers/gitlab_webhook.py"]
+
 FROM base as test
 ADD requirements-dev.txt .
 RUN pip install -r requirements-dev.txt && rm requirements-dev.txt

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=https://codium.ai/images/pr_agent/add_docs_comment.png width="768"></kbd>
+<kbd><img src=https://codium.ai/images/pr_agent/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=https://codium.ai/images/pr_agent/ask_comment.png width="768"></kbd>
+<kbd><img src=https://codium.ai/images/pr_agent/ask.png width="768"></kbd>

docs/DESCRIBE.md

@@ -0,0 +1,70 @@
+# Describe Tool
+
+The `describe` tool scans the PR code changes, and automatically generates PR description - title, type, summary, walkthrough and labels.
+It can be invoked manually by commenting on any PR:
+```
+/describe
+```
+For example:
+
+<kbd><img src=https://codium.ai/images/pr_agent/describe_comment.png width="768"></kbd>
+
+<kbd><img src=https://codium.ai/images/pr_agent/describe.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 ...".
+
+- To enable `custom labels`, apply the configuration changes described [here](./GENERATE_CUSTOM_LABELS.md#configuration-changes)
+
+- `enable_pr_type`: if set to false, it will not show the `PR type` as a text value in the description content. Default is true.
+
+- `final_update_message`: if set to true, it will add a comment message [`PR Description updated to latest commit...`](https://github.com/Codium-ai/pr-agent/pull/499#issuecomment-1837412176) after finishing calling `/describe`. Default is true.
+
+- `enable_semantic_files_types`: if set to true, "PR changes walkthrough" section will be generated. Default is true.
+  
+### 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=https://codium.ai/images/pr_agent/describe_markers_before.png width="768"></kbd>
+
+==>
+
+<kbd><img src=https://codium.ai/images/pr_agent/describe_markers_after.png width="768"></kbd>
+
+##### Configuration params:
+
+- `use_description_markers`: if set to true, the tool will use markers template. It replaces every marker of the form `pr_agent:marker_name` with the relevant content. Default is false.
+- `include_generated_by_header`: if set to true, the tool will add a dedicated header: 'Generated by PR Agent at ...' to any automatic content. Default is true.

docs/GENERATE_CUSTOM_LABELS.md

@@ -0,0 +1,41 @@
+# Generate Custom Labels
+The `generate_labels` tool scans the PR code changes, and given a list of labels and their descriptions, it automatically suggests labels that match the PR code changes.
+
+It can be invoked manually by commenting on any PR:
+```
+/generate_labels
+```
+For example:
+
+If we wish to add detect changes to SQL queries in a given PR, we can add the following custom label along with its description:
+
+<kbd><img src=https://codium.ai/images/pr_agent/custom_labels_list.png width="768"></kbd>
+
+When running the `generate_labels` tool on a PR that includes changes in SQL queries, it will automatically suggest the custom label:
+<kbd><img src=https://codium.ai/images/pr_agent/custom_label_published.png width="768"></kbd>
+
+### How to enable custom labels
+
+Note that in addition to the dedicated tool `generate_labels`, the custom labels will also be used by the `review` and `describe` tools.
+
+#### CLI
+To enable custom labels, you need to apply the [configuration changes](#configuration-changes) to the [custom_labels file](./../pr_agent/settings/custom_labels.toml):
+
+#### GitHub Action and GitHub App
+To enable custom labels, you need to apply the [configuration changes](#configuration-changes) to the local `.pr_agent.toml` file in you repository.
+
+#### Configuration changes
+ - Change `enable_custom_labels` to True: This will turn off the default labels and enable the custom labels provided in the custom_labels.toml file.
+ - Add the custom labels. It should be formatted as follows:
+
+```
+[config]
+enable_custom_labels=true
+
+[custom_labels."Custom Label Name"]
+description = "Description of when AI should suggest this label"
+
+[custom_labels."Custom Label 2"]
+description = "Description of when AI should suggest this label 2"
+```
+

docs/IMPROVE.md

@@ -0,0 +1,57 @@
+# Improve Tool
+
+The `improve` tool scans the PR code changes, and automatically generates committable suggestions for improving the PR code.
+It can be invoked manually by commenting on any PR:
+```
+/improve
+```
+For example:
+
+<kbd><img src=https://codium.ai/images/pr_agent/improve_comment.png width="768"></kbd>
+<kbd><img src=https://codium.ai/images/pr_agent/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.
+
+#### summarize mode
+- `summarize`: if set to true, the tool will present the code suggestions in a compact way. Default is false.
+
+In this mode, instead of presenting committable suggestions, the different suggestions will be combined into a single compact comment, with significantly smaller PR footprint.
+
+For example:
+
+`/improve --pr_code_suggestions.summarize=true`
+
+<kbd><img src=https://codium.ai/images/pr_agent/improved_summerize_open.png width="768"></kbd>
+
+___
+
+### A note on code suggestions quality
+
+- While the current AI for code is getting better and better (GPT-4), it's not flawless. Not all the suggestions will be perfect, and a user should not accept all of them automatically.
+
+- Suggestions are not meant to be [simplistic](./../pr_agent/settings/pr_code_suggestions_prompts.toml#L34). Instead, they aim to give deep feedback and raise questions, ideas and thoughts to the user, who can then use his judgment, experience, and understanding of the code base.
+
+- Recommended to use the '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 +1,79 @@
+# 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=https://codium.ai/images/pr_agent/review_comment.png width="768"></kbd>
+<kbd><img src=https://codium.ai/images/pr_agent/review.png width="768"></kbd>
+
+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:
+
+#### enable\\disable features
+- `require_focused_review`: if set to true, the tool will add a section - 'is the PR a focused one'. Default is false.
+- `require_score_review`: if set to true, the tool will add a section that scores the PR. Default is false.
+- `require_tests_review`: if set to true, the tool will add a section that checks if the PR contains tests. Default is true.
+- `require_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.
+#### general options
+- `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.
+- `remove_previous_review_comment`: if set to true, the tool will remove the previous review comment before adding a new one. Default is false.
+- `persistent_comment`: if set to true, the review comment will be persistent, meaning that every new review request will edit the previous one. Default is true.
+- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
+#### review labels
+- `enable_review_labels_security`: if set to true, the tool will publish a 'possible security issue' label if it detects a security issue. Default is true.
+- `enable_review_labels_effort`: if set to true, the tool will publish a 'Review effort [1-5]: x' label. Default is false.
+- To enable `custom labels`, apply the configuration changes described [here](./GENERATE_CUSTOM_LABELS.md#configuration-changes) 
+####  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:
+```
+/review -i
+```
+Note that the incremental mode is only available for GitHub.
+
+<kbd><img src=https://codium.ai/images/pr_agent/incremental_review.png width="768"></kbd>
+
+Under the section 'pr_reviewer', the [configuration file](./../pr_agent/settings/configuration.toml#L16) contains options to customize the 'review -i' tool.  
+These configurations can be used to control the rate at which the incremental review tool will create new review comments when invoked automatically, to prevent making too much noise in the PR.
+- `minimal_commits_for_incremental_review`: Minimal number of commits since the last review that are required to create incremental review.
+If there are less than the specified number of commits since the last review, the tool will not perform any action.
+Default is 0 - the tool will always run, no matter how many commits since the last review.
+- `minimal_minutes_for_incremental_review`: Minimal number of minutes that need to pass since the last reviewed commit to create incremental review.
+If less that the specified number of minutes have passed between the last reviewed commit and running this command, the tool will not perform any action. 
+Default is 0 - the tool will always run, no matter how much time have passed since the last reviewed commit.
+- `require_all_thresholds_for_incremental_review`: If set to true, all the previous thresholds must be met for incremental review to run. If false, only one is enough to run the tool.
+For example, if `minimal_commits_for_incremental_review=2` and `minimal_minutes_for_incremental_review=2`, and we have 3 commits since the last review, but the last reviewed commit is from 1 minute ago:
+When `require_all_thresholds_for_incremental_review=true` the incremental review __will not__ run, because only 1 out of 2 conditions were met (we have enough commits but the last review is too recent),
+but when `require_all_thresholds_for_incremental_review=false` the incremental review __will__ run, because one condition is enough (we have 3 commits which is more than the configured 2).
+Default is false - the tool will run as long as at least once conditions is met.
+
+#### PR Reflection
+By invoking:
+```
+/reflect_and_review
+```
+The tool will first ask the author questions about the PR, and will guide the review based on his answers.
+
+<kbd><img src=https://codium.ai/images/pr_agent/reflection_questions.png width="768"></kbd>
+<kbd><img src=https://codium.ai/images/pr_agent/reflection_answers.png width="768"></kbd>
+<kbd><img src=https://codium.ai/images/pr_agent/reflection_insights.png width="768"></kbd>
+
+
+#### 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=https://codium.ai/images/pr_agent/similar_issue_original_issue.png width="768"></kbd>
+<kbd><img src=https://codium.ai/images/pr_agent/similar_issue_comment.png width="768"></kbd>
+<kbd><img src=https://codium.ai/images/pr_agent/similar_issue.png width="768"></kbd>
+
+Note that to perform retrieval, the `similar_issue` tool indexes all the repo previous issues (once).
+
+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 +1,11 @@
+## 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)
+- [GENERATE CUSTOM LABELS](./GENERATE_CUSTOM_LABELS.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=https://codium.ai/images/pr_agent/update_changelog_comment.png width="768"></kbd>
+<kbd><img src=https://codium.ai/images/pr_agent/update_changelog.png width="768"></kbd>
+
+
+### Configuration options
+
+Under the section 'pr_update_changelog', the [configuration file](./../pr_agent/settings/configuration.toml#L50) contains options to customize the 'update changelog' tool:
+
+- `push_changelog_changes`: whether to push the changes to CHANGELOG.md, or just print them. Default is false (print only).
+- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...

pr_agent/agent/pr_agent.py

@@ -1,18 +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_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,
@@ -30,6 +30,9 @@ command2class = {
     "update_changelog": PRUpdateChangelog,
     "config": PRConfig,
     "settings": PRConfig,
+    "similar_issue": PRSimilarIssue,
+    "add_docs": PRAddDocs,
+    "generate_labels": PRGenerateLabels,
 }
 
 commands = list(command2class.keys())
@@ -40,33 +43,21 @@ 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("'", "\\'")
-        lexer = shlex.shlex(request, posix=True)
-        lexer.whitespace_split = True
-        action, *args = list(lexer)
+        if isinstance(request, str):
+            request = request.replace("'", "\\'")
+            lexer = shlex.shlex(request, posix=True)
+            lexer.whitespace_split = True
+            action, *args = list(lexer)
+        else:
+            action, *args = request
         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()
@@ -80,3 +71,4 @@ class PRAgent:
         else:
             return False
         return True
+

pr_agent/algo/__init__.py

@@ -1,4 +1,5 @@
 MAX_TOKENS = {
+    'text-embedding-ada-002': 8000,
     'gpt-3.5-turbo': 4000,
     'gpt-3.5-turbo-0613': 4000,
     'gpt-3.5-turbo-0301': 4000,
@@ -7,8 +8,17 @@ MAX_TOKENS = {
     'gpt-4': 8000,
     'gpt-4-0613': 8000,
     'gpt-4-32k': 32000,
+    'gpt-4-1106-preview': 128000, # 128K, but may be limited by config.max_model_tokens
     'claude-instant-1': 100000,
     'claude-2': 100000,
     'command-nightly': 4096,
     'replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1': 4096,
+    'meta-llama/Llama-2-7b-chat-hf': 4096,
+    'vertex_ai/codechat-bison': 6144,
+    'vertex_ai/codechat-bison-32k': 32000,
+    'codechat-bison': 6144,
+    'codechat-bison-32k': 32000,
+    'anthropic.claude-v2': 100000,
+    'anthropic.claude-instant-v1': 100000,
+    'anthropic.claude-v1': 100000,
 }

pr_agent/algo/ai_handler.py

@@ -1,12 +1,13 @@
-import logging
+import os
 
+import boto3
 import litellm
 import openai
 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
 
@@ -23,33 +24,50 @@ class AiHandler:
         Initializes the OpenAI API key and other settings from a configuration file.
         Raises a ValueError if the OpenAI key is missing.
         """
-        try:
+        self.azure = False
+        self.aws_bedrock_client = None
+
+        if get_settings().get("OPENAI.KEY", None):
             openai.api_key = get_settings().openai.key
             litellm.openai_key = get_settings().openai.key
-            litellm.debugger = get_settings().config.litellm_debugger
-            self.azure = False
-            if get_settings().get("OPENAI.ORG", None):
-                litellm.organization = get_settings().openai.org
-            if get_settings().get("OPENAI.API_TYPE", None):
-                if get_settings().openai.api_type == "azure":
-                    self.azure = True
-                    litellm.azure_key = get_settings().openai.key
-            if get_settings().get("OPENAI.API_VERSION", None):
-                litellm.api_version = get_settings().openai.api_version
-            if get_settings().get("OPENAI.API_BASE", None):
-                litellm.api_base = get_settings().openai.api_base
-            if get_settings().get("ANTHROPIC.KEY", None):
-                litellm.anthropic_key = get_settings().anthropic.key
-            if get_settings().get("COHERE.KEY", None):
-                litellm.cohere_key = get_settings().cohere.key
-            if get_settings().get("REPLICATE.KEY", None):
-                litellm.replicate_key = get_settings().replicate.key
-            if get_settings().get("REPLICATE.KEY", None):
-                litellm.replicate_key = get_settings().replicate.key
-            if get_settings().get("HUGGINGFACE.KEY", None):
-                litellm.huggingface_key = get_settings().huggingface.key
-        except AttributeError as e:
-            raise ValueError("OpenAI key is required") from e
+        if get_settings().get("litellm.use_client"):
+            litellm_token = get_settings().get("litellm.LITELLM_TOKEN")
+            assert litellm_token, "LITELLM_TOKEN is required"
+            os.environ["LITELLM_TOKEN"] = litellm_token
+            litellm.use_client = True
+        if get_settings().get("OPENAI.ORG", None):
+            litellm.organization = get_settings().openai.org
+        if get_settings().get("OPENAI.API_TYPE", None):
+            if get_settings().openai.api_type == "azure":
+                self.azure = True
+                litellm.azure_key = get_settings().openai.key
+        if get_settings().get("OPENAI.API_VERSION", None):
+            litellm.api_version = get_settings().openai.api_version
+        if get_settings().get("OPENAI.API_BASE", None):
+            litellm.api_base = get_settings().openai.api_base
+        if get_settings().get("ANTHROPIC.KEY", None):
+            litellm.anthropic_key = get_settings().anthropic.key
+        if get_settings().get("COHERE.KEY", None):
+            litellm.cohere_key = get_settings().cohere.key
+        if get_settings().get("REPLICATE.KEY", None):
+            litellm.replicate_key = get_settings().replicate.key
+        if get_settings().get("REPLICATE.KEY", None):
+            litellm.replicate_key = get_settings().replicate.key
+        if get_settings().get("HUGGINGFACE.KEY", None):
+            litellm.huggingface_key = get_settings().huggingface.key
+            if get_settings().get("HUGGINGFACE.API_BASE", None):
+                litellm.api_base = get_settings().huggingface.api_base
+        if get_settings().get("VERTEXAI.VERTEX_PROJECT", None):
+            litellm.vertex_project = get_settings().vertexai.vertex_project
+            litellm.vertex_location = get_settings().get(
+                "VERTEXAI.VERTEX_LOCATION", None
+            )
+        if get_settings().get("AWS.BEDROCK_REGION", None):
+            litellm.AmazonAnthropicConfig.max_tokens_to_sample = 2000
+            self.aws_bedrock_client = boto3.client(
+                service_name="bedrock-runtime",
+                region_name=get_settings().aws.bedrock_region,
+            )
 
     @property
     def deployment_id(self):
@@ -83,33 +101,37 @@ 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 ''}"
                 )
-            response = await acompletion(
-                model=model,
-                deployment_id=deployment_id,
-                messages=[
-                    {"role": "system", "content": system},
-                    {"role": "user", "content": user}
-                ],
-                temperature=temperature,
-                azure=self.azure,
-                force_timeout=get_settings().config.ai_timeout
-            )
+            if self.azure:
+                model = 'azure/' + model
+            messages = [{"role": "system", "content": system}, {"role": "user", "content": user}]
+            kwargs = {
+                "model": model,
+                "deployment_id": deployment_id,
+                "messages": messages,
+                "temperature": temperature,
+                "force_timeout": get_settings().config.ai_timeout,
+            }
+            if self.aws_bedrock_client:
+                kwargs["aws_bedrock_client"] = self.aws_bedrock_client
+            response = await acompletion(**kwargs)
         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 +1,36 @@
+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
+        if isinstance(patterns, str):
+            patterns = [patterns]
+        glob_setting = get_settings().ignore.glob
+        if isinstance(glob_setting, str): # --ignore.glob=[.*utils.py], --ignore.glob=.*utils.py
+            glob_setting = glob_setting.strip('[]').split(",")
+        patterns += [fnmatch.translate(glob) for glob in glob_setting]
+
+        # 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 (f.filename and 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 +1,10 @@
 from __future__ import annotations
-import logging
+
 import re
 
 from pr_agent.config_loader import get_settings
+from pr_agent.git_providers.git_provider import EDIT_TYPE
+from pr_agent.log import get_logger
 
 
 def extend_patch(original_file_str, patch_str, num_lines) -> str:
@@ -40,12 +42,16 @@ 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 +65,7 @@ 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
@@ -110,7 +116,7 @@ def omit_deletion_hunks(patch_lines) -> str:
 
 
 def handle_patch_deletions(patch: str, original_file_content_str: str,
-                           new_file_content_str: str, file_name: str) -> str:
+                           new_file_content_str: str, file_name: str, edit_type: EDIT_TYPE = EDIT_TYPE.UNKNOWN) -> str:
     """
     Handle entire file or deletion patches.
 
@@ -127,17 +133,17 @@ def handle_patch_deletions(patch: str, original_file_content_str: str,
         str: The modified patch with deletion hunks omitted.
 
     """
-    if not new_file_content_str:
+    if not new_file_content_str and edit_type != EDIT_TYPE.ADDED:
         # 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 +213,15 @@ __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/language_handler.py

@@ -3,8 +3,7 @@ from typing import Dict
 
 from pr_agent.config_loader import get_settings
 
-language_extension_map_org = get_settings().language_extension_map_org
-language_extension_map = {k.lower(): v for k, v in language_extension_map_org.items()}
+
 
 # Bad Extensions, source: https://github.com/EleutherAI/github-downloader/blob/345e7c4cbb9e0dc8a0615fd995a08bf9d73b3fe6/download_repo_text.py  # noqa: E501
 bad_extensions = get_settings().bad_extensions.default
@@ -29,6 +28,8 @@ def sort_files_by_main_languages(languages: Dict, files: list):
     # languages_sorted = sorted(languages, key=lambda x: x[1], reverse=True)
     # get all extensions for the languages
     main_extensions = []
+    language_extension_map_org = get_settings().language_extension_map_org
+    language_extension_map = {k.lower(): v for k, v in language_extension_map_org.items()}
     for language in languages_sorted_list:
         if language.lower() in language_extension_map:
             main_extensions.append(language_extension_map[language.lower()])
@@ -42,6 +43,11 @@ def sort_files_by_main_languages(languages: Dict, files: list):
     files_sorted = []
     rest_files = {}
 
+    # if no languages detected, put all files in the "Other" category
+    if not languages:
+        files_sorted = [({"language": "Other", "files": list(files_filtered)})]
+        return files_sorted
+
     main_extensions_flat = []
     for ext in main_extensions:
         main_extensions_flat.extend(ext)

pr_agent/algo/pr_processing.py

@@ -1,27 +1,29 @@
 from __future__ import annotations
 
 import difflib
-import logging
 import re
 import traceback
 from typing import Any, Callable, List, Tuple
 
 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.token_handler import TokenHandler, get_token_encoder
+from pr_agent.algo.file_filter import filter_ignored
+from pr_agent.algo.token_handler import TokenHandler
+from pr_agent.algo.utils import get_max_tokens
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers.git_provider import FilePatchInfo, GitProvider
+from pr_agent.git_providers.git_provider import FilePatchInfo, GitProvider, EDIT_TYPE
+from pr_agent.log import get_logger
 
 DELETED_FILES_ = "Deleted files:\n"
 
-MORE_MODIFIED_FILES_ = "More modified files:\n"
+MORE_MODIFIED_FILES_ = "Additional modified files (insufficient token budget to process):\n"
+
+ADDED_FILES_ = "Additional added files (insufficient token budget to process):\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:
@@ -44,31 +46,37 @@ 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]:
+    if total_tokens + OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD < get_max_tokens(model):
         return "\n".join(patches_extended)
 
     # if we are over the limit, start pruning
-    patches_compressed, modified_file_names, deleted_file_names = \
+    patches_compressed, modified_file_names, deleted_file_names, added_file_names = \
         pr_generate_compressed_diff(pr_languages, token_handler, model, add_line_numbers_to_hunks)
 
     final_diff = "\n".join(patches_compressed)
+    if added_file_names:
+        added_list_str = ADDED_FILES_ + "\n".join(added_file_names)
+        final_diff = final_diff + "\n\n" + added_list_str
     if modified_file_names:
         modified_list_str = MORE_MODIFIED_FILES_ + "\n".join(modified_file_names)
         final_diff = final_diff + "\n\n" + modified_list_str
@@ -80,7 +88,8 @@ 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 +111,7 @@ 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:
@@ -118,7 +127,7 @@ def pr_generate_extended_diff(pr_languages: list,
 
 
 def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, model: str,
-                                convert_hunks_to_line_numbers: bool) -> Tuple[list, list, list]:
+                                convert_hunks_to_line_numbers: bool) -> Tuple[list, list, list, list]:
     """
     Generate a compressed diff string for a pull request, using diff minimization techniques to reduce the number of
     tokens used.
@@ -144,6 +153,7 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
     """
 
     patches = []
+    added_files_list = []
     modified_files_list = []
     deleted_files_list = []
     # sort each one of the languages in top_langs by the number of tokens in the diff
@@ -161,7 +171,7 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
 
         # removing delete-only hunks
         patch = handle_patch_deletions(patch, original_file_content_str,
-                                       new_file_content_str, file.filename)
+                                       new_file_content_str, file.filename, file.edit_type)
         if patch is None:
             if not deleted_files_list:
                 total_tokens += token_handler.count_tokens(DELETED_FILES_)
@@ -175,21 +185,26 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
         new_patch_tokens = token_handler.count_tokens(patch)
 
         # 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}.")
+        if total_tokens > get_max_tokens(model) - OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD:
+            get_logger().warning(f"File was fully skipped, no more tokens: {file.filename}.")
             continue
 
         # If the patch is too large, just show the file name
-        if total_tokens + new_patch_tokens > MAX_TOKENS[model] - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD:
+        if total_tokens + new_patch_tokens > get_max_tokens(model) - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD:
             # Current logic is to skip the patch if it's too large
             # TODO: Option for alternative logic to remove hunks from the patch to reduce the number of tokens
             #  until we meet the requirements
             if get_settings().config.verbosity_level >= 2:
-                logging.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)
-            total_tokens += token_handler.count_tokens(file.filename) + 1
+                get_logger().warning(f"Patch too large, minimizing it, {file.filename}")
+            if file.edit_type == EDIT_TYPE.ADDED:
+                if not added_files_list:
+                    total_tokens += token_handler.count_tokens(ADDED_FILES_)
+                added_files_list.append(file.filename)
+            else:
+                if not modified_files_list:
+                    total_tokens += token_handler.count_tokens(MORE_MODIFIED_FILES_)
+                modified_files_list.append(file.filename)
+                total_tokens += token_handler.count_tokens(file.filename) + 1
             continue
 
         if patch:
@@ -200,9 +215,9 @@ 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
+    return patches, modified_files_list, deleted_files_list, added_files_list
 
 
 async def retry_with_fallback_models(f: Callable):
@@ -214,7 +229,7 @@ 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()}"
@@ -267,7 +282,7 @@ def find_line_number_of_relevant_line_in_file(diff_files: List[FilePatchInfo],
         r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
 
     for file in diff_files:
-        if file.filename.strip() == relevant_file:
+        if file.filename and (file.filename.strip() == relevant_file):
             patch = file.patch
             patch_lines = patch.splitlines()
 
@@ -311,35 +326,6 @@ def find_line_number_of_relevant_line_in_file(diff_files: List[FilePatchInfo],
     return position, absolute_position
 
 
-def clip_tokens(text: str, max_tokens: int) -> str:
-    """
-    Clip the number of tokens in a string to a maximum number of tokens.
-
-    Args:
-        text (str): The string to clip.
-        max_tokens (int): The maximum number of tokens allowed in the string.
-
-    Returns:
-        str: The clipped string.
-    """
-    if not text:
-        return text
-
-    try:
-        encoder = get_token_encoder()
-        num_input_tokens = len(encoder.encode(text))
-        if num_input_tokens <= max_tokens:
-            return text
-        num_chars = len(text)
-        chars_per_token = num_chars / num_input_tokens
-        num_output_chars = int(chars_per_token * max_tokens)
-        clipped_text = text[:num_output_chars]
-        return clipped_text
-    except Exception as e:
-        logging.warning(f"Failed to clip tokens: {e}")
-        return text
-
-
 def get_pr_multi_diffs(git_provider: GitProvider,
                        token_handler: TokenHandler,
                        model: str,
@@ -347,25 +333,27 @@ 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 +369,7 @@ 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
@@ -391,26 +379,26 @@ def get_pr_multi_diffs(git_provider: GitProvider,
             continue
 
         # Remove delete-only hunks
-        patch = handle_patch_deletions(patch, original_file_content_str, new_file_content_str, file.filename)
+        patch = handle_patch_deletions(patch, original_file_content_str, new_file_content_str, file.filename, file.edit_type)
         if patch is None:
             continue
 
         patch = convert_to_hunks_with_lines_numbers(patch, file)
         new_patch_tokens = token_handler.count_tokens(patch)
-        if patch and (total_tokens + new_patch_tokens > MAX_TOKENS[model] - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD):
+        if patch and (total_tokens + new_patch_tokens > get_max_tokens(model) - OUTPUT_BUFFER_TOKENS_SOFT_THRESHOLD):
             final_diff = "\n".join(patches)
             final_diff_list.append(final_diff)
             patches = []
             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/token_handler.py

@@ -21,7 +21,7 @@ class TokenHandler:
       method.
     """
 
-    def __init__(self, pr, vars: dict, system, user):
+    def __init__(self, pr=None, vars: dict = {}, system="", user=""):
         """
         Initializes the TokenHandler object.
 
@@ -32,7 +32,8 @@ class TokenHandler:
         - user: The user string.
         """
         self.encoder = get_token_encoder()
-        self.prompt_tokens = self._get_system_user_tokens(pr, self.encoder, vars, system, user)
+        if pr is not None:
+            self.prompt_tokens = self._get_system_user_tokens(pr, self.encoder, vars, system, user)
 
     def _get_system_user_tokens(self, pr, encoder, vars: dict, system, user):
         """

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
@@ -10,7 +9,11 @@ from typing import Any, List
 
 import yaml
 from starlette_context import context
+
+from pr_agent.algo import MAX_TOKENS
+from pr_agent.algo.token_handler import get_token_encoder
 from pr_agent.config_loader import get_settings, global_settings
+from pr_agent.log import get_logger
 
 
 def get_setting(key: str) -> Any:
@@ -20,7 +23,7 @@ def get_setting(key: str) -> Any:
     except Exception:
         return global_settings.get(key, None)
 
-def convert_to_markdown(output_data: dict) -> str:
+def convert_to_markdown(output_data: dict, gfm_supported: bool=True) -> str:
     """
     Convert a dictionary of data into markdown format.
     Args:
@@ -42,6 +45,7 @@ def convert_to_markdown(output_data: dict) -> str:
         "General suggestions": "💡",
         "Insights from user's answers": "📝",
         "Code feedback": "🤖",
+        "Estimated effort to review [1-5]": "⏱️",
     }
 
     for key, value in output_data.items():
@@ -49,27 +53,34 @@ def convert_to_markdown(output_data: dict) -> str:
             continue
         if isinstance(value, dict):
             markdown_text += f"## {key}\n\n"
-            markdown_text += convert_to_markdown(value)
+            markdown_text += convert_to_markdown(value, gfm_supported)
         elif isinstance(value, list):
             emoji = emojis.get(key, "")
             if key.lower() == 'code feedback':
-                markdown_text += f"\n\n- **<details><summary> { emoji } Code feedback:**</summary>\n\n"
+                if gfm_supported:
+                    markdown_text += f"\n\n- "
+                    markdown_text += f"<details><summary> { emoji } Code feedback:</summary>\n\n"
+                else:
+                    markdown_text += f"\n\n- **{emoji} Code feedback:**\n\n"
             else:
                 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':
-                markdown_text += "</details>\n\n"
+                if gfm_supported:
+                    markdown_text += "</details>\n\n"
+                else:
+                    markdown_text += "\n\n"
         elif value != 'n/a':
             emoji = emojis.get(key, "")
             markdown_text += f"- {emoji} **{key}:** {value}\n"
     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.
 
@@ -89,9 +100,13 @@ def parse_code_suggestion(code_suggestions: dict) -> str:
                 markdown_text += f"    - **{code_key}:**\n{code_str_indented}\n"
         else:
             if "relevant file" in sub_key.lower():
-                markdown_text += f"\n  - **{sub_key}:** {sub_value}\n"
+                markdown_text += f"\n  - **{sub_key}:** {sub_value}  \n"
             else:
-                markdown_text += f"   **{sub_key}:** {sub_value}\n"
+                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" # works for gitlab
+                        markdown_text = markdown_text.rstrip('\n') + "   \n"  # works for gitlab and bitbucker
 
     markdown_text += "\n"
     return markdown_text
@@ -149,7 +164,7 @@ 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
@@ -168,7 +183,7 @@ def fix_json_escape_char(json_message=None):
     Raises:
         None
 
-    """    
+    """
     try:
         result = json.loads(json_message)
     except Exception as e:
@@ -195,7 +210,7 @@ def convert_str_to_datetime(date_str):
     Example:
         >>> convert_str_to_datetime('Mon, 01 Jan 2022 12:00:00 UTC')
         datetime.datetime(2022, 1, 1, 12, 0, 0)
-    """    
+    """
     datetime_format = '%a, %d %b %Y %H:%M:%S %Z'
     return datetime.strptime(date_str, datetime_format)
 
@@ -220,7 +235,7 @@ 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
@@ -252,12 +267,12 @@ 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
@@ -269,28 +284,142 @@ 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().debug(f"Failed to parse YAML for config override {key}={value}", exc_info=e)
     return key, value
 
 
-def load_yaml(review_text: str) -> dict:
-    review_text = review_text.removeprefix('```yaml').rstrip('`')
+def load_yaml(response_text: str) -> dict:
+    response_text = response_text.removeprefix('```yaml').rstrip('`')
     try:
-        data = yaml.safe_load(review_text)
+        data = yaml.safe_load(response_text)
     except Exception as e:
-        logging.error(f"Failed to parse AI prediction: {e}")
-        data = try_fix_yaml(review_text)
+        get_logger().error(f"Failed to parse AI prediction: {e}")
+        data = try_fix_yaml(response_text)
     return data
 
-def try_fix_yaml(review_text: str) -> dict:
-    review_text_lines = review_text.split('\n')
+def try_fix_yaml(response_text: str) -> dict:
+    response_text_lines = response_text.split('\n')
+
+    keys = ['relevant line:', 'suggestion content:', 'relevant file:']
+    # first fallback - try to convert 'relevant line: ...' to relevant line: |-\n        ...'
+    response_text_lines_copy = response_text_lines.copy()
+    for i in range(0, len(response_text_lines_copy)):
+        for key in keys:
+            if key in response_text_lines_copy[i] and not '|-' in response_text_lines_copy[i]:
+                response_text_lines_copy[i] = response_text_lines_copy[i].replace(f'{key}',
+                                                                                  f'{key} |-\n        ')
+    try:
+        data = yaml.safe_load('\n'.join(response_text_lines_copy))
+        get_logger().info(f"Successfully parsed AI prediction after adding |-\n")
+        return data
+    except:
+        get_logger().info(f"Failed to parse AI prediction after adding |-\n")
+
+    # second fallback - try to remove last lines
     data = {}
-    for i in range(1, len(review_text_lines)):
-        review_text_lines_tmp = '\n'.join(review_text_lines[:-i])
+    for i in range(1, len(response_text_lines)):
+        response_text_lines_tmp = '\n'.join(response_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")
+            data = yaml.safe_load(response_text_lines_tmp,)
+            get_logger().info(f"Successfully parsed AI prediction after removing {i} lines")
             break
         except:
             pass
-    return data
+    
+    # thrid fallback - try to remove leading and trailing curly brackets
+    response_text_copy = response_text.strip().rstrip().removeprefix('{').removesuffix('}')
+    try:
+        data = yaml.safe_load(response_text_copy,)
+        get_logger().info(f"Successfully parsed AI prediction after removing curly brackets")
+        return data
+    except:
+        pass
+
+
+def set_custom_labels(variables):
+    if not get_settings().config.enable_custom_labels:
+        return
+
+    labels = get_settings().custom_labels
+    if not labels:
+        # set default labels
+        labels = ['Bug fix', 'Tests', 'Bug fix with tests', '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]}"
+    variables["custom_labels_class"] = "class Label(str, Enum):"
+    for k, v in labels.items():
+        description = v['description'].strip('\n').replace('\n', '\\n')
+        variables["custom_labels_class"] += f"\n    {k.lower().replace(' ', '_')} = '{k}' # {description}"
+
+def get_user_labels(current_labels: List[str] = None):
+    """
+    Only keep labels that has been added by the user
+    """
+    try:
+        if current_labels is None:
+            current_labels = []
+        user_labels = []
+        for label in current_labels:
+            if label.lower() in ['bug fix', 'tests', 'enhancement', 'documentation', 'other']:
+                continue
+            if get_settings().config.enable_custom_labels:
+                if label in get_settings().custom_labels:
+                    continue
+            user_labels.append(label)
+        if user_labels:
+            get_logger().info(f"Keeping user labels: {user_labels}")
+    except Exception as e:
+        get_logger().exception(f"Failed to get user labels: {e}")
+        return current_labels
+    return user_labels
+
+
+def get_max_tokens(model):
+    settings = get_settings()
+    if model in MAX_TOKENS:
+        max_tokens_model = MAX_TOKENS[model]
+    else:
+        raise Exception(f"MAX_TOKENS must be set for model {model} in ./pr_agent/algo/__init__.py")
+
+    if settings.config.max_model_tokens:
+        max_tokens_model = min(settings.config.max_model_tokens, max_tokens_model)
+        # get_logger().debug(f"limiting max tokens to {max_tokens_model}")
+    return max_tokens_model
+
+
+def clip_tokens(text: str, max_tokens: int, add_three_dots=True) -> str:
+    """
+    Clip the number of tokens in a string to a maximum number of tokens.
+
+    Args:
+        text (str): The string to clip.
+        max_tokens (int): The maximum number of tokens allowed in the string.
+        add_three_dots (bool, optional): A boolean indicating whether to add three dots at the end of the clipped
+    Returns:
+        str: The clipped string.
+    """
+    if not text:
+        return text
+
+    try:
+        encoder = get_token_encoder()
+        num_input_tokens = len(encoder.encode(text))
+        if num_input_tokens <= max_tokens:
+            return text
+        num_chars = len(text)
+        chars_per_token = num_chars / num_input_tokens
+        num_output_chars = int(chars_per_token * max_tokens)
+        clipped_text = text[:num_output_chars]
+        if add_three_dots:
+            clipped_text += "...(truncated)"
+        return clipped_text
+    except Exception as e:
+        get_logger().warning(f"Failed to clip tokens: {e}")
+        return text

pr_agent/cli.py

@@ -1,10 +1,13 @@
 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):
@@ -17,34 +20,46 @@ For example:
 - cli.py --pr_url=... improve
 - cli.py --pr_url=... ask "write me a poem about this PR"
 - cli.py --pr_url=... reflect
+- cli.py --issue_url=... similar_issue
 
 Supported commands:
--review / review_pr - Add a review that includes a summary of the PR and specific suggestions for improvement.
+- review / review_pr - Add a review that includes a summary of the PR and specific suggestions for improvement.
 
--ask / ask_question [question] - Ask a question about the PR.
+- ask / ask_question [question] - Ask a question about the PR.
 
--describe / describe_pr - Modify the PR title and description based on the PR's contents.
+- describe / describe_pr - Modify the PR title and description based on the PR's contents.
 
--improve / improve_code - Suggest improvements to the code in the PR as pull request comments ready to commit.
+- improve / improve_code - Suggest improvements to the code in the PR as pull request comments ready to commit.
 Extended mode ('improve --extended') employs several calls, and provides a more thorough feedback
 
--reflect - Ask the PR author questions about the PR.
+- reflect - Ask the PR author questions about the PR.
 
--update_changelog - Update the changelog based on the PR's contents.
+- update_changelog - Update the changelog based on the PR's contents.
+
+- add_docs
+
+- generate_labels
 
 
 Configuration:
 To edit any configuration parameter from 'configuration.toml', just add -config_path=<value>.
 For example: 'python cli.py --pr_url=... review --pr_reviewer.extra_instructions="focus on the file: ..."'
 """)
-    parser.add_argument('--pr_url', type=str, help='The URL of the PR to review', required=True)
+    parser.add_argument('--pr_url', type=str, help='The URL of the PR to review', default=None)
+    parser.add_argument('--issue_url', type=str, help='The URL of the Issue to review', default=None)
     parser.add_argument('command', type=str, help='The', choices=commands, default='review')
     parser.add_argument('rest', nargs=argparse.REMAINDER, default=[])
     args = parser.parse_args(inargs)
-    logging.basicConfig(level=os.environ.get("LOGLEVEL", "INFO"))
+    if not args.pr_url and not args.issue_url:
+        parser.print_help()
+        return
+
     command = args.command.lower()
     get_settings().set("CONFIG.CLI_MODE", True)
-    result = asyncio.run(PRAgent().handle_request(args.pr_url, command + " " + " ".join(args.rest)))
+    if args.issue_url:
+        result = asyncio.run(PRAgent().handle_request(args.issue_url, [command] + args.rest))
+    else:
+        result = asyncio.run(PRAgent().handle_request(args.pr_url, [command] + args.rest))
     if not result:
         parser.print_help()
 

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/__init__.py

@@ -1,18 +1,23 @@
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.bitbucket_provider import BitbucketProvider
+from pr_agent.git_providers.bitbucket_server_provider import BitbucketServerProvider
 from pr_agent.git_providers.codecommit_provider import CodeCommitProvider
 from pr_agent.git_providers.github_provider import GithubProvider
 from pr_agent.git_providers.gitlab_provider import GitLabProvider
 from pr_agent.git_providers.local_git_provider import LocalGitProvider
 from pr_agent.git_providers.azuredevops_provider import AzureDevopsProvider
+from pr_agent.git_providers.gerrit_provider import GerritProvider
+
 
 _GIT_PROVIDERS = {
     'github': GithubProvider,
     'gitlab': GitLabProvider,
     'bitbucket': BitbucketProvider,
+    'bitbucket_server': BitbucketServerProvider,
     'azure': AzureDevopsProvider,
     'codecommit': CodeCommitProvider,
-    'local' : LocalGitProvider
+    'local' : LocalGitProvider,
+    'gerrit': GerritProvider,
 }
 
 def get_git_provider():

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
@@ -13,9 +14,8 @@ try:
 except ImportError:
     AZURE_DEVOPS_AVAILABLE = False
 
-from ..algo.pr_processing import clip_tokens
 from ..config_loader import get_settings
-from ..algo.utils import load_large_diff
+from ..algo.utils import load_large_diff, clip_tokens
 from ..algo.language_handler import is_valid_file
 from .git_provider import EDIT_TYPE, FilePatchInfo
 
@@ -38,7 +38,8 @@ class AzureDevopsProvider:
             self.set_pr(pr_url)
 
     def is_supported(self, capability: str) -> bool:
-        if capability in ['get_issue_comments', 'create_inline_comment', 'publish_inline_comments', 'get_labels', 'remove_initial_comment']:
+        if capability in ['get_issue_comments', 'create_inline_comment', 'publish_inline_comments', 'get_labels',
+                          'remove_initial_comment', 'gfm_markdown']:
             return False
         return True
 
@@ -54,7 +55,7 @@ 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):
@@ -87,6 +88,8 @@ 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']
 
@@ -97,14 +100,18 @@ 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':
@@ -115,13 +122,17 @@ 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)
 
@@ -155,7 +166,7 @@ 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
@@ -224,9 +235,6 @@ 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 +6,10 @@ import requests
 from atlassian.bitbucket import Cloud
 from starlette_context import context
 
+from ..algo.pr_processing import find_line_number_of_relevant_line_in_file
 from ..config_loader import get_settings
-from .git_provider import FilePatchInfo, GitProvider
+from ..log import get_logger
+from .git_provider import FilePatchInfo, GitProvider, EDIT_TYPE
 
 
 class BitbucketProvider(GitProvider):
@@ -31,19 +32,23 @@ class BitbucketProvider(GitProvider):
         self.repo = None
         self.pr_num = None
         self.pr = None
+        self.pr_url = pr_url
         self.temp_comments = []
         self.incremental = incremental
+        self.diff_files = None
         if pr_url:
             self.set_pr(pr_url)
-        self.bitbucket_comment_api_url = self.pr._BitbucketBase__data["links"][
-            "comments"
-        ]["href"]
+        self.bitbucket_comment_api_url = self.pr._BitbucketBase__data["links"]["comments"]["href"]
+        self.bitbucket_pull_request_api_url = self.pr._BitbucketBase__data["links"]['self']['href']
 
     def get_repo_settings(self):
         try:
-            contents = self.repo_obj.get_contents(
-                ".pr_agent.toml", ref=self.pr.head.sha
-            ).decoded_content
+            url = (f"https://api.bitbucket.org/2.0/repositories/{self.workspace_slug}/{self.repo_slug}/src/"
+                   f"{self.pr.destination_branch}/.pr_agent.toml")
+            response = requests.request("GET", url, headers=self.headers)
+            if response.status_code == 404:  # not found
+                return ""
+            contents = response.text.encode('utf-8')
             return contents
         except Exception:
             return ""
@@ -61,14 +66,14 @@ 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}"
@@ -97,16 +102,11 @@ 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:
-        if capability in [
-            "get_issue_comments",
-            "create_inline_comment",
-            "publish_inline_comments",
-            "get_labels",
-        ]:
+        if capability in ['get_issue_comments', 'publish_inline_comments', 'get_labels', 'gfm_markdown']:
             return False
         return True
 
@@ -118,6 +118,9 @@ class BitbucketProvider(GitProvider):
         return [diff.new.path for diff in self.pr.diffstat()]
 
     def get_diff_files(self) -> list[FilePatchInfo]:
+        if self.diff_files:
+            return self.diff_files
+
         diffs = self.pr.diffstat()
         diff_split = [
             "diff --git%s" % x for x in self.pr.diff().split("diff --git") if x.strip()
@@ -129,16 +132,56 @@ class BitbucketProvider(GitProvider):
                 diff.old.get_data("links")
             )
             new_file_content_str = self._get_pr_file_content(diff.new.get_data("links"))
-            diff_files.append(
-                FilePatchInfo(
-                    original_file_content_str,
-                    new_file_content_str,
-                    diff_split[index],
-                    diff.new.path,
-                )
+            file_patch_canonic_structure = FilePatchInfo(
+                original_file_content_str,
+                new_file_content_str,
+                diff_split[index],
+                diff.new.path,
             )
+
+            if diff.data['status'] == 'added':
+                file_patch_canonic_structure.edit_type = EDIT_TYPE.ADDED
+            elif diff.data['status'] == 'removed':
+                file_patch_canonic_structure.edit_type = EDIT_TYPE.DELETED
+            elif diff.data['status'] == 'modified':
+                file_patch_canonic_structure.edit_type = EDIT_TYPE.MODIFIED
+            elif diff.data['status'] == 'renamed':
+                file_patch_canonic_structure.edit_type = EDIT_TYPE.RENAMED
+            diff_files.append(file_patch_canonic_structure)
+
+
+        self.diff_files = diff_files
         return diff_files
 
+    def get_latest_commit_url(self):
+        return self.pr.data['source']['commit']['links']['html']['href']
+
+    def get_comment_url(self, comment):
+        return comment.data['links']['html']['href']
+
+    def publish_persistent_comment(self, pr_comment: str, initial_header: str, update_header: bool = True):
+        try:
+            for comment in self.pr.comments():
+                body = comment.raw
+                if initial_header in body:
+                    latest_commit_url = self.get_latest_commit_url()
+                    comment_url = self.get_comment_url(comment)
+                    if update_header:
+                        updated_header = f"{initial_header}\n\n### (review updated until commit {latest_commit_url})\n"
+                        pr_comment_updated = pr_comment.replace(initial_header, updated_header)
+                    else:
+                        pr_comment_updated = pr_comment
+                    get_logger().info(f"Persistent mode- updating comment {comment_url} to latest review message")
+                    d = {"content": {"raw": pr_comment_updated}}
+                    response = comment._update_data(comment.put(None, data=d))
+                    self.publish_comment(
+                        f"**[Persistent review]({comment_url})** updated to latest commit {latest_commit_url}")
+                    return
+        except Exception as e:
+            get_logger().exception(f"Failed to update persistent review, error: {e}")
+            pass
+        self.publish_comment(pr_comment)
+
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
         comment = self.pr.comment(pr_comment)
         if is_temporary:
@@ -147,31 +190,82 @@ class BitbucketProvider(GitProvider):
     def remove_initial_comment(self):
         try:
             for comment in self.temp_comments:
-                self.pr.delete(f"comments/{comment}")
+                self.remove_comment(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}")
 
-    def publish_inline_comment(
-        self, comment: str, from_line: int, to_line: int, file: str
-    ):
-        payload = json.dumps(
-            {
-                "content": {
-                    "raw": comment,
-                },
-                "inline": {"to": from_line, "path": file},
-            }
-        )
+    def remove_comment(self, comment):
+        try:
+            self.pr.delete(f"comments/{comment}")
+        except Exception as e:
+            get_logger().exception(f"Failed to remove comment, error: {e}")
+
+    # funtion to create_inline_comment
+    def create_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
+        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:
+                get_logger().info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
+            subject_type = "FILE"
+        else:
+            subject_type = "LINE"
+        path = relevant_file.strip()
+        return dict(body=body, path=path, position=absolute_position) if subject_type == "LINE" else {}
+
+
+    def publish_inline_comment(self, comment: str, from_line: int, file: str):
+        payload = json.dumps( {
+            "content": {
+                "raw": comment,
+            },
+            "inline": {
+                "to": from_line,
+                "path": file
+            },
+        })
         response = requests.request(
             "POST", self.bitbucket_comment_api_url, data=payload, headers=self.headers
         )
         return response
 
+    def get_line_link(self, relevant_file: str, relevant_line_start: int, relevant_line_end: int = None) -> str:
+        if relevant_line_start == -1:
+            link = f"{self.pr_url}/#L{relevant_file}"
+        else:
+            link = f"{self.pr_url}/#L{relevant_file}T{relevant_line_start}"
+        return link
+
+    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 ""
+
+            diff_files = self.get_diff_files()
+            position, absolute_position = find_line_number_of_relevant_line_in_file \
+                (diff_files, relevant_file, relevant_line_str)
+
+            if absolute_position != -1 and self.pr_url:
+                link = f"{self.pr_url}/#L{relevant_file}T{absolute_position}"
+                return link
+        except Exception as e:
+            if get_settings().config.verbosity_level >= 2:
+                get_logger().info(f"Failed adding line link, error: {e}")
+
+        return ""
+
     def publish_inline_comments(self, comments: list[dict]):
         for comment in comments:
-            self.publish_inline_comment(
-                comment["body"], comment["start_line"], comment["line"], comment["path"]
-            )
+            if 'position' in comment:
+                self.publish_inline_comment(comment['body'], comment['position'], comment['path'])
+            elif 'start_line' in comment: # multi-line comment
+                # note that bitbucket does not seem to support range - only a comment on a single line - https://community.developer.atlassian.com/t/api-post-endpoint-for-inline-pull-request-comments/60452
+                self.publish_inline_comment(comment['body'], comment['start_line'], comment['path'])
+            elif 'line' in comment: # single-line comment
+                self.publish_inline_comment(comment['body'], comment['line'], comment['path'])
+            else:
+                get_logger().error(f"Could not publish inline comment {comment}")
 
     def get_title(self):
         return self.pr.title
@@ -238,16 +332,27 @@ class BitbucketProvider(GitProvider):
 
     def get_commit_messages(self):
         return ""  # not implemented yet
+    
+    # bitbucket does not support labels
+    def publish_description(self, pr_title: str, description: str):
+        payload = json.dumps({
+            "description": description,
+            "title": pr_title
 
-    def publish_description(self, pr_title: str, pr_body: str):
-        pass
-    def create_inline_comment(
-        self, body: str, relevant_file: str, relevant_line_in_file: str
-    ):
-        pass
+            })
 
-    def publish_labels(self, labels):
-        pass
+        response = requests.request("PUT", self.bitbucket_pull_request_api_url, headers=self.headers, data=payload)
+        try:
+            if response.status_code != 200:
+                get_logger().info(f"Failed to update description, error code: {response.status_code}")
+        except:
+            pass
+        return response
 
+    # bitbucket does not support labels
+    def publish_labels(self, pr_types: list):
+        pass
+    
+    # bitbucket does not support labels
     def get_labels(self):
         pass

pr_agent/git_providers/bitbucket_server_provider.py

@@ -0,0 +1,351 @@
+import json
+from typing import Optional, Tuple
+from urllib.parse import urlparse
+
+import requests
+from atlassian.bitbucket import Bitbucket
+from starlette_context import context
+
+from .git_provider import FilePatchInfo, GitProvider, EDIT_TYPE
+from ..algo.pr_processing import find_line_number_of_relevant_line_in_file
+from ..algo.utils import load_large_diff
+from ..config_loader import get_settings
+from ..log import get_logger
+
+
+class BitbucketServerProvider(GitProvider):
+    def __init__(
+        self, pr_url: Optional[str] = None, incremental: Optional[bool] = False
+    ):
+        s = requests.Session()
+        try:
+            bearer = context.get("bitbucket_bearer_token", None)
+            s.headers["Authorization"] = f"Bearer {bearer}"
+        except Exception:
+            s.headers[
+                "Authorization"
+            ] = f'Bearer {get_settings().get("BITBUCKET_SERVER.BEARER_TOKEN", None)}'
+
+        s.headers["Content-Type"] = "application/json"
+        self.headers = s.headers
+        self.bitbucket_server_url = None
+        self.workspace_slug = None
+        self.repo_slug = None
+        self.repo = None
+        self.pr_num = None
+        self.pr = None
+        self.pr_url = pr_url
+        self.temp_comments = []
+        self.incremental = incremental
+        self.diff_files = None
+        self.bitbucket_pull_request_api_url = pr_url
+
+        self.bitbucket_server_url = self._parse_bitbucket_server(url=pr_url)
+        self.bitbucket_client = Bitbucket(url=self.bitbucket_server_url,
+                                          token=get_settings().get("BITBUCKET_SERVER.BEARER_TOKEN", None))
+
+        if pr_url:
+            self.set_pr(pr_url)
+
+    def get_repo_settings(self):
+        try:
+            url = (f"{self.bitbucket_server_url}/projects/{self.workspace_slug}/repos/{self.repo_slug}/src/"
+                   f"{self.pr.destination_branch}/.pr_agent.toml")
+            response = requests.request("GET", url, headers=self.headers)
+            if response.status_code == 404:  # not found
+                return ""
+            contents = response.text.encode('utf-8')
+            return contents
+        except Exception:
+            return ""
+
+    def publish_code_suggestions(self, code_suggestions: list) -> bool:
+        """
+        Publishes code suggestions as comments on the PR.
+        """
+        post_parameters_list = []
+        for suggestion in code_suggestions:
+            body = suggestion["body"]
+            relevant_file = suggestion["relevant_file"]
+            relevant_lines_start = suggestion["relevant_lines_start"]
+            relevant_lines_end = suggestion["relevant_lines_end"]
+
+            if not relevant_lines_start or relevant_lines_start == -1:
+                if get_settings().config.verbosity_level >= 2:
+                    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:
+                    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
+
+            if relevant_lines_end > relevant_lines_start:
+                post_parameters = {
+                    "body": body,
+                    "path": relevant_file,
+                    "line": relevant_lines_end,
+                    "start_line": relevant_lines_start,
+                    "start_side": "RIGHT",
+                }
+            else:  # API is different for single line comments
+                post_parameters = {
+                    "body": body,
+                    "path": relevant_file,
+                    "line": relevant_lines_start,
+                    "side": "RIGHT",
+                }
+            post_parameters_list.append(post_parameters)
+
+        try:
+            self.publish_inline_comments(post_parameters_list)
+            return True
+        except Exception as e:
+            if get_settings().config.verbosity_level >= 2:
+                get_logger().error(f"Failed to publish code suggestion, error: {e}")
+            return False
+
+    def is_supported(self, capability: str) -> bool:
+        if capability in ['get_issue_comments', 'get_labels', 'gfm_markdown']:
+            return False
+        return True
+
+    def set_pr(self, pr_url: str):
+        self.workspace_slug, self.repo_slug, self.pr_num = self._parse_pr_url(pr_url)
+        self.pr = self._get_pr()
+
+    def get_file(self, path: str, commit_id: str):
+        file_content = ""
+        try:
+            file_content = self.bitbucket_client.get_content_of_file(self.workspace_slug,
+                                                                     self.repo_slug,
+                                                                     path,
+                                                                     commit_id)
+        except requests.HTTPError as e:
+            get_logger().debug(f"File {path} not found at commit id: {commit_id}")
+        return file_content
+
+    def get_files(self):
+        changes = self.bitbucket_client.get_pull_requests_changes(self.workspace_slug, self.repo_slug, self.pr_num)
+        diffstat = [change["path"]['toString'] for change in changes]
+        return diffstat
+
+    def get_diff_files(self) -> list[FilePatchInfo]:
+        if self.diff_files:
+            return self.diff_files
+
+        commits_in_pr = self.bitbucket_client.get_pull_requests_commits(
+            self.workspace_slug,
+            self.repo_slug,
+            self.pr_num
+        )
+
+        commit_list = list(commits_in_pr)
+        base_sha, head_sha = commit_list[0]['parents'][0]['id'], commit_list[-1]['id']
+
+        diff_files = []
+        original_file_content_str = ""
+        new_file_content_str = ""
+
+        changes = self.bitbucket_client.get_pull_requests_changes(self.workspace_slug, self.repo_slug, self.pr_num)
+        for change in changes:
+            file_path = change['path']['toString']
+            match change['type']:
+                case 'ADD':
+                    edit_type = EDIT_TYPE.ADDED
+                    new_file_content_str = self.get_file(file_path, head_sha)
+                    if isinstance(new_file_content_str, (bytes, bytearray)):
+                        new_file_content_str = new_file_content_str.decode("utf-8")
+                    original_file_content_str = ""
+                case 'DELETE':
+                    edit_type = EDIT_TYPE.DELETED
+                    new_file_content_str = ""
+                    original_file_content_str = self.get_file(file_path, base_sha)
+                    if isinstance(original_file_content_str, (bytes, bytearray)):
+                        original_file_content_str = original_file_content_str.decode("utf-8")
+                case 'RENAME':
+                    edit_type = EDIT_TYPE.RENAMED
+                case _:
+                    edit_type = EDIT_TYPE.MODIFIED
+                    original_file_content_str = self.get_file(file_path, base_sha)
+                    if isinstance(original_file_content_str, (bytes, bytearray)):
+                        original_file_content_str = original_file_content_str.decode("utf-8")
+                    new_file_content_str = self.get_file(file_path, head_sha)
+                    if isinstance(new_file_content_str, (bytes, bytearray)):
+                        new_file_content_str = new_file_content_str.decode("utf-8")
+
+            patch = load_large_diff(file_path, new_file_content_str, original_file_content_str)
+
+            diff_files.append(
+                FilePatchInfo(
+                    original_file_content_str,
+                    new_file_content_str,
+                    patch,
+                    file_path,
+                    edit_type=edit_type,
+                )
+            )
+
+        self.diff_files = diff_files
+        return diff_files
+
+    def publish_comment(self, pr_comment: str, is_temporary: bool = False):
+        if not is_temporary:
+            self.bitbucket_client.add_pull_request_comment(self.workspace_slug, self.repo_slug, self.pr_num, pr_comment)
+
+    def remove_initial_comment(self):
+        try:
+            for comment in self.temp_comments:
+                self.remove_comment(comment)
+        except ValueError as e:
+            get_logger().exception(f"Failed to remove temp comments, error: {e}")
+
+    def remove_comment(self, comment):
+        pass
+
+    # funtion to create_inline_comment
+    def create_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
+        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:
+                get_logger().info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
+            subject_type = "FILE"
+        else:
+            subject_type = "LINE"
+        path = relevant_file.strip()
+        return dict(body=body, path=path, position=absolute_position) if subject_type == "LINE" else {}
+
+    def publish_inline_comment(self, comment: str, from_line: int, file: str):
+        payload = {
+            "text": comment,
+            "severity": "NORMAL",
+            "anchor": {
+                "diffType": "EFFECTIVE",
+                "path": file,
+                "lineType": "ADDED",
+                "line": from_line,
+                "fileType": "TO"
+            }
+        }
+
+        response = requests.post(url=self._get_pr_comments_url(), json=payload, headers=self.headers)
+        return response
+
+    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 ""
+
+            diff_files = self.get_diff_files()
+            position, absolute_position = find_line_number_of_relevant_line_in_file \
+                (diff_files, relevant_file, relevant_line_str)
+
+            if absolute_position != -1 and self.pr_url:
+                link = f"{self.pr_url}/#L{relevant_file}T{absolute_position}"
+                return link
+        except Exception as e:
+            if get_settings().config.verbosity_level >= 2:
+                get_logger().info(f"Failed adding line link, error: {e}")
+
+        return ""
+
+    def publish_inline_comments(self, comments: list[dict]):
+        for comment in comments:
+            self.publish_inline_comment(comment['body'], comment['position'], comment['path'])
+
+    def get_title(self):
+        return self.pr.title
+
+    def get_languages(self):
+        return {"yaml": 0}  # devops LOL
+
+    def get_pr_branch(self):
+        return self.pr.fromRef['displayId']
+
+    def get_pr_description_full(self):
+        return self.pr.description
+
+    def get_user_id(self):
+        return 0
+
+    def get_issue_comments(self):
+        raise NotImplementedError(
+            "Bitbucket provider does not support issue comments yet"
+        )
+
+    def add_eyes_reaction(self, issue_comment_id: int) -> Optional[int]:
+        return True
+
+    def remove_reaction(self, issue_comment_id: int, reaction_id: int) -> bool:
+        return True
+
+    @staticmethod
+    def _parse_bitbucket_server(url: str) -> str:
+        parsed_url = urlparse(url)
+        return f"{parsed_url.scheme}://{parsed_url.netloc}"
+
+    @staticmethod
+    def _parse_pr_url(pr_url: str) -> Tuple[str, str, int]:
+        parsed_url = urlparse(pr_url)
+        path_parts = parsed_url.path.strip("/").split("/")
+        if len(path_parts) < 6 or path_parts[4] != "pull-requests":
+            raise ValueError(
+                "The provided URL does not appear to be a Bitbucket PR URL"
+            )
+
+        workspace_slug = path_parts[1]
+        repo_slug = path_parts[3]
+        try:
+            pr_number = int(path_parts[5])
+        except ValueError as e:
+            raise ValueError("Unable to convert PR number to integer") from e
+
+        return workspace_slug, repo_slug, pr_number
+
+    def _get_repo(self):
+        if self.repo is None:
+            self.repo = self.bitbucket_client.get_repo(self.workspace_slug, self.repo_slug)
+        return self.repo
+
+    def _get_pr(self):
+        pr = self.bitbucket_client.get_pull_request(self.workspace_slug, self.repo_slug, pull_request_id=self.pr_num)
+        return type('new_dict', (object,), pr)
+
+    def _get_pr_file_content(self, remote_link: str):
+        return ""
+
+    def get_commit_messages(self):
+        def get_commit_messages(self):
+            raise NotImplementedError("Get commit messages function not implemented yet.")
+    # bitbucket does not support labels
+    def publish_description(self, pr_title: str, description: str):
+        payload = json.dumps({
+            "description": description,
+            "title": pr_title
+        })
+
+        response = requests.put(url=self.bitbucket_pull_request_api_url, headers=self.headers, data=payload)
+        return response
+
+    # bitbucket does not support labels
+    def publish_labels(self, pr_types: list):
+        pass
+    
+    # bitbucket does not support labels
+    def get_labels(self):
+        pass
+
+    def _get_pr_comments_url(self):
+        return f"{self.bitbucket_server_url}/rest/api/latest/projects/{self.workspace_slug}/repos/{self.repo_slug}/pull-requests/{self.pr_num}/comments"

pr_agent/git_providers/codecommit_client.py

@@ -54,17 +54,22 @@ class CodeCommitClient:
     def __init__(self):
         self.boto_client = None
 
+    def is_supported(self, capability: str) -> bool:
+        if capability in ["gfm_markdown"]:
+            return False
+        return True
+
     def _connect_boto_client(self):
         try:
             self.boto_client = boto3.client("codecommit")
         except Exception as e:
-            raise ValueError(f"Failed to connect to AWS CodeCommit: {e}")
+            raise ValueError(f"Failed to connect to AWS CodeCommit: {e}") from e
 
     def get_differences(self, repo_name: int, destination_commit: str, source_commit: str):
         """
         Get the differences between two commits in CodeCommit.
 
-        Parameters:
+        Args:
         - repo_name: Name of the repository
         - destination_commit: Commit hash you want to merge into (the "before" hash) (usually on the main or master branch)
         - source_commit: Commit hash of the code you are adding (the "after" branch)
@@ -73,8 +78,8 @@ class CodeCommitClient:
         - List of CodeCommitDifferencesResponse objects
 
         Boto3 Documentation:
-        aws codecommit get-differences
-        https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/get_differences.html
+        - aws codecommit get-differences
+        - https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/get_differences.html
         """
         if self.boto_client is None:
             self._connect_boto_client()
@@ -90,7 +95,11 @@ class CodeCommitClient:
             ):
                 differences.extend(page.get("differences", []))
         except botocore.exceptions.ClientError as e:
-            raise ValueError(f"Failed to retrieve differences from CodeCommit PR #{self.pr_num}") from e
+            if e.response["Error"]["Code"] == 'RepositoryDoesNotExistException':
+                raise ValueError(f"CodeCommit cannot retrieve differences: Repository does not exist: {repo_name}") from e
+            raise ValueError(f"CodeCommit cannot retrieve differences for {source_commit}..{destination_commit}") from e
+        except Exception as e:
+            raise ValueError(f"CodeCommit cannot retrieve differences for {source_commit}..{destination_commit}") from e
 
         output = []
         for json in differences:
@@ -101,7 +110,7 @@ class CodeCommitClient:
         """
         Retrieve a file from CodeCommit.
 
-        Parameters:
+        Args:
         - repo_name: Name of the repository
         - file_path: Path to the file you are retrieving
         - sha_hash: Commit hash of the file you are retrieving
@@ -110,8 +119,8 @@ class CodeCommitClient:
         - File contents
 
         Boto3 Documentation:
-        aws codecommit get_file
-        https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/get_file.html
+        - aws codecommit get_file
+        - https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/get_file.html
         """
         if not file_path:
             return ""
@@ -122,6 +131,8 @@ class CodeCommitClient:
         try:
             response = self.boto_client.get_file(repositoryName=repo_name, commitSpecifier=sha_hash, filePath=file_path)
         except botocore.exceptions.ClientError as e:
+            if e.response["Error"]["Code"] == 'RepositoryDoesNotExistException':
+                raise ValueError(f"CodeCommit cannot retrieve PR: Repository does not exist: {repo_name}") from e
             # if the file does not exist, but is flagged as optional, then return an empty string
             if optional and e.response["Error"]["Code"] == 'FileDoesNotExistException':
                 return ""
@@ -133,19 +144,20 @@ class CodeCommitClient:
 
         return response.get("fileContent", "")
 
-    def get_pr(self, pr_number: int):
+    def get_pr(self, repo_name: str, pr_number: int):
         """
         Get a information about a CodeCommit PR.
 
-        Parameters:
+        Args:
+        - repo_name: Name of the repository
         - pr_number: The PR number you are requesting
 
         Returns:
         - CodeCommitPullRequestResponse object
 
         Boto3 Documentation:
-        aws codecommit get_pull_request
-        https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/get_pull_request.html
+        - aws codecommit get_pull_request
+        - https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/get_pull_request.html
         """
         if self.boto_client is None:
             self._connect_boto_client()
@@ -155,6 +167,8 @@ class CodeCommitClient:
         except botocore.exceptions.ClientError as e:
             if e.response["Error"]["Code"] == 'PullRequestDoesNotExistException':
                 raise ValueError(f"CodeCommit cannot retrieve PR: PR number does not exist: {pr_number}") from e
+            if e.response["Error"]["Code"] == 'RepositoryDoesNotExistException':
+                raise ValueError(f"CodeCommit cannot retrieve PR: Repository does not exist: {repo_name}") from e
             raise ValueError(f"CodeCommit cannot retrieve PR: {pr_number}: boto client error") from e
         except Exception as e:
             raise ValueError(f"CodeCommit cannot retrieve PR: {pr_number}") from e
@@ -164,35 +178,95 @@ class CodeCommitClient:
 
         return CodeCommitPullRequestResponse(response.get("pullRequest", {}))
 
-    def publish_comment(self, repo_name: str, pr_number: int, destination_commit: str, source_commit: str, comment: str):
+    def publish_description(self, pr_number: int, pr_title: str, pr_body: str):
         """
-        Publish a comment to a pull request
+        Set the title and description on a pull request
 
-        Parameters:
-        - repo_name: name of the repository
-        - pr_number: number of the pull request
-        - destination_commit: The commit hash you want to merge into (the "before" hash) (usually on the main or master branch)
-        - source_commit: The commit hash of the code you are adding (the "after" branch)
-        - pr_comment: comment
+        Args:
+        - pr_number: the AWS CodeCommit pull request number
+        - pr_title: title of the pull request
+        - pr_body: body of the pull request
 
         Returns:
         - None
 
         Boto3 Documentation:
-        aws codecommit post_comment_for_pull_request
-        https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/post_comment_for_pull_request.html
+        - aws codecommit update_pull_request_title
+        - https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/update_pull_request_title.html
+        - aws codecommit update_pull_request_description
+        - https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/update_pull_request_description.html
         """
         if self.boto_client is None:
             self._connect_boto_client()
 
         try:
-            self.boto_client.post_comment_for_pull_request(
-                pullRequestId=str(pr_number),
-                repositoryName=repo_name,
-                beforeCommitId=destination_commit,
-                afterCommitId=source_commit,
-                content=comment,
-            )
+            self.boto_client.update_pull_request_title(pullRequestId=str(pr_number), title=pr_title)
+            self.boto_client.update_pull_request_description(pullRequestId=str(pr_number), description=pr_body)
+        except botocore.exceptions.ClientError as e:
+            if e.response["Error"]["Code"] == 'PullRequestDoesNotExistException':
+                raise ValueError(f"PR number does not exist: {pr_number}") from e
+            if e.response["Error"]["Code"] == 'InvalidTitleException':
+                raise ValueError(f"Invalid title for PR number: {pr_number}") from e
+            if e.response["Error"]["Code"] == 'InvalidDescriptionException':
+                raise ValueError(f"Invalid description for PR number: {pr_number}") from e
+            if e.response["Error"]["Code"] == 'PullRequestAlreadyClosedException':
+                raise ValueError(f"PR is already closed: PR number: {pr_number}") from e
+            raise ValueError(f"Boto3 client error calling publish_description") from e
+        except Exception as e:
+            raise ValueError(f"Error calling publish_description") from e
+
+    def publish_comment(self, repo_name: str, pr_number: int, destination_commit: str, source_commit: str, comment: str, annotation_file: str = None, annotation_line: int = None):
+        """
+        Publish a comment to a pull request
+
+        Args:
+        - repo_name: name of the repository
+        - pr_number: number of the pull request
+        - destination_commit: The commit hash you want to merge into (the "before" hash) (usually on the main or master branch)
+        - source_commit: The commit hash of the code you are adding (the "after" branch)
+        - comment: The comment you want to publish
+        - annotation_file: The file you want to annotate (optional)
+        - annotation_line: The line number you want to annotate (optional)
+
+        Comment annotations for CodeCommit are different than GitHub.
+        CodeCommit only designates the starting line number for the comment.
+        It does not support the ending line number to highlight a range of lines.
+
+        Returns:
+        - None
+
+        Boto3 Documentation:
+        - aws codecommit post_comment_for_pull_request
+        - https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/post_comment_for_pull_request.html
+        """
+        if self.boto_client is None:
+            self._connect_boto_client()
+
+        try:
+            # If the comment has code annotations,
+            # then set the file path and line number in the location dictionary
+            if annotation_file and annotation_line:
+                self.boto_client.post_comment_for_pull_request(
+                    pullRequestId=str(pr_number),
+                    repositoryName=repo_name,
+                    beforeCommitId=destination_commit,
+                    afterCommitId=source_commit,
+                    content=comment,
+                    location={
+                        "filePath": annotation_file,
+                        "filePosition": annotation_line,
+                        "relativeFileVersion": "AFTER",
+                    },
+                )
+            else:
+                # The comment does not have code annotations
+                self.boto_client.post_comment_for_pull_request(
+                    pullRequestId=str(pr_number),
+                    repositoryName=repo_name,
+                    beforeCommitId=destination_commit,
+                    afterCommitId=source_commit,
+                    content=comment,
+                )
         except botocore.exceptions.ClientError as e:
             if e.response["Error"]["Code"] == 'RepositoryDoesNotExistException':
                 raise ValueError(f"Repository does not exist: {repo_name}") from e

pr_agent/git_providers/codecommit_provider.py

@@ -1,16 +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.utils import load_large_diff
+from .git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
+from ..config_loader import get_settings
+from ..log import get_logger
+
 
 class PullRequestCCMimic:
     """
@@ -61,6 +61,7 @@ class CodeCommitProvider(GitProvider):
         self.pr = None
         self.diff_files = None
         self.git_files = None
+        self.pr_url = pr_url
         if pr_url:
             self.set_pr(pr_url)
 
@@ -73,6 +74,7 @@ class CodeCommitProvider(GitProvider):
             "create_inline_comment",
             "publish_inline_comments",
             "get_labels",
+            "gfm_markdown"
         ]:
             return False
         return True
@@ -153,26 +155,63 @@ class CodeCommitProvider(GitProvider):
         return self.diff_files
 
     def publish_description(self, pr_title: str, pr_body: str):
-        return ""  # not implemented yet
+        try:
+            self.codecommit_client.publish_description(
+                pr_number=self.pr_num,
+                pr_title=pr_title,
+                pr_body=CodeCommitProvider._add_additional_newlines(pr_body),
+            )
+        except Exception as e:
+            raise ValueError(f"CodeCommit Cannot publish description for PR: {self.pr_num}") from e    
 
     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)
+        pr_comment = CodeCommitProvider._add_additional_newlines(pr_comment)
+
         try:
             self.codecommit_client.publish_comment(
                 repo_name=self.repo_name,
-                pr_number=str(self.pr_num),
+                pr_number=self.pr_num,
                 destination_commit=self.pr.destination_commit,
                 source_commit=self.pr.source_commit,
                 comment=pr_comment,
             )
         except Exception as e:
-            raise ValueError(f"CodeCommit Cannot post comment for PR: {self.pr_num}") from e
+            raise ValueError(f"CodeCommit Cannot publish comment for PR: {self.pr_num}") from e
 
     def publish_code_suggestions(self, code_suggestions: list) -> bool:
-        return [""]  # not implemented yet
+        counter = 1
+        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"]):
+                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:
+                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,
+                    destination_commit=self.pr.destination_commit,
+                    source_commit=self.pr.source_commit,
+                    comment=suggestion["body"],
+                    annotation_file=suggestion["relevant_file"],
+                    annotation_line=suggestion["relevant_lines_start"],
+                )
+            except Exception as e:
+                raise ValueError(f"CodeCommit Cannot publish code suggestions for PR: {self.pr_num}") from e
+            
+            counter += 1
+
+        # The calling function passes in a list of code suggestions, and this function publishes each suggestion one at a time.
+        # If we were to return False here, the calling function will attempt to publish the same list of code suggestions again, one at a time.
+        # Since this function publishes the suggestions one at a time anyway, we always return True here to avoid the retry.        
+        return True
 
     def publish_labels(self, labels):
         return [""]  # not implemented yet
@@ -183,7 +222,11 @@ class CodeCommitProvider(GitProvider):
     def remove_initial_comment(self):
         return ""  # not implemented yet
 
+    def remove_comment(self, comment):
+        return ""  # not implemented yet
+
     def publish_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
+        # https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/post_comment_for_compared_commit.html
         raise NotImplementedError("CodeCommit provider does not support publishing inline comments yet")
 
     def create_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
@@ -193,14 +236,26 @@ 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.
 
         Returns:
-            dict: A dictionary where each key is a language name and the corresponding value is the percentage of that language in the PR.
+        - dict: A dictionary where each key is a language name and the corresponding value is the percentage of that language in the PR.
         """
         commit_files = self.get_files()
         filenames = [ item.filename for item in commit_files ]
@@ -215,6 +270,8 @@ class CodeCommitProvider(GitProvider):
         # where each dictionary item is a language name.
         # We build that language->extension dictionary here in main_extensions_flat.
         main_extensions_flat = {}
+        language_extension_map_org = get_settings().language_extension_map_org
+        language_extension_map = {k.lower(): v for k, v in language_extension_map_org.items()}
         for language, extensions in language_extension_map.items():
             for ext in extensions:
                 main_extensions_flat[ext] = language
@@ -244,18 +301,29 @@ 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]:
+        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:
+        get_logger().info("CodeCommit provider does not support removing reactions yet")
         return True
 
     @staticmethod
     def _parse_pr_url(pr_url: str) -> Tuple[str, int]:
+        """
+        Parse the CodeCommit PR URL and return the repository name and PR number.
+
+        Args:
+        - pr_url: the full AWS CodeCommit pull request URL
+
+        Returns:
+        - Tuple[str, int]: A tuple containing the repository name and PR number.
+        """
         # Example PR URL:
         # https://us-east-1.console.aws.amazon.com/codesuite/codecommit/repositories/__MY_REPO__/pull-requests/123456"
         parsed_url = urlparse(pr_url)
 
-        if "us-east-1.console.aws.amazon.com" not in parsed_url.netloc:
+        if not CodeCommitProvider._is_valid_codecommit_hostname(parsed_url.netloc):
             raise ValueError(f"The provided URL is not a valid CodeCommit URL: {pr_url}")
 
         path_parts = parsed_url.path.strip("/").split("/")
@@ -278,17 +346,33 @@ class CodeCommitProvider(GitProvider):
 
         return repo_name, pr_number
 
+    @staticmethod
+    def _is_valid_codecommit_hostname(hostname: str) -> bool:
+        """
+        Check if the provided hostname is a valid AWS CodeCommit hostname.
+
+        This is not an exhaustive check of AWS region names, 
+        but instead uses a regex to check for matching AWS region patterns.
+
+        Args:
+        - hostname: the hostname to check
+
+        Returns:
+        - bool: True if the hostname is valid, False otherwise.
+        """
+        return re.match(r"^[a-z]{2}-(gov-)?[a-z]+-\d\.console\.aws\.amazon\.com$", hostname) is not None
+
     def _get_pr(self):
-        response = self.codecommit_client.get_pr(self.pr_num)
+        response = self.codecommit_client.get_pr(self.repo_name, self.pr_num)
 
         if len(response.targets) == 0:
             raise ValueError(f"No files found in CodeCommit PR: {self.pr_num}")
 
-        # TODO: implement support for multiple commits in one CodeCommit PR
-        #       for now, we are only using the first commit in the PR
+        # 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(
-                "Multiple commits in one PR is not supported for CodeCommit yet. Continuing, using the first commit only..."
+            get_logger().warning(
+                "Multiple targets in one PR is not supported for CodeCommit yet. Continuing, using the first target only..."
             )
 
         # Return our object that mimics PullRequest class from the PyGithub library
@@ -306,13 +390,52 @@ class CodeCommitProvider(GitProvider):
         return ""  # not implemented yet
 
     @staticmethod
-    def _get_edit_type(codecommit_change_type):
+    def _add_additional_newlines(body: str) -> str:
+        """
+        Replace single newlines in a PR body with double newlines.
+
+        CodeCommit Markdown does not seem to render as well as GitHub Markdown,
+        so we add additional newlines to the PR body to make it more readable in CodeCommit.
+
+        Args:
+        - body: the PR body
+
+        Returns:
+        - str: the PR body with the double newlines added
+        """
+        return re.sub(r'(?<!\n)\n(?!\n)', '\n\n', body)
+
+    @staticmethod
+    def _remove_markdown_html(comment: str) -> str:
+        """
+        Remove the HTML tags from a PR comment.
+
+        CodeCommit Markdown does not seem to render as well as GitHub Markdown,
+        so we remove the HTML tags from the PR comment to make it more readable in CodeCommit.
+
+        Args:
+        - comment: the PR comment
+
+        Returns:
+        - str: the PR comment with the HTML tags removed
+        """
+        comment = comment.replace("<details>", "")
+        comment = comment.replace("</details>", "")
+        comment = comment.replace("<summary>", "")
+        comment = comment.replace("</summary>", "")
+        return comment
+
+    @staticmethod
+    def _get_edit_type(codecommit_change_type: str):
         """
         Convert the CodeCommit change type string to the EDIT_TYPE enum.
         The CodeCommit change type string is returned from the get_differences SDK method.
 
+        Args:
+        - codecommit_change_type: the CodeCommit change type string
+
         Returns:
-            An EDIT_TYPE enum representing the modified, added, deleted, or renamed file in the PR diff.
+        - An EDIT_TYPE enum representing the modified, added, deleted, or renamed file in the PR diff.
         """
         t = codecommit_change_type.upper()
         edit_type = None
@@ -333,6 +456,12 @@ class CodeCommitProvider(GitProvider):
         The returned extensions will include the dot "." prefix,
         to accommodate for the dots in the existing language_extension_map settings.
         Filenames with no extension will return an empty string for the extension.
+
+        Args:
+        - filenames: a list of filenames
+
+        Returns:
+        - list: A list of file extensions, including the dot "." prefix.
         """
         extensions = []
         for filename in filenames:
@@ -349,6 +478,12 @@ class CodeCommitProvider(GitProvider):
         Return a dictionary containing the programming language name (as the key),
         and the percentage that language is used (as the value),
         given a list of file extensions.
+
+        Args:
+        - extensions: a list of file extensions
+
+        Returns:
+        - dict: A dictionary where each key is a language name and the corresponding value is the percentage of that language in the PR.
         """
         total_files = len(extensions)
         if total_files == 0:

pr_agent/git_providers/gerrit_provider.py

@@ -0,0 +1,403 @@
+import json
+import os
+import pathlib
+import shutil
+import subprocess
+import uuid
+from collections import Counter, namedtuple
+from pathlib import Path
+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 EDIT_TYPE, FilePatchInfo, GitProvider
+from pr_agent.git_providers.local_git_provider import PullRequestMimic
+from pr_agent.log import get_logger
+
+
+def _call(*command, **kwargs) -> (int, str, str):
+    res = subprocess.run(
+        command,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+        check=True,
+        **kwargs,
+    )
+    return res.stdout.decode()
+
+
+def clone(url, directory):
+    get_logger().info("Cloning %s to %s", url, directory)
+    stdout = _call('git', 'clone', "--depth", "1", url, directory)
+    get_logger().info(stdout)
+
+
+def fetch(url, refspec, cwd):
+    get_logger().info("Fetching %s %s", url, refspec)
+    stdout = _call(
+        'git', 'fetch', '--depth', '2', url, refspec,
+        cwd=cwd
+    )
+    get_logger().info(stdout)
+
+
+def checkout(cwd):
+    get_logger().info("Checking out")
+    stdout = _call('git', 'checkout', "FETCH_HEAD", cwd=cwd)
+    get_logger().info(stdout)
+
+
+def show(*args, cwd=None):
+    get_logger().info("Show")
+    return _call('git', 'show', *args, cwd=cwd)
+
+
+def diff(*args, cwd=None):
+    get_logger().info("Diff")
+    patch = _call('git', 'diff', *args, cwd=cwd)
+    if not patch:
+        get_logger().warning("No changes found")
+        return
+    return patch
+
+
+def reset_local_changes(cwd):
+    get_logger().info("Reset local changes")
+    _call('git', 'checkout', "--force", cwd=cwd)
+
+
+def add_comment(url: urllib3.util.Url, refspec, message):
+    *_, patchset, changenum = refspec.rsplit("/")
+    message = "'" + message.replace("'", "'\"'\"'") + "'"
+    return _call(
+        "ssh",
+        "-p", str(url.port),
+        f"{url.auth}@{url.host}",
+        "gerrit", "review",
+        "--message", message,
+        # "--code-review", score,
+        f"{patchset},{changenum}",
+    )
+
+
+def list_comments(url: urllib3.util.Url, refspec):
+    *_, patchset, _ = refspec.rsplit("/")
+    stdout = _call(
+        "ssh",
+        "-p", str(url.port),
+        f"{url.auth}@{url.host}",
+        "gerrit", "query",
+        "--comments",
+        "--current-patch-set", patchset,
+        "--format", "JSON",
+    )
+    change_set, *_ = stdout.splitlines()
+    return json.loads(change_set)["currentPatchSet"]["comments"]
+
+
+def prepare_repo(url: urllib3.util.Url, project, refspec):
+    repo_url = (f"{url.scheme}://{url.auth}@{url.host}:{url.port}/{project}")
+
+    directory = pathlib.Path(mkdtemp())
+    clone(repo_url, directory),
+    fetch(repo_url, refspec, cwd=directory)
+    checkout(cwd=directory)
+    return directory
+
+
+def adopt_to_gerrit_message(message):
+    lines = message.splitlines()
+    buf = []
+    for line in lines:
+        # remove markdown formatting
+        line = (line.replace("*", "")
+                .replace("``", "`")
+                .replace("<details>", "")
+                .replace("</details>", "")
+                .replace("<summary>", "")
+                .replace("</summary>", ""))
+
+        line = line.strip()
+        if line.startswith('#'):
+            buf.append("\n" +
+                       line.replace('#', '').removesuffix(":").strip() +
+                       ":")
+            continue
+        elif line.startswith('-'):
+            buf.append(line.removeprefix('-').strip())
+            continue
+        else:
+            buf.append(line)
+    return "\n".join(buf).strip()
+
+
+def add_suggestion(src_filename, context: str, start, end: int):
+    with (
+        NamedTemporaryFile("w", delete=False) as tmp,
+        open(src_filename, "r") as src
+    ):
+        lines = src.readlines()
+        tmp.writelines(lines[:start - 1])
+        if context:
+            tmp.write(context)
+        tmp.writelines(lines[end:])
+
+    shutil.copy(tmp.name, src_filename)
+    os.remove(tmp.name)
+
+
+def upload_patch(patch, path):
+    patch_server_endpoint = get_settings().get(
+        'gerrit.patch_server_endpoint')
+    patch_server_token = get_settings().get(
+        'gerrit.patch_server_token')
+
+    response = requests.post(
+        patch_server_endpoint,
+        json={
+            "content": patch,
+            "path": path,
+        },
+        headers={
+            "Content-Type": "application/json",
+            "Authorization": f"Bearer {patch_server_token}",
+        }
+    )
+    response.raise_for_status()
+    patch_server_endpoint = patch_server_endpoint.rstrip("/")
+    return patch_server_endpoint + "/" + path
+
+
+class GerritProvider(GitProvider):
+
+    def __init__(self, key: str, incremental=False):
+        self.project, self.refspec = key.split(':')
+        assert self.project, "Project name is required"
+        assert self.refspec, "Refspec is required"
+        base_url = get_settings().get('gerrit.url')
+        assert base_url, "Gerrit URL is required"
+        user = get_settings().get('gerrit.user')
+        assert user, "Gerrit user is required"
+
+        parsed = urllib3.util.parse_url(base_url)
+        self.parsed_url = urllib3.util.parse_url(
+            f"{parsed.scheme}://{user}@{parsed.host}:{parsed.port}"
+        )
+
+        self.repo_path = prepare_repo(
+            self.parsed_url, self.project, self.refspec
+        )
+        self.repo = Repo(self.repo_path)
+        assert self.repo
+        self.pr_url = base_url
+        self.pr = PullRequestMimic(self.get_pr_title(), self.get_diff_files())
+
+    def get_pr_title(self):
+        """
+        Substitutes the branch-name as the PR-mimic title.
+        """
+        return self.repo.branches[0].name
+
+    def get_issue_comments(self):
+        comments = list_comments(self.parsed_url, self.refspec)
+        Comments = namedtuple('Comments', ['reversed'])
+        Comment = namedtuple('Comment', ['body'])
+        return Comments([Comment(c['message']) for c in reversed(comments)])
+
+    def get_labels(self):
+        raise NotImplementedError(
+            'Getting labels is not implemented for the gerrit provider')
+
+    def add_eyes_reaction(self, issue_comment_id: int):
+        raise NotImplementedError(
+            'Adding reactions is not implemented for the gerrit provider')
+
+    def remove_reaction(self, issue_comment_id: int, reaction_id: int):
+        raise NotImplementedError(
+            'Removing reactions is not implemented for the gerrit provider')
+
+    def get_commit_messages(self):
+        return [self.repo.head.commit.message]
+
+    def get_repo_settings(self):
+        try:
+            with open(self.repo_path / ".pr_agent.toml", 'rb') as f:
+                contents = f.read()
+            return contents
+        except OSError:
+            return b""
+
+    def get_diff_files(self) -> list[FilePatchInfo]:
+        diffs = self.repo.head.commit.diff(
+            self.repo.head.commit.parents[0],  # previous commit
+            create_patch=True,
+            R=True
+        )
+
+        diff_files = []
+        for diff_item in diffs:
+            if diff_item.a_blob is not None:
+                original_file_content_str = (
+                    diff_item.a_blob.data_stream.read().decode('utf-8')
+                )
+            else:
+                original_file_content_str = ""  # empty file
+            if diff_item.b_blob is not None:
+                new_file_content_str = diff_item.b_blob.data_stream.read(). \
+                    decode('utf-8')
+            else:
+                new_file_content_str = ""  # empty file
+            edit_type = EDIT_TYPE.MODIFIED
+            if diff_item.new_file:
+                edit_type = EDIT_TYPE.ADDED
+            elif diff_item.deleted_file:
+                edit_type = EDIT_TYPE.DELETED
+            elif diff_item.renamed_file:
+                edit_type = EDIT_TYPE.RENAMED
+            diff_files.append(
+                FilePatchInfo(
+                    original_file_content_str,
+                    new_file_content_str,
+                    diff_item.diff.decode('utf-8'),
+                    diff_item.b_path,
+                    edit_type=edit_type,
+                    old_filename=None
+                    if diff_item.a_path == diff_item.b_path
+                    else diff_item.a_path
+                )
+            )
+        self.diff_files = diff_files
+        return diff_files
+
+    def get_files(self):
+        diff_index = self.repo.head.commit.diff(
+            self.repo.head.commit.parents[0],  # previous commit
+            R=True
+        )
+        # Get the list of changed files
+        diff_files = [item.a_path for item in diff_index]
+        return diff_files
+
+    def get_languages(self):
+        """
+        Calculate percentage of languages in repository. Used for hunk
+        prioritisation.
+        """
+        # Get all files in repository
+        filepaths = [Path(item.path) for item in
+                     self.repo.tree().traverse() if item.type == 'blob']
+        # Identify language by file extension and count
+        lang_count = Counter(
+            ext.lstrip('.') for filepath in filepaths for ext in
+            [filepath.suffix.lower()])
+        # Convert counts to percentages
+        total_files = len(filepaths)
+        lang_percentage = {lang: count / total_files * 100 for lang, count
+                           in lang_count.items()}
+        return lang_percentage
+
+    def get_pr_description_full(self):
+        return self.repo.head.commit.message
+
+    def get_user_id(self):
+        return self.repo.head.commit.author.email
+
+    def is_supported(self, capability: str) -> bool:
+        if capability in [
+            # 'get_issue_comments',
+            'create_inline_comment',
+            'publish_inline_comments',
+            'get_labels',
+            'gfm_markdown'
+        ]:
+            return False
+        return True
+
+    def split_suggestion(self, msg) -> tuple[str, str]:
+        is_code_context = False
+        description = []
+        context = []
+        for line in msg.splitlines():
+            if line.startswith('```suggestion'):
+                is_code_context = True
+                continue
+            if line.startswith('```'):
+                is_code_context = False
+                continue
+            if is_code_context:
+                context.append(line)
+            else:
+                description.append(
+                    line.replace('*', '')
+                )
+
+        return (
+            '\n'.join(description),
+            '\n'.join(context) + '\n' if context else ''
+        )
+
+    def publish_code_suggestions(self, code_suggestions: list):
+        msg = []
+        for suggestion in code_suggestions:
+            description, code = self.split_suggestion(suggestion['body'])
+            add_suggestion(
+                pathlib.Path(self.repo_path) / suggestion["relevant_file"],
+                code,
+                suggestion["relevant_lines_start"],
+                suggestion["relevant_lines_end"],
+            )
+            patch = diff(cwd=self.repo_path)
+            patch_id = uuid.uuid4().hex[0:4]
+            path = "/".join(["codium-ai", self.refspec, patch_id])
+            full_path = upload_patch(patch, path)
+            reset_local_changes(self.repo_path)
+            msg.append(f'* {description}\n{full_path}')
+
+        if msg:
+            add_comment(self.parsed_url, self.refspec, "\n".join(msg))
+            return True
+
+    def publish_comment(self, pr_comment: str, is_temporary: bool = False):
+        if not is_temporary:
+            msg = adopt_to_gerrit_message(pr_comment)
+            add_comment(self.parsed_url, self.refspec, msg)
+
+    def publish_description(self, pr_title: str, pr_body: str):
+        msg = adopt_to_gerrit_message(pr_body)
+        add_comment(self.parsed_url, self.refspec, pr_title + '\n' + msg)
+
+    def publish_inline_comments(self, comments: list[dict]):
+        raise NotImplementedError(
+            'Publishing inline comments is not implemented for the gerrit '
+            'provider')
+
+    def publish_inline_comment(self, body: str, relevant_file: str,
+                               relevant_line_in_file: str):
+        raise NotImplementedError(
+            'Publishing inline comments is not implemented for the gerrit '
+            'provider')
+
+    def create_inline_comment(self, body: str, relevant_file: str,
+                              relevant_line_in_file: str):
+        raise NotImplementedError(
+            'Creating inline comments is not implemented for the gerrit '
+            'provider')
+
+    def publish_labels(self, labels):
+        # Not applicable to the local git provider,
+        # but required by the interface
+        pass
+
+    def remove_initial_comment(self):
+        # remove repo, cloned in previous steps
+        # shutil.rmtree(self.repo_path)
+        pass
+
+    def remove_comment(self, comment):
+        pass
+
+    def get_pr_branch(self):
+        return self.repo.head

pr_agent/git_providers/git_provider.py

@@ -1,4 +1,3 @@
-import logging
 from abc import ABC, abstractmethod
 from dataclasses import dataclass
 
@@ -6,12 +5,16 @@ from dataclasses import dataclass
 from enum import Enum
 from typing import Optional
 
+from pr_agent.config_loader import get_settings
+from pr_agent.log import get_logger
+
 
 class EDIT_TYPE(Enum):
     ADDED = 1
     DELETED = 2
     MODIFIED = 3
     RENAMED = 4
+    UNKNOWN = 5
 
 
 @dataclass
@@ -21,8 +24,10 @@ class FilePatchInfo:
     patch: str
     filename: str
     tokens: int = -1
-    edit_type: EDIT_TYPE = EDIT_TYPE.MODIFIED
+    edit_type: EDIT_TYPE = EDIT_TYPE.UNKNOWN
     old_filename: str = None
+    num_plus_lines: int = -1
+    num_minus_lines: int = -1
 
 
 class GitProvider(ABC):
@@ -38,38 +43,10 @@ class GitProvider(ABC):
     def publish_description(self, pr_title: str, pr_body: str):
         pass
 
-    @abstractmethod
-    def publish_comment(self, pr_comment: str, is_temporary: bool = False):
-        pass
-
-    @abstractmethod
-    def publish_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
-        pass
-
-    @abstractmethod
-    def create_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
-        pass
-
-    @abstractmethod
-    def publish_inline_comments(self, comments: list[dict]):
-        pass
-
     @abstractmethod
     def publish_code_suggestions(self, code_suggestions: list) -> bool:
         pass
 
-    @abstractmethod
-    def publish_labels(self, labels):
-        pass
-
-    @abstractmethod
-    def get_labels(self):
-        pass
-
-    @abstractmethod
-    def remove_initial_comment(self):
-        pass
-
     @abstractmethod
     def get_languages(self):
         pass
@@ -86,19 +63,19 @@ class GitProvider(ABC):
     def get_pr_description_full(self) -> str:
         pass
 
-    def get_pr_description(self) -> str:
+    def get_pr_description(self, *, full: bool = True) -> str:
         from pr_agent.config_loader import get_settings
-        from pr_agent.algo.pr_processing import clip_tokens
-        max_tokens = get_settings().get("CONFIG.MAX_DESCRIPTION_TOKENS", None)
-        description = self.get_pr_description_full()
-        if max_tokens:
-            return clip_tokens(description, max_tokens)
+        from pr_agent.algo.utils import clip_tokens
+        max_tokens_description = get_settings().get("CONFIG.MAX_DESCRIPTION_TOKENS", None)
+        description = self.get_pr_description_full() if full else self.get_user_description()
+        if max_tokens_description:
+            return clip_tokens(description, max_tokens_description)
         return description
 
     def get_user_description(self) -> str:
         description = (self.get_pr_description_full() or "").strip()
         # if the existing description wasn't generated by the pr-agent, just return it as-is
-        if not description.startswith("## PR Type"):
+        if not any(description.startswith(header) for header in ("## PR Type", "## PR Description")):
             return description
         # if the existing description was generated by the pr-agent, but it doesn't contain the user description,
         # return nothing (empty string) because it means there is no user description
@@ -108,11 +85,57 @@ class GitProvider(ABC):
         return description.split("## User Description:", 1)[1].strip()
 
     @abstractmethod
-    def get_issue_comments(self):
+    def get_repo_settings(self):
+        pass
+
+    def get_pr_id(self):
+        return ""
+
+    def get_line_link(self, relevant_file: str, relevant_line_start: int, relevant_line_end: int = None) -> str:
+        return ""
+
+    #### comments operations ####
+    @abstractmethod
+    def publish_comment(self, pr_comment: str, is_temporary: bool = False):
+        pass
+
+    def publish_persistent_comment(self, pr_comment: str, initial_header: str, update_header: bool):
+        self.publish_comment(pr_comment)
+
+    @abstractmethod
+    def publish_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
         pass
 
     @abstractmethod
-    def get_repo_settings(self):
+    def create_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
+        pass
+
+    @abstractmethod
+    def publish_inline_comments(self, comments: list[dict]):
+        pass
+
+    @abstractmethod
+    def remove_initial_comment(self):
+        pass
+
+    @abstractmethod
+    def remove_comment(self, comment):
+        pass
+
+    @abstractmethod
+    def get_issue_comments(self):
+        pass
+
+    def get_comment_url(self, comment) -> str:
+        return ""
+
+    #### labels operations ####
+    @abstractmethod
+    def publish_labels(self, labels):
+        pass
+
+    @abstractmethod
+    def get_labels(self):
         pass
 
     @abstractmethod
@@ -123,50 +146,78 @@ class GitProvider(ABC):
     def remove_reaction(self, issue_comment_id: int, reaction_id: int) -> bool:
         pass
 
+    #### commits operations ####
     @abstractmethod
     def get_commit_messages(self):
         pass
 
+    def get_latest_commit_url(self) -> str:
+        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:
+        get_logger().info("No languages detected")
+        return main_language_str
+    if not files:
+        get_logger().info("No files in diff")
+        return main_language_str
+
     try:
         top_language = max(languages, key=languages.get).lower()
 
         # validate that the specific commit uses the main language
         extension_list = []
         for file in files:
+            if not file:
+                continue
             if isinstance(file, str):
                 file = FilePatchInfo(base_file=None, head_file=None, patch=None, filename=file)
             extension_list.append(file.filename.rsplit('.')[-1])
 
         # get the most common extension
-        most_common_extension = max(set(extension_list), key=extension_list.count)
+        most_common_extension = '.' + max(set(extension_list), key=extension_list.count)
+        try:
+            language_extension_map_org = get_settings().language_extension_map_org
+            language_extension_map = {k.lower(): v for k, v in language_extension_map_org.items()}
 
-        # look for a match. TBD: add more languages, do this systematically
-        if most_common_extension == 'py' and top_language == 'python' or \
-                most_common_extension == 'js' and top_language == 'javascript' or \
-                most_common_extension == 'ts' and top_language == 'typescript' or \
-                most_common_extension == 'go' and top_language == 'go' or \
-                most_common_extension == 'java' and top_language == 'java' or \
-                most_common_extension == 'c' and top_language == 'c' or \
-                most_common_extension == 'cpp' and top_language == 'c++' or \
-                most_common_extension == 'cs' and top_language == 'c#' or \
-                most_common_extension == 'swift' and top_language == 'swift' or \
-                most_common_extension == 'php' and top_language == 'php' or \
-                most_common_extension == 'rb' and top_language == 'ruby' or \
-                most_common_extension == 'rs' and top_language == 'rust' or \
-                most_common_extension == 'scala' and top_language == 'scala' or \
-                most_common_extension == 'kt' and top_language == 'kotlin' or \
-                most_common_extension == 'pl' and top_language == 'perl' or \
-                most_common_extension == 'swift' and top_language == 'swift' or \
-                most_common_extension == top_language:
-            main_language_str = top_language
+            if top_language in language_extension_map and most_common_extension in language_extension_map[top_language]:
+                main_language_str = top_language
+            else:
+                for language, extensions in language_extension_map.items():
+                    if most_common_extension in extensions:
+                        main_language_str = language
+                        break
+        except Exception as e:
+            get_logger().exception(f"Failed to get main language: {e}")
+            pass
+
+        ## old approach:
+        # most_common_extension = max(set(extension_list), key=extension_list.count)
+        # if most_common_extension == 'py' and top_language == 'python' or \
+        #         most_common_extension == 'js' and top_language == 'javascript' or \
+        #         most_common_extension == 'ts' and top_language == 'typescript' or \
+        #         most_common_extension == 'tsx' and top_language == 'typescript' or \
+        #         most_common_extension == 'go' and top_language == 'go' or \
+        #         most_common_extension == 'java' and top_language == 'java' or \
+        #         most_common_extension == 'c' and top_language == 'c' or \
+        #         most_common_extension == 'cpp' and top_language == 'c++' or \
+        #         most_common_extension == 'cs' and top_language == 'c#' or \
+        #         most_common_extension == 'swift' and top_language == 'swift' or \
+        #         most_common_extension == 'php' and top_language == 'php' or \
+        #         most_common_extension == 'rb' and top_language == 'ruby' or \
+        #         most_common_extension == 'rs' and top_language == 'rust' or \
+        #         most_common_extension == 'scala' and top_language == 'scala' or \
+        #         most_common_extension == 'kt' and top_language == 'kotlin' or \
+        #         most_common_extension == 'pl' and top_language == 'perl' or \
+        #         most_common_extension == top_language:
+        #     main_language_str = top_language
 
     except Exception as e:
-        logging.exception(e)
+        get_logger().exception(e)
         pass
 
     return main_language_str
@@ -176,6 +227,13 @@ class IncrementalPR:
     def __init__(self, is_incremental: bool = False):
         self.is_incremental = is_incremental
         self.commits_range = None
-        self.first_new_commit_sha = None
-        self.last_seen_commit_sha = None
+        self.first_new_commit = None
+        self.last_seen_commit = None
 
+    @property
+    def first_new_commit_sha(self):
+        return None if self.first_new_commit is None else self.first_new_commit.sha
+
+    @property
+    def last_seen_commit_sha(self):
+        return None if self.last_seen_commit is None else self.last_seen_commit.sha

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.utils import load_large_diff
-from ..algo.pr_processing import find_line_number_of_relevant_line_in_file, clip_tokens
+from ..algo.pr_processing import find_line_number_of_relevant_line_in_file
+from ..algo.utils import load_large_diff, 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, EDIT_TYPE
 
 
 class GithubProvider(GitProvider):
@@ -32,9 +31,10 @@ class GithubProvider(GitProvider):
         self.diff_files = None
         self.git_files = None
         self.incremental = incremental
-        if pr_url:
+        if pr_url and 'pull' in pr_url:
             self.set_pr(pr_url)
             self.last_commit_id = list(self.pr.get_commits())[-1]
+            self.pr_url = self.get_pr_url() # pr_url for github actions can be as api.github.com, so we need to get the url from the pr object
 
     def is_supported(self, capability: str) -> bool:
         return True
@@ -51,36 +51,44 @@ class GithubProvider(GitProvider):
     def get_incremental_commits(self):
         self.commits = list(self.pr.get_commits())
 
-        self.get_previous_review()
+        self.previous_review = self.get_previous_review(full=True, incremental=True)
         if self.previous_review:
             self.incremental.commits_range = self.get_commit_range()
             # Get all files changed during the commit range
             self.file_set = dict()
             for commit in self.incremental.commits_range:
                 if commit.commit.message.startswith(f"Merge branch '{self._get_repo().default_branch}'"):
-                    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})
+        else:
+            raise ValueError("No previous review found")
 
     def get_commit_range(self):
         last_review_time = self.previous_review.created_at
-        first_new_commit_index = 0
+        first_new_commit_index = None
         for index in range(len(self.commits) - 1, -1, -1):
             if self.commits[index].commit.author.date > last_review_time:
-                self.incremental.first_new_commit_sha = self.commits[index].sha
+                self.incremental.first_new_commit = self.commits[index]
                 first_new_commit_index = index
             else:
-                self.incremental.last_seen_commit_sha = self.commits[index].sha
+                self.incremental.last_seen_commit = self.commits[index]
                 break
-        return self.commits[first_new_commit_index:]
+        return self.commits[first_new_commit_index:] if first_new_commit_index is not None else []
 
-    def get_previous_review(self):
-        self.previous_review = None
-        self.comments = list(self.pr.get_issue_comments())
+    def get_previous_review(self, *, full: bool, incremental: bool):
+        if not (full or incremental):
+            raise ValueError("At least one of full or incremental must be True")
+        if not getattr(self, "comments", None):
+            self.comments = list(self.pr.get_issue_comments())
+        prefixes = []
+        if full:
+            prefixes.append("## PR Analysis")
+        if incremental:
+            prefixes.append("## Incremental PR Review")
         for index in range(len(self.comments) - 1, -1, -1):
-            if self.comments[index].body.startswith("## PR Analysis"):
-                self.previous_review = self.comments[index]
-                break
+            if any(self.comments[index].body.startswith(prefix) for prefix in prefixes):
+                return self.comments[index]
 
     def get_files(self):
         if self.incremental.is_incremental and self.file_set:
@@ -124,22 +132,68 @@ class GithubProvider(GitProvider):
                     if not patch:
                         patch = load_large_diff(file.filename, new_file_content_str, original_file_content_str)
 
-                diff_files.append(FilePatchInfo(original_file_content_str, new_file_content_str, patch, file.filename))
+                if file.status == 'added':
+                    edit_type = EDIT_TYPE.ADDED
+                elif file.status == 'removed':
+                    edit_type = EDIT_TYPE.DELETED
+                elif file.status == 'renamed':
+                    edit_type = EDIT_TYPE.RENAMED
+                elif file.status == 'modified':
+                    edit_type = EDIT_TYPE.MODIFIED
+                else:
+                    get_logger().error(f"Unknown edit type: {file.status}")
+                    edit_type = EDIT_TYPE.UNKNOWN
+
+                # count number of lines added and removed
+                patch_lines = patch.splitlines(keepends=True)
+                num_plus_lines = len([line for line in patch_lines if line.startswith('+')])
+                num_minus_lines = len([line for line in patch_lines if line.startswith('-')])
+                file_patch_canonical_structure = FilePatchInfo(original_file_content_str, new_file_content_str, patch,
+                                                               file.filename, edit_type=edit_type,
+                                                               num_plus_lines=num_plus_lines,
+                                                               num_minus_lines=num_minus_lines,)
+                diff_files.append(file_patch_canonical_structure)
 
             self.diff_files = diff_files
             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):
         self.pr.edit(title=pr_title, body=pr_body)
 
+    def get_latest_commit_url(self) -> str:
+        return self.last_commit_id.html_url
+
+    def get_comment_url(self, comment) -> str:
+        return comment.html_url
+
+    def publish_persistent_comment(self, pr_comment: str, initial_header: str, update_header: bool = True):
+        prev_comments = list(self.pr.get_issue_comments())
+        for comment in prev_comments:
+            body = comment.body
+            if body.startswith(initial_header):
+                latest_commit_url = self.get_latest_commit_url()
+                comment_url = self.get_comment_url(comment)
+                if update_header:
+                    updated_header = f"{initial_header}\n\n### (review updated until commit {latest_commit_url})\n"
+                    pr_comment_updated = pr_comment.replace(initial_header, updated_header)
+                else:
+                    pr_comment_updated = pr_comment
+                get_logger().info(f"Persistent mode- updating comment {comment_url} to latest review message")
+                response = comment.edit(pr_comment_updated)
+                self.publish_comment(
+                    f"**[Persistent review]({comment_url})** updated to latest commit {latest_commit_url}")
+                return
+        self.publish_comment(pr_comment)
+
     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"):
             self.github_user_id = response.user.login
@@ -156,7 +210,7 @@ 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 +233,13 @@ 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
@@ -212,16 +266,22 @@ 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):
         try:
             for comment in getattr(self.pr, 'comments_list', []):
                 if comment.is_temporary:
-                    comment.delete()
+                    self.remove_comment(comment)
         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 remove_comment(self, comment):
+        try:
+            comment.delete()
+        except Exception as e:
+            get_logger().exception(f"Failed to remove comment, error: {e}")
 
     def get_title(self):
         return self.pr.title
@@ -239,9 +299,10 @@ 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 +319,10 @@ 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 +332,7 @@ 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 +340,7 @@ 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
 
 
@@ -309,6 +373,35 @@ class GithubProvider(GitProvider):
 
         return repo_name, pr_number
 
+    @staticmethod
+    def _parse_issue_url(issue_url: str) -> Tuple[str, int]:
+        parsed_url = urlparse(issue_url)
+
+        if 'github.com' not in parsed_url.netloc:
+            raise ValueError("The provided URL is not a valid GitHub URL")
+
+        path_parts = parsed_url.path.strip('/').split('/')
+        if 'api.github.com' in parsed_url.netloc:
+            if len(path_parts) < 5 or path_parts[3] != 'issues':
+                raise ValueError("The provided URL does not appear to be a GitHub ISSUE URL")
+            repo_name = '/'.join(path_parts[1:3])
+            try:
+                issue_number = int(path_parts[4])
+            except ValueError as e:
+                raise ValueError("Unable to convert issue number to integer") from e
+            return repo_name, issue_number
+
+        if len(path_parts) < 4 or path_parts[2] != 'issues':
+            raise ValueError("The provided URL does not appear to be a GitHub PR issue")
+
+        repo_name = '/'.join(path_parts[:2])
+        try:
+            issue_number = int(path_parts[3])
+        except ValueError as e:
+            raise ValueError("Unable to convert issue number to integer") from e
+
+        return repo_name, issue_number
+
     def _get_github_client(self):
         deployment_type = get_settings().get("GITHUB.DEPLOYMENT_TYPE", "user")
 
@@ -322,7 +415,7 @@ class GithubProvider(GitProvider):
                 raise ValueError("GitHub app installation ID is required when using GitHub app deployment")
             auth = AppAuthentication(app_id=app_id, private_key=private_key,
                                      installation_id=self.installation_id)
-            return Github(app_auth=auth)
+            return Github(app_auth=auth, base_url=get_settings().github.base_url)
 
         if deployment_type == 'user':
             try:
@@ -331,7 +424,7 @@ class GithubProvider(GitProvider):
                 raise ValueError(
                     "GitHub token is required when using user deployment. See: "
                     "https://github.com/Codium-ai/pr-agent#method-2-run-from-source") from e
-            return Github(auth=Auth.Token(token))
+            return Github(auth=Auth.Token(token), base_url=get_settings().github.base_url)
 
     def _get_repo(self):
         if hasattr(self, 'repo_obj') and \
@@ -356,7 +449,7 @@ class GithubProvider(GitProvider):
     def publish_labels(self, pr_types):
         try:
             label_color_map = {"Bug fix": "1d76db", "Tests": "e99695", "Bug fix with tests": "c5def5",
-                               "Refactoring": "bfdadc", "Enhancement": "bfd4f2", "Documentation": "d4c5f9",
+                               "Enhancement": "bfd4f2", "Documentation": "d4c5f9",
                                "Other": "d1bcf9"}
             post_parameters = []
             for p in pr_types:
@@ -366,13 +459,13 @@ 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):
@@ -414,6 +507,24 @@ 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_line_link(self, relevant_file: str, relevant_line_start: int, relevant_line_end: int = None) -> str:
+        sha_file = hashlib.sha256(relevant_file.encode('utf-8')).hexdigest()
+        if relevant_line_start == -1:
+            link = f"https://github.com/{self.repo}/pull/{self.pr_num}/files#diff-{sha_file}"
+        elif relevant_line_end:
+            link = f"https://github.com/{self.repo}/pull/{self.pr_num}/files#diff-{sha_file}R{relevant_line_start}-R{relevant_line_end}"
+        else:
+            link = f"https://github.com/{self.repo}/pull/{self.pr_num}/files#diff-{sha_file}R{relevant_line_start}"
+        return link
+
+
+    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.utils import load_large_diff
+from ..algo.pr_processing import find_line_number_of_relevant_line_in_file
+from ..algo.utils import load_large_diff, clip_tokens
 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."""
@@ -37,13 +37,14 @@ class GitLabProvider(GitProvider):
         self.diff_files = None
         self.git_files = None
         self.temp_comments = []
+        self.pr_url = merge_request_url
         self._set_merge_request(merge_request_url)
         self.RE_HUNK_HEADER = re.compile(
             r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
         self.incremental = incremental
 
     def is_supported(self, capability: str) -> bool:
-        if capability in ['get_issue_comments', 'create_inline_comment', 'publish_inline_comments']:
+        if capability in ['get_issue_comments', 'create_inline_comment', 'publish_inline_comments']: # gfm_markdown is supported in gitlab !
             return False
         return True
 
@@ -58,7 +59,7 @@ 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 +99,7 @@ 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
@@ -114,12 +115,20 @@ class GitLabProvider(GitProvider):
                 if not patch:
                     patch = load_large_diff(filename, new_file_content_str, original_file_content_str)
 
+
+                # count number of lines added and removed
+                patch_lines = patch.splitlines(keepends=True)
+                num_plus_lines = len([line for line in patch_lines if line.startswith('+')])
+                num_minus_lines = len([line for line in patch_lines if line.startswith('-')])
                 diff_files.append(
                     FilePatchInfo(original_file_content_str, new_file_content_str,
                                   patch=patch,
                                   filename=filename,
                                   edit_type=edit_type,
-                                  old_filename=None if diff['old_path'] == diff['new_path'] else diff['old_path']))
+                                  old_filename=None if diff['old_path'] == diff['new_path'] else diff['old_path'],
+                                  num_plus_lines=num_plus_lines,
+                                  num_minus_lines=num_minus_lines, ))
+
         self.diff_files = diff_files
         return diff_files
 
@@ -134,7 +143,34 @@ 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 get_latest_commit_url(self):
+        return self.mr.commits().next().web_url
+
+    def get_comment_url(self, comment):
+        return f"{self.mr.web_url}#note_{comment.id}"
+
+    def publish_persistent_comment(self, pr_comment: str, initial_header: str, update_header: bool = True):
+        try:
+            for comment in self.mr.notes.list(get_all=True)[::-1]:
+                if comment.body.startswith(initial_header):
+                    latest_commit_url = self.get_latest_commit_url()
+                    comment_url = self.get_comment_url(comment)
+                    if update_header:
+                        updated_header = f"{initial_header}\n\n### (review updated until commit {latest_commit_url})\n"
+                        pr_comment_updated = pr_comment.replace(initial_header, updated_header)
+                    else:
+                        pr_comment_updated = pr_comment
+                    get_logger().info(f"Persistent mode- updating comment {comment_url} to latest review message")
+                    response = self.mr.notes.update(comment.id, {'body': pr_comment_updated})
+                    self.publish_comment(
+                        f"**[Persistent review]({comment_url})** updated to latest commit {latest_commit_url}")
+                    return
+        except Exception as e:
+            get_logger().exception(f"Failed to update persistent review, error: {e}")
+            pass
+        self.publish_comment(pr_comment)
 
     def publish_comment(self, mr_comment: str, is_temporary: bool = False):
         comment = self.mr.notes.create({'body': mr_comment})
@@ -156,12 +192,12 @@ 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 +210,23 @@ 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 +261,10 @@ 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
@@ -285,9 +323,15 @@ class GitLabProvider(GitProvider):
     def remove_initial_comment(self):
         try:
             for comment in self.temp_comments:
-                comment.delete()
+                self.remove_comment(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}")
+
+    def remove_comment(self, comment):
+        try:
+            comment.delete()
+        except Exception as e:
+            get_logger().exception(f"Failed to remove comment, error: {e}")
 
     def get_title(self):
         return self.mr.title
@@ -307,7 +351,7 @@ class GitLabProvider(GitProvider):
 
     def get_repo_settings(self):
         try:
-            contents = self.gl.projects.get(self.id_project).files.get(file_path='.pr_agent.toml', ref=self.mr.source_branch)
+            contents = self.gl.projects.get(self.id_project).files.get(file_path='.pr_agent.toml', ref=self.mr.target_branch).decode()
             return contents
         except Exception:
             return ""
@@ -355,7 +399,7 @@ 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 +422,45 @@ 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 get_line_link(self, relevant_file: str, relevant_line_start: int, relevant_line_end: int = None) -> str:
+        if relevant_line_start == -1:
+            link = f"https://gitlab.com/codiumai/pr-agent/-/blob/{self.mr.source_branch}/{relevant_file}?ref_type=heads"
+        elif relevant_line_end:
+            link = f"https://gitlab.com/codiumai/pr-agent/-/blob/{self.mr.source_branch}/{relevant_file}?ref_type=heads#L{relevant_line_start}-L{relevant_line_end}"
+        else:
+            link = f"https://gitlab.com/codiumai/pr-agent/-/blob/{self.mr.source_branch}/{relevant_file}?ref_type=heads#L{relevant_line_start}"
+        return link
+
+
+    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:
@@ -49,14 +49,15 @@ 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:
             raise KeyError(f'Branch: {self.target_branch_name} does not exist')
 
     def is_supported(self, capability: str) -> bool:
-        if capability in ['get_issue_comments', 'create_inline_comment', 'publish_inline_comments', 'get_labels']:
+        if capability in ['get_issue_comments', 'create_inline_comment', 'publish_inline_comments', 'get_labels',
+                          'gfm_markdown']:
             return False
         return True
 
@@ -139,6 +140,9 @@ class LocalGitProvider(GitProvider):
     def remove_initial_comment(self):
         pass  # Not applicable to the local git provider, but required by the interface
 
+    def remove_comment(self, comment):
+        pass  # Not applicable to the local git provider, but required by the interface
+
     def get_languages(self):
         """
         Calculate percentage of languages in repository. Used for hunk prioritisation.

pr_agent/git_providers/utils.py

@@ -0,0 +1,37 @@
+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}")
+        except Exception as e:
+            get_logger().exception("Failed to apply repo settings", e)
+        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/bitbucket_server_webhook.py

@@ -0,0 +1,64 @@
+import json
+
+import uvicorn
+from fastapi import APIRouter, FastAPI
+from fastapi.encoders import jsonable_encoder
+from starlette import status
+from starlette.background import BackgroundTasks
+from starlette.middleware import Middleware
+from starlette.requests import Request
+from starlette.responses import JSONResponse
+from starlette_context.middleware import RawContextMiddleware
+
+from pr_agent.agent.pr_agent import PRAgent
+from pr_agent.config_loader import get_settings
+from pr_agent.log import get_logger
+
+router = APIRouter()
+
+
+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 handle_webhook(background_tasks: BackgroundTasks, request: Request):
+    log_context = {"server_type": "bitbucket_server"}
+    data = await request.json()
+    get_logger().info(json.dumps(data))
+
+    pr_id = data['pullRequest']['id']
+    repository_name = data['pullRequest']['toRef']['repository']['slug']
+    project_name = data['pullRequest']['toRef']['repository']['project']['key']
+    bitbucket_server = get_settings().get("BITBUCKET_SERVER.URL")
+    pr_url = f"{bitbucket_server}/projects/{project_name}/repos/{repository_name}/pull-requests/{pr_id}"
+
+    log_context["api_url"] = pr_url
+    log_context["event"] = "pull_request"
+
+    handle_request(background_tasks, pr_url, "review", log_context)
+    return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
+
+
+@router.get("/")
+async def root():
+    return {"status": "ok"}
+
+
+def start():
+    bitbucket_server_url = get_settings().get("BITBUCKET_SERVER.URL", None)
+    if not bitbucket_server_url:
+        raise ValueError("BITBUCKET_SERVER.URL is not set")
+    get_settings().config.git_provider = "bitbucket_server"
+    middleware = [Middleware(RawContextMiddleware)]
+    app = FastAPI(middleware=middleware)
+    app.include_router(router)
+    uvicorn.run(app, host="0.0.0.0", port=3000)
+
+
+if __name__ == '__main__':
+    start()

pr_agent/servers/gerrit_server.py

@@ -0,0 +1,77 @@
+import copy
+from enum import Enum
+from json import JSONDecodeError
+
+import uvicorn
+from fastapi import APIRouter, FastAPI, HTTPException
+from pydantic import BaseModel
+from starlette.middleware import Middleware
+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 get_settings, global_settings
+from pr_agent.log import get_logger, setup_logger
+
+setup_logger()
+router = APIRouter()
+
+
+class Action(str, Enum):
+    review = "review"
+    describe = "describe"
+    ask = "ask"
+    improve = "improve"
+    reflect = "reflect"
+    answer = "answer"
+
+
+class Item(BaseModel):
+    refspec: str
+    project: str
+    msg: str
+
+
+@router.post("/api/v1/gerrit/{action}")
+async def handle_gerrit_request(action: Action, item: Item):
+    get_logger().debug("Received a Gerrit request")
+    context["settings"] = copy.deepcopy(global_settings)
+
+    if action == Action.ask:
+        if not item.msg:
+            return HTTPException(
+                status_code=400,
+                detail="msg is required for ask command"
+            )
+    await PRAgent().handle_request(
+        f"{item.project}:{item.refspec}",
+        f"/{item.msg.strip()}"
+    )
+
+
+async def get_body(request):
+    try:
+        body = await request.json()
+    except JSONDecodeError as e:
+        get_logger().error("Error parsing request body", e)
+        return {}
+    return body
+
+
+@router.get("/")
+async def root():
+    return {"status": "ok"}
+
+
+def start():
+    # to prevent adding help messages with the output
+    get_settings().set("CONFIG.CLI_MODE", True)
+    middleware = [Middleware(RawContextMiddleware)]
+    app = FastAPI(middleware=middleware)
+    app.include_router(router)
+
+    uvicorn.run(app, host="0.0.0.0", port=3000)
+
+
+if __name__ == '__main__':
+    start()

pr_agent/servers/github_action_runner.py

@@ -1,23 +1,43 @@
 import asyncio
 import json
 import os
+from typing import Union
 
 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
 
 
+def is_true(value: Union[str, bool]) -> bool:
+    if isinstance(value, bool):
+        return value
+    if isinstance(value, str):
+        return value.lower() == 'true'
+    return False
+
+
+def get_setting_or_env(key: str, default: Union[str, bool] = None) -> Union[str, bool]:
+    try:
+        value = get_settings().get(key, default)
+    except AttributeError:  # TBD still need to debug why this happens on GitHub Actions
+        value = os.getenv(key, None) or os.getenv(key.upper(), None) or os.getenv(key.lower(), None) or default
+    return value
+
+
 async def run_action():
     # Get environment variables
     GITHUB_EVENT_NAME = os.environ.get('GITHUB_EVENT_NAME')
     GITHUB_EVENT_PATH = os.environ.get('GITHUB_EVENT_PATH')
-    OPENAI_KEY = os.environ.get('OPENAI_KEY')
-    OPENAI_ORG = os.environ.get('OPENAI_ORG')
+    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)
 
-
     # Check if required environment variables are set
     if not GITHUB_EVENT_NAME:
         print("GITHUB_EVENT_NAME not set")
@@ -47,13 +67,30 @@ 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 = get_setting_or_env("GITHUB_ACTION.AUTO_REVIEW", None)
+                if auto_review is None or is_true(auto_review):
+                    await PRReviewer(pr_url).run()
+                auto_describe = get_setting_or_env("GITHUB_ACTION.AUTO_DESCRIBE", None)
+                if is_true(auto_describe):
+                    await PRDescription(pr_url).run()
+                auto_improve = get_setting_or_env("GITHUB_ACTION.AUTO_IMPROVE", None)
+                if is_true(auto_improve):
+                    await PRCodeSuggestions(pr_url).run()
 
     # Handle issue comment event
     elif GITHUB_EVENT_NAME == "issue_comment":
@@ -61,13 +98,22 @@ async def run_action():
         if action in ["created", "edited"]:
             comment_body = event_payload.get("comment", {}).get("body")
             if comment_body:
-                pr_url = event_payload.get("issue", {}).get("pull_request", {}).get("url")
-                if pr_url:
+                is_pr = False
+                # check if issue is pull request
+                if event_payload.get("issue", {}).get("pull_request"):
+                    url = event_payload.get("issue", {}).get("pull_request", {}).get("url")
+                    is_pr = True
+                else:
+                    url = event_payload.get("issue", {}).get("url")
+                if url:
                     body = comment_body.strip().lower()
                     comment_id = event_payload.get("comment", {}).get("id")
-                    provider = get_git_provider()(pr_url=pr_url)
-                    await PRAgent().handle_request(pr_url, body, notify=lambda: provider.add_eyes_reaction(comment_id))
+                    provider = get_git_provider()(pr_url=url)
+                    if is_pr:
+                        await PRAgent().handle_request(url, body, notify=lambda: provider.add_eyes_reaction(comment_id))
+                    else:
+                        await PRAgent().handle_request(url, body)
 
 
 if __name__ == '__main__':
-    asyncio.run(run_action())
+    asyncio.run(run_action())

pr_agent/servers/github_app.py

@@ -1,9 +1,7 @@
 import copy
-import logging
-import sys
 import os
-import time
-from typing import Any, Dict
+import asyncio.locks
+from typing import Any, Dict, List, Tuple
 
 import uvicorn
 from fastapi import APIRouter, FastAPI, HTTPException, Request, Response
@@ -15,9 +13,13 @@ 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.servers.utils import verify_signature
+from pr_agent.git_providers.utils import apply_repo_settings
+from pr_agent.git_providers.git_provider import IncrementalPR
+from pr_agent.log import LoggingFormat, get_logger, setup_logger
+from pr_agent.servers.utils import verify_signature, DefaultDictWithTimeout
+
+setup_logger(fmt=LoggingFormat.JSON)
 
-logging.basicConfig(stream=sys.stdout, level=logging.INFO)
 router = APIRouter()
 
 
@@ -28,11 +30,11 @@ 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 +46,14 @@ 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:
@@ -60,7 +63,9 @@ async def get_body(request):
     return body
 
 
-_duplicate_requests_cache = {}
+_duplicate_requests_cache = DefaultDictWithTimeout(ttl=get_settings().github_app.duplicate_requests_cache_ttl)
+_duplicate_push_triggers = DefaultDictWithTimeout(ttl=get_settings().github_app.push_trigger_pending_tasks_ttl)
+_pending_task_duplicate_push_conditions = DefaultDictWithTimeout(asyncio.locks.Condition, ttl=get_settings().github_app.push_trigger_pending_tasks_ttl)
 
 
 async def handle_request(body: Dict[str, Any], event: str):
@@ -76,8 +81,8 @@ 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 {}
@@ -87,71 +92,143 @@ 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(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,
     #   as well as direct review requests from the bot
-    elif event == 'pull_request':
-        pull_request = body.get("pull_request")
-        if not pull_request:
-            return {}
-        api_url = pull_request.get("url")
-        if not api_url:
-            return {}
-        if pull_request.get("draft", True) or pull_request.get("state") != "open" or pull_request.get("user", {}).get("login", "") == bot_user:
+    elif event == 'pull_request' and action != 'synchronize':
+        pull_request, api_url = _check_pull_request_event(action, body, log_context, bot_user)
+        if not (pull_request and api_url):
             return {}
         if action in get_settings().github_app.handle_pr_actions:
             if action == "review_requested":
                 if body.get("requested_reviewer", {}).get("login", "") != bot_user:
                     return {}
-                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}")
-            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(f"Performing command: {new_command}")
-                await agent.handle_request(api_url, new_command)
+            get_logger().info(f"Performing review for {api_url=} because of {event=} and {action=}")
+            await _perform_commands("pr_commands", agent, body, api_url, log_context)
 
-    logging.info("event or action does not require handling")
+    # handle pull_request event with synchronize action - "push trigger" for new commits
+    elif event == 'pull_request' and action == 'synchronize' and get_settings().github_app.handle_push_trigger:
+        pull_request, api_url = _check_pull_request_event(action, body, log_context, bot_user)
+        if not (pull_request and api_url):
+            return {}
+
+        # TODO: do we still want to get the list of commits to filter bot/merge commits?
+        before_sha = body.get("before")
+        after_sha = body.get("after")
+        merge_commit_sha = pull_request.get("merge_commit_sha")
+        if before_sha == after_sha:
+            return {}
+        if get_settings().github_app.push_trigger_ignore_merge_commits and after_sha == merge_commit_sha:
+            return {}
+        if get_settings().github_app.push_trigger_ignore_bot_commits and body.get("sender", {}).get("login", "") == bot_user:
+            return {}
+
+        # Prevent triggering multiple times for subsequent push triggers when one is enough:
+        # The first push will trigger the processing, and if there's a second push in the meanwhile it will wait.
+        # Any more events will be discarded, because they will all trigger the exact same processing on the PR.
+        # We let the second event wait instead of discarding it because while the first event was being processed,
+        # more commits may have been pushed that led to the subsequent events,
+        # so we keep just one waiting as a delegate to trigger the processing for the new commits when done waiting.
+        current_active_tasks = _duplicate_push_triggers.setdefault(api_url, 0)
+        max_active_tasks = 2 if get_settings().github_app.push_trigger_pending_tasks_backlog else 1
+        if current_active_tasks < max_active_tasks:
+            # first task can enter, and second tasks too if backlog is enabled
+            get_logger().info(
+                f"Continue processing push trigger for {api_url=} because there are {current_active_tasks} active tasks"
+            )
+            _duplicate_push_triggers[api_url] += 1
+        else:
+            get_logger().info(
+                f"Skipping push trigger for {api_url=} because another event already triggered the same processing"
+            )
+            return {}
+        async with _pending_task_duplicate_push_conditions[api_url]:
+            if current_active_tasks == 1:
+                # second task waits
+                get_logger().info(
+                    f"Waiting to process push trigger for {api_url=} because the first task is still in progress"
+                )
+                await _pending_task_duplicate_push_conditions[api_url].wait()
+                get_logger().info(f"Finished waiting to process push trigger for {api_url=} - continue with flow")
+
+        try:
+            if get_settings().github_app.push_trigger_wait_for_initial_review and not get_git_provider()(api_url, incremental=IncrementalPR(True)).previous_review:
+                get_logger().info(f"Skipping incremental review because there was no initial review for {api_url=} yet")
+                return {}
+            get_logger().info(f"Performing incremental review for {api_url=} because of {event=} and {action=}")
+            await _perform_commands("push_commands", agent, body, api_url, log_context)
+
+        finally:
+            # release the waiting task block
+            async with _pending_task_duplicate_push_conditions[api_url]:
+                _pending_task_duplicate_push_conditions[api_url].notify(1)
+                _duplicate_push_triggers[api_url] -= 1
+
+    get_logger().info("event or action does not require handling")
     return {}
 
 
+def _check_pull_request_event(action: str, body: dict, log_context: dict, bot_user: str) -> Tuple[Dict[str, Any], str]:
+    invalid_result = {}, ""
+    pull_request = body.get("pull_request")
+    if not pull_request:
+        return invalid_result
+    api_url = pull_request.get("url")
+    if not api_url:
+        return invalid_result
+    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 invalid_result
+    if action in ("review_requested", "synchronize") and pull_request.get("created_at") == pull_request.get("updated_at"):
+        # avoid double reviews when opening a PR for the first time
+        return invalid_result
+    return pull_request, api_url
+
+
+async def _perform_commands(commands_conf: str, agent: PRAgent, body: dict, api_url: str, log_context: dict):
+    apply_repo_settings(api_url)
+    commands = get_settings().get(f"github_app.{commands_conf}")
+    for command in 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)
+        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)
+
+
 def _is_duplicate_request(body: Dict[str, Any]) -> bool:
     """
     In some deployments its possible to get duplicate requests if the handling is long,
     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}")
-    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]
-    for key in to_delete:
-        del _duplicate_requests_cache[key]
-    is_duplicate = request_hash in _duplicate_requests_cache
-    _duplicate_requests_cache[request_hash] = request_time
+    get_logger().info(f"request_hash: {request_hash}")
+    is_duplicate = _duplicate_requests_cache.get(request_hash, False)
+    _duplicate_requests_cache[request_hash] = True
     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

@@ -1,43 +1,84 @@
-import logging
+import copy
+import json
 
 import uvicorn
 from fastapi import APIRouter, FastAPI, Request, status
 from fastapi.encoders import jsonable_encoder
 from fastapi.responses import JSONResponse
 from starlette.background import BackgroundTasks
+from starlette.middleware import Middleware
+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 get_settings
+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
 
-app = FastAPI()
+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.get("token_name", secret_dict.get("id", "unknown"))
+            context["settings"] = copy.deepcopy(global_settings)
+            context["settings"].gitlab.personal_access_token = gitlab_token
+        except Exception as e:
+            get_logger().error(f"Failed to validate secret {request_token}: {e}")
+            return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
+    elif get_settings().get("GITLAB.SHARED_SECRET"):
+        secret = get_settings().get("GITLAB.SHARED_SECRET")
+        if not request.headers.get("X-Gitlab-Token") == secret:
+            return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
+    else:
+        return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
+    gitlab_token = get_settings().get("GITLAB.PERSONAL_ACCESS_TOKEN", None)
+    if not gitlab_token:
+        return JSONResponse(status_code=status.HTTP_401_UNAUTHORIZED, content=jsonable_encoder({"message": "unauthorized"}))
     data = await request.json()
+    get_logger().info(json.dumps(data))
     if data.get('object_kind') == 'merge_request' and data['object_attributes'].get('action') in ['open', 'reopen']:
-        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", log_context)
     elif data.get('object_kind') == 'note' and data['event_type'] == 'note':
         if 'merge_request' in data:
             mr = data['merge_request']
             url = mr.get('url')
             body = data.get('object_attributes', {}).get('note')
-            background_tasks.add_task(PRAgent().handle_request, url, body)
+            handle_request(background_tasks, url, body, log_context)
     return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
 
+
+@router.get("/")
+async def root():
+    return {"status": "ok"}
+
 def start():
     gitlab_url = get_settings().get("GITLAB.URL", None)
     if not gitlab_url:
         raise ValueError("GITLAB.URL is not set")
-    gitlab_token = get_settings().get("GITLAB.PERSONAL_ACCESS_TOKEN", None)
-    if not gitlab_token:
-        raise ValueError("GITLAB.PERSONAL_ACCESS_TOKEN is not set")
     get_settings().config.git_provider = "gitlab"
-
-    app = FastAPI()
+    middleware = [Middleware(RawContextMiddleware)]
+    app = FastAPI(middleware=middleware)
     app.include_router(router)
 
     uvicorn.run(app, host="0.0.0.0", port=3000)

pr_agent/servers/help.py

@@ -1,17 +1,19 @@
-commands_text = "> **/review [-i]**: Request a review of your Pull Request. For an incremental review, which only " \
-                "considers changes since the last review, include the '-i' option.\n" \
-                "> **/describe**: Modify the PR title and description based on the contents of the PR.\n" \
-                "> **/improve [--extended]**: Suggest improvements to the code in the PR. Extended mode employs several calls, and provides a more thorough feedback. \n" \
-                "> **/ask \\<QUESTION\\>**: Pose a question about the PR.\n" \
-                "> **/update_changelog**: Update the changelog based on the PR's contents.\n\n" \
-                ">To edit any configuration parameter from **configuration.toml**, add --config_path=new_value\n" \
-                ">For example: /review --pr_reviewer.extra_instructions=\"focus on the file: ...\" \n" \
-                ">To list the possible configuration parameters, use the **/config** command.\n" \
+commands_text = "> **/review**: Request a review of your Pull Request.   \n" \
+                "> **/describe**: Update the PR title and description based on the contents of the PR.   \n" \
+                "> **/improve [--extended]**: Suggest code improvements. Extended mode provides a higher quality feedback.   \n" \
+                "> **/ask \\<QUESTION\\>**: Ask a question about the PR.   \n" \
+                "> **/update_changelog**: Update the changelog based on the PR's contents.   \n" \
+                "> **/add_docs**: Generate docstring for new components introduced in the PR.   \n" \
+                "> **/generate_labels**: Generate labels for the PR based on the PR's contents.   \n" \
+                "> see the [tools guide](https://github.com/Codium-ai/pr-agent/blob/main/docs/TOOLS_GUIDE.md) for more details.\n\n" \
+                ">To edit any configuration parameter from the [configuration.toml](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml), add --config_path=new_value.  \n" \
+                ">For example: /review --pr_reviewer.extra_instructions=\"focus on the file: ...\"    \n" \
+                ">To list the possible configuration parameters, add a **/config** comment.   \n" \
 
 
 def bot_help_text(user: str):
-    return f"> Tag me in a comment '@{user}' and add one of the following commands:\n" + commands_text
+    return f"> Tag me in a comment '@{user}' and add one of the following commands:  \n" + commands_text
 
 
-actions_help_text = "> To invoke the PR-Agent, add a comment using one of the following commands:\n" + \
+actions_help_text = "> To invoke the PR-Agent, add a comment using one of the following commands:  \n" + \
                     commands_text

pr_agent/servers/serverless.py

@@ -1,14 +1,13 @@
-import logging
-
 from fastapi import FastAPI
 from mangum import Mangum
+from starlette.middleware import Middleware
+from starlette_context.middleware import RawContextMiddleware
 
 from pr_agent.servers.github_app import router
 
-logger = logging.getLogger()
-logger.setLevel(logging.DEBUG)
 
-app = FastAPI()
+middleware = [Middleware(RawContextMiddleware)]
+app = FastAPI(middleware=middleware)
 app.include_router(router)
 
 handler = Mangum(app, lifespan="off")

pr_agent/servers/utils.py

@@ -1,5 +1,8 @@
 import hashlib
 import hmac
+import time
+from collections import defaultdict
+from typing import Callable, Any
 
 from fastapi import HTTPException
 
@@ -25,3 +28,59 @@ def verify_signature(payload_body, secret_token, signature_header):
 class RateLimitExceeded(Exception):
     """Raised when the git provider API rate limit has been exceeded."""
     pass
+
+
+class DefaultDictWithTimeout(defaultdict):
+    """A defaultdict with a time-to-live (TTL)."""
+
+    def __init__(
+        self,
+        default_factory: Callable[[], Any] = None,
+        ttl: int = None,
+        refresh_interval: int = 60,
+        update_key_time_on_get: bool = True,
+        *args,
+        **kwargs,
+    ):
+        """
+        Args:
+            default_factory: The default factory to use for keys that are not in the dictionary.
+            ttl: The time-to-live (TTL) in seconds.
+            refresh_interval: How often to refresh the dict and delete items older than the TTL.
+            update_key_time_on_get: Whether to update the access time of a key also on get (or only when set).
+        """
+        super().__init__(default_factory, *args, **kwargs)
+        self.__key_times = dict()
+        self.__ttl = ttl
+        self.__refresh_interval = refresh_interval
+        self.__update_key_time_on_get = update_key_time_on_get
+        self.__last_refresh = self.__time() - self.__refresh_interval
+
+    @staticmethod
+    def __time():
+        return time.monotonic()
+
+    def __refresh(self):
+        if self.__ttl is None:
+            return
+        request_time = self.__time()
+        if request_time - self.__last_refresh > self.__refresh_interval:
+            return
+        to_delete = [key for key, key_time in self.__key_times.items() if request_time - key_time > self.__ttl]
+        for key in to_delete:
+            del self[key]
+        self.__last_refresh = request_time
+
+    def __getitem__(self, __key):
+        if self.__update_key_time_on_get:
+            self.__key_times[__key] = self.__time()
+        self.__refresh()
+        return super().__getitem__(__key)
+
+    def __setitem__(self, __key, __value):
+        self.__key_times[__key] = self.__time()
+        return super().__setitem__(__key, __value)
+
+    def __delitem__(self, __key):
+        del self.__key_times[__key]
+        return super().__delitem__(__key)

pr_agent/settings/.secrets_template.toml

@@ -16,6 +16,10 @@ key = ""  # Acquire through https://platform.openai.com
 #deployment_id = ""  # The deployment name you chose when you deployed the engine
 #fallback_deployments = []  # For each fallback model specified in configuration.toml in the [config] section, specify the appropriate deployment_id
 
+[pinecone]
+api_key = "..."
+environment = "gcp-starter"
+
 [anthropic]
 key = "" # Optional, uncomment if you want to use Anthropic. Acquire through https://www.anthropic.com/
 
@@ -24,6 +28,21 @@ key = "" # Optional, uncomment if you want to use Cohere. Acquire through https:
 
 [replicate]
 key = "" # Optional, uncomment if you want to use Replicate. Acquire through https://replicate.com/
+
+[huggingface]
+key = "" # Optional, uncomment if you want to use Huggingface Inference API. Acquire through https://huggingface.co/docs/api-inference/quicktour
+api_base = "" # the base url for your huggingface inference endpoint 
+
+[ollama]
+api_base = "" # the base url for your local Llama 2, Code Llama, and other models inference endpoint. Acquire through https://ollama.ai/
+
+[vertexai]
+vertex_project = "" # the google cloud platform project name for your vertexai deployment
+vertex_location = "" # the google cloud platform location for your vertexai deployment
+
+[aws]
+bedrock_region = "" # the AWS region to call Bedrock APIs
+
 [github]
 # ---- Set the following only for deployment type == "user"
 user_token = ""  # A GitHub personal access token with 'repo' scope.
@@ -43,5 +62,12 @@ webhook_secret = "<WEBHOOK SECRET>"  # Optional, may be commented out.
 personal_access_token = ""
 
 [bitbucket]
-# Bitbucket personal bearer token
+# For Bitbucket personal/repository bearer token
 bearer_token = ""
+
+# For Bitbucket app
+app_key = ""
+base_url = ""
+
+[litellm]
+LITELLM_TOKEN = "" # see https://docs.litellm.ai/docs/debugging/hosted_debugging for details and instructions on how to get a token

pr_agent/settings/configuration.toml

@@ -1,5 +1,5 @@
 [config]
-model="gpt-4"
+model="gpt-4" # "gpt-4-1106-preview"
 fallback_models=["gpt-3.5-turbo-16k"]
 git_provider="github"
 publish_output=true
@@ -10,30 +10,58 @@ use_repo_settings_file=true
 ai_timeout=180
 max_description_tokens = 500
 max_commits_tokens = 500
-litellm_debugger=false
+max_model_tokens = 32000 # Limits the maximum number of tokens that can be used by any model, regardless of the model's default capabilities.
+patch_extra_lines = 3
 secret_provider="google_cloud_storage"
+cli_mode=false
 
 [pr_reviewer] # /review #
+# enable/disable features
 require_focused_review=false
 require_score_review=false
 require_tests_review=true
 require_security_review=true
+require_estimate_effort_to_review=true
+# general options
 num_code_suggestions=4
 inline_code_comments = false
 ask_and_reflect=false
 automatic_review=true
+remove_previous_review_comment=false
+persistent_comment=true
 extra_instructions = ""
+# review labels
+enable_review_labels_security=true
+enable_review_labels_effort=false
+# specific configurations for incremental review (/review -i)
+require_all_thresholds_for_incremental_review=false
+minimal_commits_for_incremental_review=0
+minimal_minutes_for_incremental_review=0
 
 [pr_description] # /describe #
+publish_labels=true
 publish_description_as_comment=false
 add_original_user_description=false
 keep_original_user_title=false
+use_bullet_points=true
 extra_instructions = ""
+enable_pr_type=true
+enable_file_walkthrough=false
+enable_semantic_files_types=true
+final_update_message = true
+
+
+# markers
+use_description_markers=false
+include_generated_by_header=true
+
+#custom_labels = ['Bug fix', 'Tests', 'Bug fix with tests', 'Enhancement', 'Documentation', 'Other']
 
 [pr_questions] # /ask #
 
 [pr_code_suggestions] # /improve #
 num_code_suggestions=4
+summarize = false
 extra_instructions = ""
 rank_suggestions = false
 # params for '/improve --extended' mode
@@ -42,6 +70,10 @@ 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 = ""
@@ -52,6 +84,12 @@ extra_instructions = ""
 # The type of deployment to create. Valid values are 'app' or 'user'.
 deployment_type = "user"
 ratelimit_retries = 5
+base_url = "https://api.github.com"
+
+[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
@@ -67,6 +105,30 @@ pr_commands = [
     "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
     "/auto_review",
 ]
+# settings for "pull_request" event with "synchronize" action - used to detect and handle push triggers for new commits
+handle_push_trigger = false
+push_trigger_ignore_bot_commits = true
+push_trigger_ignore_merge_commits = true
+push_trigger_wait_for_initial_review = true
+push_trigger_pending_tasks_backlog = true
+push_trigger_pending_tasks_ttl = 300
+push_commands = [
+    "/describe --pr_description.add_original_user_description=true --pr_description.keep_original_user_title=true",
+    """/auto_review -i \
+       --pr_reviewer.require_focused_review=false \
+       --pr_reviewer.require_score_review=false \
+       --pr_reviewer.require_tests_review=false \
+       --pr_reviewer.require_security_review=false \
+       --pr_reviewer.require_estimate_effort_to_review=false \
+       --pr_reviewer.num_code_suggestions=0 \
+       --pr_reviewer.inline_code_comments=false \
+       --pr_reviewer.remove_previous_review_comment=true \
+       --pr_reviewer.require_all_thresholds_for_incremental_review=false \
+       --pr_reviewer.minimal_commits_for_incremental_review=5 \
+       --pr_reviewer.minimal_minutes_for_incremental_review=30 \
+       --pr_reviewer.extra_instructions='' \
+    """
+]
 
 [gitlab]
 # URL to the gitlab service
@@ -84,4 +146,27 @@ polling_interval_seconds = 30
 [local]
 # LocalGitProvider settings - uncomment to use paths other than default
 # description_path= "path/to/description.md"
-# review_path= "path/to/review.md"
+# review_path= "path/to/review.md"
+
+[gerrit]
+# endpoint to the gerrit service
+# url = "ssh://gerrit.example.com:29418"
+# user for gerrit authentication
+# user = "ai-reviewer"
+# patch server where patches will be saved
+# patch_server_endpoint = "http://127.0.0.1:5000/patch"
+# token to authenticate in the patch server
+# patch_server_token = ""
+
+[litellm]
+#use_client = false
+
+[pr_similar_issue]
+skip_comments = false
+force_update_dataset = false
+max_issues_to_scan = 500
+
+[pinecone]
+# fill and place in .secrets.toml
+#api_key = ...
+# environment = "gcp-starter"

pr_agent/settings/custom_labels.toml

@@ -0,0 +1,16 @@
+[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."Enhancement"]
+#description = """Adds new features or modifies existing ones"""
+#[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 +1,126 @@
+[pr_add_docs_prompt]
+system="""You are PR-Doc, a language model that specializes in generating documentation for code components in a Pull Request (PR).
+Your task is to generate {{ docs_for_language }} for code components in the PR Diff.
+
+
+Example for the PR Diff format:
+======
+## src/file1.py
+
+@@ -12,3 +12,4 @@ def func1():
+__new hunk__
+12  code line1 that remained unchanged in the PR
+14 +new code line1 added in the PR
+15 +new code line2 added in the PR
+16  code line2 that remained unchanged in the PR
+__old hunk__
+ code line1 that remained unchanged in the PR
+-code line that was removed in the PR
+ code line2 that remained unchanged in the PR
+
+
+@@ ... @@ 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 }}'
+
+{%- if description %}
+
+Description:
+======
+{{ description|trim }}
+======
+{%- endif %}
+
+{%- if language %}
+
+Main PR 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

@@ -1,22 +1,21 @@
 [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.
+system="""You are PR-Reviewer, a language model that specializes in suggesting code improvements for a Pull Request (PR).
+Your task is to provide meaningful and actionable code suggestions, to improve the new code presented in a PR diff (lines starting with '+').
 
-Example for a PR Diff input:
-'
+Example for the PR Diff format:
+======
 ## src/file1.py
 
-@@ -12,3 +12,5 @@ def func1():
+@@ -12,3 +12,4 @@ def func1():
 __new hunk__
-12  code line that already existed in the file...
-13  code line that already existed in the file....
+12  code line1 that remained unchanged in the PR
 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...
+16  code line2 that remained unchanged in the PR
 __old hunk__
- code line that already existed in the file...
+ code line1 that remained unchanged in the PR
 -code line that was removed in the PR
- code line that already existed in the file...
+ code line2 that remained unchanged in the PR
 
 
 @@ ... @@ def func2():
@@ -28,27 +27,29 @@ __old hunk__
 
 ## src/file2.py
 ...
-'
+======
+
 
 Specific instructions:
-- Provide up to {{ num_code_suggestions }} code 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.
+- 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, 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.
-- Provide the exact line numbers range (inclusive) for each issue.
+- 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 suggestion.
 - Assume there is additional relevant code, that is not included in the diff.
 
 
 {%- if extra_instructions %}
 
 Extra instructions from the user:
+======
 {{ extra_instructions }}
+======
 {%- endif %}
 
+
 You must use the following YAML schema to format your answer:
 ```yaml
 Code suggestions:
@@ -68,12 +69,17 @@ Code suggestions:
       type: string
       description: |-
         a code snippet showing the relevant code lines from a '__new hunk__' section.
-        It must be continuous, correctly formatted and indented, and without line numbers.
-    relevant lines:
-      type: string
+        It must be contiguous, correctly formatted and indented, and without line numbers.
+    relevant lines start:
+      type: integer
       description: |-
-        the relevant lines from a '__new hunk__' section, in the format of 'start_line-end_line'.
-        For example: '10-15'. They should be derived from the hunk line numbers, and correspond to the 'existing code' snippet above.
+        The relevant line number from a '__new hunk__' section where the suggestion starts (inclusive).
+        Should be derived from the hunk line numbers, and correspond to the 'existing code' snippet above.
+    relevant lines end:
+      type: integer
+      description: |-
+        The relevant line number from a '__new hunk__' section where the suggestion ends (inclusive).
+        Should be derived from the hunk line numbers, and correspond to the 'existing code' snippet above.
     improved code:
       type: string
       description: |-
@@ -84,15 +90,19 @@ Code suggestions:
 Example output:
 ```yaml
 Code suggestions:
-  - relevant file: |-
-        src/file1.py
-    suggestion content: |-
-        Add a docstring to func1()
-    existing code: |-
-        def func1():
-    relevant lines: '12-12'
-    improved code: |-
-        ...
+- relevant file: |-
+    src/file1.py
+  suggestion content: |-
+    Add a docstring to func1()
+  existing code: |-
+    def func1():
+  relevant lines start: |-
+    12
+  relevant lines end: |-
+    12
+  improved code: |-
+    ...
+...
 ```
 
 
@@ -106,18 +116,25 @@ Title: '{{title}}'
 
 Branch: '{{branch}}'
 
-Description: '{{description}}'
+{%- if description %}
+
+Description:
+======
+{{ description|trim }}
+======
+{%- endif %}
 
 {%- if language %}
 
-Main language: {{language}}
+Main PR language: '{{ language }}'
 {%- endif %}
 
 
 The PR Diff:
-```
-{{- diff|trim }}
-```
+======
+{{ diff|trim }}
+======
+
 
 Response (should be a valid YAML, and nothing else):
 ```yaml

pr_agent/settings/pr_custom_labels.toml

@@ -0,0 +1,86 @@
+[pr_custom_labels_prompt]
+system="""You are PR-Reviewer, a language model designed to review a Git Pull Request (PR).
+Your task is to provide labels that describe the PR content.
+{%- if enable_custom_labels %}
+Thoroughly read the labels name and the provided description, and decide whether the label is relevant to the PR.
+{%- endif %}
+
+{%- if extra_instructions %}
+
+Extra instructions from the user:
+======
+{{ extra_instructions }}
+======
+{% endif %}
+
+
+The output must be a YAML object equivalent to type $Labels, according to the following Pydantic definitions:
+======
+{%- if enable_custom_labels %}
+
+{{ custom_labels_class }}
+
+{%- else %}
+class Label(str, Enum):
+    bug_fix = "Bug fix"
+    tests = "Tests"
+    enhancement = "Enhancement"
+    documentation = "Documentation"
+    other = "Other"
+{%- endif %}
+
+class Labels(BaseModel):
+    labels: List[Label] = Field(min_items=0, description="custom labels that describe the PR. Return the label value, not the name.")
+======
+
+
+Example output:
+
+```yaml
+labels:
+- ...
+- ...
+```
+
+Answer should be a valid YAML, and nothing else.
+"""
+
+user="""PR Info:
+
+Previous title: '{{title}}'
+
+Branch: '{{ branch }}'
+
+{%- if description %}
+
+Description:
+======
+{{ description|trim }}
+======
+{%- endif %}
+
+{%- if language %}
+
+Main PR language: '{{ language }}'
+{%- endif %}
+{%- if commit_messages_str %}
+
+
+Commit messages:
+======
+{{ commit_messages_str|trim }}
+======
+{%- endif %}
+
+
+The PR Git Diff:
+======
+{{ diff|trim }}
+======
+
+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

@@ -1,86 +1,133 @@
 [pr_description_prompt]
-system="""You are CodiumAI-PR-Reviewer, a language model designed to review git pull requests.
-Your task is to provide full description of the PR content.
-- Make sure not to focus the new PR code (the '+' lines).
-- Notice that the 'Previous title', 'Previous description' and 'Commit messages' sections may be partial, simplistic, non-informative or not up-to-date. Hence, compare them to the PR diff code, and use them only as a reference.
--  If needed, each YAML output should be in block scalar format ('|-')
+system="""You are PR-Reviewer, a language model designed to review a Git Pull Request (PR).
+Your task is to provide a full description for the PR content - title, type, description, and main files walkthrough.
+- Focus on the new PR code (lines starting with '+').
+- Keep in mind that the 'Previous title', 'Previous description' and 'Commit messages' sections may be partial, simplistic, non-informative or out of date. Hence, compare them to the PR diff code, and use them only as a reference.
+- The generated title and description should prioritize the most significant changes.
+- If needed, each YAML output should be in block scalar indicator ('|-')
+
 {%- if extra_instructions %}
 
 Extra instructions from the user:
+=====
 {{ extra_instructions }}
+=====
 {% endif %}
 
-You must use the following YAML schema to format your answer:
-```yaml
-PR Title:
-  type: string
-  description: an informative title for the PR, describing its main theme
-PR Type:
-  type: array
-  items:
-    type: string
-    enum:
-      - Bug fix
-      - Tests
-      - Bug fix with tests
-      - Refactoring
-      - Enhancement
-      - Documentation
-      - Other
-PR Description:
-  type: string
-  description: an informative and concise description of the PR
-PR Main Files Walkthrough:
-  type: array
-  maxItems: 10
-  description: |-
-    a walkthrough of the PR changes. Review main files, and shortly describe the changes in each file (up to 10 most important files).
-  items:
-    filename:
-      type: string
-      description: the relevant file full path
-    changes in file:
-      type: string
-      description: minimal and concise description of the changes in the relevant file
+
+The output must be a YAML object equivalent to type $PRDescription, according to the following Pydantic definitions:
+=====
+class PRType(str, Enum):
+    bug_fix = "Bug fix"
+    tests = "Tests"
+    enhancement = "Enhancement"
+    documentation = "Documentation"
+    other = "Other"
+
+{%- if enable_custom_labels %}
+
+{{ custom_labels_class }}
+
+{%- endif %}
+
+{%- if enable_file_walkthrough %}
+class FileWalkthrough(BaseModel):
+    filename: str = Field(description="the relevant file full path")
+    changes_in_file: str = Field(description="minimal and concise summary of the changes in the relevant file")
+{%- endif %}
+
+{%- if enable_semantic_files_types %}
+Class FileDescription(BaseModel):
+    filename: str = Field(description="the relevant file full path")
+    changes_summary: str = Field(description="minimal and concise summary of the changes in the relevant file")
+    label: str = Field(description="a single semantic label that represents a type of code changes that occurred in the File. Possible values (partial list): 'bug fix', 'tests', 'enhancement', 'documentation', 'error handling', 'configuration changes', 'dependencies', 'formatting', 'miscellaneous', ...")
+{%- endif %}
+
+Class PRDescription(BaseModel):
+    title: str = Field(description="an informative title for the PR, describing its main theme")
+    type: List[PRType] = Field(description="one or more types that describe the PR type. Return the label value, not the name.")
+    description: str = Field(description="an informative and concise description of the PR. {%- if use_bullet_points %} Use bullet points.{% endif %}")
+{%- if enable_custom_labels %}
+    labels: List[Label] = Field(min_items=0, description="custom labels that describe the PR. Return the label value, not the name.")
+{%- endif %}
+{%- if enable_file_walkthrough %}
+    main_files_walkthrough: List[FileWalkthrough] = Field(max_items=10)
+{%- endif %}
+{%- if enable_semantic_files_types %}
+    pr_files[List[FileDescription]] = Field(max_items=15")
+{%- endif %}
+=====
 
 
 Example output:
+
 ```yaml
-PR Title: |-
+title: |-
   ...
-PR Type:
-  - Bug fix
-PR Description: |-
+type:
+- ...
+- ...
+{%- if enable_custom_labels %}
+labels:
+- ...
+- ...
+{%- endif %}
+description: |-
   ...
-PR Main Files Walkthrough:
-  - ...
-  - ...
+{%- if enable_file_walkthrough %}
+main_files_walkthrough:
+- ...
+- ...
+{%- endif %}
+{%- if enable_semantic_files_types %}
+pr_files:
+- filename: |
+    ...
+  changes_summary: |
+    ...
+  label: |
+    ...
+...
+{%- endif %}
 ```
 
-Make sure to output a valid YAML. Don't repeat the prompt in the answer, and avoid outputting the 'type' and 'description' fields.
+Answer should be a valid YAML, and nothing else. Each YAML output MUST be after a newline, with proper indent, and block scalar indicator ('|-')
 """
 
 user="""PR Info:
+
 Previous title: '{{title}}'
-Previous description: '{{description}}'
+
+{%- if description %}
+
+Previous description:
+=====
+{{ description|trim }}
+=====
+{%- endif %}
+
 Branch: '{{branch}}'
 {%- if language %}
 
-Main language: {{language}}
+Main PR language: '{{ language }}'
 {%- endif %}
 {%- if commit_messages_str %}
 
 Commit messages:
-{{commit_messages_str}}
+=====
+{{ commit_messages_str|trim }}
+=====
 {%- endif %}
 
 
-The PR Git Diff:
-```
-{{diff}}
-```
+The PR Diff:
+=====
+{{ diff|trim }}
+=====
+
 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_information_from_user_prompts.toml

@@ -1,5 +1,5 @@
 [pr_information_from_user_prompt]
-system="""You are CodiumAI-PR-Reviewer, a language model designed to review git pull requests.
+system="""You are PR-Reviewer, a language model designed to review a Git Pull Request (PR).
 Given the PR Info and the PR Git Diff, generate 3 short questions about the PR code for the PR author.
 The goal of the questions is to help the language model understand the PR better, so the questions should be insightful, informative, non-trivial, and relevant to the PR.
 You should prefer asking yes\\no questions, or multiple choice questions. Also add at least one open-ended question, but make sure they are not too difficult, and can be answered in a sentence or two.
@@ -16,22 +16,36 @@ Questions to better understand the PR:
 
 user="""PR Info:
 Title: '{{title}}'
+
 Branch: '{{branch}}'
-Description: '{{description}}'
+
+{%- if description %}
+
+Description:
+======
+{{ description|trim }}
+======
+{%- endif %}
+
 {%- if language %}
-Main language: {{language}}
+
+Main PR language: '{{ language }}'
 {%- endif %}
 {%- if commit_messages_str %}
 
+
 Commit messages:
-{{commit_messages_str}}
+======
+{{ commit_messages_str|trim }}
+======
 {%- endif %}
 
 
 The PR Git Diff:
-```
-{{diff}}
-```
+======
+{{ diff|trim }}
+======
+
 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
 
 

pr_agent/settings/pr_questions_prompts.toml

@@ -1,36 +1,42 @@
 [pr_questions_prompt]
-system="""You are CodiumAI-PR-Reviewer, a language model designed to review git pull requests.
-Your task is to answer questions about the new PR code (the '+' lines), and provide feedback.
+system="""You are PR-Reviewer, a language model designed to review a Git Pull Request (PR).
+
+Your goal is to answer questions\\tasks about the new PR code (lines starting with '+'), and provide feedback.
 Be informative, constructive, and give examples. Try to be as specific as possible.
-Don't avoid answering the questions. You must answer the questions, as best as you can, without adding unrelated content.
-Make sure not to repeat modifications already implemented in the new PR code (the '+' lines).
+Don't avoid answering the questions. You must answer the questions, as best as you can, without adding any unrelated content.
 """
 
 user="""PR Info:
-Title: '{{title}}'
-Branch: '{{branch}}'
-Description: '{{description}}'
-{%- if language %}
-Main language: {{language}}
-{%- endif %}
-{%- if commit_messages_str %}
 
-Commit messages:
-{{commit_messages_str}}
+Title: '{{title}}'
+
+Branch: '{{branch}}'
+
+{%- if description %}
+
+Description:
+======
+{{ description|trim }}
+======
+{%- endif %}
+
+{%- if language %}
+
+Main PR language: '{{ language }}'
 {%- endif %}
 
 
 The PR Git Diff:
-```
-{{diff}}
-```
+======
+{{ diff|trim }}
+======
 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
 
 
 The PR Questions:
-```
-{{ questions }}
-```
+======
+{{ questions|trim }}
+======
 
-Response:
+Response to the PR Questions:
 """

pr_agent/settings/pr_reviewer_prompts.toml

@@ -1,18 +1,19 @@
 [pr_review_prompt]
-system="""You are PR-Reviewer, a language model designed to review git pull requests.
+system="""You are PR-Reviewer, a language model designed to review a Git Pull Request (PR).
 Your task is to provide constructive and concise feedback for the PR, and also provide meaningful code suggestions.
+The review should focus on new code added in the PR diff (lines starting with '+')
 
-Example PR Diff input:
-'
+Example PR Diff:
+======
 ## src/file1.py
 
 @@ -12,5 +12,5 @@ def func1():
-code line that already existed in the file...
-code line that already existed in the file....
+code line 1 that remained unchanged in the PR
+code line 2 that remained unchanged in the PR
 -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 added in the PR
+code line 3 that remained unchanged in the PR
+
 
 @@ ... @@ def func2():
 ...
@@ -20,24 +21,28 @@ code line that already existed in the file....
 
 ## src/file2.py
 ...
-'
-
-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).
+======
 
 {%- if num_code_suggestions > 0 %}
-- Provide up to {{ num_code_suggestions }} code suggestions.
+
+
+Code suggestions guidelines:
+- 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.
-- Suggestions should focus on improving the new code added in the PR (lines starting with '+')
+- Don't suggest to add docstring, type hints, or comments.
+- Suggestions should focus on the new code added in the PR diff (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:
 ```yaml
 PR Analysis:
@@ -52,7 +57,6 @@ PR Analysis:
     enum:
       - Bug fix
       - Tests
-      - Refactoring
       - Enhancement
       - Documentation
       - Other
@@ -85,14 +89,22 @@ PR Analysis:
       code diff changes are too scattered, then the PR is not focused. Explain
       your answer shortly.
 {%- endif %}
+{%- if require_estimate_effort_to_review %}
+  Estimated effort to review [1-5]:
+    type: string
+    description: >-
+      Estimate, on a scale of 1-5 (inclusive), the time and effort required to review this PR by an experienced and knowledgeable developer. 1 means short and easy review , 5 means long and hard review.
+      Take into account the size, complexity, quality, and the needed changes of the PR code diff.
+      Explain your answer shortly (1-2 sentences). Use the format: '1, because ...'
+{%- endif %}
 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
@@ -105,11 +117,10 @@ 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: |-
@@ -121,8 +132,8 @@ 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
+      does this PR code introduce possible vulnerabilities such as exposure of sensitive information (e.g., API keys, secrets, passwords), or security concerns like SQL injection, XSS, CSRF, and others ? Answer 'No' if there are no possible issues.
+      Answer 'Yes, because ...' if there are security concerns or issues. Explain your answer shortly.
 {%- endif %}
 ```
 
@@ -134,7 +145,7 @@ PR Analysis:
   PR summary: |-
     xxx
   Type of PR: |-
-    Bug fix
+    ...
 {%- if require_score %}
   Score: 89
 {%- endif %}
@@ -143,6 +154,10 @@ 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: |-
     ...
@@ -166,34 +181,50 @@ Don't repeat the prompt in the answer, and avoid outputting the 'type' and 'desc
 """
 
 user="""PR Info:
+
 Title: '{{title}}'
+
 Branch: '{{branch}}'
-Description: '{{description}}'
+
+{%- if description %}
+
+Description:
+======
+{{ description|trim }}
+======
+{%- endif %}
+
 {%- if language %}
-Main language: {{language}}
+
+Main PR language: '{{ language }}'
 {%- endif %}
 {%- if commit_messages_str %}
 
 Commit messages:
+======
 {{commit_messages_str}}
+======
 {%- endif %}
 
 {%- if question_str %}
-######
+=====
 Here are questions to better understand the PR. Use the answers to provide better feedback.
 
-{{question_str|trim}}
+{{ question_str|trim }}
 
 User answers:
-{{answer_str|trim}}
-######
+'
+{{ answer_str|trim }}
+'
+=====
 {%- 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. Focus on the '+' lines.
+
+The PR Diff:
+======
+{{ diff|trim }}
+======
+
 
 Response (should be a valid YAML, and nothing else):
 ```yaml

pr_agent/settings/pr_sort_code_suggestions_prompts.toml

@@ -2,10 +2,10 @@
 system="""
 """
 
-user="""You are given a list of code suggestions to improve a PR:
-
+user="""You are given a list of code suggestions to improve a Git Pull Request (PR):
+======
 {{ suggestion_str|trim }}
-
+======
 
 Your task is to sort the code suggestions by their order of importance, and return a list with sorting order.
 The sorting order is a list of pairs, where each pair contains the index of the suggestion in the original list.

pr_agent/settings/pr_update_changelog_prompts.toml

@@ -1,5 +1,5 @@
 [pr_update_changelog_prompt]
-system="""You are a language model called CodiumAI-PR-Changlog-summarizer.
+system="""You are a language model called PR-Changelog-Updater.
 Your task is to update the CHANGELOG.md file of the project, to shortly summarize important changes introduced in this PR (the '+' lines).
 - The output should match the existing CHANGELOG.md format, style and conventions, so it will look like a natural part of the file. For example, if previous changes were summarized in a single line, you should do the same.
 - Don't repeat previous changes. Generate only new content, that is not already in the CHANGELOG.md file.
@@ -8,28 +8,44 @@ 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 }}
+======
+{{ extra_instructions|trim }}
+======
 {%- endif %}
 """
 
 user="""PR Info:
+
 Title: '{{title}}'
+
 Branch: '{{branch}}'
-Description: '{{description}}'
+
+{%- if description %}
+
+Description:
+======
+{{ description|trim }}
+======
+{%- endif %}
+
 {%- if language %}
-Main language: {{language}}
+
+Main PR language: '{{ language }}'
 {%- endif %}
 {%- if commit_messages_str %}
 
+
 Commit messages:
-{{commit_messages_str}}
+======
+{{ commit_messages_str|trim }}
+======
 {%- endif %}
 
 
-The PR Diff:
-```
-{{diff}}
-```
+The PR Git Diff:
+======
+{{ diff|trim }}
+======
 
 Current date:
 ```
@@ -37,9 +53,10 @@ Current date:
 ```
 
 The current CHANGELOG.md:
-```
+======
 {{ changelog_file_str }}
-```
+======
+
 
 Response:
 """

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 +1,16 @@
 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 +22,10 @@ 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:
@@ -48,37 +51,47 @@ class PRCodeSuggestions:
                                           get_settings().pr_code_suggestions_prompt.user)
 
     async def run(self):
-        logging.info('Generating code suggestions for PR...')
-        if get_settings().config.publish_output:
-            self.git_provider.publish_comment("Preparing review...", is_temporary=True)
+        try:
+            get_logger().info('Generating code suggestions for PR...')
+            if get_settings().config.publish_output:
+                self.git_provider.publish_comment("Preparing suggestions...", is_temporary=True)
 
-        logging.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)
+            get_logger().info('Preparing PR code suggestions...')
+            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):
+                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...')
-            data['Code suggestions'] = await self.rank_suggestions(data['Code suggestions'])
+            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):
+                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...')
-            self.git_provider.remove_initial_comment()
-            logging.info('Pushing inline code suggestions...')
-            self.push_inline_code_suggestions(data)
+            if get_settings().config.publish_output:
+                get_logger().info('Pushing PR code suggestions...')
+                self.git_provider.remove_initial_comment()
+                if get_settings().pr_code_suggestions.summarize:
+                    get_logger().info('Pushing summarize code suggestions...')
+                    self.publish_summarizes_suggestions(data)
+                else:
+                    get_logger().info('Pushing inline code suggestions...')
+                    self.push_inline_code_suggestions(data)
+        except Exception as 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):
@@ -88,8 +101,8 @@ 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)
 
@@ -106,18 +119,16 @@ class PRCodeSuggestions:
         code_suggestions = []
 
         if not data['Code suggestions']:
+            get_logger().info('No suggestions found to improve this PR.')
             return self.git_provider.publish_comment('No suggestions found to improve this PR.')
 
         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_str = d['relevant lines'].strip()
-                if ',' in relevant_lines_str:  # handling 'relevant lines': '181, 190' or '178-184, 188-194'
-                    relevant_lines_str = relevant_lines_str.split(',')[0]
-                relevant_lines_start = int(relevant_lines_str.split('-')[0])  # absolute position
-                relevant_lines_end = int(relevant_lines_str.split('-')[-1])
+                relevant_lines_start = int(d['relevant lines start'])  # absolute position
+                relevant_lines_end = int(d['relevant lines end'])
                 content = d['suggestion content']
                 new_code_snippet = d['improved code']
 
@@ -130,11 +141,11 @@ 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])
 
@@ -156,19 +167,19 @@ 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)
@@ -216,8 +227,8 @@ 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)
 
@@ -232,9 +243,46 @@ 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
 
+    def publish_summarizes_suggestions(self, data: Dict):
+        try:
+            data_markdown = "## PR Code Suggestions\n\n"
+
+            language_extension_map_org = get_settings().language_extension_map_org
+            extension_to_language = {}
+            for language, extensions in language_extension_map_org.items():
+                for ext in extensions:
+                    extension_to_language[ext] = language
+
+            for s in data['Code suggestions']:
+                try:
+                    extension_s = s['relevant file'].rsplit('.')[-1]
+                    code_snippet_link = self.git_provider.get_line_link(s['relevant file'], s['relevant lines start'],
+                                                                        s['relevant lines end'])
+                    data_markdown += f"\n💡 Suggestion:\n\n**{s['suggestion content']}**\n\n"
+                    if code_snippet_link:
+                        data_markdown += f" File: [{s['relevant file']} ({s['relevant lines start']}-{s['relevant lines end']})]({code_snippet_link})\n\n"
+                    else:
+                        data_markdown += f"File: {s['relevant file']} ({s['relevant lines start']}-{s['relevant lines end']})\n\n"
+                    if self.git_provider.is_supported("gfm_markdown"):
+                        data_markdown += "<details> <summary> Example code:</summary>\n\n"
+                        data_markdown += f"___\n\n"
+                    language_name = "python"
+                    if extension_s and (extension_s in extension_to_language):
+                        language_name = extension_to_language[extension_s]
+                    data_markdown += f"Existing code:\n```{language_name}\n{s['existing code']}\n```\n"
+                    data_markdown += f"Improved code:\n```{language_name}\n{s['improved code']}\n```\n"
+                    if self.git_provider.is_supported("gfm_markdown"):
+                        data_markdown += "</details>\n"
+                    data_markdown += "\n___\n\n"
+                except Exception as e:
+                    get_logger().error(f"Could not parse suggestion: {s}, error: {e}")
+            self.git_provider.publish_comment(data_markdown)
+        except Exception as e:
+            get_logger().info(f"Failed to publish summarized code suggestions, error: {e}")
+
 

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

@@ -1,6 +1,5 @@
 import copy
-import json
-import logging
+import re
 from typing import List, Tuple
 
 from jinja2 import Environment, StrictUndefined
@@ -8,10 +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, get_user_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:
@@ -28,6 +28,12 @@ class PRDescription:
         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()
+
+        if get_settings().pr_description.enable_semantic_files_types and not self.git_provider.is_supported(
+                "gfm_markdown"):
+            get_logger().debug(f"Disabling semantic files types for {self.pr_id}")
+            get_settings().pr_description.enable_semantic_files_types = False
 
         # Initialize the AI handler
         self.ai_handler = AiHandler()
@@ -36,11 +42,16 @@ class PRDescription:
         self.vars = {
             "title": self.git_provider.pr.title,
             "branch": self.git_provider.get_pr_branch(),
-            "description": self.git_provider.get_pr_description(),
+            "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_class": "",  # will be filled if necessary in 'set_custom_labels' function
+            "enable_file_walkthrough": get_settings().pr_description.enable_file_walkthrough,
+            "enable_semantic_files_types": get_settings().pr_description.enable_semantic_files_types,
         }
 
         self.user_description = self.git_provider.get_user_description()
@@ -61,27 +72,53 @@ class PRDescription:
         """
         Generates a PR description using an AI model and publishes it to the PR.
         """
-        logging.info('Generating a PR description...')
-        if get_settings().config.publish_output:
-            self.git_provider.publish_comment("Preparing pr description...", is_temporary=True)
-        
-        await retry_with_fallback_models(self._prepare_prediction)
-        
-        logging.info('Preparing answer...')
-        pr_title, pr_body, pr_types, markdown_text = self._prepare_pr_answer()
-        
-        if get_settings().config.publish_output:
-            logging.info('Pushing answer...')
-            if get_settings().pr_description.publish_description_as_comment:
-                self.git_provider.publish_comment(markdown_text)
+
+        try:
+            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)
+
+            await retry_with_fallback_models(self._prepare_prediction)
+
+            get_logger().info(f"Preparing answer {self.pr_id}")
+            if self.prediction:
+                self._prepare_data()
             else:
-                self.git_provider.publish_description(pr_title, pr_body)
-                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_types + current_labels)
-            self.git_provider.remove_initial_comment()
+                return None
+
+            if get_settings().pr_description.enable_semantic_files_types:
+                self._prepare_file_labels()
+
+            pr_labels = []
+            if get_settings().pr_description.publish_labels:
+                pr_labels = self._prepare_labels()
+
+            if get_settings().pr_description.use_description_markers:
+                pr_title, pr_body = self._prepare_pr_answer_with_markers()
+            else:
+                pr_title, pr_body,  = self._prepare_pr_answer()
+            full_markdown_description = f"## Title\n\n{pr_title}\n\n___\n{pr_body}"
+
+            if get_settings().config.publish_output:
+                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:
+                    self.git_provider.publish_description(pr_title, pr_body)
+                    if get_settings().pr_description.publish_labels and self.git_provider.is_supported("get_labels"):
+                        current_labels = self.git_provider.get_labels()
+                        user_labels = get_user_labels(current_labels)
+                        self.git_provider.publish_labels(pr_labels + user_labels)
+
+                    if (get_settings().pr_description.final_update_message and
+                            hasattr(self.git_provider, 'pr_url') and self.git_provider.pr_url):
+                        latest_commit_url = self.git_provider.get_latest_commit_url()
+                        if latest_commit_url:
+                            self.git_provider.publish_comment(
+                                f"**[PR Description]({self.git_provider.pr_url})** updated to latest commit ({latest_commit_url})")
+                self.git_provider.remove_initial_comment()
+        except Exception as e:
+            get_logger().error(f"Error generating PR description {self.pr_id}: {e}")
         
         return ""
 
@@ -99,9 +136,12 @@ class PRDescription:
             Any exceptions raised by the 'get_pr_diff' and '_get_prediction' functions.
 
         """
-        logging.info('Getting PR diff...')
+        if get_settings().pr_description.use_description_markers and 'pr_agent:' not in self.user_description:
+            return None
+
+        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('Getting AI prediction...')
+        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:
@@ -118,12 +158,13 @@ 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,
@@ -132,36 +173,89 @@ class PRDescription:
             user=user_prompt
         )
 
+        if get_settings().config.verbosity_level >= 2:
+            get_logger().info(f"\nAI response:\n{response}")
+
         return response
 
-    def _prepare_pr_answer(self) -> Tuple[str, str, List[str], str]:
+    def _prepare_data(self):
+        # Load the AI prediction data into a dictionary
+        self.data = load_yaml(self.prediction.strip())
+
+        if get_settings().pr_description.add_original_user_description and self.user_description:
+            self.data["User Description"] = self.user_description
+
+
+    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 'labels' in self.data:
+            if type(self.data['labels']) == list:
+                pr_types = self.data['labels']
+            elif type(self.data['labels']) == str:
+                pr_types = self.data['labels'].split(',')
+        elif 'type' in self.data:
+            if type(self.data['type']) == list:
+                pr_types = self.data['type']
+            elif type(self.data['type']) == str:
+                pr_types = self.data['type'].split(',')
+        return pr_types
+
+    def _prepare_pr_answer_with_markers(self) -> Tuple[str, str]:
+        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:
+            ai_header = f"### 🤖 Generated by PR Agent at {self.git_provider.last_commit_id.sha}\n\n"
+        else:
+            ai_header = ""
+
+        ai_type = self.data.get('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('description')
+        if ai_summary and not re.search(r'<!--\s*pr_agent:summary\s*-->', body):
+            summary = f"{ai_header}{ai_summary}"
+            body = body.replace('pr_agent:summary', summary)
+
+        if not re.search(r'<!--\s*pr_agent:walkthrough\s*-->', body):
+            ai_walkthrough = self.data.get('PR Main Files Walkthrough')
+            if ai_walkthrough:
+                walkthrough = str(ai_header)
+                for file in ai_walkthrough:
+                    filename = file['filename'].replace("'", "`")
+                    description = file['changes in file'].replace("'", "`")
+                    walkthrough += f'- `{filename}`: {description}\n'
+
+                body = body.replace('pr_agent:walkthrough', walkthrough)
+
+        return title, body
+
+    def _prepare_pr_answer(self) -> Tuple[str, str]:
         """
         Prepare the PR description based on the AI prediction data.
 
         Returns:
         - title: a string containing the PR title.
-        - pr_body: a string containing the PR body in a markdown format.
-        - pr_types: a list of strings containing the PR types.
-        - markdown_text: a string containing the AI prediction data in a markdown format. used for publishing a comment
+        - pr_body: a string containing the PR description body in a markdown format.
         """
-        # Load the AI prediction data into a dictionary
-        data = load_yaml(self.prediction.strip())
 
-        if get_settings().pr_description.add_original_user_description and self.user_description:
-            data["User Description"] = self.user_description
-
-        # Initialization
-        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 data:
-            if type(data['PR Type']) == list:
-                pr_types = data['PR Type']
-            elif type(data['PR Type']) == str:
-                pr_types = data['PR Type'].split(',')
+        # Iterate over the dictionary items and append the key and value to 'markdown_text' in a markdown format
+        markdown_text = ""
+        # Don't display 'PR Labels'
+        if 'labels' in self.data and self.git_provider.is_supported("get_labels"):
+            self.data.pop('labels')
+        if not get_settings().pr_description.enable_pr_type:
+            self.data.pop('type')
+        for key, value in self.data.items():
+            markdown_text += f"## {key}\n\n"
+            markdown_text += f"{value}\n\n"
 
         # Remove the 'PR Title' key from the dictionary
-        ai_title = data.pop('PR Title')
+        ai_title = self.data.pop('title', self.vars["title"])
         if get_settings().pr_description.keep_original_user_title:
             # Assign the original PR title to the 'title' variable
             title = self.vars["title"]
@@ -172,25 +266,132 @@ class PRDescription:
         # Iterate over the remaining dictionary items and append the key and value to 'pr_body' in a markdown format,
         # except for the items containing the word 'walkthrough'
         pr_body = ""
-        for idx, (key, value) in enumerate(data.items()):
-            pr_body += f"## {key}:\n"
+        for idx, (key, value) in enumerate(self.data.items()):
+            if key == 'pr_files':
+                value = self.file_label_dict
+                key_publish = "PR changes walkthrough"
+            else:
+                key_publish = key.rstrip(':').replace("_", " ").capitalize()
+            pr_body += f"## {key_publish}\n"
             if 'walkthrough' in key.lower():
-                # for filename, description in value.items():
+                if self.git_provider.is_supported("gfm_markdown"):
+                    pr_body += "<details> <summary>files:</summary>\n\n"
                 for file in value:
                     filename = file['filename'].replace("'", "`")
-                    description = file['changes in file']
-                    pr_body += f'`{filename}`: {description}\n'
+                    description = file['changes_in_file']
+                    pr_body += f'- `{filename}`: {description}\n'
+                if self.git_provider.is_supported("gfm_markdown"):
+                    pr_body += "</details>\n"
+            elif 'pr_files' in key.lower():
+                pr_body = self.process_pr_files_prediction(pr_body, value)
             else:
                 # if the value is a list, join its items by comma
-                if type(value) == list:
+                if isinstance(value, list):
                     value = ', '.join(v for v in value)
                 pr_body += f"{value}\n"
-            if idx < len(data) - 1:
+            if idx < len(self.data) - 1:
                 pr_body += "\n___\n"
 
-        markdown_text = f"## Title\n\n{title}\n\n___\n{pr_body}"
-
         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_types, markdown_text
+        return title, pr_body
+
+    def _prepare_file_labels(self):
+        self.file_label_dict = {}
+        for file in self.data['pr_files']:
+            try:
+                filename = file['filename'].replace("'", "`").replace('"', '`')
+                changes_summary = file['changes_summary']
+                label = file['label']
+                if label not in self.file_label_dict:
+                    self.file_label_dict[label] = []
+                self.file_label_dict[label].append((filename, changes_summary))
+            except Exception as e:
+                get_logger().error(f"Error preparing file label dict {self.pr_id}: {e}")
+                pass
+
+    def process_pr_files_prediction(self, pr_body, value):
+        if not self.git_provider.is_supported("gfm_markdown"):
+            get_logger().info(f"Disabling semantic files types for {self.pr_id} since gfm_markdown is not supported")
+            return pr_body
+
+        try:
+            pr_body += "<table>"
+            header = f"Relevant files"
+            delta = 65
+            header += "&nbsp; " * delta
+            pr_body += f"""<thead><tr><th></th><th>{header}</th></tr></thead>"""
+            pr_body += """<tbody>"""
+            for semantic_label in value.keys():
+                s_label = semantic_label.strip("'").strip('"')
+                pr_body += f"""<tr><td><strong>{s_label.capitalize()}</strong></td>"""
+                list_tuples = value[semantic_label]
+                pr_body += f"""<td><details><summary>{len(list_tuples)} files</summary><table>"""
+                for filename, file_change_description in list_tuples:
+                    filename = filename.replace("'", "`")
+                    filename_publish = filename.split("/")[-1]
+                    filename_publish = f"{filename_publish}"
+                    if len(filename_publish) < (delta - 5):
+                        filename_publish += "&nbsp; " * ((delta - 5) - len(filename_publish))
+                    diff_plus_minus = ""
+                    diff_files = self.git_provider.diff_files
+                    for f in diff_files:
+                        if f.filename.lower() == filename.lower():
+                            num_plus_lines = f.num_plus_lines
+                            num_minus_lines = f.num_minus_lines
+                            diff_plus_minus += f"+{num_plus_lines}/-{num_minus_lines}"
+                            break
+
+                    # try to add line numbers link to code suggestions
+                    link = ""
+                    if hasattr(self.git_provider, 'get_line_link'):
+                        filename = filename.strip()
+                        link = self.git_provider.get_line_link(filename, relevant_line_start=-1)
+
+                    file_change_description = self._insert_br_after_x_chars(file_change_description, x=(delta - 5))
+                    pr_body += f"""
+<tr>
+  <td>
+    <details>
+      <summary><strong>{filename_publish}</strong></summary>
+      <ul>
+        {filename}<br><br>
+        <strong>{file_change_description}</strong>
+      </ul>
+    </details>
+  </td>
+  <td><a href="{link}"> {diff_plus_minus}</a></td>
+
+</tr>                    
+"""
+                pr_body += """</table></details></td></tr>"""
+            pr_body += """</tr></tbody></table>"""
+
+        except Exception as e:
+            get_logger().error(f"Error processing pr files to markdown {self.pr_id}: {e}")
+            pass
+        return pr_body
+
+    def _insert_br_after_x_chars(self, text, x=70):
+        """
+        Insert <br> into a string after a word that increases its length above x characters.
+        """
+        if len(text) < x:
+            return text
+
+        words = text.split(' ')
+        new_text = ""
+        current_length = 0
+
+        for word in words:
+            # Check if adding this word exceeds x characters
+            if current_length + len(word) > x:
+                new_text += "<br>"  # Insert line break
+                current_length = 0  # Reset counter
+
+            # Add the word to the new text
+            new_text += word + " "
+            current_length += len(word) + 1  # Add 1 for the space
+
+        return new_text.strip()  # Remove trailing space

pr_agent/tools/pr_generate_labels.py

@@ -0,0 +1,171 @@
+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, get_user_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(),
+            "enable_custom_labels": get_settings().config.enable_custom_labels,
+            "custom_labels_class": "",  # will be filled if necessary in 'set_custom_labels' function
+        }
+
+        # 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}")
+
+                current_labels = self.git_provider.get_labels()
+                user_labels = get_user_labels(current_labels)
+                pr_labels = pr_labels + user_labels
+
+                if self.git_provider.is_supported("get_labels"):
+                    self.git_provider.publish_labels(pr_labels)
+                elif pr_labels:
+                    value = ', '.join(v for v in pr_labels)
+                    pr_labels_text = f"## PR Labels:\n{value}\n"
+                    self.git_provider.publish_comment(pr_labels_text, is_temporary=False)
+                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
+        )
+
+        if get_settings().config.verbosity_level >= 2:
+            get_logger().info(f"\nAI response:\n{response}")
+
+        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 'labels' key is present in the dictionary, split its value by comma and assign it to 'pr_types'
+        if 'labels' in self.data:
+            if type(self.data['labels']) == list:
+                pr_types = self.data['labels']
+            elif type(self.data['labels']) == str:
+                pr_types = self.data['labels'].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 +1,5 @@
 import copy
-import json
-import logging
+import datetime
 from collections import OrderedDict
 from typing import List, Tuple
 
@@ -9,13 +8,13 @@ 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, get_user_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
 
 
@@ -59,11 +58,14 @@ class PRReviewer:
             "require_tests": get_settings().pr_reviewer.require_tests_review,
             "require_security": get_settings().pr_reviewer.require_security_review,
             "require_focused": get_settings().pr_reviewer.require_focused_review,
+            "require_estimate_effort_to_review": get_settings().pr_reviewer.require_estimate_effort_to_review,
             'num_code_suggestions': get_settings().pr_reviewer.num_code_suggestions,
             'question_str': question_str,
             '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(
@@ -94,28 +96,44 @@ class PRReviewer:
         """
         Review the pull request and generate feedback.
         """
-        if self.is_auto and not get_settings().pr_reviewer.automatic_review:
-            logging.info(f'Automatic review is disabled {self.pr_url}')
-            return None
 
-        logging.info(f'Reviewing PR: {self.pr_url} ...')
+        try:
+            if self.is_auto and not get_settings().pr_reviewer.automatic_review:
+                get_logger().info(f'Automatic review is disabled {self.pr_url}')
+                return None
+            if self.incremental.is_incremental and not self._can_run_incremental_review():
+                return None
 
-        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...')
-        pr_comment = self._prepare_pr_review()
-    
-        if get_settings().config.publish_output:
-            logging.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...')
-                self._publish_inline_code_comments()
+            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)
+
+            get_logger().info('Preparing PR review...')
+            pr_comment = self._prepare_pr_review()
+
+            if get_settings().config.publish_output:
+                get_logger().info('Pushing PR review...')
+                previous_review_comment = self._get_previous_review_comment()
+
+                # publish the review
+                if get_settings().pr_reviewer.persistent_comment and not self.incremental.is_incremental:
+                    self.git_provider.publish_persistent_comment(pr_comment,
+                                                                 initial_header="## PR Analysis",
+                                                                 update_header=True)
+                else:
+                    self.git_provider.publish_comment(pr_comment)
+
+                self.git_provider.remove_initial_comment()
+                if previous_review_comment:
+                    self._remove_previous_review_comment(previous_review_comment)
+                if get_settings().pr_reviewer.inline_code_comments:
+                    get_logger().info('Pushing inline code comments...')
+                    self._publish_inline_code_comments()
+        except Exception as e:
+            get_logger().error(f"Failed to review PR: {e}")
 
     async def _prepare_prediction(self, model: str) -> None:
         """
@@ -127,9 +145,9 @@ 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:
@@ -150,8 +168,8 @@ class PRReviewer:
         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,
@@ -160,6 +178,9 @@ class PRReviewer:
             user=user_prompt
         )
 
+        if get_settings().config.verbosity_level >= 2:
+            get_logger().info(f"\nAI response:\n{response}")
+
         return response
 
     def _prepare_pr_review(self) -> str:
@@ -204,30 +225,46 @@ 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
+
 
         # Add incremental review section
         if self.incremental.is_incremental:
             last_commit_url = f"{self.git_provider.get_pr_url()}/commits/" \
                               f"{self.git_provider.incremental.first_new_commit_sha}"
+            last_commit_msg = self.incremental.commits_range[0].commit.message if self.incremental.commits_range else ""
+            incremental_review_markdown_text = f"Starting from commit {last_commit_url}"
+            if last_commit_msg:
+                replacement = last_commit_msg.splitlines(keepends=False)[0].replace('_', r'\_')
+                incremental_review_markdown_text += f"  \n_({replacement})_"
             data = OrderedDict(data)
             data.update({'Incremental PR Review': {
-                "⏮️ Review for commits since previous PR-Agent review": f"Starting from commit {last_commit_url}"}})
+                "⏮️ Review for commits since previous PR-Agent review": incremental_review_markdown_text}})
             data.move_to_end('Incremental PR Review', last=False)
 
-        markdown_text = convert_to_markdown(data)
+        markdown_text = convert_to_markdown(data, self.git_provider.is_supported("gfm_markdown"))
         user = self.git_provider.get_user_id()
 
         # 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:
+            if self.git_provider.is_supported("gfm_markdown"):
+                markdown_text += "\n <details> <summary> Instructions</summary>\n\n"
+            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
+            if self.git_provider.is_supported("gfm_markdown"):
+                markdown_text += "\n</details>\n"
+
+        # Add custom labels from the review prediction (effort, security)
+        self.set_review_labels(data)
 
         # 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 = ""
@@ -241,21 +278,14 @@ class PRReviewer:
         if get_settings().pr_reviewer.num_code_suggestions == 0:
             return
 
-        review_text = self.prediction.strip()
-        review_text = review_text.removeprefix('```yaml').rstrip('`')
-        try:
-            data = yaml.load(review_text, Loader=SafeLoader)
-        except Exception as e:
-            logging.error(f"Failed to parse AI prediction: {e}")
-            data = try_fix_yaml(review_text)
-
+        data = load_yaml(self.prediction.strip())
         comments: List[str] = []
         for suggestion in data.get('PR Feedback', {}).get('Code feedback', []):
             relevant_file = suggestion.get('relevant file', '').strip()
             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"):
@@ -266,7 +296,7 @@ class PRReviewer:
                 self.git_provider.publish_inline_comment(content, relevant_file, relevant_line_in_file)
 
         if comments:
-            self.git_provider.publish_inline_comments(comments)
+                self.git_provider.publish_inline_comments(comments)
 
     def _get_user_answers(self) -> Tuple[str, str]:
         """
@@ -291,3 +321,83 @@ class PRReviewer:
                     break
 
         return question_str, answer_str
+
+    def _get_previous_review_comment(self):
+        """
+        Get the previous review comment if it exists.
+        """
+        try:
+            if get_settings().pr_reviewer.remove_previous_review_comment and hasattr(self.git_provider, "get_previous_review"):
+                return self.git_provider.get_previous_review(
+                    full=not self.incremental.is_incremental,
+                    incremental=self.incremental.is_incremental,
+                )
+        except Exception as e:
+            get_logger().exception(f"Failed to get previous review comment, error: {e}")
+
+    def _remove_previous_review_comment(self, comment):
+        """
+        Remove the previous review comment if it exists.
+        """
+        try:
+            if get_settings().pr_reviewer.remove_previous_review_comment and comment:
+                self.git_provider.remove_comment(comment)
+        except Exception as e:
+            get_logger().exception(f"Failed to remove previous review comment, error: {e}")
+
+    def _can_run_incremental_review(self) -> bool:
+        """Checks if we can run incremental review according the various configurations and previous review"""
+        # checking if running is auto mode but there are no new commits
+        if self.is_auto and not self.incremental.first_new_commit_sha:
+            get_logger().info(f"Incremental review is enabled for {self.pr_url} but there are no new commits")
+            return False
+        # checking if there are enough commits to start the review
+        num_new_commits = len(self.incremental.commits_range)
+        num_commits_threshold = get_settings().pr_reviewer.minimal_commits_for_incremental_review
+        not_enough_commits = num_new_commits < num_commits_threshold
+        # checking if the commits are not too recent to start the review
+        recent_commits_threshold = datetime.datetime.now() - datetime.timedelta(
+            minutes=get_settings().pr_reviewer.minimal_minutes_for_incremental_review
+        )
+        last_seen_commit_date = (
+            self.incremental.last_seen_commit.commit.author.date if self.incremental.last_seen_commit else None
+        )
+        all_commits_too_recent = (
+            last_seen_commit_date > recent_commits_threshold if self.incremental.last_seen_commit else False
+        )
+        # check all the thresholds or just one to start the review
+        condition = any if get_settings().pr_reviewer.require_all_thresholds_for_incremental_review else all
+        if condition((not_enough_commits, all_commits_too_recent)):
+            get_logger().info(
+                f"Incremental review is enabled for {self.pr_url} but didn't pass the threshold check to run:"
+                f"\n* Number of new commits = {num_new_commits} (threshold is {num_commits_threshold})"
+                f"\n* Last seen commit date = {last_seen_commit_date} (threshold is {recent_commits_threshold})"
+            )
+            return False
+        return True
+
+    def set_review_labels(self, data):
+        if (get_settings().pr_reviewer.enable_review_labels_security or
+                get_settings().pr_reviewer.enable_review_labels_effort):
+            try:
+                review_labels = []
+                if get_settings().pr_reviewer.enable_review_labels_effort:
+                    estimated_effort = data['PR Analysis']['Estimated effort to review [1-5]']
+                    estimated_effort_number = int(estimated_effort.split(',')[0])
+                    if 1 <= estimated_effort_number <= 5: # 1, because ...
+                        review_labels.append(f'Review effort [1-5]: {estimated_effort_number}')
+                if get_settings().pr_reviewer.enable_review_labels_security:
+                    security_concerns = data['PR Analysis']['Security concerns'] # yes, because ...
+                    security_concerns_bool = 'yes' in security_concerns.lower() or 'true' in security_concerns.lower()
+                    if security_concerns_bool:
+                        review_labels.append('Possible security concern')
+
+                current_labels = self.git_provider.get_labels()
+                current_labels_filtered = [label for label in current_labels if
+                                           not label.lower().startswith('review effort [1-5]:') and not label.lower().startswith(
+                                               'possible security concern')]
+                if current_labels or review_labels:
+                    get_logger().info(f"Setting review labels: {review_labels + current_labels_filtered}")
+                    self.git_provider.publish_labels(review_labels + current_labels_filtered)
+            except Exception as e:
+                get_logger().error(f"Failed to set review labels, error: {e}")

pr_agent/tools/pr_similar_issue.py

@@ -0,0 +1,295 @@
+import time
+from enum import Enum
+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.algo.utils import get_max_tokens
+from pr_agent.config_loader import get_settings
+from pr_agent.git_providers import get_git_provider
+from pr_agent.log import get_logger
+
+MODEL = "text-embedding-ada-002"
+
+
+class PRSimilarIssue:
+    def __init__(self, issue_url: str, args: list = None):
+        if get_settings().config.git_provider != "github":
+            raise Exception("Only github is supported for similar issue tool")
+
+        self.cli_mode = get_settings().CONFIG.CLI_MODE
+        self.max_issues_to_scan = get_settings().pr_similar_issue.max_issues_to_scan
+        self.issue_url = issue_url
+        self.git_provider = get_git_provider()()
+        repo_name, issue_number = self.git_provider._parse_issue_url(issue_url.split('=')[-1])
+        self.git_provider.repo = repo_name
+        self.git_provider.repo_obj = self.git_provider.github_client.get_repo(repo_name)
+        self.token_handler = TokenHandler()
+        repo_obj = self.git_provider.repo_obj
+        repo_name_for_index = self.repo_name_for_index = repo_obj.full_name.lower().replace('/', '-').replace('_/', '-')
+        index_name = self.index_name = "codium-ai-pr-agent-issues"
+
+        # assuming pinecone api key and environment are set in secrets file
+        try:
+            api_key = get_settings().pinecone.api_key
+            environment = get_settings().pinecone.environment
+        except Exception:
+            if not self.cli_mode:
+                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_main.create_comment("Please set pinecone api key and environment in secrets file")
+            raise Exception("Please set pinecone api key and environment in secrets file")
+
+        # 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():
+            run_from_scratch = True
+            upsert = False
+        else:
+            if get_settings().pr_similar_issue.force_update_dataset:
+                upsert = True
+            else:
+                pinecone_index = pinecone.Index(index_name=index_name)
+                res = pinecone_index.fetch([f"example_issue_{repo_name_for_index}"]).to_dict()
+                if res["vectors"]:
+                    upsert = False
+
+        if run_from_scratch or upsert:  # index the entire repo
+            get_logger().info('Indexing the entire repo...')
+
+            get_logger().info('Getting issues...')
+            issues = list(repo_obj.get_issues(state='all'))
+            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)
+            issues_to_update = []
+            issues_paginated_list = repo_obj.get_issues(state='all')
+            counter = 1
+            for issue in issues_paginated_list:
+                if issue.pull_request:
+                    continue
+                issue_str, comments, number = self._process_issue(issue)
+                issue_key = f"issue_{number}"
+                id = issue_key + "." + "issue"
+                res = pinecone_index.fetch([id]).to_dict()
+                is_new_issue = True
+                for vector in res["vectors"].values():
+                    if vector['metadata']['repo'] == repo_name_for_index:
+                        is_new_issue = False
+                        break
+                if is_new_issue:
+                    counter += 1
+                    issues_to_update.append(issue)
+                else:
+                    break
+
+            if issues_to_update:
+                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:
+                get_logger().info('No new issues to update')
+
+    async def run(self):
+        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
+        get_logger().info('Done')
+
+        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)
+        res = pinecone_index.query(embeds[0],
+                                   top_k=5,
+                                   filter={"repo": self.repo_name_for_index},
+                                   include_metadata=True).to_dict()
+        relevant_issues_number_list = []
+        relevant_comment_number_list = []
+        score_list = []
+        for r in res['matches']:
+            # 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:
+                relevant_issues_number_list.append(issue_number)
+            if 'comment' in r["id"]:
+                relevant_comment_number_list.append(int(r["id"].split('.')[1].split('_')[-1]))
+            else:
+                relevant_comment_number_list.append(-1)
+            score_list.append(str("{:.2f}".format(r['score'])))
+        get_logger().info('Done')
+
+        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)
+            title = issue.title
+            url = issue.html_url
+            if relevant_comment_number_list[i] != -1:
+                url = list(issue.get_comments())[relevant_comment_number_list[i]].html_url
+            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)
+        get_logger().info(similar_issues_str)
+        get_logger().info('Done')
+
+    def _process_issue(self, issue):
+        header = issue.title
+        body = issue.body
+        number = issue.number
+        if get_settings().pr_similar_issue.skip_comments:
+            comments = []
+        else:
+            comments = list(issue.get_comments())
+        issue_str = f"Issue Header: \"{header}\"\n\nIssue Body:\n{body}"
+        return issue_str, comments, number
+
+    def _update_index_with_issues(self, issues_list, repo_name_for_index, upsert=False):
+        get_logger().info('Processing issues...')
+        corpus = Corpus()
+        example_issue_record = Record(
+            id=f"example_issue_{repo_name_for_index}",
+            text="example_issue",
+            metadata=Metadata(repo=repo_name_for_index)
+        )
+        corpus.append(example_issue_record)
+
+        counter = 0
+        for issue in issues_list:
+            if issue.pull_request:
+                continue
+
+            counter += 1
+            if counter % 100 == 0:
+                get_logger().info(f"Scanned {counter} issues")
+            if counter >= self.max_issues_to_scan:
+                get_logger().info(f"Scanned {self.max_issues_to_scan} issues, stopping")
+                break
+
+            issue_str, comments, number = self._process_issue(issue)
+            issue_key = f"issue_{number}"
+            username = issue.user.login
+            created_at = str(issue.created_at)
+            if len(issue_str) < 8000 or \
+                    self.token_handler.count_tokens(issue_str) < get_max_tokens(MODEL):  # fast reject first
+                issue_record = Record(
+                    id=issue_key + "." + "issue",
+                    text=issue_str,
+                    metadata=Metadata(repo=repo_name_for_index,
+                                      username=username,
+                                      created_at=created_at,
+                                      level=IssueLevel.ISSUE)
+                )
+                corpus.append(issue_record)
+                if comments:
+                    for j, comment in enumerate(comments):
+                        comment_body = comment.body
+                        num_words_comment = len(comment_body.split())
+                        if num_words_comment < 10 or not isinstance(comment_body, str):
+                            continue
+
+                        if len(comment_body) < 8000 or \
+                                self.token_handler.count_tokens(comment_body) < MAX_TOKENS[MODEL]:
+                            comment_record = Record(
+                                id=issue_key + ".comment_" + str(j + 1),
+                                text=comment_body,
+                                metadata=Metadata(repo=repo_name_for_index,
+                                                  username=username,  # use issue username for all comments
+                                                  created_at=created_at,
+                                                  level=IssueLevel.COMMENT)
+                            )
+                            corpus.append(comment_record)
+        df = pd.DataFrame(corpus.dict()["documents"])
+        get_logger().info('Done')
+
+        get_logger().info('Embedding...')
+        openai.api_key = get_settings().openai.key
+        list_to_encode = list(df["text"].values)
+        try:
+            res = openai.Embedding.create(input=list_to_encode, engine=MODEL)
+            embeds = [record['embedding'] for record in res['data']]
+        except:
+            embeds = []
+            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)
+                    embeds.append(res['data'][0]['embedding'])
+                except:
+                    embeds.append([0] * 1536)
+        df["values"] = embeds
+        meta = DatasetMetadata.empty()
+        meta.dense_model.dimension = len(embeds[0])
+        ds = Dataset.from_pandas(df, meta)
+        get_logger().info('Done')
+
+        api_key = get_settings().pinecone.api_key
+        environment = get_settings().pinecone.environment
+        if not upsert:
+            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:
+            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)
+            time.sleep(5)  # wait for pinecone to finalize upserting before querying
+        get_logger().info('Done')
+
+
+class IssueLevel(str, Enum):
+    ISSUE = "issue"
+    COMMENT = "comment"
+
+
+class Metadata(BaseModel):
+    repo: str
+    username: str = Field(default="@codium")
+    created_at: str = Field(default="01-01-1970 00:00:00.00000")
+    level: IssueLevel = Field(default=IssueLevel.ISSUE)
+
+    class Config:
+        use_enum_values = True
+
+
+class Record(BaseModel):
+    id: str
+    text: str
+    metadata: Metadata
+
+
+class Corpus(BaseModel):
+    documents: List[Record] = Field(default=[])
+
+    def append(self, r: Record):
+        self.documents.append(r)

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
 
@@ -46,28 +46,28 @@ class PRUpdateChangelog:
                                           get_settings().pr_update_changelog_prompt.user)
 
     async def run(self):
-        assert type(self.git_provider) == GithubProvider, "Currently only Github is supported"
+        # 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

@@ -1,19 +1,25 @@
-dynaconf==3.1.12
-fastapi==0.99.0
-PyGithub==1.59.*
-retry==0.9.2
-openai==0.27.8
-Jinja2==3.1.2
-tiktoken==0.4.0
-uvicorn==0.22.0
-python-gitlab==3.15.0
-pytest~=7.4.0
-aiohttp~=3.8.4
+aiohttp==3.9.1
 atlassian-python-api==3.39.0
-GitPython~=3.1.32
-PyYAML==6.0
-starlette-context==0.3.6
-litellm~=0.1.445
-boto3~=1.28.25
+azure-devops==7.1.0b3
+boto3==1.33.6
+dynaconf==3.2.4
+fastapi==0.99.0
+GitPython==3.1.32
+google-cloud-aiplatform==1.35.0
 google-cloud-storage==2.10.0
+Jinja2==3.1.2
+litellm==0.12.5
+loguru==0.7.2
+msrest==0.7.1
+openai==0.27.8
+pinecone-client
+pinecone-datasets @ git+https://github.com/mrT23/pinecone-datasets.git@main
+pytest==7.4.0
+PyGithub==1.59.*
+PyYAML==6.0.1
+python-gitlab==3.15.0
+retry==0.9.2
+starlette-context==0.3.6
+tiktoken==0.5.2
 ujson==5.8.0
+uvicorn==0.22.0

tests/unittest/test_bitbucket_provider.py

@@ -1,3 +1,4 @@
+from pr_agent.git_providers import BitbucketServerProvider
 from pr_agent.git_providers.bitbucket_provider import BitbucketProvider
 
 
@@ -8,3 +9,10 @@ class TestBitbucketProvider:
         assert workspace_slug == "WORKSPACE_XYZ"
         assert repo_slug == "MY_TEST_REPO"
         assert pr_number == 321
+
+    def test_bitbucket_server_pr_url(self):
+        url = "https://git.onpreminstance.com/projects/AAA/repos/my-repo/pull-requests/1"
+        workspace_slug, repo_slug, pr_number = BitbucketServerProvider._parse_pr_url(url)
+        assert workspace_slug == "AAA"
+        assert repo_slug == "my-repo"
+        assert pr_number == 1

tests/unittest/test_clip_tokens.py

@@ -0,0 +1,19 @@
+
+# Generated by CodiumAI
+
+import pytest
+
+from pr_agent.algo.utils import clip_tokens
+
+
+class TestClipTokens:
+    def test_clip(self):
+        text = "line1\nline2\nline3\nline4\nline5\nline6"
+        max_tokens = 25
+        result = clip_tokens(text, max_tokens)
+        assert result == text
+
+        max_tokens = 10
+        result = clip_tokens(text, max_tokens)
+        expected_results = 'line1\nline2\nline3\nli...(truncated)'
+        assert result == expected_results

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": [
@@ -125,7 +125,7 @@ class TestCodeCommitProvider:
             }
         }
 
-        pr = api.get_pr(321)
+        pr = api.get_pr("my_test_repo", 321)
 
         assert pr.title == "My PR"
         assert pr.description == "My PR description"

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
 
 
@@ -25,12 +27,64 @@ 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"
         repo_name, pr_number = CodeCommitProvider._parse_pr_url(url)
         assert repo_name == "my_test_repo"
         assert pr_number == 321
 
+    def test_is_valid_codecommit_hostname(self):
+        # Test the various AWS regions
+        assert CodeCommitProvider._is_valid_codecommit_hostname("af-south-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ap-east-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ap-northeast-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ap-northeast-2.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ap-northeast-3.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ap-south-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ap-south-2.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ap-southeast-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ap-southeast-2.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ap-southeast-3.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ap-southeast-4.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("ca-central-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("eu-central-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("eu-central-2.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("eu-north-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("eu-south-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("eu-south-2.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("eu-west-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("eu-west-2.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("eu-west-3.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("il-central-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("me-central-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("me-south-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("sa-east-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("us-east-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("us-east-2.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("us-gov-east-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("us-gov-west-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("us-west-1.console.aws.amazon.com")
+        assert CodeCommitProvider._is_valid_codecommit_hostname("us-west-2.console.aws.amazon.com")
+        # Test non-AWS regions
+        assert not CodeCommitProvider._is_valid_codecommit_hostname("no-such-region.console.aws.amazon.com")
+        assert not CodeCommitProvider._is_valid_codecommit_hostname("console.aws.amazon.com")
+
     # Test that an error is raised when an invalid CodeCommit URL is provided to the set_pr() method of the CodeCommitProvider class.
     # Generated by CodiumAI
     def test_invalid_codecommit_url(self):
@@ -106,6 +160,7 @@ class TestCodeCommitProvider:
         assert percentages == {}
 
     def test_get_edit_type(self):
+        # Test that the _get_edit_type() function can convert a CodeCommit letter to an EDIT_TYPE enum
         assert CodeCommitProvider._get_edit_type("A") == EDIT_TYPE.ADDED
         assert CodeCommitProvider._get_edit_type("D") == EDIT_TYPE.DELETED
         assert CodeCommitProvider._get_edit_type("M") == EDIT_TYPE.MODIFIED
@@ -117,3 +172,18 @@ class TestCodeCommitProvider:
         assert CodeCommitProvider._get_edit_type("r") == EDIT_TYPE.RENAMED
 
         assert CodeCommitProvider._get_edit_type("X") is None
+
+    def test_add_additional_newlines(self):
+        # a short string to test adding double newlines
+        input = "abc\ndef\n\n___\nghi\njkl\nmno\n\npqr\n"
+        expect = "abc\n\ndef\n\n___\n\nghi\n\njkl\n\nmno\n\npqr\n\n"
+        assert CodeCommitProvider._add_additional_newlines(input) == expect
+        # a test example from a real PR
+        input = "## PR Type:\nEnhancement\n\n___\n## PR Description:\nThis PR introduces a new feature to the script, allowing users to filter servers by name.\n\n___\n## PR Main Files Walkthrough:\n`foo`: The foo script has been updated to include a new command line option `-f` or `--filter`.\n`bar`: The bar script has been updated to list stopped servers.\n"
+        expect = "## PR Type:\n\nEnhancement\n\n___\n\n## PR Description:\n\nThis PR introduces a new feature to the script, allowing users to filter servers by name.\n\n___\n\n## PR Main Files Walkthrough:\n\n`foo`: The foo script has been updated to include a new command line option `-f` or `--filter`.\n\n`bar`: The bar script has been updated to list stopped servers.\n\n"
+        assert CodeCommitProvider._add_additional_newlines(input) == expect
+
+    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

tests/unittest/test_convert_to_markdown.py

@@ -71,7 +71,7 @@ class TestConvertToMarkdown:
 - 📌 **Type of PR:** Test type\n\
 - 🧪 **Relevant tests added:** no\n\
 - ✨ **Focused PR:** Yes\n\
--  **General PR suggestions:** general suggestion...\n\n\n- **<details><summary> 🤖 Code feedback:**</summary>\n\n  - **Code example:**\n    - **Before:**\n        ```\n        Code before\n        ```\n    - **After:**\n        ```\n        Code after\n        ```\n\n  - **Code example:**\n    - **Before:**\n        ```\n        Code before 2\n        ```\n    - **After:**\n        ```\n        Code after 2\n        ```\n\n</details>\
+-  **General PR suggestions:** general suggestion...\n\n\n- <details><summary> 🤖 Code feedback:</summary>\n\n  - **Code example:**\n    - **Before:**\n        ```\n        Code before\n        ```\n    - **After:**\n        ```\n        Code after\n        ```\n\n  - **Code example:**\n    - **Before:**\n        ```\n        Code before 2\n        ```\n    - **After:**\n        ```\n        Code after 2\n        ```\n\n</details>\
 """
         assert convert_to_markdown(input_data).strip() == expected_output.strip()
 

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'

tests/unittest/test_language_handler.py

@@ -61,7 +61,7 @@ class TestSortFilesByMainLanguages:
             type('', (object,), {'filename': 'file1.py'})(),
             type('', (object,), {'filename': 'file2.java'})()
         ]
-        expected_output = [{'language': 'Other', 'files': []}]
+        expected_output = [{'language': 'Other', 'files': files}]
         assert sort_files_by_main_languages(languages, files) == expected_output
 
     # Tests that function handles empty files list

tests/unittest/test_load_yaml.py

@@ -2,6 +2,9 @@
 # Generated by CodiumAI
 
 import pytest
+import yaml
+from yaml.scanner import ScannerError
+
 from pr_agent.algo.utils import load_yaml
 
 
@@ -12,7 +15,7 @@ class TestLoadYaml:
         expected_output = {'name': 'John Smith', 'age': 35}
         assert load_yaml(yaml_str) == expected_output
 
-    def test_load_complicated_yaml(self):
+    def test_load_invalid_yaml1(self):
         yaml_str = \
 '''\
 PR Analysis:
@@ -26,7 +29,23 @@ PR Feedback:
   Code feedback:
     - relevant file: pr_agent/settings/pr_description_prompts.toml
       suggestion: Consider using a more descriptive variable name than 'user' for the command prompt. A more descriptive name would make the code more readable and maintainable. [medium]
-      relevant line: 'user="""PR Info:'
+      relevant line: user="""PR Info: aaa
   Security concerns: No'''
-        expected_output = {'PR Analysis': {'Main theme': 'Enhancing the `/describe` command prompt by adding title and description', 'Type of PR': 'Enhancement', 'Relevant tests added': False, 'Focused PR': 'Yes, the PR is focused on enhancing the `/describe` command prompt.'}, 'PR Feedback': {'General suggestions': 'The PR seems to be well-structured and focused on a specific enhancement. However, it would be beneficial to add tests to ensure the new feature works as expected.', 'Code feedback': [{'relevant file': 'pr_agent/settings/pr_description_prompts.toml', 'suggestion': "Consider using a more descriptive variable name than 'user' for the command prompt. A more descriptive name would make the code more readable and maintainable. [medium]", 'relevant line': 'user="""PR Info:'}], 'Security concerns': False}}
+        with pytest.raises(ScannerError):
+            yaml.safe_load(yaml_str)
+
+        expected_output = {'PR Analysis': {'Main theme': 'Enhancing the `/describe` command prompt by adding title and description', 'Type of PR': 'Enhancement', 'Relevant tests added': False, 'Focused PR': 'Yes, the PR is focused on enhancing the `/describe` command prompt.'}, 'PR Feedback': {'General suggestions': 'The PR seems to be well-structured and focused on a specific enhancement. However, it would be beneficial to add tests to ensure the new feature works as expected.', 'Code feedback': [{'relevant file': 'pr_agent/settings/pr_description_prompts.toml', 'suggestion': "Consider using a more descriptive variable name than 'user' for the command prompt. A more descriptive name would make the code more readable and maintainable. [medium]", 'relevant line': 'user="""PR Info: aaa'}], 'Security concerns': False}}
         assert load_yaml(yaml_str) == expected_output
+
+    def test_load_invalid_yaml2(self):
+        yaml_str = '''\
+- relevant file: src/app.py:
+  suggestion content: The print statement is outside inside the if __name__ ==: \
+  '''
+        with pytest.raises(ScannerError):
+            yaml.safe_load(yaml_str)
+
+        expected_output =[{'relevant file': 'src/app.py:',
+  'suggestion content': 'The print statement is outside inside the if __name__ ==:   '}]
+        assert load_yaml(yaml_str) == expected_output
+

tests/unittest/test_parse_code_suggestion.py

@@ -61,7 +61,7 @@ class TestParseCodeSuggestion:
             'before': 'Before 1',
             'after': 'After 1'
         }
-        expected_output = "   **suggestion:** Suggestion 1\n   **description:** Description 1\n   **before:** Before 1\n   **after:** After 1\n\n"  # noqa: E501
+        expected_output = '   **suggestion:** Suggestion 1  \n   **description:** Description 1  \n   **before:** Before 1  \n   **after:** After 1  \n\n'  # noqa: E501
         assert parse_code_suggestion(code_suggestions) == expected_output
 
     # Tests that function returns correct output when input dictionary has 'code example' key
@@ -74,5 +74,5 @@ class TestParseCodeSuggestion:
                 'after': 'After 2'
             }
         }
-        expected_output = "   **suggestion:** Suggestion 2\n   **description:** Description 2\n  - **code example:**\n    - **before:**\n        ```\n        Before 2\n        ```\n    - **after:**\n        ```\n        After 2\n        ```\n\n"  # noqa: E501
+        expected_output = '   **suggestion:** Suggestion 2  \n   **description:** Description 2  \n  - **code example:**\n    - **before:**\n        ```\n        Before 2\n        ```\n    - **after:**\n        ```\n        After 2\n        ```\n\n'  # noqa: E501
         assert parse_code_suggestion(code_suggestions) == expected_output

tests/unittest/try_fix_yaml.py

@@ -0,0 +1,31 @@
+
+# Generated by CodiumAI
+from pr_agent.algo.utils import try_fix_yaml
+
+
+import pytest
+
+class TestTryFixYaml:
+
+    # The function successfully parses a valid YAML string.
+    def test_valid_yaml(self):
+        review_text = "key: value\n"
+        expected_output = {"key": "value"}
+        assert try_fix_yaml(review_text) == expected_output
+
+    # The function adds '|-' to 'relevant line:' if it is not already present and successfully parses the YAML string.
+    def test_add_relevant_line(self):
+        review_text = "relevant line: value: 3\n"
+        expected_output = {"relevant line": "value: 3"}
+        assert try_fix_yaml(review_text) == expected_output
+
+    # The function removes the last line(s) of the YAML string and successfully parses the YAML string.
+    def test_remove_last_line(self):
+        review_text = "key: value\nextra invalid line\n"
+        expected_output = {"key": "value"}
+        assert try_fix_yaml(review_text) == expected_output
+
+    # The YAML string is empty.
+    def test_empty_yaml_fixed(self):
+        review_text = ""
+        assert try_fix_yaml(review_text) is None