test

Fix `get_user_description` in case `pr_description.enable_pr_type=false`

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

@@ -2,6 +2,8 @@ name: Build-and-test
 
 on:
   push:
+  pull_request:
+    types: [ opened, reopened ]
 
 jobs:
   build-and-test:

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

@@ -24,4 +24,7 @@ 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 }}
+
 

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

@@ -1,80 +1,76 @@
 
-## Installation
+### Installation
+
+To get started with PR-Agent quickly, you first need to acquire two tokens:
+
+1. An OpenAI key from [here](https://platform.openai.com/), with access to GPT-4.
+2. A GitHub\GitLab\BitBucket personal access token (classic) with the repo scope.
+
+There are several ways to use PR-Agent:
+
+**Locally**
+- [Using Docker image (no installation required)](INSTALL.md#use-docker-image-no-installation-required)
+- [Run from source](INSTALL.md#run-from-source)
+
+**GitHub specific methods**
+- [Run as a GitHub Action](INSTALL.md#run-as-a-github-action)
+- [Run as a 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)
+---
+
+### Use Docker image (no installation required)
+
+A list of the relevant tools can be found in the [tools guide](./docs/TOOLS_GUIDE.md).
+
+To invoke a tool (for example `review`), you can run directly from the Docker image. Here's how:
+
+- For GitHub:
+```
+docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
+```
+
+- For GitLab:
+```
+docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
+```
+
+Note: If you have a dedicated GitLab instance, you need to specify the custom url as variable:
+```
+docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> 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.
 
 ---
 
-#### Method 1: Use Docker image (no installation required)
 
-To request a review for a PR, or ask a question about a PR, you can run directly from the Docker image. Here's how:
-
-1. To request a review for a PR, run the following command:
-
-```
-docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent --pr_url <pr_url> review
+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, run the following command:
-
+Or you can run a [specific released versions](./RELEASE_NOTES.md) of pr-agent, for example:
 ```
-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>"
-```
-
-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
-    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 }}
-```
-
-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:
 
@@ -100,18 +96,92 @@ chmod 600 pr_agent/settings/.secrets.toml
 
 ```
 export PYTHONPATH=[$PYTHONPATH:]<PATH to pr_agent folder>
-python pr_agent/cli.py --pr_url <pr_url> review
-python pr_agent/cli.py --pr_url <pr_url> ask <your question>
-python pr_agent/cli.py --pr_url <pr_url> describe
-python pr_agent/cli.py --pr_url <pr_url> improve
+python3 -m pr_agent.cli --pr_url <pr_url> review
+python3 -m pr_agent.cli --pr_url <pr_url> ask <your question>
+python3 -m pr_agent.cli --pr_url <pr_url> describe
+python3 -m pr_agent.cli --pr_url <pr_url> improve
+python3 -m pr_agent.cli --pr_url <pr_url> add_docs
+python3 -m pr_agent.cli --issue_url <issue_url> similar_issue
+...
 ```
 
 ---
 
-#### Method 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`:
+
+```
+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](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:
 
 ```
@@ -120,7 +190,7 @@ 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).
@@ -200,11 +270,14 @@ 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)
 ---
 
-####  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
@@ -216,5 +289,130 @@ docker push codiumai/pr-agent:github_app  # Push to your Docker repository
     ```
 4. Create a lambda function that uses the uploaded image. Set the lambda timeout to be at least 3m.
 5. Configure the lambda function to have a Function URL.
-6. Go back to steps 8-9 of [Method 5](#method-5-run-as-a-github-app) with the function url as your Webhook URL.
+6. Go back to steps 8-9 of [Method 5](#run-as-a-github-app) with the function url as your Webhook URL.
     The Webhook URL would look like `https://<LAMBDA_FUNCTION_URL>/api/v1/github_webhooks`
+
+---
+
+### AWS CodeCommit Setup
+
+Not all features have been added to CodeCommit yet.  As of right now, CodeCommit has been implemented to run the pr-agent CLI on the command line, using AWS credentials stored in environment variables.  (More features will be added in the future.)  The following is a set of instructions to have pr-agent do a review of your CodeCommit pull request from the command line:
+
+1. Create an IAM user that you will use to read CodeCommit pull requests and post comments
+    * Note: That user should have CLI access only, not Console access
+2. Add IAM permissions to that user, to allow access to CodeCommit (see IAM Role example below)
+3. Generate an Access Key for your IAM user
+4. Set the Access Key and Secret using environment variables (see Access Key example below)
+5. Set the `git_provider` value to `codecommit` in the `pr_agent/settings/configuration.toml` settings file
+6. Set the `PYTHONPATH` to include your `pr-agent` project directory
+    * Option A: Add `PYTHONPATH="/PATH/TO/PROJECTS/pr-agent` to your `.env` file
+    * Option B: Set `PYTHONPATH` and run the CLI in one command, for example:
+        * `PYTHONPATH="/PATH/TO/PROJECTS/pr-agent python pr_agent/cli.py [--ARGS]`
+
+##### AWS CodeCommit IAM Role Example
+
+Example IAM permissions to that user to allow access to CodeCommit:
+
+* Note: The following is a working example of IAM permissions that has read access to the repositories and write access to allow posting comments
+* Note: If you only want pr-agent to review your pull requests, you can tighten the IAM permissions further, however this IAM example will work, and allow the pr-agent to post comments to the PR
+* Note: You may want to replace the `"Resource": "*"` with your list of repos, to limit access to only those repos
+
+```
+{
+    "Version": "2012-10-17",
+    "Statement": [
+        {
+            "Effect": "Allow",
+            "Action": [
+                "codecommit:BatchDescribe*",
+                "codecommit:BatchGet*",
+                "codecommit:Describe*",
+                "codecommit:EvaluatePullRequestApprovalRules",
+                "codecommit:Get*",
+                "codecommit:List*",
+                "codecommit:PostComment*",
+                "codecommit:PutCommentReaction",
+                "codecommit:UpdatePullRequestDescription",
+                "codecommit:UpdatePullRequestTitle"
+            ],
+            "Resource": "*"
+        }
+    ]
+}
+```
+
+##### AWS CodeCommit Access Key and Secret
+
+Example setting the Access Key and Secret using environment variables
+
+```sh
+export AWS_ACCESS_KEY_ID="XXXXXXXXXXXXXXXX"
+export AWS_SECRET_ACCESS_KEY="XXXXXXXXXXXXXXXX"
+export AWS_DEFAULT_REGION="us-east-1"
+```
+
+##### AWS CodeCommit CLI Example
+
+After you set up AWS CodeCommit using the instructions above, here is an example CLI run that tells pr-agent to **review** a given pull request.
+(Replace your specific PYTHONPATH and PR URL in the example)
+
+```sh
+PYTHONPATH="/PATH/TO/PROJECTS/pr-agent" python pr_agent/cli.py \
+  --pr_url https://us-east-1.console.aws.amazon.com/codesuite/codecommit/repositories/MY_REPO_NAME/pull-requests/321 \
+  review
+```
+
+---
+
+### Run a GitLab webhook server
+
+1. From the GitLab workspace or group, create an access token. Enable the "api" scope only.
+2. Generate a random secret for your app, and save it for later. For example, you can use:
+
+```
+WEBHOOK_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
+```
+3. Follow the instructions to build the Docker image, setup a secrets file and deploy on your own server from [Method 5](#run-as-a-github-app) steps 4-7.
+4. In the secrets file, fill in the following:
+    - Your OpenAI key.
+    - In the [gitlab] section, fill in personal_access_token and shared_secret. The access token can be a personal access token, or a group or project access token.
+    - Set deployment_type to 'gitlab' in [configuration.toml](./pr_agent/settings/configuration.toml)
+5. Create a webhook in GitLab. Set the URL to the URL of your app's server. Set the secret token to the generated secret from step 2.
+In the "Trigger" section, check the ‘comments’ and ‘merge request events’ boxes.
+6. Test your installation by opening a merge request or commenting or a merge request using one of CodiumAI's commands.
+
+
+
+### Run as a Bitbucket Pipeline
+
+
+You can use the Bitbucket Pipeline system to run PR-Agent on every pull request open or update.
+
+1. Add the following file in your repository bitbucket_pipelines.yml
+
+```yaml
+pipelines:
+    pull-requests:
+      '**':
+        - step:
+            name: PR Agent Review
+            image: python:3.10
+            services:
+              - docker
+            script:
+              - docker run -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$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.
+
+
+### Run on a hosted Bitbucket app
+
+Please contact <support@codium.ai> if you're interested in a hosted BitBucket app solution that provides full functionality including PR reviews and comment handling. It's based on the [bitbucket_app.py](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/git_providers/bitbucket_provider.py) implmentation.
+
+
+=======

PR_COMPRESSION.md

@@ -1,4 +1,4 @@
-# Git Patch Logic
+# PR Compression Strategy
 There are two scenarios:
 1. The PR is small enough to fit in a single prompt (including system and user prompt)
 2. The PR is too large to fit in a single prompt (including system and user prompt)
@@ -16,7 +16,7 @@ We prioritize the languages of the repo based on the following criteria:
 ## Small PR
 In this case, we can fit the entire PR in a single prompt:
 1. Exclude binary files and non code files (e.g. images, pdfs, etc)
-2. We Expand the surrounding context of each patch to 6 lines above and below the patch
+2. We Expand the surrounding context of each patch to 3 lines above and below the patch
 ## Large PR
 
 ### Motivation
@@ -25,7 +25,7 @@ We want to be able to pack as much information as possible in a single LMM promp
 
 
 
-#### PR compression strategy
+#### Compression strategy
 We prioritize additions over deletions:
  - Combine all deleted files into a single list (`deleted files`)
  - File patches are a list of hunks, remove all hunks of type deletion-only from the hunks in the file patch

README.md

@@ -9,112 +9,143 @@ Making pull requests less painful with an AI agent
 
 [![GitHub license](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://github.com/Codium-ai/pr-agent/blob/main/LICENSE)
 [![Discord](https://badgen.net/badge/icon/discord?icon=discord&label&color=purple)](https://discord.com/channels/1057273017547378788/1126104260430528613)
+[![Twitter](https://img.shields.io/twitter/follow/codiumai)](https://twitter.com/codiumai)
     <a href="https://github.com/Codium-ai/pr-agent/commits/main">
     <img alt="GitHub" src="https://img.shields.io/github/last-commit/Codium-ai/pr-agent/main?style=for-the-badge" height="20">
     </a>
 </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 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 - title, type, summary, code walkthrough and PR labels.
+‣ **Auto Description ([`/describe`](./docs/DESCRIBE.md))**: Automatically generating PR description - title, type, summary, code walkthrough and labels.
 \
-**PR Review**: Adjustable feedback about the PR main theme, type, relevant tests, security issues, focus, 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 about the PR.
+‣ **Question Answering ([`/ask ...`](./docs/ASK.md))**: Answering free-text questions about the PR.
 \
-**Code Suggestions**: Committable code suggestions 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.
+‣ **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>/describe:</h4>
+<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1687561986">/describe:</a></h4>
 <div align="center">
 <p float="center">
 <img src="https://www.codium.ai/images/describe-2.gif" width="800">
 </p>
 </div>
-<h4>/review:</h4>
+
+<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>/reflect_and_review:</h4>
-<div align="center">
-<p float="center">
-<img src="https://www.codium.ai/images/reflect_and_review.gif" width="800">
-</p>
-</div>
-<h4>/ask:</h4>
-<div align="center">
-<p float="center">
-<img src="https://www.codium.ai/images/ask-2.gif" width="800">
-</p>
-</div>
-<h4>/improve:</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 |
-|-------|---------------------------------------------|:------:|:------:|:---------:|
-| TOOLS | Review                                      |   :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:    |           |
-|       | Reflect and Review                          |   :white_check_mark:    |                         |           |
-|       | Update CHANGELOG.md                         |   :white_check_mark:    |                         |           |
-|       |                                             |        |        |           |
-| USAGE | CLI                                         |   :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.
 
 ---
 
@@ -128,19 +159,22 @@ 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://www.codium.ai/wp-content/uploads/2023/10/codiumai-diagram-v5.png)
 
 Check out the [PR Compression strategy](./PR_COMPRESSION.md) page for more details on how we convert a code diff to a manageable LLM prompt
 
@@ -152,16 +186,17 @@ 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.
-- We support **multiple git providers** (GitHub, Gitlab, Bitbucket), **multiple ways** to use the tool (CLI, GitHub Action, GitHub App, Docker, ...), and **multiple models** (GPT-4, GPT-3.5, Anthropic, Cohere, Llama2).
+- 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.
 
 
 ## Roadmap
 
 - [x] Support additional models, as a replacement for OpenAI (see [here](https://github.com/Codium-ai/pr-agent/pull/172))
-- [ ] Develop additional logic for handling large PRs
+- [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)
+- [x] PR-Agent for issues
 - [ ] Adding more tools. Possible directions:
   - [x] PR description
   - [x] Inline code suggestions
@@ -169,13 +204,31 @@ 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 self-host PR-Agent, e.g. via CLI running on your computer, with your OpenAI API key, it is between you and OpenAI. You can read their API data privacy policy here:
+https://openai.com/enterprise-privacy
+
+## Links
+
+[![Join our Discord community](https://raw.githubusercontent.com/Codium-ai/codiumai-vscode-release/main/media/docs/Joincommunity.png)](https://discord.gg/kG35uSHDBc)
+
+- 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 +1,66 @@
+## Unreleased
+- review tool now posts persistent comments by default
+
+## [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 +1,363 @@
+## 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)
+- [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 is also exposed the following environment variables:
+
+ - `IGNORE.GLOB`
+ - `IGNORE.REGEX`
+
+See [dynaconf envvars documentation](https://www.dynaconf.com/envvars/).
+
+#### git provider
+The [git_provider](pr_agent/settings/configuration.toml#L4) field in the configuration file determines the GIT provider that will be used by PR-Agent. Currently, the following providers are supported:
+`
+"github", "gitlab", "azure", "codecommit", "local", "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 for 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 the 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, you can edit and customize any configuration parameter.
+
+For example, if you set in `.pr_agent.toml`:
+
+```
+[pr_reviewer]
+num_code_suggestions=1
+```
+
+Than you will overwrite the default number of code suggestions to be 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 action 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",
+]
+```
+The 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 paramteres 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
+```
+
+
+### 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:
+```
+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
+```
+[config]
+model="" # the OpenAI model you've deployed on Azure (e.g. gpt-3.5-turbo)
+```
+in the configuration.toml
+
+#### 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={
+    ...,
+    "llama2": 4096
+}
+
+
+[config] # in configuration.toml
+model = "ollama/llama2"
+
+[ollama] # in .secrets.toml
+api_base = ... # the base url for your huggingface inference endpoint
+```
+
+**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.
+
+### 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

@@ -2,17 +2,26 @@ 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
 
 FROM base as github_app
 ADD pr_agent pr_agent
 CMD ["python", "pr_agent/servers/github_app.py"]
 
+FROM base as bitbucket_app
+ADD pr_agent pr_agent
+CMD ["python", "pr_agent/servers/bitbucket_app.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=./../pics/add_docs_comment.png width="768"></kbd>
+<kbd><img src=./../pics/add_docs.png width="768"></kbd>
+
+### Configuration options
+ - `docs_style`: The exact style of the documentation (for python docstring). you can choose between: `google`, `numpy`, `sphinx`, `restructuredtext`, `plain`. Default is `sphinx`.
+ - `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".

docs/ASK.md

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

docs/DESCRIBE.md

@@ -0,0 +1,64 @@
+# Describe Tool
+
+The `describe` tool scans the PR code changes, and automatically generates PR description - title, type, summary, code walkthrough and labels.
+It can be invoked manually by commenting on any PR:
+```
+/describe
+```
+For example:
+
+<kbd><img src=./../pics/describe_comment.png width="768"></kbd>
+
+<kbd><img src=./../pics/describe.png width="768"></kbd>
+
+The `describe` tool can also be triggered automatically every time a new PR is opened. See examples for automatic triggers for [GitHub App](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools) and [GitHub Action](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-action)
+
+### Configuration options
+
+Under the section 'pr_description', the [configuration file](./../pr_agent/settings/configuration.toml#L28) contains options to customize the 'describe' tool:
+
+- `publish_labels`: if set to true, the tool will publish the labels to the PR. Default is true.
+
+- `publish_description_as_comment`: if set to true, the tool will publish the description as a comment to the PR. If false, it will overwrite the origianl description. Default is false.
+
+- `add_original_user_description`: if set to true, the tool will add the original user description to the generated description. Default is false.
+
+- `keep_original_user_title`: if set to true, the tool will keep the original PR title, and won't change it. Default is false.
+
+- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
+- 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.
+  
+### Markers template
+
+markers enable to easily integrate user's content and auto-generated content, with a template-like mechanism.
+
+For example, if the PR original description was:
+```
+User content...
+
+
+## PR Description:
+pr_agent:summary
+
+## PR Walkthrough:
+pr_agent:walkthrough
+```
+The marker `pr_agent:summary` will be replaced with the PR summary, and `pr_agent:walkthrough` will be replaced with the PR walkthrough.
+
+##### Example:
+```
+        env:
+          pr_description.use_description_markers: 'true'
+```          
+
+<kbd><img src=./../pics/describe_markers_before.png width="768"></kbd>
+
+==>
+
+<kbd><img src=./../pics/describe_markers_after.png width="768"></kbd>
+
+##### Configuration params:
+
+- `use_description_markers`: if set to true, the tool will use markers template. It replaces every marker of the form `pr_agent:marker_name` with the relevant content. Default is false.
+- `include_generated_by_header`: if set to true, the tool will add a dedicated header: 'Generated by PR Agent at ...' to any automatic content. Default is true.

docs/GENERATE_CUSTOM_LABELS.md

@@ -0,0 +1,41 @@
+# 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=./../pics/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=./../pics/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 +1,45 @@
+# Improve Tool
+
+The `improve` tool scans the PR code changes, and automatically generate committable suggestions for improving the PR code.
+It can be invoked manually by commenting on any PR:
+```
+/improve
+```
+For example:
+
+<kbd><img src=./../pics/improve_comment.png width="768"></kbd>
+<kbd><img src=./../pics/improve.png width="768"></kbd>
+
+The `improve` tool can also be triggered automatically every time a new PR is opened. See examples for automatic triggers for [GitHub App](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools) and [GitHub Action](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-action)
+
+An extended mode, which does not involve PR Compression and provides more comprehensive suggestions, can be invoked by commenting on any PR:
+```
+/improve --extended
+```
+Note that the extended mode divides the PR code changes into chunks, up to the token limits, where each chunk is handled separately (multiple calls to GPT-4).
+Hence, the total number of suggestions is proportional to the number of chunks, i.e. the size of the PR.
+
+### Configuration options
+
+Under the section 'pr_code_suggestions', the [configuration file](./../pr_agent/settings/configuration.toml#L40) contains options to customize the 'improve' tool:
+
+- `num_code_suggestions`: number of code suggestions provided by the 'improve' tool. Default is 4.
+- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
+- `rank_suggestions`: if set to true, the tool will rank the suggestions, based on importance. Default is false.
+
+#### params for '/improve --extended' mode
+- `num_code_suggestions_per_chunk`: number of code suggestions provided by the 'improve' tool, per chunk. Default is 8.
+- `rank_extended_suggestions`: if set to true, the tool will rank the suggestions, based on importance. Default is true.
+- `max_number_of_calls`: maximum number of chunks. Default is 5.
+- `final_clip_factor`: factor to remove suggestions with low confidence. Default is 0.9.
+
+
+#### A note on code suggestions quality
+
+- With current level of AI for code (GPT-4), mistakes can happen. Not all the suggestions will be perfect, and a user should not accept all of them automatically.
+
+- Suggestions are not meant to be [simplistic](./../pr_agent/settings/pr_code_suggestions_prompts.toml#L34). Instead, they aim to give deep feedback and raise questions, ideas and thoughts to the user, who can then use his judgment, experience, and understanding of the code base.
+
+- Recommended to use the 'extra_instructions' field to guide the model to suggestions that are more relevant to the specific needs of the project.
+
+- Best quality will be obtained by using 'improve --extended' mode.

docs/REVIEW.md

@@ -0,0 +1,74 @@
+# Review Tool
+
+The `review` tool scans the PR code changes, and automatically generates a PR review.
+It can be invoked manually by commenting on any PR:
+```
+/review
+```
+For example:
+
+<kbd><img src=./../pics/review_comment.png width="768"></kbd>
+<kbd><img src=./../pics/describe.png width="768"></kbd>
+
+The `review` tool can also be triggered automatically every time a new PR is opened. See examples for automatic triggers for [GitHub App](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#github-app-automatic-tools) and [GitHub Action](https://github.com/Codium-ai/pr-agent/blob/main/Usage.md#working-with-github-action)
+
+### Configuration options
+
+Under the section 'pr_reviewer', the [configuration file](./../pr_agent/settings/configuration.toml#L16) contains options to customize the 'review' tool:
+
+- `require_focused_review`: if set to true, the tool will add a section - 'is the PR a focused one'. Default is false.
+- `require_score_review`: if set to true, the tool will add a section that scores the PR. Default is false.
+- `require_tests_review`: if set to true, the tool will add a section that checks if the PR contains tests. Default is true.
+- `require_security_review`: if set to true, the tool will add a section that checks if the PR contains security issues. Default is true.
+- `require_estimate_effort_to_review`: if set to true, the tool will add a section that estimates thed effort needed to review the PR. Default is true.
+- `num_code_suggestions`: number of code suggestions provided by the 'review' tool. Default is 4.
+- `inline_code_comments`: if set to true, the tool will publish the code suggestions as comments on the code diff. Default is false.
+- `automatic_review`: if set to false, no automatic reviews will be done. Default is true.
+- `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. Default is true.
+- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
+- To enable `custom labels`, apply the configuration changes described [here](./GENERATE_CUSTOM_LABELS.md#configuration-changes) 
+####  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=./../pics/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=./../pics/reflection_questions.png width="768"></kbd>
+<kbd><img src=./../pics/reflection_answers.png width="768"></kbd>
+<kbd><img src=./../pics/reflection_insights.png width="768"></kbd>
+
+
+#### A note on code suggestions quality
+
+- With current level of AI for code (GPT-4), mistakes can happen. Not all the suggestions will be perfect, and a user should not accept all of them automatically.
+
+- Suggestions are not meant to be [simplistic](./../pr_agent/settings/pr_reviewer_prompts.toml#L29). Instead, they aim to give deep feedback and raise questions, ideas and thoughts to the user, who can then use his judgment, experience, and understanding of the code base.
+
+- Recommended to use the 'extra_instructions' field to guide the model to suggestions that are more relevant to the specific needs of the project.
+
+- Unlike the 'review' feature, which does a lot of things, the ['improve --extended'](./IMPROVE.md) feature is dedicated only to suggestions, and usually gives better results.

docs/SIMILAR_ISSUE.md

@@ -0,0 +1,31 @@
+# Similar Issue Tool
+The similar issue tool retrieves the most similar issues to the current issue.
+It can be invoked manually by commenting on any PR:
+```
+/similar_issue
+```
+For example:
+
+<kbd><img src=./../pics/similar_issue_original_issue.png width="768"></kbd>
+<kbd><img src=./../pics/similar_issue_comment.png width="768"></kbd>
+<kbd><img src=./../pics/similar_issue.png width="768"></kbd>
+
+Note that to perform retrieval, the `similar_issue` tool indexes all the repo previous issues (once).
+
+To enable usage of the '**similar issue**' tool, you need to set the following keys in `.secrets.toml` (or in the relevant environment variables):
+```
+[pinecone]
+api_key = "..."
+environment = "..."
+```
+These parameters can be obtained by registering to [Pinecone](https://app.pinecone.io/?sessionType=signup/).
+
+
+### How to use:
+- To invoke the 'similar issue' tool from **CLI**, run:
+`python3 cli.py --issue_url=... similar_issue`
+
+- To invoke the 'similar' issue tool via online usage, [comment](https://github.com/Codium-ai/pr-agent/issues/178#issuecomment-1716934893) on a PR:
+`/similar_issue`
+
+- You can also enable the 'similar issue' tool to run automatically when a new issue is opened, by adding it to the [pr_commands list in the github_app section](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L66)

docs/TOOLS_GUIDE.md

@@ -0,0 +1,11 @@
+## 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=./../pics/update_changelog_comment.png width="768"></kbd>
+<kbd><img src=./../pics/update_changelog.png width="768"></kbd>
+
+
+### Configuration options
+
+Under the section 'pr_update_changelog', the [configuration file](./../pr_agent/settings/configuration.toml#L50) contains options to customize the 'update changelog' tool:
+
+- `push_changelog_changes`: whether to push the changes to CHANGELOG.md, or just print them. Default is false (print only).
+- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...

pr_agent/agent/pr_agent.py

@@ -1,20 +1,21 @@
-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,
     "answer": PRReviewer,
     "review": PRReviewer,
     "review_pr": PRReviewer,
@@ -29,6 +30,9 @@ command2class = {
     "update_changelog": PRUpdateChangelog,
     "config": PRConfig,
     "settings": PRConfig,
+    "similar_issue": PRSimilarIssue,
+    "add_docs": PRAddDocs,
+    "generate_labels": PRGenerateLabels,
 }
 
 commands = list(command2class.keys())
@@ -39,37 +43,27 @@ 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
+        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()
             await PRReviewer(pr_url, is_answer=True, args=args).run()
+        elif action == "auto_review":
+            await PRReviewer(pr_url, is_auto=True, args=args).run()
         elif action in command2class:
             if notify:
                 notify()
@@ -77,3 +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 +8,10 @@ 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
 }

pr_agent/algo/ai_handler.py

@@ -1,12 +1,12 @@
-import logging
+import os
 
 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
 
@@ -26,6 +26,11 @@ class AiHandler:
         try:
             openai.api_key = get_settings().openai.key
             litellm.openai_key = get_settings().openai.key
+            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
             self.azure = False
             if get_settings().get("OPENAI.ORG", None):
                 litellm.organization = get_settings().openai.org
@@ -43,6 +48,12 @@ class AiHandler:
                 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
         except AttributeError as e:
             raise ValueError("OpenAI key is required") from e
 
@@ -55,7 +66,7 @@ class AiHandler:
 
     @retry(exceptions=(APIError, Timeout, TryAgain, AttributeError, RateLimitError),
            tries=OPENAI_RETRIES, delay=2, backoff=2, jitter=(1, 3))
-    async def chat_completion(self, model: str, temperature: float, system: str, user: str):
+    async def chat_completion(self, model: str, system: str, user: str, temperature: float = 0.2):
         """
         Performs a chat completion using the OpenAI ChatCompletion API.
         Retries in case of API errors or timeouts.
@@ -78,33 +89,34 @@ class AiHandler:
         try:
             deployment_id = self.deployment_id
             if get_settings().config.verbosity_level >= 2:
-                logging.debug(
+                get_logger().debug(
                     f"Generating completion with {model}"
                     f"{(' from deployment ' + deployment_id) if deployment_id else ''}"
                 )
+            if self.azure:
+                model = 'azure/' + model
+            messages = [{"role": "system", "content": system}, {"role": "user", "content": user}]
             response = await acompletion(
                 model=model,
                 deployment_id=deployment_id,
-                messages=[
-                    {"role": "system", "content": system},
-                    {"role": "user", "content": user}
-                ],
+                messages=messages,
                 temperature=temperature,
-                azure=self.azure,
                 force_timeout=get_settings().config.ai_timeout
             )
         except (APIError, Timeout, TryAgain) as e:
-            logging.error("Error during OpenAI inference: ", e)
+            get_logger().error("Error during OpenAI inference: ", e)
             raise
         except (RateLimitError) as e:
-            logging.error("Rate limit error during OpenAI inference: ", e)
+            get_logger().error("Rate limit error during OpenAI inference: ", e)
             raise
         except (Exception) as e:
-            logging.error("Unknown error during OpenAI inference: ", e)
+            get_logger().error("Unknown error during OpenAI inference: ", e)
             raise TryAgain from e
         if response is None or len(response["choices"]) == 0:
             raise TryAgain
         resp = response["choices"][0]['message']['content']
         finish_reason = response["choices"][0]["finish_reason"]
-        print(resp, finish_reason)
+        usage = response.get("usage")
+        get_logger().info("AI response", response=resp, messages=messages, finish_reason=finish_reason,
+                          model=model, usage=usage)
         return resp, finish_reason

pr_agent/algo/file_filter.py

@@ -0,0 +1,31 @@
+import fnmatch
+import re
+
+from pr_agent.config_loader import get_settings
+
+def filter_ignored(files):
+    """
+    Filter out files that match the ignore patterns.
+    """
+
+    try:
+        # load regex patterns, and translate glob patterns to regex
+        patterns = get_settings().ignore.regex
+        patterns += [fnmatch.translate(glob) for glob in get_settings().ignore.glob]
+
+        # compile all valid patterns
+        compiled_patterns = []
+        for r in patterns:
+            try:
+                compiled_patterns.append(re.compile(r))
+            except re.error:
+                pass
+
+        # keep filenames that _don't_ match the ignore regex
+        for r in compiled_patterns:
+            files = [f for f in files if (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

@@ -1,9 +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:
@@ -41,12 +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)
@@ -60,7 +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
@@ -111,7 +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.
 
@@ -128,17 +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
 
@@ -157,7 +162,7 @@ def convert_to_hunks_with_lines_numbers(patch: str, file) -> str:
 
     example output:
 ## src/file.ts
---new hunk--
+__new hunk__
 881        line1
 882        line2
 883        line3
@@ -166,7 +171,7 @@ def convert_to_hunks_with_lines_numbers(patch: str, file) -> str:
 889        line6
 890        line7
 ...
---old hunk--
+__old hunk__
         line1
         line2
 -       line3
@@ -176,8 +181,7 @@ def convert_to_hunks_with_lines_numbers(patch: str, file) -> str:
            ...
     """
     
-    patch_with_lines_str = f"## {file.filename}\n"
-    import re
+    patch_with_lines_str = f"\n\n## {file.filename}\n"
     patch_lines = patch.splitlines()
     RE_HUNK_HEADER = re.compile(
         r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
@@ -185,27 +189,39 @@ def convert_to_hunks_with_lines_numbers(patch: str, file) -> str:
     old_content_lines = []
     match = None
     start1, size1, start2, size2 = -1, -1, -1, -1
+    prev_header_line = []
+    header_line =[]
     for line in patch_lines:
         if 'no newline at end of file' in line.lower():
             continue
 
         if line.startswith('@@'):
+            header_line = line
             match = RE_HUNK_HEADER.match(line)
             if match and new_content_lines:  # found a new hunk, split the previous lines
                 if new_content_lines:
-                    patch_with_lines_str += '\n--new hunk--\n'
+                    if prev_header_line:
+                        patch_with_lines_str += f'\n{prev_header_line}\n'
+                    patch_with_lines_str += '__new hunk__\n'
                     for i, line_new in enumerate(new_content_lines):
                         patch_with_lines_str += f"{start2 + i} {line_new}\n"
                 if old_content_lines:
-                    patch_with_lines_str += '--old hunk--\n'
+                    patch_with_lines_str += '__old hunk__\n'
                     for line_old in old_content_lines:
                         patch_with_lines_str += f"{line_old}\n"
                 new_content_lines = []
                 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('+'):
@@ -219,12 +235,13 @@ def convert_to_hunks_with_lines_numbers(patch: str, file) -> str:
     # finishing last hunk
     if match and new_content_lines:
         if new_content_lines:
-            patch_with_lines_str += '\n--new hunk--\n'
+            patch_with_lines_str += f'\n{header_line}\n'
+            patch_with_lines_str += '\n__new hunk__\n'
             for i, line_new in enumerate(new_content_lines):
                 patch_with_lines_str += f"{start2 + i} {line_new}\n"
         if old_content_lines:
-            patch_with_lines_str += '\n--old hunk--\n'
+            patch_with_lines_str += '\n__old hunk__\n'
             for line_old in old_content_lines:
                 patch_with_lines_str += f"{line_old}\n"
 
-    return patch_with_lines_str.strip()
+    return patch_with_lines_str.rstrip()

pr_agent/algo/language_handler.py

@@ -42,6 +42,11 @@ 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.file_filter import filter_ignored
 from pr_agent.algo.token_handler import TokenHandler, get_token_encoder
+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 = 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
@@ -78,9 +86,10 @@ def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler, model: s
     return final_diff
 
 
-def pr_generate_extended_diff(pr_languages: list, token_handler: TokenHandler,
-                              add_line_numbers_to_hunks: bool) -> \
-        Tuple[list, int]:
+def pr_generate_extended_diff(pr_languages: list,
+                              token_handler: TokenHandler,
+                              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.
@@ -90,13 +99,10 @@ def pr_generate_extended_diff(pr_languages: list, token_handler: TokenHandler,
       files.
     - token_handler: An object of the TokenHandler class used for handling tokens in the context of the pull request.
     - add_line_numbers_to_hunks: A boolean indicating whether to add line numbers to the hunks in the diff.
-
-    Returns:
-    - patches_extended: A list of extended patches for each file in the pull request.
-    - total_tokens: The total number of tokens used in the extended patches.
     """
     total_tokens = token_handler.prompt_tokens  # initial tokens
     patches_extended = []
+    patches_extended_tokens = []
     for lang in pr_languages:
         for file in lang['files']:
             original_file_content_str = file.base_file
@@ -105,8 +111,8 @@ def pr_generate_extended_diff(pr_languages: list, token_handler: TokenHandler,
                 continue
 
             # extend each patch with extra lines of context
-            extended_patch = extend_patch(original_file_content_str, patch, num_lines=PATCH_EXTRA_LINES)
-            full_extended_patch = f"## {file.filename}\n\n{extended_patch}\n"
+            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:
                 full_extended_patch = convert_to_hunks_with_lines_numbers(extended_patch, file)
@@ -114,13 +120,14 @@ def pr_generate_extended_diff(pr_languages: list, token_handler: TokenHandler,
             patch_tokens = token_handler.count_tokens(full_extended_patch)
             file.tokens = patch_tokens
             total_tokens += patch_tokens
+            patches_extended_tokens.append(patch_tokens)
             patches_extended.append(full_extended_patch)
 
-    return patches_extended, total_tokens
+    return patches_extended, total_tokens, patches_extended_tokens
 
 
 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.
@@ -146,6 +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
@@ -163,7 +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_)
@@ -177,17 +185,22 @@ 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}")
+                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)
@@ -202,9 +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):
@@ -216,7 +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()}"
@@ -324,7 +337,9 @@ def clip_tokens(text: str, max_tokens: int) -> str:
     Returns:
         str: The clipped string.
     """
-    # We'll estimate the number of tokens by hueristically assuming 2.5 tokens per word
+    if not text:
+        return text
+
     try:
         encoder = get_token_encoder()
         num_input_tokens = len(encoder.encode(text))
@@ -336,5 +351,87 @@ def clip_tokens(text: str, max_tokens: int) -> str:
         clipped_text = text[:num_output_chars]
         return clipped_text
     except Exception as e:
-        logging.warning(f"Failed to clip tokens: {e}")
+        get_logger().warning(f"Failed to clip tokens: {e}")
         return text
+
+
+def get_pr_multi_diffs(git_provider: GitProvider,
+                       token_handler: TokenHandler,
+                       model: str,
+                       max_calls: int = 5) -> List[str]:
+    """
+    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:
+        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)
+
+    # Sort files within each language group by tokens in descending order
+    sorted_files = []
+    for lang in pr_languages:
+        sorted_files.extend(sorted(lang['files'], key=lambda x: x.tokens, reverse=True))
+
+    patches = []
+    final_diff_list = []
+    total_tokens = token_handler.prompt_tokens
+    call_number = 1
+    for file in sorted_files:
+        if call_number > max_calls:
+            if get_settings().config.verbosity_level >= 2:
+                get_logger().info(f"Reached max calls ({max_calls})")
+            break
+
+        original_file_content_str = file.base_file
+        new_file_content_str = file.head_file
+        patch = file.patch
+        if not patch:
+            continue
+
+        # Remove delete-only hunks
+        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 > 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:
+                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:
+                get_logger().info(f"Tokens: {total_tokens}, last filename: {file.filename}")
+
+    # Add the last chunk
+    if patches:
+        final_diff = "\n".join(patches)
+        final_diff_list.append(final_diff)
+
+    return final_diff_list

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.
 
@@ -32,6 +32,7 @@ class TokenHandler:
         - user: The user string.
         """
         self.encoder = get_token_encoder()
+        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 +9,10 @@ from typing import Any, List
 
 import yaml
 from starlette_context import context
+
+from pr_agent.algo import MAX_TOKENS
 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 +22,7 @@ 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:
@@ -32,40 +34,51 @@ def convert_to_markdown(output_data: dict) -> str:
 
     emojis = {
         "Main theme": "🎯",
+        "PR summary": "📝",
         "Type of PR": "📌",
         "Score": "🏅",
         "Relevant tests added": "🧪",
         "Unrelated changes": "⚠️",
         "Focused PR": "✨",
         "Security concerns": "🔒",
-        "General PR suggestions": "💡",
+        "General suggestions": "💡",
         "Insights from user's answers": "📝",
         "Code feedback": "🤖",
+        "Estimated effort to review [1-5]": "⏱️",
     }
 
     for key, value in output_data.items():
-        if not value:
+        if value is None or value == '' or value == {}:
             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):
-            if key.lower() == 'code feedback':
-                markdown_text += "\n"  # just looks nicer with additional line breaks
             emoji = emojis.get(key, "")
+            if key.lower() == 'code feedback':
+                if gfm_supported:
+                    markdown_text += f"\n\n- **<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':
+                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.
 
@@ -88,6 +101,10 @@ def parse_code_suggestion(code_suggestions: dict) -> str:
                 markdown_text += f"\n  - **{sub_key}:** {sub_value}\n"
             else:
                 markdown_text += f"   **{sub_key}:** {sub_value}\n"
+            if not gfm_supported:
+                if "relevant line" not in sub_key.lower(): # nicer presentation
+                        # markdown_text = markdown_text.rstrip('\n') + "\\\n" # works for gitlab
+                        markdown_text = markdown_text.rstrip('\n') + "   \n"  # works for gitlab and bitbucker
 
     markdown_text += "\n"
     return markdown_text
@@ -145,7 +162,7 @@ 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
@@ -216,7 +233,7 @@ 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
@@ -245,39 +262,115 @@ def update_settings_from_args(args: List[str]) -> List[str]:
             arg = arg.strip()
             if arg.startswith('--'):
                 arg = arg.strip('-').strip()
-                vals = arg.split('=')
+                vals = arg.split('=', 1)
                 if len(vals) != 2:
-                    logging.error(f'Invalid argument format: {arg}')
+                    if len(vals) > 2: # --extended is a valid argument
+                        get_logger().error(f'Invalid argument format: {arg}')
                     other_args.append(arg)
                     continue
-                key, value = vals
-                key = key.strip().upper()
-                value = value.strip()
+                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
 
 
+def _fix_key_value(key: str, value: str):
+    key = key.strip().upper()
+    value = value.strip()
+    try:
+        value = yaml.safe_load(value)
+    except Exception as e:
+        get_logger().error(f"Failed to parse YAML for config override {key}={value}", exc_info=e)
+    return key, value
+
+
 def load_yaml(review_text: str) -> dict:
+    test = 1
     review_text = review_text.removeprefix('```yaml').rstrip('`')
     try:
-        data = yaml.load(review_text, Loader=yaml.SafeLoader)
+        data = yaml.safe_load(review_text)
     except Exception as e:
-        logging.error(f"Failed to parse AI prediction: {e}")
+        get_logger().error(f"Failed to parse AI prediction: {e}")
         data = try_fix_yaml(review_text)
     return data
 
 def try_fix_yaml(review_text: str) -> dict:
     review_text_lines = review_text.split('\n')
+
+    # first fallback - try to convert 'relevant line: ...' to relevant line: |-\n        ...'
+    review_text_lines_copy = review_text_lines.copy()
+    for i in range(0, len(review_text_lines_copy)):
+        if 'relevant line:' in review_text_lines_copy[i] and not '|-' in review_text_lines_copy[i]:
+            review_text_lines_copy[i] = review_text_lines_copy[i].replace('relevant line: ',
+                                                    'relevant line: |-\n        ')
+    try:
+        data = yaml.load('\n'.join(review_text_lines_copy), Loader=yaml.SafeLoader)
+        get_logger().info(f"Successfully parsed AI prediction after adding |-\n        to relevant line")
+        return data
+    except:
+        get_logger().debug(f"Failed to parse AI prediction after adding |-\n        to relevant line")
+
+    # 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])
         try:
             data = yaml.load(review_text_lines_tmp, Loader=yaml.SafeLoader)
-            logging.info(f"Successfully parsed AI prediction after removing {i} lines")
+            get_logger().info(f"Successfully parsed AI prediction after removing {i} lines")
             break
         except:
             pass
     return data
+
+
+def set_custom_labels(variables):
+    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', 'Refactoring', 'Enhancement', 'Documentation', 'Other']
+        labels_list = "\n      - ".join(labels) if labels else ""
+        labels_list = f"      - {labels_list}" if labels_list else ""
+        variables["custom_labels"] = labels_list
+        return
+    final_labels = ""
+    for k, v in labels.items():
+        final_labels += f"      - {k} ({v['description']})\n"
+    variables["custom_labels"] = final_labels
+    variables["custom_labels_examples"] = f"      - {list(labels.keys())[0]}"
+
+
+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', 'refactoring', '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()
+    max_tokens_model = MAX_TOKENS[model]
+    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

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):
@@ -17,26 +20,42 @@ 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.
-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.
-improve / improve_code - Suggest improvements to the code in the PR as pull request comments ready to commit.
-reflect - Ask the PR author questions about the PR.
-update_changelog - Update the changelog based on the PR's contents.
+-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.
+
+-describe / describe_pr - Modify the PR title and description based on the PR's contents.
+
+-improve / improve_code - Suggest improvements to the code in the PR as pull request comments ready to commit.
+Extended mode ('improve --extended') employs several calls, and provides a more thorough feedback
+
+-reflect - Ask the PR author questions about the PR.
+
+-update_changelog - Update the changelog based on the PR's contents.
+
+
+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

@@ -14,14 +14,19 @@ 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",
         "settings/pr_description_prompts.toml",
         "settings/pr_code_suggestions_prompts.toml",
+        "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

@@ -1,14 +1,21 @@
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.bitbucket_provider import BitbucketProvider
+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,
-    'local' : LocalGitProvider
+    'azure': AzureDevopsProvider,
+    'codecommit': CodeCommitProvider,
+    'local' : LocalGitProvider,
+    'gerrit': GerritProvider,
 }
 
 def get_git_provider():

pr_agent/git_providers/azuredevops_provider.py

@@ -0,0 +1,278 @@
+import json
+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
+    from azure.devops.connection import Connection
+    from azure.devops.v7_1.git.models import Comment, CommentThread, GitVersionDescriptor, GitPullRequest
+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.language_handler import is_valid_file
+from .git_provider import EDIT_TYPE, FilePatchInfo
+
+
+class AzureDevopsProvider:
+    def __init__(self, pr_url: Optional[str] = None, incremental: Optional[bool] = False):
+        if not AZURE_DEVOPS_AVAILABLE:
+            raise ImportError("Azure DevOps provider is not available. Please install the required dependencies.")
+
+        self.azure_devops_client = self._get_azure_devops_client()
+
+        self.workspace_slug = None
+        self.repo_slug = None
+        self.repo = None
+        self.pr_num = None
+        self.pr = None
+        self.temp_comments = []
+        self.incremental = incremental
+        if pr_url:
+            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', '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_repo_settings(self):
+        try:
+            contents = self.azure_devops_client.get_item_content(repository_id=self.repo_slug,
+                                                                 project=self.workspace_slug, download=False,
+                                                                 include_content_metadata=False, include_content=True,
+                                                                 path=".pr_agent.toml")
+            return contents
+        except Exception as e:
+            get_logger().exception("get repo settings error")
+            return ""
+
+    def get_files(self):
+        files = []
+        for i in self.azure_devops_client.get_pull_request_commits(project=self.workspace_slug,
+                                                                   repository_id=self.repo_slug,
+                                                                   pull_request_id=self.pr_num):
+
+            changes_obj = self.azure_devops_client.get_changes(project=self.workspace_slug,
+                                                               repository_id=self.repo_slug, commit_id=i.commit_id)
+
+            for c in changes_obj.changes:
+                files.append(c['item']['path'])
+        return list(set(files))
+
+    def get_diff_files(self) -> list[FilePatchInfo]:
+        try:
+            base_sha = self.pr.last_merge_target_commit
+            head_sha = self.pr.last_merge_source_commit
+
+            commits = self.azure_devops_client.get_pull_request_commits(project=self.workspace_slug,
+                                                                        repository_id=self.repo_slug,
+                                                                        pull_request_id=self.pr_num)
+
+            diff_files = []
+            diffs = []
+            diff_types = {}
+
+            for c in commits:
+                changes_obj = self.azure_devops_client.get_changes(project=self.workspace_slug,
+                                                                   repository_id=self.repo_slug, commit_id=c.commit_id)
+                for i in changes_obj.changes:
+                    if(i['item']['gitObjectType'] == 'tree'):
+                        continue
+                    diffs.append(i['item']['path'])
+                    diff_types[i['item']['path']] = i['changeType']
+
+            diffs = list(set(diffs))
+
+            for file in diffs:
+                if not is_valid_file(file):
+                    continue
+
+                version = GitVersionDescriptor(version=head_sha.commit_id, version_type='commit')
+                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
+                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':
+                    edit_type = EDIT_TYPE.ADDED
+                elif diff_types[file] == 'delete':
+                    edit_type = EDIT_TYPE.DELETED
+                elif diff_types[file] == 'rename':
+                    edit_type = EDIT_TYPE.RENAMED
+
+                version = GitVersionDescriptor(version=base_sha.commit_id, version_type='commit')
+                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
+                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)
+
+                diff_files.append(FilePatchInfo(original_file_content_str, new_file_content_str,
+                                                patch=patch,
+                                                filename=file,
+                                                edit_type=edit_type))
+
+            self.diff_files = diff_files
+            return diff_files
+        except Exception as e:
+            print(f"Error: {str(e)}")
+            return []
+
+    def publish_comment(self, pr_comment: str, is_temporary: bool = False):
+        comment = Comment(content=pr_comment)
+        thread = CommentThread(comments=[comment])
+        thread_response = self.azure_devops_client.create_thread(comment_thread=thread, project=self.workspace_slug,
+                                                                 repository_id=self.repo_slug,
+                                                                 pull_request_id=self.pr_num)
+        if is_temporary:
+            self.temp_comments.append({'thread_id': thread_response.id, 'comment_id': comment.id})
+
+    def publish_description(self, pr_title: str, pr_body: str):
+        try:
+            updated_pr = GitPullRequest()
+            updated_pr.title = pr_title
+            updated_pr.description = pr_body
+            self.azure_devops_client.update_pull_request(project=self.workspace_slug,
+                                                         repository_id=self.repo_slug,
+                                                         pull_request_id=self.pr_num,
+                                                         git_pull_request_to_update=updated_pr)
+        except Exception as e:
+            get_logger().exception(f"Could not update pull request {self.pr_num} description: {e}")
+
+    def remove_initial_comment(self):
+        return ""  # not implemented yet
+
+    def publish_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
+        raise NotImplementedError("Azure DevOps provider does not support publishing inline comment yet")
+
+    def create_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
+        raise NotImplementedError("Azure DevOps provider does not support creating inline comments yet")
+
+    def publish_inline_comments(self, comments: list[dict]):
+        raise NotImplementedError("Azure DevOps provider does not support publishing inline comments yet")
+
+    def get_title(self):
+        return self.pr.title
+
+    def get_languages(self):
+        languages = []
+        files = self.azure_devops_client.get_items(project=self.workspace_slug, repository_id=self.repo_slug,
+                                                   recursion_level="Full", include_content_metadata=True,
+                                                   include_links=False, download=False)
+        for f in files:
+            if f.git_object_type == 'blob':
+                file_name, file_extension = os.path.splitext(f.path)
+                languages.append(file_extension[1:])
+
+        extension_counts = {}
+        for ext in languages:
+            if ext != '':
+                extension_counts[ext] = extension_counts.get(ext, 0) + 1
+
+        total_extensions = sum(extension_counts.values())
+
+        extension_percentages = {ext: (count / total_extensions) * 100 for ext, count in extension_counts.items()}
+
+        return extension_percentages
+
+    def get_pr_branch(self):
+        pr_info = self.azure_devops_client.get_pull_request_by_id(project=self.workspace_slug,
+                                                                  pull_request_id=self.pr_num)
+        source_branch = pr_info.source_ref_name.split('/')[-1]
+        return source_branch
+
+    def get_pr_description(self):
+        max_tokens = get_settings().get("CONFIG.MAX_DESCRIPTION_TOKENS", None)
+        if max_tokens:
+            return clip_tokens(self.pr.description, max_tokens)
+        return self.pr.description
+
+    def get_user_id(self):
+        return 0
+
+    def get_issue_comments(self):
+        raise NotImplementedError("Azure DevOps 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
+
+    def get_issue_comments(self):
+        raise NotImplementedError("Azure DevOps provider does not support issue comments yet")
+
+    @staticmethod
+    def _parse_pr_url(pr_url: str) -> Tuple[str, int]:
+        parsed_url = urlparse(pr_url)
+
+        path_parts = parsed_url.path.strip('/').split('/')
+
+        if len(path_parts) < 6 or path_parts[4] != 'pullrequest':
+            raise ValueError("The provided URL does not appear to be a Azure DevOps 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_azure_devops_client(self):
+        try:
+            pat = get_settings().azure_devops.pat
+            org = get_settings().azure_devops.org
+        except AttributeError as e:
+            raise ValueError(
+                "Azure DevOps PAT token is required ") from e
+
+        credentials = BasicAuthentication('', pat)
+        azure_devops_connection = Connection(base_url=org, creds=credentials)
+        azure_devops_client = azure_devops_connection.clients.get_git_client()
+
+        return azure_devops_client
+
+    def _get_repo(self):
+        if self.repo is None:
+            self.repo = self.azure_devops_client.get_repository(project=self.workspace_slug,
+                                                                repository_id=self.repo_slug)
+        return self.repo
+
+    def _get_pr(self):
+        self.pr = self.azure_devops_client.get_pull_request_by_id(pull_request_id=self.pr_num, project=self.workspace_slug)
+        return self.pr
+
+    def get_commit_messages(self):
+        return ""  # not implemented yet

pr_agent/git_providers/bitbucket_provider.py

@@ -1,40 +1,112 @@
-import logging
+import json
 from typing import Optional, Tuple
 from urllib.parse import urlparse
 
 import requests
 from atlassian.bitbucket import Cloud
+from starlette_context import context
 
-from ..algo.pr_processing import clip_tokens
+from ..algo.pr_processing import find_line_number_of_relevant_line_in_file
 from ..config_loader import get_settings
-from .git_provider import FilePatchInfo
+from ..log import get_logger
+from .git_provider import FilePatchInfo, GitProvider, EDIT_TYPE
 
 
-class BitbucketProvider:
-    def __init__(self, pr_url: Optional[str] = None, incremental: Optional[bool] = False):
+class BitbucketProvider(GitProvider):
+    def __init__(
+        self, pr_url: Optional[str] = None, incremental: Optional[bool] = False
+    ):
         s = requests.Session()
-        s.headers['Authorization'] = f'Bearer {get_settings().get("BITBUCKET.BEARER_TOKEN", None)}'
+        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.BEARER_TOKEN", None)}'
+        s.headers["Content-Type"] = "application/json"
+        self.headers = s.headers
         self.bitbucket_client = Cloud(session=s)
-
         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
         if pr_url:
             self.set_pr(pr_url)
+        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 ""
 
+    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', '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
 
@@ -46,66 +118,148 @@ class BitbucketProvider:
         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()]
+        diff_split = [
+            "diff --git%s" % x for x in self.pr.diff().split("diff --git") if x.strip()
+        ]
 
         diff_files = []
         for index, diff in enumerate(diffs):
-            original_file_content_str = self._get_pr_file_content(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))
+            original_file_content_str = self._get_pr_file_content(
+                diff.old.get_data("links")
+            )
+            new_file_content_str = self._get_pr_file_content(diff.new.get_data("links"))
+            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 publish_persistent_comment(self, pr_comment: str, initial_text: str, updated_text: str):
+        try:
+            for comment in self.pr.comments():
+                body = comment.raw
+                if initial_text in body:
+                    if updated_text:
+                        pr_comment_updated = pr_comment.replace(initial_text, updated_text)
+                    else:
+                        pr_comment_updated = pr_comment
+                    d = {"content": {"raw": pr_comment_updated}}
+                    response = comment._update_data(comment.put(None, data=d))
+                    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:
-            self.temp_comments.append(comment['id'])
+            self.temp_comments.append(comment["id"])
 
     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, body: str, relevant_file: str, relevant_line_in_file: str):
-        pass
+    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):
-        raise NotImplementedError("Bitbucket provider does not support creating inline comments yet")
+        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 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]):
-        raise NotImplementedError("Bitbucket provider does not support publishing inline comments yet")
+        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):
-        languages = {self._get_repo().get_data('language'): 0}
+        languages = {self._get_repo().get_data("language"): 0}
         return languages
 
     def get_pr_branch(self):
         return self.pr.source_branch
 
-    def get_pr_description(self):
-        max_tokens = get_settings().get("CONFIG.MAX_DESCRIPTION_TOKENS", None)
-        if max_tokens:
-            return clip_tokens(self.pr.description, max_tokens)
+    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 get_repo_settings(self):
-        try:
-            contents = self.repo_obj.get_contents(".pr_agent.toml", ref=self.pr.head.sha).decoded_content
-            return contents
-        except Exception:
-            return ""
+        raise NotImplementedError(
+            "Bitbucket provider does not support issue comments yet"
+        )
 
     def add_eyes_reaction(self, issue_comment_id: int) -> Optional[int]:
         return True
@@ -117,13 +271,15 @@ class BitbucketProvider:
     def _parse_pr_url(pr_url: str) -> Tuple[str, int]:
         parsed_url = urlparse(pr_url)
 
-        if 'bitbucket.org' not in parsed_url.netloc:
+        if "bitbucket.org" not in parsed_url.netloc:
             raise ValueError("The provided URL is not a valid Bitbucket URL")
 
-        path_parts = parsed_url.path.strip('/').split('/')
+        path_parts = parsed_url.path.strip("/").split("/")
 
-        if len(path_parts) < 4 or path_parts[2] != 'pull-requests':
-            raise ValueError("The provided URL does not appear to be a Bitbucket PR URL")
+        if len(path_parts) < 4 or path_parts[2] != "pull-requests":
+            raise ValueError(
+                "The provided URL does not appear to be a Bitbucket PR URL"
+            )
 
         workspace_slug = path_parts[0]
         repo_slug = path_parts[1]
@@ -136,7 +292,9 @@ class BitbucketProvider:
 
     def _get_repo(self):
         if self.repo is None:
-            self.repo = self.bitbucket_client.workspaces.get(self.workspace_slug).repositories.get(self.repo_slug)
+            self.repo = self.bitbucket_client.workspaces.get(
+                self.workspace_slug
+            ).repositories.get(self.repo_slug)
         return self.repo
 
     def _get_pr(self):
@@ -147,3 +305,27 @@ class BitbucketProvider:
 
     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
+
+            })
+
+        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/codecommit_client.py

@@ -0,0 +1,277 @@
+import boto3
+import botocore
+
+
+class CodeCommitDifferencesResponse:
+    """
+    CodeCommitDifferencesResponse is the response object returned from our get_differences() function.
+    It maps the JSON response to member variables of this class.
+    """
+
+    def __init__(self, json: dict):
+        before_blob = json.get("beforeBlob", {})
+        after_blob = json.get("afterBlob", {})
+
+        self.before_blob_id = before_blob.get("blobId", "")
+        self.before_blob_path = before_blob.get("path", "")
+        self.after_blob_id = after_blob.get("blobId", "")
+        self.after_blob_path = after_blob.get("path", "")
+        self.change_type = json.get("changeType", "")
+
+
+class CodeCommitPullRequestResponse:
+    """
+    CodeCommitPullRequestResponse is the response object returned from our get_pr() function.
+    It maps the JSON response to member variables of this class.
+    """
+
+    def __init__(self, json: dict):
+        self.title = json.get("title", "")
+        self.description = json.get("description", "")
+
+        self.targets = []
+        for target in json.get("pullRequestTargets", []):
+            self.targets.append(CodeCommitPullRequestResponse.CodeCommitPullRequestTarget(target))
+
+    class CodeCommitPullRequestTarget:
+        """
+        CodeCommitPullRequestTarget is a subclass of CodeCommitPullRequestResponse that
+        holds details about an individual target commit.
+        """
+
+        def __init__(self, json: dict):
+            self.source_commit = json.get("sourceCommit", "")
+            self.source_branch = json.get("sourceReference", "")
+            self.destination_commit = json.get("destinationCommit", "")
+            self.destination_branch = json.get("destinationReference", "")
+
+
+class CodeCommitClient:
+    """
+    CodeCommitClient is a wrapper around the AWS boto3 SDK for the CodeCommit client
+    """
+
+    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}") from e
+
+    def get_differences(self, repo_name: int, destination_commit: str, source_commit: str):
+        """
+        Get the differences between two commits in CodeCommit.
+
+        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)
+
+        Returns:
+        - 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
+        """
+        if self.boto_client is None:
+            self._connect_boto_client()
+
+        # The differences response from AWS is paginated, so we need to iterate through the pages to get all the differences.
+        differences = []
+        try:
+            paginator = self.boto_client.get_paginator("get_differences")
+            for page in paginator.paginate(
+                repositoryName=repo_name,
+                beforeCommitSpecifier=destination_commit,
+                afterCommitSpecifier=source_commit,
+            ):
+                differences.extend(page.get("differences", []))
+        except botocore.exceptions.ClientError as 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:
+            output.append(CodeCommitDifferencesResponse(json))
+        return output
+
+    def get_file(self, repo_name: str, file_path: str, sha_hash: str, optional: bool = False):
+        """
+        Retrieve a file from CodeCommit.
+
+        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
+
+        Returns:
+        - File contents
+
+        Boto3 Documentation:
+        - aws codecommit get_file
+        - https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/codecommit/client/get_file.html
+        """
+        if not file_path:
+            return ""
+
+        if self.boto_client is None:
+            self._connect_boto_client()
+
+        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 ""
+            raise ValueError(f"CodeCommit cannot retrieve file '{file_path}' from repository '{repo_name}'") from e
+        except Exception as e:
+            raise ValueError(f"CodeCommit cannot retrieve file '{file_path}' from repository '{repo_name}'") from e
+        if "fileContent" not in response:
+            raise ValueError(f"File content is empty for file: {file_path}")
+
+        return response.get("fileContent", "")
+
+    def get_pr(self, repo_name: str, pr_number: int):
+        """
+        Get a information about a CodeCommit PR.
+
+        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
+        """
+        if self.boto_client is None:
+            self._connect_boto_client()
+
+        try:
+            response = self.boto_client.get_pull_request(pullRequestId=str(pr_number))
+        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
+
+        if "pullRequest" not in response:
+            raise ValueError("CodeCommit PR number not found: {pr_number}")
+
+        return CodeCommitPullRequestResponse(response.get("pullRequest", {}))
+
+    def publish_description(self, pr_number: int, pr_title: str, pr_body: str):
+        """
+        Set the title and description on a pull request
+
+        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 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.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
+            if e.response["Error"]["Code"] == 'PullRequestDoesNotExistException':
+                raise ValueError(f"PR number does not exist: {pr_number}") from e
+            raise ValueError(f"Boto3 client error calling post_comment_for_pull_request") from e
+        except Exception as e:
+            raise ValueError(f"Error calling post_comment_for_pull_request") from e

pr_agent/git_providers/codecommit_provider.py

@@ -0,0 +1,495 @@
+import os
+import re
+from collections import Counter
+from typing import List, Optional, Tuple
+from urllib.parse import urlparse
+
+from pr_agent.git_providers.codecommit_client import CodeCommitClient
+
+from ..algo.language_handler import is_valid_file, language_extension_map
+from ..algo.utils import load_large_diff
+from .git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
+from ..log import get_logger
+
+
+class PullRequestCCMimic:
+    """
+    This class mimics the PullRequest class from the PyGithub library for the CodeCommitProvider.
+    """
+
+    def __init__(self, title: str, diff_files: List[FilePatchInfo]):
+        self.title = title
+        self.diff_files = diff_files
+        self.description = None
+        self.source_commit = None
+        self.source_branch = None  # the branch containing your new code changes
+        self.destination_commit = None
+        self.destination_branch = None  # the branch you are going to merge into
+
+
+class CodeCommitFile:
+    """
+    This class represents a file in a pull request in CodeCommit.
+    """
+
+    def __init__(
+        self,
+        a_path: str,
+        a_blob_id: str,
+        b_path: str,
+        b_blob_id: str,
+        edit_type: EDIT_TYPE,
+    ):
+        self.a_path = a_path
+        self.a_blob_id = a_blob_id
+        self.b_path = b_path
+        self.b_blob_id = b_blob_id
+        self.edit_type: EDIT_TYPE = edit_type
+        self.filename = b_path if b_path else a_path
+
+
+class CodeCommitProvider(GitProvider):
+    """
+    This class implements the GitProvider interface for AWS CodeCommit repositories.
+    """
+
+    def __init__(self, pr_url: Optional[str] = None, incremental: Optional[bool] = False):
+        self.codecommit_client = CodeCommitClient()
+        self.aws_client = None
+        self.repo_name = None
+        self.pr_num = None
+        self.pr = None
+        self.diff_files = None
+        self.git_files = None
+        if pr_url:
+            self.set_pr(pr_url)
+
+    def provider_name(self):
+        return "CodeCommit"
+
+    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 set_pr(self, pr_url: str):
+        self.repo_name, self.pr_num = self._parse_pr_url(pr_url)
+        self.pr = self._get_pr()
+
+    def get_files(self) -> list[CodeCommitFile]:
+        # bring files from CodeCommit only once
+        if self.git_files:
+            return self.git_files
+
+        self.git_files = []
+        differences = self.codecommit_client.get_differences(self.repo_name, self.pr.destination_commit, self.pr.source_commit)
+        for item in differences:
+            self.git_files.append(CodeCommitFile(item.before_blob_path,
+                                                 item.before_blob_id,
+                                                 item.after_blob_path,
+                                                 item.after_blob_id,
+                                                 CodeCommitProvider._get_edit_type(item.change_type)))
+        return self.git_files
+
+    def get_diff_files(self) -> list[FilePatchInfo]:
+        """
+        Retrieves the list of files that have been modified, added, deleted, or renamed in a pull request in CodeCommit,
+        along with their content and patch information.
+
+        Returns:
+            diff_files (List[FilePatchInfo]): List of FilePatchInfo objects representing the modified, added, deleted,
+            or renamed files in the merge request.
+        """
+        # bring files from CodeCommit only once
+        if self.diff_files:
+            return self.diff_files
+
+        self.diff_files = []
+
+        files = self.get_files()
+        for diff_item in files:
+            patch_filename = ""
+            if diff_item.a_blob_id is not None:
+                patch_filename = diff_item.a_path
+                original_file_content_str = self.codecommit_client.get_file(
+                    self.repo_name, diff_item.a_path, self.pr.destination_commit)
+                if isinstance(original_file_content_str, (bytes, bytearray)):
+                    original_file_content_str = original_file_content_str.decode("utf-8")
+            else:
+                original_file_content_str = ""
+
+            if diff_item.b_blob_id is not None:
+                patch_filename = diff_item.b_path
+                new_file_content_str = self.codecommit_client.get_file(self.repo_name, diff_item.b_path, self.pr.source_commit)
+                if isinstance(new_file_content_str, (bytes, bytearray)):
+                    new_file_content_str = new_file_content_str.decode("utf-8")
+            else:
+                new_file_content_str = ""
+
+            patch = load_large_diff(patch_filename, new_file_content_str, original_file_content_str)
+
+            # Store the diffs as a list of FilePatchInfo objects
+            info = FilePatchInfo(
+                original_file_content_str,
+                new_file_content_str,
+                patch,
+                diff_item.b_path,
+                edit_type=diff_item.edit_type,
+                old_filename=None
+                if diff_item.a_path == diff_item.b_path
+                else diff_item.a_path,
+            )
+            # Only add valid files to the diff list
+            # "bad extensions" are set in the language_extensions.toml file
+            # a "valid file" is one that is not in the "bad extensions" list
+            if is_valid_file(info.filename):
+                self.diff_files.append(info)
+
+        return self.diff_files
+
+    def publish_description(self, pr_title: str, pr_body: str):
+        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:
+            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=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 publish comment for PR: {self.pr_num}") from e
+
+    def publish_code_suggestions(self, code_suggestions: list) -> bool:
+        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
+
+    def get_labels(self):
+        return [""]  # not implemented yet
+
+    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):
+        raise NotImplementedError("CodeCommit provider does not support creating inline comments yet")
+
+    def publish_inline_comments(self, comments: list[dict]):
+        raise NotImplementedError("CodeCommit provider does not support publishing inline comments yet")
+
+    def get_title(self):
+        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.
+        """
+        commit_files = self.get_files()
+        filenames = [ item.filename for item in commit_files ]
+        extensions = CodeCommitProvider._get_file_extensions(filenames)
+
+        # Calculate the percentage of each file extension in the PR
+        percentages = CodeCommitProvider._get_language_percentages(extensions)
+
+        # The global language_extension_map is a dictionary of languages,
+        # where each dictionary item is a BoxList of extensions.
+        # We want a dictionary of extensions,
+        # where each dictionary item is a language name.
+        # We build that language->extension dictionary here in main_extensions_flat.
+        main_extensions_flat = {}
+        for language, extensions in language_extension_map.items():
+            for ext in extensions:
+                main_extensions_flat[ext] = language
+
+        # Map the file extension/languages to percentages
+        languages = {}
+        for ext, pct in percentages.items():
+            languages[main_extensions_flat.get(ext, "")] = pct
+
+        return languages
+
+    def get_pr_branch(self):
+        return self.pr.source_branch
+
+    def get_pr_description_full(self) -> str:
+        return self.pr.description
+
+    def get_user_id(self):
+        return -1  # not implemented yet
+
+    def get_issue_comments(self):
+        raise NotImplementedError("CodeCommit provider does not support issue comments yet")
+
+    def get_repo_settings(self):
+        # a local ".pr_agent.toml" settings file is optional
+        settings_filename = ".pr_agent.toml"
+        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 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("/")
+
+        if (
+            len(path_parts) < 6
+            or path_parts[0] != "codesuite"
+            or path_parts[1] != "codecommit"
+            or path_parts[2] != "repositories"
+            or path_parts[4] != "pull-requests"
+        ):
+            raise ValueError(f"The provided URL does not appear to be a CodeCommit PR URL: {pr_url}")
+
+        repo_name = path_parts[3]
+
+        try:
+            pr_number = int(path_parts[5])
+        except ValueError as e:
+            raise ValueError(f"Unable to convert PR number to integer: '{path_parts[5]}'") from e
+
+        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.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 targets in one CodeCommit PR
+        #       for now, we are only using the first target in the PR
+        if len(response.targets) > 1:
+            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
+        # (This strategy was copied from the LocalGitProvider)
+        mimic = PullRequestCCMimic(response.title, self.diff_files)
+        mimic.description = response.description
+        mimic.source_commit = response.targets[0].source_commit
+        mimic.source_branch = response.targets[0].source_branch
+        mimic.destination_commit = response.targets[0].destination_commit
+        mimic.destination_branch = response.targets[0].destination_branch
+
+        return mimic
+
+    def get_commit_messages(self):
+        return ""  # not implemented yet
+
+    @staticmethod
+    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.
+        """
+        t = codecommit_change_type.upper()
+        edit_type = None
+        if t == "A":
+            edit_type = EDIT_TYPE.ADDED
+        elif t == "D":
+            edit_type = EDIT_TYPE.DELETED
+        elif t == "M":
+            edit_type = EDIT_TYPE.MODIFIED
+        elif t == "R":
+            edit_type = EDIT_TYPE.RENAMED
+        return edit_type
+
+    @staticmethod
+    def _get_file_extensions(filenames):
+        """
+        Return a list of file extensions from a list of filenames.
+        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:
+            filename, ext = os.path.splitext(filename)
+            if ext:
+                extensions.append(ext.lower())
+            else:
+                extensions.append("")
+        return extensions
+
+    @staticmethod
+    def _get_language_percentages(extensions):
+        """
+        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:
+            return {}
+
+        # Identify language by file extension and count
+        lang_count = Counter(extensions)
+        # Convert counts to percentages
+        lang_percentage = {
+            lang: round(count / total_files * 100) for lang, count in lang_count.items()
+        }
+        return lang_percentage

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 = 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

@@ -5,12 +5,15 @@ from dataclasses import dataclass
 from enum import Enum
 from typing import Optional
 
+from pr_agent.log import get_logger
+
 
 class EDIT_TYPE(Enum):
     ADDED = 1
     DELETED = 2
     MODIFIED = 3
     RENAMED = 4
+    UNKNOWN = 5
 
 
 @dataclass
@@ -20,7 +23,7 @@ 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
 
 
@@ -41,6 +44,9 @@ class GitProvider(ABC):
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
         pass
 
+    def publish_persistent_comment(self, pr_comment: str, initial_text: str, updated_text: str):
+        self.publish_comment(pr_comment)
+
     @abstractmethod
     def publish_inline_comment(self, body: str, relevant_file: str, relevant_line_in_file: str):
         pass
@@ -54,7 +60,7 @@ class GitProvider(ABC):
         pass
 
     @abstractmethod
-    def publish_code_suggestions(self, code_suggestions: list):
+    def publish_code_suggestions(self, code_suggestions: list) -> bool:
         pass
 
     @abstractmethod
@@ -69,6 +75,10 @@ class GitProvider(ABC):
     def remove_initial_comment(self):
         pass
 
+    @abstractmethod
+    def remove_comment(self, comment):
+        pass
+
     @abstractmethod
     def get_languages(self):
         pass
@@ -82,9 +92,30 @@ class GitProvider(ABC):
         pass
 
     @abstractmethod
-    def get_pr_description(self):
+    def get_pr_description_full(self) -> str:
         pass
 
+    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_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 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
+        if "## User Description:" not in description:
+            return ""
+        # otherwise, extract the original user description from the existing pr-agent description and return it
+        return description.split("## User Description:", 1)[1].strip()
+
     @abstractmethod
     def get_issue_comments(self):
         pass
@@ -105,17 +136,31 @@ class GitProvider(ABC):
     def get_commit_messages(self):
         pass
 
+    def get_pr_id(self):
+        return ""
+
 def get_main_pr_language(languages, files) -> str:
     """
     Get the main language of the commit. Return an empty string if cannot determine.
     """
     main_language_str = ""
+    if not languages:
+        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
@@ -137,10 +182,11 @@ def get_main_pr_language(languages, files) -> str:
                 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':
+                most_common_extension == top_language:
             main_language_str = top_language
 
-    except Exception:
+    except Exception as e:
+        get_logger().exception(e)
         pass
 
     return main_language_str
@@ -150,6 +196,13 @@ 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.pr_processing import clip_tokens, find_line_number_of_relevant_line_in_file
 from ..algo.utils import load_large_diff
-from ..algo.pr_processing import find_line_number_of_relevant_line_in_file, clip_tokens
 from ..config_loader import get_settings
+from ..log import get_logger
 from ..servers.utils import RateLimitExceeded
+from .git_provider import FilePatchInfo, GitProvider, IncrementalPR, EDIT_TYPE
 
 
 class GithubProvider(GitProvider):
@@ -32,7 +31,7 @@ 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]
 
@@ -51,36 +50,42 @@ 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})
 
     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
+    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 +129,49 @@ 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
+                file_patch_canonical_structure = FilePatchInfo(original_file_content_str, new_file_content_str, patch,
+                                                               file.filename, edit_type=edit_type)
+                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 publish_persistent_comment(self, pr_comment: str, initial_text: str, updated_text: str):
+        prev_comments = list(self.pr.get_issue_comments())
+        for comment in prev_comments:
+            body = comment.body
+            if body.startswith(initial_text):
+                if updated_text:
+                    pr_comment_updated = pr_comment.replace(initial_text, updated_text)
+                else:
+                    pr_comment_updated = pr_comment
+                response = comment.edit(pr_comment_updated)
+                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 +188,7 @@ 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"
@@ -166,7 +198,7 @@ class GithubProvider(GitProvider):
     def publish_inline_comments(self, comments: list[dict]):
         self.pr.create_review(commit=self.last_commit_id, comments=comments)
 
-    def publish_code_suggestions(self, code_suggestions: list):
+    def publish_code_suggestions(self, code_suggestions: list) -> bool:
         """
         Publishes code suggestions as comments on the PR.
         """
@@ -179,13 +211,13 @@ 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 +244,22 @@ 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:
+                    self.remove_comment(comment)
+        except Exception as e:
+            get_logger().exception(f"Failed to remove initial comment, error: {e}")
+
+    def remove_comment(self, comment):
+        try:
             comment.delete()
         except Exception as e:
-            logging.exception(f"Failed to remove initial comment, error: {e}")
+            get_logger().exception(f"Failed to remove comment, error: {e}")
 
     def get_title(self):
         return self.pr.title
@@ -233,18 +271,16 @@ class GithubProvider(GitProvider):
     def get_pr_branch(self):
         return self.pr.head.ref
 
-    def get_pr_description(self):
-        max_tokens = get_settings().get("CONFIG.MAX_DESCRIPTION_TOKENS", None)
-        if max_tokens:
-            return clip_tokens(self.pr.body, max_tokens)
+    def get_pr_description_full(self):
         return self.pr.body
 
     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):
@@ -261,7 +297,10 @@ 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 ""
@@ -271,7 +310,7 @@ 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:
@@ -279,7 +318,7 @@ 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
 
 
@@ -312,6 +351,35 @@ 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")
 
@@ -369,13 +437,13 @@ 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):
@@ -417,6 +485,13 @@ class GithubProvider(GitProvider):
                 return link
         except Exception as e:
             if get_settings().config.verbosity_level >= 2:
-                logging.info(f"Failed adding line link, error: {e}")
+                get_logger().info(f"Failed adding line link, error: {e}")
 
         return ""
+
+    def get_pr_id(self):
+        try:
+            pr_id = f"{self.repo}/{self.pr_num}"
+            return pr_id
+        except:
+            return ""

pr_agent/git_providers/gitlab_provider.py

@@ -1,4 +1,4 @@
-import logging
+import hashlib
 import re
 from typing import Optional, Tuple
 from urllib.parse import urlparse
@@ -7,12 +7,12 @@ import gitlab
 from gitlab import GitlabGetError
 
 from ..algo.language_handler import is_valid_file
-from ..algo.pr_processing import clip_tokens
+from ..algo.pr_processing import clip_tokens, find_line_number_of_relevant_line_in_file
 from ..algo.utils import load_large_diff
 from ..config_loader import get_settings
 from .git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
+from ..log import get_logger
 
-logger = logging.getLogger()
 
 class DiffNotFoundError(Exception):
     """Raised when the diff for a merge request cannot be found."""
@@ -43,7 +43,7 @@ class GitLabProvider(GitProvider):
         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']:
             return False
         return True
 
@@ -58,7 +58,7 @@ class GitLabProvider(GitProvider):
         try:
             self.last_diff = self.mr.diffs.list(get_all=True)[-1]
         except IndexError as e:
-            logger.error(f"Could not get diff for merge request {self.id_mr}")
+            get_logger().error(f"Could not get diff for merge request {self.id_mr}")
             raise DiffNotFoundError(f"Could not get diff for merge request {self.id_mr}") from e
 
 
@@ -98,7 +98,7 @@ class GitLabProvider(GitProvider):
                     if isinstance(new_file_content_str, bytes):
                         new_file_content_str = bytes.decode(new_file_content_str, 'utf-8')
                 except UnicodeDecodeError:
-                    logging.warning(
+                    get_logger().warning(
                         f"Cannot decode file {diff['old_path']} or {diff['new_path']} in merge request {self.id_mr}")
 
                 edit_type = EDIT_TYPE.MODIFIED
@@ -134,7 +134,22 @@ class GitLabProvider(GitProvider):
             self.mr.description = pr_body
             self.mr.save()
         except Exception as e:
-            logging.exception(f"Could not update merge request {self.id_mr} description: {e}")
+            get_logger().exception(f"Could not update merge request {self.id_mr} description: {e}")
+
+    def publish_persistent_comment(self, pr_comment: str, initial_text: str, updated_text: str):
+        try:
+            for comment in self.mr.notes.list(get_all=True)[::-1]:
+                if comment.body.startswith(initial_text):
+                    if updated_text:
+                        pr_comment_updated = pr_comment.replace(initial_text, updated_text)
+                    else:
+                        pr_comment_updated = pr_comment
+                    response = self.mr.notes.update(comment.id, {'body': pr_comment_updated})
+                    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 +171,12 @@ 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,
@@ -174,28 +189,27 @@ 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
 
-    def publish_code_suggestions(self, code_suggestions: list):
+    def publish_code_suggestions(self, code_suggestions: list) -> bool:
         for suggestion in code_suggestions:
             try:
                 body = suggestion['body']
@@ -226,7 +240,10 @@ 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 +302,15 @@ class GitLabProvider(GitProvider):
     def remove_initial_comment(self):
         try:
             for comment in self.temp_comments:
+                self.remove_comment(comment)
+        except Exception as e:
+            get_logger().exception(f"Failed to remove temp comments, error: {e}")
+
+    def remove_comment(self, comment):
+        try:
             comment.delete()
         except Exception as e:
-            logging.exception(f"Failed to remove temp comments, error: {e}")
+            get_logger().exception(f"Failed to remove comment, error: {e}")
 
     def get_title(self):
         return self.mr.title
@@ -299,10 +322,7 @@ class GitLabProvider(GitProvider):
     def get_pr_branch(self):
         return self.mr.source_branch
 
-    def get_pr_description(self):
-        max_tokens = get_settings().get("CONFIG.MAX_DESCRIPTION_TOKENS", None)
-        if max_tokens:
-            return clip_tokens(self.mr.description, max_tokens)
+    def get_pr_description_full(self):
         return self.mr.description
 
     def get_issue_comments(self):
@@ -310,7 +330,7 @@ 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 ""
@@ -358,7 +378,7 @@ 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
@@ -382,3 +402,34 @@ class GitLabProvider(GitProvider):
         if max_tokens:
             commit_messages_str = clip_tokens(commit_messages_str, max_tokens)
         return commit_messages_str
+
+    def get_pr_id(self):
+        try:
+            pr_id = self.mr.web_url
+            return pr_id
+        except:
+            return ""
+
+    def generate_link_to_relevant_line_number(self, suggestion) -> str:
+        try:
+            relevant_file = suggestion['relevant file'].strip('`').strip("'")
+            relevant_line_str = suggestion['relevant line']
+            if not relevant_line_str:
+                return ""
+
+            position, absolute_position = find_line_number_of_relevant_line_in_file \
+                (self.diff_files, relevant_file, relevant_line_str)
+
+            if absolute_position != -1:
+                # link to right file only
+                link = f"https://gitlab.com/codiumai/pr-agent/-/blob/{self.mr.source_branch}/{relevant_file}?ref_type=heads#L{absolute_position}"
+
+                # # link to diff
+                # sha_file = hashlib.sha1(relevant_file.encode('utf-8')).hexdigest()
+                # link = f"{self.pr.web_url}/diffs#{sha_file}_{absolute_position}_{absolute_position}"
+                return link
+        except Exception as e:
+            if get_settings().config.verbosity_level >= 2:
+                get_logger().info(f"Failed adding line link, error: {e}")
+
+        return ""

pr_agent/git_providers/local_git_provider.py

@@ -1,4 +1,3 @@
-import logging
 from collections import Counter
 from pathlib import Path
 from typing import List
@@ -7,6 +6,7 @@ from git import Repo
 
 from pr_agent.config_loader import _find_repository_root, get_settings
 from pr_agent.git_providers.git_provider import EDIT_TYPE, FilePatchInfo, GitProvider
+from pr_agent.log import get_logger
 
 
 class PullRequestMimic:
@@ -49,14 +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
 
@@ -130,7 +131,7 @@ class LocalGitProvider(GitProvider):
                                 relevant_lines_start: int, relevant_lines_end: int):
         raise NotImplementedError('Publishing code suggestions is not implemented for the local git provider')
 
-    def publish_code_suggestions(self, code_suggestions: list):
+    def publish_code_suggestions(self, code_suggestions: list) -> bool:
         raise NotImplementedError('Publishing code suggestions is not implemented for the local git provider')
 
     def publish_labels(self, labels):
@@ -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.
@@ -158,7 +162,7 @@ class LocalGitProvider(GitProvider):
     def get_user_id(self):
         return -1  # Not used anywhere for the local provider, but required by the interface
 
-    def get_pr_description(self):
+    def get_pr_description_full(self):
         commits_diff = list(self.repo.iter_commits(self.target_branch_name + '..HEAD'))
         # Get the commit messages and concatenate
         commit_messages = " ".join([commit.message for commit in commits_diff])

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/__init__.py

@@ -0,0 +1,16 @@
+from pr_agent.config_loader import get_settings
+
+
+def get_secret_provider():
+    try:
+        provider_id = get_settings().config.secret_provider
+    except AttributeError as e:
+        raise ValueError("secret_provider is a required attribute in the configuration file") from e
+    try:
+        if provider_id == 'google_cloud_storage':
+            from pr_agent.secret_providers.google_cloud_storage_secret_provider import GoogleCloudStorageSecretProvider
+            return GoogleCloudStorageSecretProvider()
+        else:
+            raise ValueError(f"Unknown secret provider: {provider_id}")
+    except Exception as e:
+        raise ValueError(f"Failed to initialize secret provider {provider_id}") from e

pr_agent/secret_providers/google_cloud_storage_secret_provider.py

@@ -0,0 +1,34 @@
+import ujson
+from google.cloud import storage
+
+from pr_agent.config_loader import get_settings
+from pr_agent.log import get_logger
+from pr_agent.secret_providers.secret_provider import SecretProvider
+
+
+class GoogleCloudStorageSecretProvider(SecretProvider):
+    def __init__(self):
+        try:
+            self.client = storage.Client.from_service_account_info(ujson.loads(get_settings().google_cloud_storage.
+                                                                               service_account))
+            self.bucket_name = get_settings().google_cloud_storage.bucket_name
+            self.bucket = self.client.bucket(self.bucket_name)
+        except Exception as e:
+            get_logger().error(f"Failed to initialize Google Cloud Storage Secret Provider: {e}")
+            raise e
+
+    def get_secret(self, secret_name: str) -> str:
+        try:
+            blob = self.bucket.blob(secret_name)
+            return blob.download_as_string()
+        except Exception as 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):
+        try:
+            blob = self.bucket.blob(secret_name)
+            blob.upload_from_string(secret_value)
+        except Exception as e:
+            get_logger().error(f"Failed to store secret {secret_name} in Google Cloud Storage: {e}")
+            raise e

pr_agent/secret_providers/secret_provider.py

@@ -0,0 +1,12 @@
+from abc import ABC, abstractmethod
+
+
+class SecretProvider(ABC):
+
+    @abstractmethod
+    def get_secret(self, secret_name: str) -> str:
+        pass
+
+    @abstractmethod
+    def store_secret(self, secret_name: str, secret_value: str):
+        pass

pr_agent/servers/atlassian-connect.json

@@ -0,0 +1,33 @@
+{
+  "name": "CodiumAI PR-Agent",
+  "description": "CodiumAI PR-Agent",
+  "key": "app_key",
+  "vendor": {
+    "name": "CodiumAI",
+    "url": "https://codium.ai"
+  },
+  "authentication": {
+    "type": "jwt"
+  },
+  "baseUrl": "base_url",
+  "lifecycle": {
+    "installed": "/installed",
+    "uninstalled": "/uninstalled"
+  },
+  "scopes": [
+    "account",
+    "repository",
+    "pullrequest"
+  ],
+  "contexts": [
+    "account"
+  ],
+  "modules": {
+    "webhooks": [
+      {
+        "event": "*",
+        "url": "/webhook"
+      }
+    ]
+  }
+}

pr_agent/servers/bitbucket_app.py

@@ -0,0 +1,149 @@
+import copy
+import hashlib
+import json
+import os
+import time
+
+import jwt
+import requests
+import uvicorn
+from fastapi import APIRouter, FastAPI, Request, Response
+from starlette.background import BackgroundTasks
+from starlette.middleware import Middleware
+from starlette.responses import JSONResponse
+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 LoggingFormat, get_logger, setup_logger
+from pr_agent.secret_providers import get_secret_provider
+
+setup_logger(fmt=LoggingFormat.JSON)
+router = APIRouter()
+secret_provider = get_secret_provider()
+
+async def get_bearer_token(shared_secret: str, client_key: str):
+    try:
+        now = int(time.time())
+        url = "https://bitbucket.org/site/oauth2/access_token"
+        canonical_url = "GET&/site/oauth2/access_token&"
+        qsh = hashlib.sha256(canonical_url.encode("utf-8")).hexdigest()
+        app_key = get_settings().bitbucket.app_key
+
+        payload = {
+            "iss": app_key,
+            "iat": now,
+            "exp": now + 240,
+            "qsh": qsh,
+            "sub": client_key,
+            }
+        token = jwt.encode(payload, shared_secret, algorithm="HS256")
+        payload = 'grant_type=urn%3Abitbucket%3Aoauth2%3Ajwt'
+        headers = {
+            'Authorization': f'JWT {token}',
+            'Content-Type': 'application/x-www-form-urlencoded'
+        }
+        response = requests.request("POST", url, headers=headers, data=payload)
+        bearer_token = response.json()["access_token"]
+        return bearer_token
+    except Exception as e:
+        get_logger().error(f"Failed to get bearer token: {e}")
+        raise e
+
+@router.get("/")
+async def handle_manifest(request: Request, response: Response):
+    cur_dir = os.path.dirname(os.path.abspath(__file__))
+    manifest = open(os.path.join(cur_dir, "atlassian-connect.json"), "rt").read()
+    try:
+        manifest = manifest.replace("app_key", get_settings().bitbucket.app_key)
+        manifest = manifest.replace("base_url", get_settings().bitbucket.base_url)
+    except:
+        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):
+    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()
+    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"]
+            jwt.decode(input_jwt, shared_secret, audience=client_key, algorithms=["HS256"])
+            bearer_token = await get_bearer_token(shared_secret, client_key)
+            context['bitbucket_bearer_token'] = bearer_token
+            context["settings"] = copy.deepcopy(global_settings)
+            event = data["event"]
+            agent = PRAgent()
+            if event == "pullrequest:created":
+                pr_url = data["data"]["pullrequest"]["links"]["html"]["href"]
+                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"]
+                with get_logger().contextualize(**log_context):
+                    await agent.handle_request(pr_url, comment_body)
+        except Exception as e:
+            get_logger().error(f"Failed to handle webhook: {e}")
+    background_tasks.add_task(inner)
+    return "OK"
+
+@router.get("/webhook")
+async def handle_github_webhooks(request: Request, response: Response):
+    return "Webhook server online!"
+
+@router.post("/installed")
+async def handle_installed_webhooks(request: Request, response: Response):
+    try:
+        get_logger().info("handle_installed_webhooks")
+        get_logger().info(request.headers)
+        data = await request.json()
+        get_logger().info(data)
+        shared_secret = data["sharedSecret"]
+        client_key = data["clientKey"]
+        username = data["principal"]["username"]
+        secrets = {
+            "shared_secret": shared_secret,
+            "client_key": client_key
+        }
+        secret_provider.store_secret(username, json.dumps(secrets))
+    except Exception as 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()
+    get_logger().info(data)
+
+
+def start():
+    get_settings().set("CONFIG.PUBLISH_OUTPUT_PROGRESS", False)
+    get_settings().set("CONFIG.GIT_PROVIDER", "bitbucket")
+    get_settings().set("PR_DESCRIPTION.PUBLISH_DESCRIPTION_AS_COMMENT", True)
+    middleware = [Middleware(RawContextMiddleware)]
+    app = FastAPI(middleware=middleware)
+    app.include_router(router)
+
+    uvicorn.run(app, host="0.0.0.0", port=int(os.getenv("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

@@ -5,6 +5,10 @@ import os
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
+from pr_agent.git_providers.utils import apply_repo_settings
+from pr_agent.log import get_logger
+from pr_agent.tools.pr_code_suggestions import PRCodeSuggestions
+from pr_agent.tools.pr_description import PRDescription
 from pr_agent.tools.pr_reviewer import PRReviewer
 
 
@@ -12,12 +16,11 @@ 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 +50,30 @@ 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:
+                auto_review = os.environ.get('github_action.auto_review', None)
+                if auto_review is None or (isinstance(auto_review, str) and auto_review.lower() == 'true'):
                     await PRReviewer(pr_url).run()
+                auto_describe = os.environ.get('github_action.auto_describe', None)
+                if isinstance(auto_describe, str) and auto_describe.lower() == 'true':
+                    await PRDescription(pr_url).run()
+                auto_improve = os.environ.get('github_action.auto_improve', None)
+                if isinstance(auto_improve, str) and auto_improve.lower() == 'true':
+                    await PRCodeSuggestions(pr_url).run()
 
     # Handle issue comment event
     elif GITHUB_EVENT_NAME == "issue_comment":
@@ -61,12 +81,21 @@ 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__':

pr_agent/servers/github_app.py

@@ -1,7 +1,7 @@
 import copy
-import logging
-import sys
-from typing import Any, Dict
+import os
+import asyncio.locks
+from typing import Any, Dict, List, Tuple
 
 import uvicorn
 from fastapi import APIRouter, FastAPI, HTTPException, Request, Response
@@ -10,11 +10,16 @@ from starlette_context import context
 from starlette_context.middleware import RawContextMiddleware
 
 from pr_agent.agent.pr_agent import PRAgent
+from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings, global_settings
 from pr_agent.git_providers 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.DEBUG)
 router = APIRouter()
 
 
@@ -25,77 +30,206 @@ 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)
 
-    return await handle_request(body)
+    response = await handle_request(body, event=request.headers.get("X-GitHub-Event", None))
+    return response or {}
 
 
 @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
-    body_bytes = await request.body()
-    signature_header = request.headers.get('x-hub-signature-256', None)
     webhook_secret = getattr(get_settings().github, 'webhook_secret', None)
     if webhook_secret:
+        body_bytes = await request.body()
+        signature_header = request.headers.get('x-hub-signature-256', None)
         verify_signature(body_bytes, webhook_secret, signature_header)
     return body
 
 
+_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]):
+async def handle_request(body: Dict[str, Any], event: str):
     """
     Handle incoming GitHub webhook requests.
 
     Args:
         body: The request body.
+        event: The GitHub event type.
     """
     action = body.get("action")
     if not action:
         return {}
     agent = PRAgent()
+    bot_user = get_settings().github_app.bot_user
+    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 {}
+
+    # handle all sorts of comment events (e.g. issue_comment)
     if action == 'created':
         if "comment" not in body:
             return {}
         comment_body = body.get("comment", {}).get("body")
-        sender = body.get("sender", {}).get("login")
-        if sender and 'bot' in sender:
+        if sender and bot_user in sender:
+            get_logger().info(f"Ignoring comment from {bot_user} user")
             return {}
-        if "issue" not in body or "pull_request" not in body["issue"]:
+        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 {}
-        pull_request = body["issue"]["pull_request"]
-        api_url = pull_request.get("url")
+        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)
+        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' 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 {}
+            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)
 
-    elif action == "opened" or 'reopened' in action:
+    # 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 {}
+        return invalid_result
     api_url = pull_request.get("url")
     if not api_url:
-            return {}
-        await agent.handle_request(api_url, "/review")
+        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
 
-    return {}
+
+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))
+    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:
+        get_logger().info(f"Ignoring duplicate request {request_hash}")
+    return is_duplicate
 
 
 @router.get("/")
@@ -104,6 +238,7 @@ async def root():
 
 
 def start():
+    if get_settings().github_app.override_deployment_type:
         # Override the deployment type to app
         get_settings().set("GITHUB.DEPLOYMENT_TYPE", "app")
     get_settings().set("CONFIG.PUBLISH_OUTPUT_PROGRESS", False)
@@ -111,7 +246,7 @@ def start():
     app = FastAPI(middleware=middleware)
     app.include_router(router)
 
-    uvicorn.run(app, host="0.0.0.0", port=3000)
+    uvicorn.run(app, host="0.0.0.0", port=int(os.environ.get("PORT", "3000")))
 
 
 if __name__ == '__main__':

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["id"]
+            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

@@ -1,7 +1,7 @@
 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**: Suggest improvements to the code in 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" \

pr_agent/servers/serverless.py

@@ -1,14 +1,15 @@
-import logging
-
 from fastapi import FastAPI
 from mangum import Mangum
+from starlette.middleware import Middleware
+from starlette_context.middleware import RawContextMiddleware
 
+from pr_agent.log import setup_logger
 from pr_agent.servers.github_app import router
 
-logger = logging.getLogger()
-logger.setLevel(logging.DEBUG)
+setup_logger()
 
-app = FastAPI()
+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 +28,14 @@ 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/
+
 [github]
 # ---- Set the following only for deployment type == "user"
 user_token = ""  # A GitHub personal access token with 'repo' scope.
@@ -43,5 +55,12 @@ 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

@@ -1,35 +1,68 @@
 [config]
-model="gpt-4"
+model="gpt-4" # "gpt-4-1106-preview"
 fallback_models=["gpt-3.5-turbo-16k"]
 git_provider="github"
 publish_output=true
 publish_output_progress=true
-verbosity_level=0 # 0,1,2
+verbosity_level=2 # 0,1,2
 use_extra_bad_extensions=false
 use_repo_settings_file=true
 ai_timeout=180
 max_description_tokens = 500
 max_commits_tokens = 500
+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 #
-require_focused_review=true
+require_focused_review=false
 require_score_review=false
 require_tests_review=true
 require_security_review=true
-num_code_suggestions=3
+require_estimate_effort_to_review=true
+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 = ""
+# 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
+
+# markers
+use_description_markers=false
+include_generated_by_header=true
+
+#custom_labels = ['Bug fix', 'Tests', 'Bug fix with tests', 'Refactoring', 'Enhancement', 'Documentation', 'Other']
 
 [pr_questions] # /ask #
 
 [pr_code_suggestions] # /improve #
 num_code_suggestions=4
 extra_instructions = ""
+rank_suggestions = false
+# params for '/improve --extended' mode
+num_code_suggestions_per_chunk=8
+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
@@ -42,6 +75,50 @@ extra_instructions = ""
 deployment_type = "user"
 ratelimit_retries = 5
 
+[github_action]
+# auto_review = true    # set as env var in .github/workflows/pr-agent.yaml
+# auto_describe = true  # set as env var in .github/workflows/pr-agent.yaml
+# auto_improve = true   # set as env var in .github/workflows/pr-agent.yaml
+
+[github_app]
+# these toggles allows running the github app from custom deployments
+bot_user = "github-actions[bot]"
+override_deployment_type = true
+# in some deployments it's possible to get duplicate requests if the handling is long,
+# these settings are used to avoid handling duplicate requests.
+duplicate_requests_cache = false
+duplicate_requests_cache_ttl = 60  # in seconds
+# settings for "pull_request" event
+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",
+]
+# 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
 url = "https://gitlab.com"
@@ -59,3 +136,26 @@ polling_interval_seconds = 30
 # LocalGitProvider settings - uncomment to use paths other than default
 # description_path= "path/to/description.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 +1,18 @@
+[config]
+enable_custom_labels=false
+
+## template for custom labels
+#[custom_labels."Bug fix"]
+#description = "Fixes a bug in the code"
+#[custom_labels."Tests"]
+#description = "Adds or modifies tests"
+#[custom_labels."Bug fix with tests"]
+#description = "Fixes a bug in the code and adds or modifies tests"
+#[custom_labels."Refactoring"]
+#description = "Code refactoring without changing functionality"
+#[custom_labels."Enhancement"]
+#description = "Adds new features or functionality"
+#[custom_labels."Documentation"]
+#description = "Adds or modifies documentation"
+#[custom_labels."Other"]
+#description = "Other changes that do not fit in any of the above categories"

pr_agent/settings/ignore.toml

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

pr_agent/settings/language_extensions.toml

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

pr_agent/settings/pr_add_docs.toml

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

pr_agent/settings/pr_code_suggestions_prompts.toml

@@ -1,90 +1,131 @@
 [pr_code_suggestions_prompt]
-system="""You are a language model called CodiumAI-PR-Code-Reviewer.
-Your task is to provide meaningfull non-trivial code suggestions to improve the new code in a PR (the '+' lines).
-- Try to give important suggestions like fixing code problems, issues and bugs. As a second priority, provide suggestions for meaningfull code improvements, like performance, vulnerability, modularity, and best practices.
-- Suggestions should refer only to the 'new hunk' code, and focus on improving the new added code lines, with '+'.
-- Provide the exact line number range (inclusive) for each issue.
-- Assume there is additional code in the relevant file that is not included in the diff.
-- Provide up to {{ num_code_suggestions }} code suggestions.
-- Make sure not to provide suggestions repeating modifications already implemented in the new PR code (the '+' lines).
-- Don't output line numbers in the 'improved code' snippets.
+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 (the '+' lines in the diff).
+
+Example for a PR Diff input:
+'
+## src/file1.py
+
+@@ -12,3 +12,5 @@ def func1():
+__new hunk__
+12  code line that already existed in the file...
+13  code line that already existed in the file....
+14 +new code line1 added in the PR
+15 +new code line2 added in the PR
+16  code line that already existed in the file...
+__old hunk__
+ code line that already existed in the file...
+-code line that was removed in the PR
+ code line that already existed in the file...
+
+
+@@ ... @@ def func2():
+__new hunk__
+...
+__old hunk__
+...
+
+
+## src/file2.py
+...
+'
+
+Specific instructions:
+- 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.
+- 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 JSON schema to format your answer:
-```json
-{
-    "Code suggestions": {
-      "type": "array",
-      "minItems": 1,
-      "maxItems": {{ num_code_suggestions }},
-      "uniqueItems": "true",
-      "items": {
-        "relevant file": {
-          "type": "string",
-          "description": "the relevant file full path"
-        },
-        "suggestion content": {
-          "type": "string",
-          "description": "a concrete suggestion for meaningfully improving the new PR code."
-        },
-        "existing code": {
-          "type": "string",
-          "description": "a code snippet showing authentic relevant code lines from a 'new hunk' section. It must be continuous, correctly formatted and indented, and without line numbers."
-        },
-        "relevant lines": {
-          "type": "string",
-          "description": "the relevant lines in the 'new hunk' sections, 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."
-        },
-        "improved code": {
-          "type": "string",
-          "description": "a new code snippet that can be used to replace the relevant lines in 'new hunk' code. Replacement suggestions should be complete, correctly formatted and indented, and without line numbers."
-        }
-      }
-    }
-}
-```
-
-Example input:
 '
-## src/file1.py
----new_hunk---
-```
-[new hunk code, annotated with line numbers]
-```
----old_hunk---
-```
-[old hunk code]
+{%- endif %}
+
+You must use the following YAML schema to format your answer:
+```yaml
+Code suggestions:
+  type: array
+  minItems: 1
+  maxItems: {{ num_code_suggestions }}
+  uniqueItems: true
+  items:
+    relevant file:
+      type: string
+      description: the relevant file full path
+    suggestion content:
+      type: string
+      description: |-
+        a concrete suggestion for meaningfully improving the new PR code.
+    existing code:
+      type: string
+      description: |-
+        a code snippet showing the relevant code lines from a '__new hunk__' section.
+        It must be contiguous, correctly formatted and indented, and without line numbers.
+    relevant lines start:
+      type: integer
+      description: |-
+        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: |-
+        a new code snippet that can be used to replace the relevant lines in '__new hunk__' code.
+        Replacement suggestions should be complete, correctly formatted and indented, and without line numbers.
 ```
+
+Example output:
+```yaml
+Code suggestions:
+  - 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: |-
         ...
-'
+```
 
+
+Each YAML output MUST be after a newline, indented, with block scalar indicator ('|-').
 Don't repeat the prompt in the answer, and avoid outputting the 'type' and 'description' fields.
 """
 
 user="""PR Info:
-Title: '{{title}}'
-Branch: '{{branch}}'
-Description: '{{description}}'
-{%- if language %}
-Main language: {{language}}
-{%- endif %}
-{%- if commit_messages_str %}
 
-Commit messages:
-{{commit_messages_str}}
+Title: '{{title}}'
+
+Branch: '{{branch}}'
+
+Description: '{{description}}'
+
+{%- if language %}
+
+Main language: {{language}}
 {%- endif %}
 
 
 The PR Diff:
 ```
-{{diff}}
+{{- diff|trim }}
 ```
 
-Response (should be a valid JSON, and nothing else):
-```json
+Response (should be a valid YAML, and nothing else):
+```yaml
 """

pr_agent/settings/pr_custom_labels.toml

@@ -0,0 +1,71 @@
+[pr_custom_labels_prompt]
+system="""You are CodiumAI-PR-Reviewer, a language model designed to review git pull requests.
+Your task is to label the type of the PR content.
+- Make sure not to focus the new PR code (the '+' lines).
+- If needed, each YAML output should be in block scalar format ('|-')
+{%- if extra_instructions %}
+
+Extra instructions from the user:
+'
+{{ extra_instructions }}
+'
+{% endif %}
+
+You must use the following YAML schema to format your answer:
+```yaml
+PR Type:
+  type: array
+{%- if enable_custom_labels %}
+  description: Labels that are applicable to the Pull Request. Don't output the description in the parentheses. If none of the labels is relevant to the PR, output an empty array.
+{%- endif %}
+  items:
+    type: string
+    enum:
+{%- if enable_custom_labels %}
+{{ custom_labels }}
+{%- else %}
+      - Bug fix
+      - Tests
+      - Refactoring
+      - Enhancement
+      - Documentation
+      - Other
+{%- endif %}
+
+Example output:
+```yaml
+PR Type:
+{%- if enable_custom_labels %}
+{{ custom_labels_examples }}
+{%- else %}
+  - Bug fix
+{%- endif %}
+```
+
+Make sure to output a valid YAML. Don't repeat the prompt in the answer, and avoid outputting the 'type' and 'description' fields.
+"""
+
+user="""PR Info:
+Previous title: '{{title}}'
+Previous description: '{{description}}'
+Branch: '{{branch}}'
+{%- if language %}
+
+Main language: {{language}}
+{%- endif %}
+{%- if commit_messages_str %}
+
+Commit messages:
+{{commit_messages_str}}
+{%- endif %}
+
+
+The PR Git Diff:
+```
+{{diff}}
+```
+Note that lines in the diff body are prefixed with a symbol that represents the type of change: '-' for deletions, '+' for additions, and ' ' (a space) for unchanged lines.
+
+Response (should be a valid YAML, and nothing else):
+```yaml
+"""

pr_agent/settings/pr_description_prompts.toml

@@ -1,13 +1,16 @@
 [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).
+Your task is to provide full description of a Pull Request (PR) content.
+- Make sure to focus on 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.
+- Emphasize first the most important changes, and then the less important ones.
 - If needed, each YAML output should be in block scalar format ('|-')
 {%- if extra_instructions %}
 
 Extra instructions from the user:
+'
 {{ extra_instructions }}
+'
 {% endif %}
 
 You must use the following YAML schema to format your answer:
@@ -16,20 +19,27 @@ 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
+{%- if enable_custom_labels %}
+PR Labels:
+  type: array
+  description: Labels that are applicable to the Pull Request. Don't output the description in the parentheses. If none of the labels is relevant to the PR, output an empty array.
+  items:
+    type: string
+    enum:
+{{ custom_labels }}
+{%- endif %}
 PR Description:
   type: string
-  description: an informative and concise description of the PR
+  description: an informative and concise description of the PR.
+  {%- if use_bullet_points %} Use bullet points. {% endif %}
 PR Main Files Walkthrough:
   type: array
   maxItems: 10
@@ -42,6 +52,7 @@ PR Main Files Walkthrough:
     changes in file:
       type: string
       description: minimal and concise description of the changes in the relevant file
+```
 
 
 Example output:
@@ -49,7 +60,12 @@ Example output:
 PR Title: |-
   ...
 PR Type:
-  - Bug fix
+  ...
+{%- if enable_custom_labels %}
+PR Labels:
+- ...
+- ...
+{%- endif %}
 PR Description: |-
   ...
 PR Main Files Walkthrough:

pr_agent/settings/pr_reviewer_prompts.toml

@@ -1,18 +1,43 @@
 [pr_review_prompt]
-system="""You are CodiumAI-PR-Reviewer, a language model designed to review git pull requests.
-Your task is to provide constructive and concise feedback for the PR, and also provide meaningfull code suggestions to improve the new PR code (the '+' lines).
+system="""You are PR-Reviewer, a language model designed to review git pull requests.
+Your task is to provide constructive and concise feedback for the PR, and also provide meaningful code suggestions.
+
+Example PR Diff input:
+'
+## 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 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...
+
+@@ ... @@ def func2():
+...
+
+
+## src/file2.py
+...
+'
+
+The review should focus on new code added in the PR (lines starting with '+'), and not on code that already existed in the file (lines starting with '-', or without prefix).
+
 {%- if num_code_suggestions > 0 %}
-- Provide up to {{ num_code_suggestions }} code suggestions.
-- Try to focus on the most important suggestions, like fixing code problems, issues and bugs. As a second priority, provide suggestions for meaningfull code improvements, like performance, vulnerability, modularity, and best practices.
-- Suggestions should focus on improving the new added code lines.
-- Make sure not to provide suggestions repeating modifications already implemented in the new PR code (the '+' lines).
+- 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, type hints, or comments.
+- Suggestions should focus on improving the new code added in the PR (lines starting with '+')
 {%- endif %}
-- If needed, each YAML output should be in block scalar format ('|-')
 
 {%- if extra_instructions %}
 
 Extra instructions from the user:
+'
 {{ extra_instructions }}
+'
 {% endif %}
 
 You must use the following YAML schema to format your answer:
@@ -21,6 +46,9 @@ PR Analysis:
   Main theme:
     type: string
     description: a short explanation of the PR
+  PR summary:
+    type: string
+    description: summary of the PR in 2-3 sentences.
   Type of PR:
     type: string
     enum:
@@ -33,7 +61,7 @@ PR Analysis:
 {%- if require_score %}
   Score:
     type: int
-    description: >-
+    description: |-
       Rate this PR on a scale of 0-100 (inclusive), where 0 means the worst
       possible PR code, and 100 means PR code of the highest quality, without
       any bugs or performance issues, that is ready to be merged immediately and
@@ -47,27 +75,34 @@ PR Analysis:
 {%- if question_str %}
   Insights from user's answer:
     type: string
-    description: >-
+    description: |-
       shortly summarize the insights you gained from the user's answers to the questions
 {%- endif %}
 {%- if require_focused %}
   Focused PR:
     type: string
-    description: >-
+    description: |-
       Is this a focused PR, in the sense that all the PR code diff changes are
       united under a single focused theme ? If the theme is too broad, or the PR
       code diff changes are too scattered, then the PR is not focused. Explain
       your answer shortly.
 {%- endif %}
+{%- 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).
+{%- 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.
+    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.
 {%- if num_code_suggestions > 0 %}
   Code feedback:
     type: array
@@ -79,47 +114,56 @@ PR Feedback:
         description: the relevant file full path
       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.
+        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.
       relevant line:
         type: string
-        description: |
+        description: |-
           a single code line taken from the relevant file, to which the suggestion applies.
-          The line should be a '+' line.
+          The code line should start with a '+'.
           Make sure to output the line exactly as it appears in the relevant file
 {%- endif %}
 {%- if require_security %}
   Security concerns:
     type: string
     description: >-
-      yes\\no question: does this PR code introduce possible security concerns or
-      issues, like SQL injection, XSS, CSRF, and others ? If answered 'yes',explain your answer shortly
+      yes\\no question: does this PR code introduce possible vulnerabilities such as exposure of sensitive information (e.g., API keys, secrets, passwords), or security concerns like SQL injection, XSS, CSRF, and others ? If answered 'yes', explain your answer briefly.
 {%- endif %}
 ```
 
 Example output:
 ```yaml
 PR Analysis:
-  Main theme: xxx
-  Type of PR: Bug fix
+  Main theme: |-
+    xxx
+  PR summary: |-
+    xxx
+  Type of PR: |-
+    ...
 {%- if require_score %}
   Score: 89
 {%- endif %}
-  Relevant tests added: No
+  Relevant tests added: |-
+    No
 {%- 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: ...
+  General PR suggestions: |-
+    ...
 {%- if num_code_suggestions > 0 %}
   Code feedback:
     - relevant file: |-
         directory/xxx.py
-      suggestion: xxx [important]
+      suggestion: |-
+        xxx [important]
       relevant line: |-
         xxx
     ...
@@ -129,7 +173,7 @@ PR Feedback:
 {%- endif %}
 ```
 
-Make sure to output a valid YAML. Use multi-line block scalar ('|') if needed.
+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.
 """
 
@@ -153,7 +197,9 @@ Here are questions to better understand the PR. Use the answers to provide bette
 {{question_str|trim}}
 
 User answers:
+'
 {{answer_str|trim}}
+'
 ######
 {%- endif %}
 
@@ -161,7 +207,7 @@ The PR Git Diff:
 ```
 {{diff}}
 ```
-Note that lines in the diff body are prefixed with a symbol that represents the type of change: '-' for deletions, '+' for additions, and ' ' (a space) for unchanged lines.
+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.
 
 Response (should be a valid YAML, and nothing else):
 ```yaml

pr_agent/settings/pr_sort_code_suggestions_prompts.toml

@@ -0,0 +1,46 @@
+[pr_sort_code_suggestions_prompt]
+system="""
+"""
+
+user="""You are given a list of code suggestions to improve a 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.
+Rank the suggestions based on their importance to improving the PR, with critical issues first and minor issues last.
+
+You must use the following YAML schema to format your answer:
+```yaml
+Sort Order:
+    type: array
+    maxItems: {{ suggestion_list|length }}
+    uniqueItems: true
+    items:
+        suggestion number:
+            type: integer
+            minimum: 1
+            maximum: {{ suggestion_list|length }}
+        importance order:
+            type: integer
+            minimum: 1
+            maximum: {{ suggestion_list|length }}
+```
+
+Example output:
+```yaml
+Sort Order:
+    - suggestion number: 1
+      importance order: 2
+    - suggestion number: 2
+      importance order: 3
+    - suggestion number: 3
+      importance order: 1
+```
+
+Make sure to output a valid YAML. Use multi-line block scalar ('|') if needed.
+Don't repeat the prompt in the answer, and avoid outputting the 'type' and 'description' fields.
+Response (should be a valid YAML, and nothing else):
+```yaml
+"""

pr_agent/settings/pr_update_changelog_prompts.toml

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

pr_agent/tools/pr_add_docs.py

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

pr_agent/tools/pr_code_suggestions.py

@@ -1,17 +1,17 @@
 import copy
-import json
-import logging
 import textwrap
+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
+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 try_fix_json
+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:
@@ -22,6 +22,16 @@ class PRCodeSuggestions:
             self.git_provider.get_languages(), self.git_provider.get_files()
         )
 
+        # extended mode
+        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:
+            num_code_suggestions = get_settings().pr_code_suggestions.num_code_suggestions
+
         self.ai_handler = AiHandler()
         self.patches_diff = None
         self.prediction = None
@@ -32,7 +42,7 @@ class PRCodeSuggestions:
             "description": self.git_provider.get_pr_description(),
             "language": self.main_language,
             "diff": "",  # empty diff for initial calculation
-            "num_code_suggestions": get_settings().pr_code_suggestions.num_code_suggestions,
+            "num_code_suggestions": num_code_suggestions,
             "extra_instructions": get_settings().pr_code_suggestions.extra_instructions,
             "commit_messages_str": self.git_provider.get_commit_messages(),
         }
@@ -42,29 +52,43 @@ class PRCodeSuggestions:
                                           get_settings().pr_code_suggestions_prompt.user)
 
     async def run(self):
-        assert type(self.git_provider) != BitbucketProvider, "Bitbucket is not supported for now"
-
-        logging.info('Generating code suggestions for PR...')
+        try:
+            get_logger().info('Generating code suggestions for PR...')
             if get_settings().config.publish_output:
                 self.git_provider.publish_comment("Preparing review...", is_temporary=True)
+
+            get_logger().info('Preparing PR review...')
+            if not self.is_extended:
                 await retry_with_fallback_models(self._prepare_prediction)
-        logging.info('Preparing PR review...')
                 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):
+                get_logger().info('Ranking Suggestions...')
+                data['Code suggestions'] = await self.rank_suggestions(data['Code suggestions'])
+
             if get_settings().config.publish_output:
-            logging.info('Pushing PR review...')
+                get_logger().info('Pushing PR review...')
                 self.git_provider.remove_initial_comment()
-            logging.info('Pushing inline code comments...')
+                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):
@@ -74,21 +98,18 @@ 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)
 
         return response
 
-    def _prepare_pr_code_suggestions(self) -> str:
+    def _prepare_pr_code_suggestions(self) -> Dict:
         review = self.prediction.strip()
-        try:
-            data = json.loads(review)
-        except json.decoder.JSONDecodeError:
-            if get_settings().config.verbosity_level >= 2:
-                logging.info(f"Could not parse json response: {review}")
-            data = try_fix_json(review, code_suggestions=True)
+        data = load_yaml(review)
+        if isinstance(data, list):
+            data = {'Code suggestions': data}
         return data
 
     def push_inline_code_suggestions(self, data):
@@ -100,13 +121,10 @@ class PRCodeSuggestions:
         for d in data['Code suggestions']:
             try:
                 if get_settings().config.verbosity_level >= 2:
-                    logging.info(f"suggestion: {d}")
+                    get_logger().info(f"suggestion: {d}")
                 relevant_file = d['relevant file'].strip()
-                relevant_lines_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']
 
@@ -119,9 +137,13 @@ 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}")
 
-        self.git_provider.publish_code_suggestions(code_suggestions)
+        is_successful = self.git_provider.publish_code_suggestions(code_suggestions)
+        if not is_successful:
+            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])
 
     def dedent_code(self, relevant_file, relevant_lines_start, new_code_snippet):
         try:  # dedent code snippet
@@ -141,7 +163,85 @@ 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:
+        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)
+
+        get_logger().info('Getting multi AI predictions...')
+        prediction_list = []
+        for i, patches_diff in enumerate(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)
+        self.prediction_list = prediction_list
+
+        data = {}
+        for prediction in prediction_list:
+            self.prediction = prediction
+            data_per_chunk = self._prepare_pr_code_suggestions()
+            if "Code suggestions" in data:
+                data["Code suggestions"].extend(data_per_chunk["Code suggestions"])
+            else:
+                data.update(data_per_chunk)
+        self.data = data
+        return data
+
+    async def rank_suggestions(self, data: List) -> List:
+        """
+        Call a model to rank (sort) code suggestions based on their importance order.
+
+        Args:
+            data (List): A list of code suggestions to be ranked.
+
+        Returns:
+            List: The ranked list of code suggestions.
+        """
+
+        suggestion_list = []
+        # remove invalid suggestions
+        for i, suggestion in enumerate(data):
+            if suggestion['existing code'] != suggestion['improved code']:
+                suggestion_list.append(suggestion)
+
+        data_sorted = [[]] * len(suggestion_list)
+
+        try:
+            suggestion_str = ""
+            for i, suggestion in enumerate(suggestion_list):
+                suggestion_str += f"suggestion {i + 1}: " + str(suggestion) + '\n\n'
+
+            variables = {'suggestion_list': suggestion_list, 'suggestion_str': suggestion_str}
+            model = get_settings().config.model
+            environment = Environment(undefined=StrictUndefined)
+            system_prompt = environment.from_string(get_settings().pr_sort_code_suggestions_prompt.system).render(
+                variables)
+            user_prompt = environment.from_string(get_settings().pr_sort_code_suggestions_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, system=system_prompt,
+                                                                            user=user_prompt)
+
+            sort_order = load_yaml(response)
+            for s in sort_order['Sort Order']:
+                suggestion_number = s['suggestion number']
+                importance_order = s['importance order']
+                data_sorted[importance_order - 1] = suggestion_list[suggestion_number - 1]
+
+            if get_settings().pr_code_suggestions.final_clip_factor != 1:
+                new_len = int(0.5 + len(data_sorted) * get_settings().pr_code_suggestions.final_clip_factor)
+                data_sorted = data_sorted[:new_len]
+        except Exception as e:
+            if get_settings().config.verbosity_level >= 1:
+                get_logger().info(f"Could not sort suggestions, error: {e}")
+            data_sorted = suggestion_list
+
+        return data_sorted
+
+

pr_agent/tools/pr_config.py

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

pr_agent/tools/pr_description.py

@@ -1,6 +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 +28,7 @@ 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()
 
         # Initialize the AI handler
         self.ai_handler = AiHandler()
@@ -36,13 +37,19 @@ 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": "",
+            "custom_labels_examples": "",
         }
 
+        self.user_description = self.git_provider.get_user_description()
+    
         # Initialize the token handler
         self.token_handler = TokenHandler(
             self.git_provider.pr,
@@ -59,27 +66,44 @@ class PRDescription:
         """
         Generates a PR description using an AI model and publishes it to the PR.
         """
-        logging.info('Generating a PR description...')
+
+        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)
+                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()
+            get_logger().info(f"Preparing answer {self.pr_id}")
+            if self.prediction:
+                self._prepare_data()
+            else:
+                return None
+
+            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:
-            logging.info('Pushing answer...')
+                get_logger().info(f"Pushing answer {self.pr_id}")
                 if get_settings().pr_description.publish_description_as_comment:
-                self.git_provider.publish_comment(markdown_text)
+                    self.git_provider.publish_comment(full_markdown_description)
                 else:
                     self.git_provider.publish_description(pr_title, pr_body)
-                if self.git_provider.is_supported("get_labels"):
+                    if get_settings().pr_description.publish_labels and 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)
+                        user_labels = get_user_labels(current_labels)
+
+                        self.git_provider.publish_labels(pr_labels + user_labels)
                 self.git_provider.remove_initial_comment()
+        except Exception as e:
+            get_logger().error(f"Error generating PR description {self.pr_id}: {e}")
         
         return ""
 
@@ -97,9 +121,12 @@ 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:
@@ -116,12 +143,13 @@ class PRDescription:
         variables["diff"] = self.patches_diff  # update diff
 
         environment = Environment(undefined=StrictUndefined)
+        set_custom_labels(variables)
         system_prompt = environment.from_string(get_settings().pr_description_prompt.system).render(variables)
         user_prompt = environment.from_string(get_settings().pr_description_prompt.user).render(variables)
 
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"\nSystem prompt:\n{system_prompt}")
-            logging.info(f"\nUser prompt:\n{user_prompt}")
+            get_logger().info(f"\nSystem prompt:\n{system_prompt}")
+            get_logger().info(f"\nUser prompt:\n{user_prompt}")
 
         response, finish_reason = await self.ai_handler.chat_completion(
             model=model,
@@ -132,56 +160,115 @@ class PRDescription:
 
         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 'PR Labels' in self.data:
+            if type(self.data['PR Labels']) == list:
+                pr_types = self.data['PR Labels']
+            elif type(self.data['PR Labels']) == str:
+                pr_types = self.data['PR Labels'].split(',')
+        elif 'PR Type' in self.data:
+            if type(self.data['PR Type']) == list:
+                pr_types = self.data['PR Type']
+            elif type(self.data['PR Type']) == str:
+                pr_types = self.data['PR Type'].split(',')
+        return pr_types
+
+    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('PR Type')
+        if ai_type and not re.search(r'<!--\s*pr_agent:type\s*-->', body):
+            pr_type = f"{ai_header}{ai_type}"
+            body = body.replace('pr_agent:type', pr_type)
+
+        ai_summary = self.data.get('PR Description')
+        if ai_summary and not re.search(r'<!--\s*pr_agent:summary\s*-->', body):
+            summary = f"{ai_header}{ai_summary}"
+            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())
-
-        # Initialization
-        pr_types = []
 
         # Iterate over the dictionary items and append the key and value to 'markdown_text' in a markdown format
         markdown_text = ""
-        for key, value in data.items():
+        # Don't display 'PR Labels'
+        if 'PR Labels' in self.data and self.git_provider.is_supported("get_labels"):
+            self.data.pop('PR Labels')
+        if not get_settings().pr_description.enable_pr_type:
+            self.data.pop('PR Type')
+        for key, value in self.data.items():
             markdown_text += f"## {key}\n\n"
             markdown_text += f"{value}\n\n"
 
-        # 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(',')
-
-        # Assign the value of the 'PR Title' key to 'title' variable and remove it from the dictionary
-        title = data.pop('PR Title')
+        # Remove the 'PR Title' key from the dictionary
+        ai_title = self.data.pop('PR 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"]
+        else:
+            # Assign the value of the 'PR Title' key to 'title' variable
+            title = ai_title
 
         # 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 key, value in data.items():
+        for idx, (key, value) in enumerate(self.data.items()):
             pr_body += f"## {key}:\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'
+                    pr_body += f'- `{filename}`: {description}\n'
+                if self.git_provider.is_supported("gfm_markdown"):
+                    pr_body +="</details>\n"
             else:
                 # if the value is a list, join its items by comma
                 if type(value) == list:
                     value = ', '.join(v for v in value)
-                pr_body += f"{value}\n\n___\n"
+                pr_body += f"{value}\n"
+            if idx < len(self.data) - 1:
+                pr_body += "\n___\n"
 
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"title:\n{title}\n{pr_body}")
+            get_logger().info(f"title:\n{title}\n{pr_body}")
 
-        return title, pr_body, pr_types, markdown_text
+        return title, pr_body

pr_agent/tools/pr_generate_labels.py

@@ -0,0 +1,169 @@
+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(),
+            "custom_labels": "",
+            "custom_labels_examples": "",
+            "enable_custom_labels": get_settings().config.enable_custom_labels,
+        }
+
+        # Initialize the token handler
+        self.token_handler = TokenHandler(
+            self.git_provider.pr,
+            self.vars,
+            get_settings().pr_custom_labels_prompt.system,
+            get_settings().pr_custom_labels_prompt.user,
+        )
+    
+        # Initialize patches_diff and prediction attributes
+        self.patches_diff = None
+        self.prediction = None
+
+    async def run(self):
+        """
+        Generates a PR labels using an AI model and publishes it to the PR.
+        """
+
+        try:
+            get_logger().info(f"Generating a PR labels {self.pr_id}")
+            if get_settings().config.publish_output:
+                self.git_provider.publish_comment("Preparing PR labels...", is_temporary=True)
+
+            await retry_with_fallback_models(self._prepare_prediction)
+
+            get_logger().info(f"Preparing answer {self.pr_id}")
+            if self.prediction:
+                self._prepare_data()
+            else:
+                return None
+
+            pr_labels = self._prepare_labels()
+
+            if get_settings().config.publish_output:
+                get_logger().info(f"Pushing labels {self.pr_id}")
+
+                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
+        )
+
+        return response
+
+    def _prepare_data(self):
+        # Load the AI prediction data into a dictionary
+        self.data = load_yaml(self.prediction.strip())
+
+
+
+    def _prepare_labels(self) -> List[str]:
+        pr_types = []
+
+        # If the 'PR Type' key is present in the dictionary, split its value by comma and assign it to 'pr_types'
+        if 'PR Type' in self.data:
+            if type(self.data['PR Type']) == list:
+                pr_types = self.data['PR Type']
+            elif type(self.data['PR Type']) == str:
+                pr_types = self.data['PR Type'].split(',')
+
+        return pr_types

pr_agent/tools/pr_information_from_user.py

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

pr_agent/tools/pr_questions.py

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

pr_agent/tools/pr_reviewer.py

@@ -1,6 +1,5 @@
 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
 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
 
 
@@ -23,7 +22,7 @@ class PRReviewer:
     """
     The PRReviewer class is responsible for reviewing a pull request and generating feedback using an AI model.
     """
-    def __init__(self, pr_url: str, is_answer: bool = False, args: list = None):
+    def __init__(self, pr_url: str, is_answer: bool = False, is_auto: bool = False, args: list = None):
         """
         Initialize the PRReviewer object with the necessary attributes and objects to review a pull request.
 
@@ -40,6 +39,7 @@ class PRReviewer:
         )
         self.pr_url = pr_url
         self.is_answer = is_answer
+        self.is_auto = is_auto
 
         if self.is_answer and not self.git_provider.is_supported("get_issue_comments"):
             raise Exception(f"Answer mode is not supported for {get_settings().config.git_provider} for now")
@@ -58,11 +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(
@@ -93,24 +96,44 @@ class PRReviewer:
         """
         Review the pull request and generate feedback.
         """
-        logging.info('Reviewing PR...')
+
+        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
+
+            get_logger().info(f'Reviewing PR: {self.pr_url} ...')
 
             if get_settings().config.publish_output:
                 self.git_provider.publish_comment("Preparing review...", is_temporary=True)
 
             await retry_with_fallback_models(self._prepare_prediction)
 
-        logging.info('Preparing PR review...')
+            get_logger().info('Preparing PR review...')
             pr_comment = self._prepare_pr_review()
 
             if get_settings().config.publish_output:
-            logging.info('Pushing PR review...')
-            self.git_provider.publish_comment(pr_comment)
-            self.git_provider.remove_initial_comment()
+                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_text="## PR Analysis",
+                                                                 updated_text="## PR Analysis (updated)")
+                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:
-                logging.info('Pushing 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:
         """
@@ -122,9 +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:
@@ -145,8 +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,
@@ -199,30 +222,39 @@ 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:
+            bot_user = "[bot]" if get_settings().github_app.override_deployment_type else get_settings().github_app.bot_user
+            if user and bot_user not in user:
                 markdown_text += bot_help_text(user)
             else:
                 markdown_text += actions_help_text
 
         # Log markdown response if verbosity level is high
         if get_settings().config.verbosity_level >= 2:
-            logging.info(f"Markdown response:\n{markdown_text}")
+            get_logger().info(f"Markdown response:\n{markdown_text}")
 
         if markdown_text == None or len(markdown_text) == 0:
             markdown_text = ""
@@ -241,7 +273,7 @@ class PRReviewer:
         try:
             data = yaml.load(review_text, Loader=SafeLoader)
         except Exception as e:
-            logging.error(f"Failed to parse AI prediction: {e}")
+            get_logger().error(f"Failed to parse AI prediction: {e}")
             data = try_fix_yaml(review_text)
 
         comments: List[str] = []
@@ -250,7 +282,7 @@ class PRReviewer:
             relevant_line_in_file = suggestion.get('relevant line', '').strip()
             content = suggestion.get('suggestion', '')
             if not relevant_file or not relevant_line_in_file or not content:
-                logging.info("Skipping inline comment with missing file/line/content")
+                get_logger().info("Skipping inline comment with missing file/line/content")
                 continue
 
             if self.git_provider.is_supported("create_inline_comment"):
@@ -286,3 +318,57 @@ 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

pr_agent/tools/pr_similar_issue.py

@@ -0,0 +1,294 @@
+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.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="",