Update setup.py

Tr/docs best practice

.gitignore

@@ -1,6 +1,7 @@
 .idea/
 .lsp/
 .vscode/
+.env
 venv/
 pr_agent/settings/.secrets.toml
 __pycache__
@@ -9,3 +10,4 @@ dist/
 build/
 .DS_Store
 docs/.cache/
+.qodo

README.md

@@ -10,45 +10,79 @@
 
 </picture>
 <br/>
-Qode Merge PR-Agent aims to help efficiently review and handle pull requests, by providing AI feedback and suggestions
+PR-Agent aims to help efficiently review and handle pull requests, by providing AI feedback and suggestions
 </div>
 
-[![GitHub license](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://github.com/Codium-ai/pr-agent/blob/main/LICENSE)
-[![Static Badge](https://img.shields.io/badge/Chrome-Extension-violet)](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl)
-[![Static Badge](https://img.shields.io/badge/Code-Benchmark-blue)](https://pr-agent-docs.codium.ai/finetuning_benchmark/)
+[![Static Badge](https://img.shields.io/badge/Chrome-Extension-violet)](https://chromewebstore.google.com/detail/qodo-merge-ai-powered-cod/ephlnjeghhogofkifjloamocljapahnl)
+[![Static Badge](https://img.shields.io/badge/Pro-App-blue)](https://github.com/apps/qodo-merge-pro/)
+[![Static Badge](https://img.shields.io/badge/OpenSource-App-red)](https://github.com/apps/qodo-merge-pro-for-open-source/)
 [![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)
-[![Cheat Sheet](https://img.shields.io/badge/Cheat-Sheet-red)](https://www.codium.ai/images/pr_agent/cheat_sheet.pdf)
-    <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>
+<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>
 
-### [Documentation](https://pr-agent-docs.codium.ai/)
-- See the [Installation Guide](https://qodo-merge-docs.qodo.ai/installation/) for instructions on installing Qode Merge PR-Agent on different platforms.
+### [Documentation](https://qodo-merge-docs.qodo.ai/)
 
-- See the [Usage Guide](https://qodo-merge-docs.qodo.ai/usage-guide/) for instructions on running Qode Merge PR-Agent tools via different interfaces, such as CLI, PR Comments, or by automatically triggering them when a new PR is opened.
+- See the [Installation Guide](https://qodo-merge-docs.qodo.ai/installation/) for instructions on installing PR-Agent on different platforms.
+
+- See the [Usage Guide](https://qodo-merge-docs.qodo.ai/usage-guide/) for instructions on running PR-Agent tools via different interfaces, such as CLI, PR Comments, or by automatically triggering them when a new PR is opened.
 
 - See the [Tools Guide](https://qodo-merge-docs.qodo.ai/tools/) for a detailed description of the different tools, and the available configurations for each tool.
 
 
 ## Table of Contents
+
 - [News and Updates](#news-and-updates)
 - [Overview](#overview)
 - [Example results](#example-results)
 - [Try it now](#try-it-now)
-- [PR-Agent Pro 💎](https://pr-agent-docs.codium.ai/overview/pr_agent_pro/)
+- [Qodo Merge 💎](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/)
 - [How it works](#how-it-works)
 - [Why use PR-Agent?](#why-use-pr-agent)
 
 ## News and Updates
 
+### Jan 25, 2025
+
+The open-source GitHub organization was updated:
+`https://github.com/codium-ai/pr-agent` →
+`https://github.com/qodo-ai/pr-agent`
+
+The docker should be redirected automatically to the new location. 
+However, if you have any issues, please update the GitHub action docker image from
+`uses: Codium-ai/pr-agent@main`
+to
+`uses: qodo-ai/pr-agent@main`
+
+
+### Jan 2, 2025
+
+New tool  [/Implement](https://qodo-merge-docs.qodo.ai/tools/implement/) (💎), which converts human code review discussions and feedback into ready-to-commit code changes.
+
+<kbd><img src="https://www.qodo.ai/images/pr_agent/implement1.png" width="512"></kbd>
+
+
+### Jan 1, 2025
+
+Update logic and [documentation](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/#ollama) for running local models via Ollama.
+
+### December 30, 2024
+
+Following [feedback](https://research.kudelskisecurity.com/2024/08/29/careful-where-you-code-multiple-vulnerabilities-in-ai-powered-pr-agent/) from the community, we have addressed two vulnerabilities identified in the open-source PR-Agent project. The fixes are now included in the newly released version (v0.26), available as of today.
+
+### December 25, 2024
+
+The `review` tool previously included a legacy feature for providing code suggestions (controlled by '--pr_reviewer.num_code_suggestion'). This functionality has been deprecated. Use instead the [`improve`](https://qodo-merge-docs.qodo.ai/tools/improve/) tool, which offers higher quality and more actionable code suggestions.
+
 ### December 2, 2024
 
-Open-source repositories can now freely use Qodo Merge Pro, and enjoy easy one-click installation using our dedicated [app](https://github.com/apps/qodo-merge-pro-for-open-source).
+Open-source repositories can now freely use Qodo Merge, and enjoy easy one-click installation using a marketplace [app](https://github.com/apps/qodo-merge-pro-for-open-source).
 
 <kbd><img src="https://github.com/user-attachments/assets/b0838724-87b9-43b0-ab62-73739a3a855c" width="512"></kbd>
 
+See [here](https://qodo-merge-docs.qodo.ai/installation/pr_agent_pro/) for more details about installing Qodo Merge for private repositories.
+
 
 ### November 18, 2024
 
@@ -71,80 +105,81 @@ Focused mode
 <kbd><img src="https://qodo.ai/images/pr_agent/code_suggestions_focused_mode.png" width="512"></kbd>
 
 
-### November 4, 2024
-
-Qodo Merge PR Agent will now leverage context from Jira or GitHub tickets to enhance the PR Feedback. Read more about this feature 
-[here](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/)
-
-
 ## Overview
 <div style="text-align:left;">
 
 Supported commands per platform:
 
-|       |                                                                                                         | GitHub             | Gitlab             | Bitbucket          | Azure DevOps |
+|       |                                                                                                         | GitHub             | GitLab             | Bitbucket          | Azure DevOps |
 |-------|---------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:--------------------:|:------------:|
-| TOOLS | Review                                                                                                  | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ Incremental                                                                                           | ✅ |                    |                    |              |
-|       | Describe                                                                                                | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ [Inline File Summary](https://pr-agent-docs.codium.ai/tools/describe#inline-file-summary) 💎          | ✅ |                    |                    |              |
-|       | Improve                                                                                                 | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ Extended                                                                                              | ✅ | ✅ | ✅ |      ✅       |
-|       | Ask                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ [Ask on code lines](https://pr-agent-docs.codium.ai/tools/ask#ask-lines)                              | ✅ | ✅ |                    |              |
-|       | [Custom Prompt](https://pr-agent-docs.codium.ai/tools/custom_prompt/) 💎                                | ✅ | ✅ | ✅ |              |
-|       | [Test](https://pr-agent-docs.codium.ai/tools/test/) 💎                                                  | ✅ | ✅ |                    |              |
-|       | Reflect and Review                                                                                      | ✅ | ✅ | ✅ |      ✅       |
-|       | Update CHANGELOG.md                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | Find Similar Issue                                                                                      | ✅ |                    |                    |              |
-|       | [Add PR Documentation](https://pr-agent-docs.codium.ai/tools/documentation/) 💎                         | ✅ | ✅ |                   |              |
-|       | [Custom Labels](https://pr-agent-docs.codium.ai/tools/custom_labels/) 💎                                | ✅ | ✅ |                    |              |
-|       | [Analyze](https://pr-agent-docs.codium.ai/tools/analyze/) 💎                                            | ✅ | ✅ |                    |              |
-|       | [CI Feedback](https://pr-agent-docs.codium.ai/tools/ci_feedback/) 💎                                    | ✅ |                    |                    |              |
-|       | [Similar Code](https://pr-agent-docs.codium.ai/tools/similar_code/) 💎                                  | ✅ |                    |                    |              |
+| TOOLS | [Review](https://qodo-merge-docs.qodo.ai/tools/review/)                                                                                                  | ✅ | ✅ | ✅ |      ✅       |
+|       | [Describe](https://qodo-merge-docs.qodo.ai/tools/describe/)                                                                                                | ✅ | ✅ | ✅ |      ✅       |
+|       | [Improve](https://qodo-merge-docs.qodo.ai/tools/improve/)                                                                                                 | ✅ | ✅ | ✅ |      ✅       |
+|       | [Ask](https://qodo-merge-docs.qodo.ai/tools/ask/)                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
+|       | ⮑ [Ask on code lines](https://qodo-merge-docs.qodo.ai/tools/ask/#ask-lines)                              | ✅ | ✅ |                    |              |
+|       | [Update CHANGELOG](https://qodo-merge-docs.qodo.ai/tools/update_changelog/)                                                                                     | ✅ | ✅ | ✅ |      ✅       |
+|       | [Ticket Context](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/) 💎  | ✅ | ✅ |  ✅                  |   |
+|       | [Utilizing Best Practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) 💎  | ✅ | ✅ |  ✅                  |   |
+|       | [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) 💎  | ✅ |  |                    |   |
+|       | [Suggestion Tracking](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking) 💎  | ✅ | ✅ |                    |   |
+|       | [CI Feedback](https://qodo-merge-docs.qodo.ai/tools/ci_feedback/) 💎                                    | ✅ |                    |                    |              |
+|       | [PR Documentation](https://qodo-merge-docs.qodo.ai/tools/documentation/) 💎                         | ✅ | ✅ |                   |              |
+|       | [Custom Labels](https://qodo-merge-docs.qodo.ai/tools/custom_labels/) 💎                                | ✅ | ✅ |                    |              |
+|       | [Analyze](https://qodo-merge-docs.qodo.ai/tools/analyze/) 💎                                            | ✅ | ✅ |                    |              |
+|       | [Similar Code](https://qodo-merge-docs.qodo.ai/tools/similar_code/) 💎                                  | ✅ |                    |                    |              |
+|       | [Custom Prompt](https://qodo-merge-docs.qodo.ai/tools/custom_prompt/) 💎                                | ✅ | ✅ | ✅ |              |
+|       | [Test](https://qodo-merge-docs.qodo.ai/tools/test/) 💎                                                  | ✅ | ✅ |                    |              |
+|       | [Implement](https://qodo-merge-docs.qodo.ai/tools/implement/) 💎                                        | ✅ | ✅ |         ✅          |              |
 |       |                                                                                                         |                    |                    |                    |              |
-| USAGE | CLI                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | App / webhook                                                                                           | ✅ | ✅ | ✅ |      ✅       |
-|       | Tagging bot                                                                                             | ✅ |                    |                    |              |
-|       | Actions                                                                                                 | ✅ |✅| ✅ |✅|
+| USAGE | [CLI](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#local-repo-cli)                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
+|       | [App / webhook](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#github-app)                                                                                           | ✅ | ✅ | ✅ |      ✅       |
+|       | [Tagging bot](https://github.com/Codium-ai/pr-agent#try-it-now)                                                                                             | ✅ |                    |                    |              |
+|       | [Actions](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-action)                                                                                                 | ✅ |✅| ✅ |✅|
 |       |                                                                                                         |                    |                    |                    |              |
-| CORE  | PR compression                                                                                          | ✅ | ✅ | ✅ |      ✅       |
-|       | Repo language prioritization                                                                            | ✅ | ✅ | ✅ |      ✅       |
+| CORE  | [PR compression](https://qodo-merge-docs.qodo.ai/core-abilities/compression_strategy/)                                                                  | ✅ | ✅ | ✅ |      ✅       |
 |       | Adaptive and token-aware file patch fitting                                                             | ✅ | ✅ | ✅ |      ✅       |
-|       | Multiple models support                                                                                 | ✅ | ✅ | ✅ |      ✅       |
-|       | [Static code analysis](https://pr-agent-docs.codium.ai/core-abilities/#static-code-analysis) 💎         | ✅ | ✅ | ✅ |              |
-|       | [Global and wiki configurations](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/) 💎 | ✅ | ✅ | ✅ |              |
-|       | [PR interactive actions](https://www.codium.ai/images/pr_agent/pr-actions.mp4) 💎                       | ✅ |        ✅           |                    |              |
-- 💎 means this feature is available only in [PR-Agent Pro](https://www.codium.ai/pricing/)
+|       | [Multiple models support](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/)                                                                                 | ✅ | ✅ | ✅ |      ✅       |
+|       | [Local and global metadata](https://qodo-merge-docs.qodo.ai/core-abilities/metadata/)          | ✅ | ✅ | ✅ | ✅             |
+|       | [Dynamic context](https://qodo-merge-docs.qodo.ai/core-abilities/dynamic_context/)          | ✅ | ✅ | ✅ | ✅             |
+|       | [Self reflection](https://qodo-merge-docs.qodo.ai/core-abilities/self_reflection/)          | ✅ | ✅ | ✅ | ✅             |
+|       | [Static code analysis](https://qodo-merge-docs.qodo.ai/core-abilities/static_code_analysis/) 💎         | ✅ | ✅ | ✅ |              |
+|       | [Global and wiki configurations](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/) 💎 | ✅ | ✅ | ✅ |              |
+|       | [PR interactive actions](https://www.qodo.ai/images/pr_agent/pr-actions.mp4) 💎                       | ✅ |        ✅           |                    |              |
+|       | [Impact Evaluation](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/) 💎  | ✅ | ✅ |                    |   |
+- 💎 means this feature is available only in [Qodo-Merge](https://www.qodo.ai/pricing/)
 
 [//]: # (- Support for additional git providers is described in [here]&#40;./docs/Full_environments.md&#41;)
 ___
 
-‣ **Auto Description ([`/describe`](https://pr-agent-docs.codium.ai/tools/describe/))**: Automatically generating PR description - title, type, summary, code walkthrough and labels.
+‣ **Auto Description ([`/describe`](https://qodo-merge-docs.qodo.ai/tools/describe/))**: Automatically generating PR description - title, type, summary, code walkthrough and labels.
 \
-‣ **Auto Review ([`/review`](https://pr-agent-docs.codium.ai/tools/review/))**: Adjustable feedback about the PR, possible issues, security concerns, review effort and more.
+‣ **Auto Review ([`/review`](https://qodo-merge-docs.qodo.ai/tools/review/))**: Adjustable feedback about the PR, possible issues, security concerns, review effort and more.
 \
-‣ **Code Suggestions ([`/improve`](https://pr-agent-docs.codium.ai/tools/improve/))**: Code suggestions for improving the PR.
+‣ **Code Suggestions ([`/improve`](https://qodo-merge-docs.qodo.ai/tools/improve/))**: Code suggestions for improving the PR.
 \
-‣ **Question Answering ([`/ask ...`](https://pr-agent-docs.codium.ai/tools/ask/))**: Answering free-text questions about the PR.
+‣ **Question Answering ([`/ask ...`](https://qodo-merge-docs.qodo.ai/tools/ask/))**: Answering free-text questions about the PR.
 \
-‣ **Update Changelog ([`/update_changelog`](https://pr-agent-docs.codium.ai/tools/update_changelog/))**: Automatically updating the CHANGELOG.md file with the PR changes.
+‣ **Update Changelog ([`/update_changelog`](https://qodo-merge-docs.qodo.ai/tools/update_changelog/))**: Automatically updating the CHANGELOG.md file with the PR changes.
 \
-‣ **Find Similar Issue ([`/similar_issue`](https://pr-agent-docs.codium.ai/tools/similar_issues/))**: Automatically retrieves and presents similar issues.
+‣ **Find Similar Issue ([`/similar_issue`](https://qodo-merge-docs.qodo.ai/tools/similar_issues/))**: Automatically retrieves and presents similar issues.
 \
-‣ **Add Documentation 💎  ([`/add_docs`](https://pr-agent-docs.codium.ai/tools/documentation/))**: Generates documentation to methods/functions/classes that changed in the PR.
+‣ **Add Documentation 💎  ([`/add_docs`](https://qodo-merge-docs.qodo.ai/tools/documentation/))**: Generates documentation to methods/functions/classes that changed in the PR.
 \
-‣ **Generate Custom Labels 💎 ([`/generate_labels`](https://pr-agent-docs.codium.ai/tools/custom_labels/))**: Generates custom labels for the PR, based on specific guidelines defined by the user.
+‣ **Generate Custom Labels 💎 ([`/generate_labels`](https://qodo-merge-docs.qodo.ai/tools/custom_labels/))**: Generates custom labels for the PR, based on specific guidelines defined by the user.
 \
-‣ **Analyze 💎 ([`/analyze`](https://pr-agent-docs.codium.ai/tools/analyze/))**: Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component.
+‣ **Analyze 💎 ([`/analyze`](https://qodo-merge-docs.qodo.ai/tools/analyze/))**: Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component.
 \
-‣ **Custom Prompt 💎 ([`/custom_prompt`](https://pr-agent-docs.codium.ai/tools/custom_prompt/))**: Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user.
+‣ **Test 💎 ([`/test`](https://qodo-merge-docs.qodo.ai/tools/test/))**: Generate tests for a selected component, based on the PR code changes.
 \
-‣ **Generate Tests 💎 ([`/test component_name`](https://pr-agent-docs.codium.ai/tools/test/))**: Generates unit tests for a selected component, based on the PR code changes.
+‣ **Custom Prompt 💎 ([`/custom_prompt`](https://qodo-merge-docs.qodo.ai/tools/custom_prompt/))**: Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user.
 \
-‣ **CI Feedback 💎 ([`/checks ci_job`](https://pr-agent-docs.codium.ai/tools/ci_feedback/))**: Automatically generates feedback and analysis for a failed CI job.
+‣ **Generate Tests 💎 ([`/test component_name`](https://qodo-merge-docs.qodo.ai/tools/test/))**: Generates unit tests for a selected component, based on the PR code changes.
 \
-‣ **Similar Code 💎 ([`/find_similar_component`](https://pr-agent-docs.codium.ai/tools/similar_code/))**: Retrieves the most similar code components from inside the organization's codebase, or from open-source code.
+‣ **CI Feedback 💎 ([`/checks ci_job`](https://qodo-merge-docs.qodo.ai/tools/ci_feedback/))**: Automatically generates feedback and analysis for a failed CI job.
+\
+‣ **Similar Code 💎 ([`/find_similar_component`](https://qodo-merge-docs.qodo.ai/tools/similar_code/))**: Retrieves the most similar code components from inside the organization's codebase, or from open-source code.
+\
+‣ **Implement 💎 ([`/implement`](https://qodo-merge-docs.qodo.ai/tools/implement/))**: Generates implementation code from review suggestions.
 ___
 
 ## Example results
@@ -175,50 +210,8 @@ ___
 </kbd>
 </p>
 </div>
-<hr>
 
-<h4><a href="https://github.com/Codium-ai/pr-agent/pull/530">/generate_labels</a></h4>
-<div align="center">
-<p float="center">
-<kbd><img src="https://www.codium.ai/images/pr_agent/geneare_custom_labels_main_short.png" width="300"></kbd>
-</p>
-</div>
 
-[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/78#issuecomment-1639739496">/reflect_and_review:</a></h4>)
-
-[//]: # (<div align="center">)
-
-[//]: # (<p float="center">)
-
-[//]: # (<img src="https://www.codium.ai/images/reflect_and_review.gif" width="800">)
-
-[//]: # (</p>)
-
-[//]: # (</div>)
-
-[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695020538">/ask:</a></h4>)
-
-[//]: # (<div align="center">)
-
-[//]: # (<p float="center">)
-
-[//]: # (<img src="https://www.codium.ai/images/ask-2.gif" width="800">)
-
-[//]: # (</p>)
-
-[//]: # (</div>)
-
-[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695024952">/improve:</a></h4>)
-
-[//]: # (<div align="center">)
-
-[//]: # (<p float="center">)
-
-[//]: # (<img src="https://www.codium.ai/images/improve-2.gif" width="800">)
-
-[//]: # (</p>)
-
-[//]: # (</div>)
 <div align="left">
 
 
@@ -242,19 +235,19 @@ It does not have 'edit' access to your repo, for example, so it cannot update th
 ![Review generation process](https://www.codium.ai/images/demo-2.gif)
 
 
-To set up your own PR-Agent, see the [Installation](https://pr-agent-docs.codium.ai/installation/) section below.
-Note that when you set your own PR-Agent or use CodiumAI hosted PR-Agent, there is no need to mention `@CodiumAI-Agent ...`. Instead, directly start with the command, e.g., `/ask ...`.
+To set up your own PR-Agent, see the [Installation](https://qodo-merge-docs.qodo.ai/installation/) section below.
+Note that when you set your own PR-Agent or use Qodo hosted PR-Agent, there is no need to mention `@CodiumAI-Agent ...`. Instead, directly start with the command, e.g., `/ask ...`.
 
 ---
 
 
-## PR-Agent Pro 💎
-[PR-Agent Pro](https://www.codium.ai/pricing/) is a hosted version of PR-Agent, provided by CodiumAI. It is available for a monthly fee, and provides the following benefits:
-1. **Fully managed** - We take care of everything for you - hosting, models, regular updates, and more. Installation is as simple as signing up and adding the PR-Agent app to your GitHub\GitLab\BitBucket repo.
-2. **Improved privacy** - No data will be stored or used to train models. PR-Agent Pro will employ zero data retention, and will use an OpenAI account with zero data retention.
-3. **Improved support** - PR-Agent Pro users will receive priority support, and will be able to request new features and capabilities.
-4. **Extra features** -In addition to the benefits listed above, PR-Agent Pro will emphasize more customization, and the usage of static code analysis, in addition to LLM logic, to improve results.
-See [here](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) for a list of features available in PR-Agent Pro.
+## Qodo Merge 💎
+[Qodo Merge](https://www.qodo.ai/pricing/) is a hosted version of PR-Agent, provided by Qodo. It is available for a monthly fee, and provides the following benefits:
+1. **Fully managed** - We take care of everything for you - hosting, models, regular updates, and more. Installation is as simple as signing up and adding the Qodo Merge app to your GitHub\GitLab\BitBucket repo.
+2. **Improved privacy** - No data will be stored or used to train models. Qodo Merge will employ zero data retention, and will use an OpenAI account with zero data retention.
+3. **Improved support** - Qodo Merge users will receive priority support, and will be able to request new features and capabilities.
+4. **Extra features** -In addition to the benefits listed above, Qodo Merge will emphasize more customization, and the usage of static code analysis, in addition to LLM logic, to improve results.
+See [here](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) for a list of features available in Qodo Merge.
 
 
 
@@ -262,9 +255,9 @@ See [here](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) for a list of
 
 The following diagram illustrates PR-Agent tools and their flow:
 
-![PR-Agent Tools](https://codium.ai/images/pr_agent/diagram-v0.9.png)
+![PR-Agent Tools](https://www.qodo.ai/images/pr_agent/diagram-v0.9.png)
 
-Check out the [PR Compression strategy](https://pr-agent-docs.codium.ai/core-abilities/#pr-compression-strategy) page for more details on how we convert a code diff to a manageable LLM prompt
+Check out the [PR Compression strategy](https://qodo-merge-docs.qodo.ai/core-abilities/#pr-compression-strategy) page for more details on how we convert a code diff to a manageable LLM prompt
 
 ## Why use PR-Agent?
 
@@ -273,7 +266,7 @@ A reasonable question that can be asked is: `"Why use PR-Agent? What makes it st
 Here are some advantages of PR-Agent:
 
 - We emphasize **real-life practical usage**. Each tool (review, improve, ask, ...) has a single GPT-4 call, no more. We feel that this is critical for realistic team usage - obtaining an answer quickly (~30 seconds) and affordably.
-- Our [PR Compression strategy](https://pr-agent-docs.codium.ai/core-abilities/#pr-compression-strategy)  is a core ability that enables to effectively tackle both short and long PRs.
+- Our [PR Compression strategy](https://qodo-merge-docs.qodo.ai/core-abilities/#pr-compression-strategy)  is a core ability that enables to effectively tackle both short and long PRs.
 - Our JSON prompting strategy enables to have **modular, customizable tools**. For example, the '/review' tool categories can be controlled via the [configuration](pr_agent/settings/configuration.toml) file. Adding additional categories is easy and accessible.
 - We support **multiple git providers** (GitHub, Gitlab, Bitbucket), **multiple ways** to use the tool (CLI, GitHub Action, GitHub App, Docker, ...), and **multiple models** (GPT-4, GPT-3.5, Anthropic, Cohere, Llama2).
 
@@ -285,24 +278,24 @@ Here are some advantages of PR-Agent:
 - If you host PR-Agent with your OpenAI API key, it is between you and OpenAI. You can read their API data privacy policy here:
 https://openai.com/enterprise-privacy
 
-### CodiumAI-hosted PR-Agent Pro 💎
+### Qodo-hosted Qodo Merge 💎
 
-- When using PR-Agent Pro 💎, hosted by CodiumAI, we will not store any of your data, nor will we use it for training. You will also benefit from an OpenAI account with zero data retention.
+- When using Qodo Merge 💎, hosted by Qodo, we will not store any of your data, nor will we use it for training. You will also benefit from an OpenAI account with zero data retention.
 
-- For certain clients, CodiumAI-hosted PR-Agent Pro will use CodiumAI’s proprietary models — if this is the case, you will be notified.
+- For certain clients, Qodo-hosted Qodo Merge will use Qodo’s proprietary models — if this is the case, you will be notified.
 
-- No passive collection of Code and Pull Requests’ data — PR-Agent will be active only when you invoke it, and it will then extract and analyze only data relevant to the executed command and queried pull request.
+- No passive collection of Code and Pull Requests’ data — Qodo Merge will be active only when you invoke it, and it will then extract and analyze only data relevant to the executed command and queried pull request.
 
-### PR-Agent Chrome extension
+### Qodo Merge Chrome extension
 
-- The [PR-Agent Chrome extension](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl) serves solely to modify the visual appearance of a GitHub PR screen. It does not transmit any user's repo or pull request code. Code is only sent for processing when a user submits a GitHub comment that activates a PR-Agent tool, in accordance with the standard privacy policy of PR-Agent.
+- The [Qodo Merge Chrome extension](https://chromewebstore.google.com/detail/qodo-merge-ai-powered-cod/ephlnjeghhogofkifjloamocljapahnl) serves solely to modify the visual appearance of a GitHub PR screen. It does not transmit any user's repo or pull request code. Code is only sent for processing when a user submits a GitHub comment that activates a PR-Agent tool, in accordance with the standard privacy policy of Qodo-Merge.
 
 ## 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
+- Qodo site: https://www.qodo.ai/
+- Blog: https://www.qodo.ai/blog/
+- Troubleshooting: https://www.qodo.ai/blog/technical-faq-and-troubleshooting/
+- Support: support@qodo.ai

docs/docs/chrome-extension/data_privacy.md

@@ -1,4 +1,4 @@
 We take your code's security and privacy seriously:
 
 - The Chrome extension will not send your code to any external servers.
-- For private repositories, we will first validate the user's identity and permissions. After authentication, we generate responses using the existing Qodo Merge Pro integration.
+- For private repositories, we will first validate the user's identity and permissions. After authentication, we generate responses using the existing Qodo Merge integration.

docs/docs/chrome-extension/features.md

@@ -8,7 +8,7 @@ To enable private chat, simply install the Qodo Merge Chrome extension. After in
 This chat session is **private**, and won't be visible to other users.
 
 All open-source repositories are supported.
-For private repositories, you will also need to install Qodo Merge Pro, After installation, make sure to open at least one new PR to fully register your organization. Once done, you can chat with both new and existing PRs across all installed repositories.
+For private repositories, you will also need to install Qodo Merge. After installation, make sure to open at least one new PR to fully register your organization. Once done, you can chat with both new and existing PRs across all installed repositories.
 
 #### Context-aware PR chat
 

docs/docs/chrome-extension/index.md

@@ -1,11 +1,11 @@
-[Qodo Merge Chrome extension](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl) is a collection of tools that integrates seamlessly with your GitHub environment, aiming to enhance your Git usage experience, and providing AI-powered capabilities to your PRs.
+[Qodo Merge Chrome extension](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl){:target="_blank"} is a collection of tools that integrates seamlessly with your GitHub environment, aiming to enhance your Git usage experience, and providing AI-powered capabilities to your PRs.
 
 With a single-click installation you will gain access to a context-aware chat on your pull requests code, a toolbar extension with multiple AI feedbacks, Qodo Merge filters, and additional abilities.
 
 The extension is powered by top code models like Claude 3.5 Sonnet and GPT4. All the extension's features are free to use on public repositories.
 
-For private repositories, you will need to install [Qodo Merge Pro](https://github.com/apps/codiumai-pr-agent-pro) in addition to the extension  (Quick GitHub app setup with a 14-day free trial. No credit card needed).
-For a demonstration of how to install Qodo Merge Pro and use it with the Chrome extension, please refer to the tutorial video at the provided [link](https://codium.ai/images/pr_agent/private_repos.mp4).
+For private repositories, you will need to install [Qodo Merge](https://github.com/apps/qodo-merge-pro){:target="_blank"} in addition to the extension  (Quick GitHub app setup with a 14-day free trial. No credit card needed).
+For a demonstration of how to install Qodo Merge and use it with the Chrome extension, please refer to the tutorial video at the provided [link](https://codium.ai/images/pr_agent/private_repos.mp4){:target="_blank"}.
 
 <img src="https://codium.ai/images/pr_agent/PR-AgentChat.gif" width="768">
 

docs/docs/core-abilities/auto_best_practices.md

@@ -0,0 +1,69 @@
+# Auto Best Practices 💎
+`Supported Git Platforms: GitHub`
+
+## Overview
+
+![Auto best practice suggestion graph](https://www.qodo.ai/images/pr_agent/auto_best_practices_graph.png){width=684}
+
+> Note - enabling a [Wiki](https://qodo-merge-docs.qodo.ai/usage-guide/enabling_a_wiki/) is required for this feature.
+
+### Finding Code Problems - Exploration Phase
+
+The `improve` tool identifies potential issues, problems and bugs in Pull Request (PR) code changes. 
+Rather than focusing on minor issues like code style or formatting, the tool intelligently analyzes code to detect meaningful problems. 
+
+The analysis intentionally takes a flexible, _exploratory_ approach to identify meaningful potential issues, allowing the tool to surface relevant code suggestions without being constrained by predefined categories.
+
+### Tracking Implemented Suggestions
+
+Qodo Merge features a novel [tracking system](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking) that automatically detects when PR authors implement AI-generated code suggestions. 
+All accepted suggestions are aggregated in a repository-specific wiki page called [`.pr_agent_accepted_suggestions`](https://github.com/qodo-ai/pr-agent/wiki/.pr_agent_accepted_suggestions)
+
+
+### Learning and Applying Auto Best Practices
+
+Monthly, Qodo Merge analyzes the collection of accepted suggestions to generate repository-specific best practices, stored in [`.pr_agent_auto_best_practices`](https://github.com/qodo-ai/pr-agent/wiki/.pr_agent_auto_best_practices) wiki file.
+These best practices reflect recurring patterns in accepted code improvements.
+
+The `improve` tool will incorporate these best practices as an additional analysis layer, checking PR code changes against known patterns of previously accepted improvements.
+This creates a two-phase analysis:
+
+1. Open exploration for general code issues
+2. Targeted checking against established best practices - exploiting the knowledge gained from past suggestions
+
+By keeping these phases decoupled, the tool remains free to discover new or unseen issues and problems, while also learning from past experiences.
+
+
+When presenting the suggestions generated by the `improve` tool, Qodo Merge will add a dedicated label for each suggestion generated from the auto best practices - 'Learned best practice':
+
+![Auto best practice suggestion](https://www.qodo.ai/images/pr_agent/auto_best_practices.png){width=684}
+
+
+## Auto Best Practices vs Custom Best Practices
+
+Teams and companies can also manually define their own [custom best practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) in Qodo Merge. 
+
+When custom best practices exist, Qodo Merge will still generate an 'auto best practices' wiki file, though it won't be used by the `improve` tool. 
+However, this auto-generated file can still serve two valuable purposes:
+
+1. It can help enhance your custom best practices with additional insights derived from suggestions your team found valuable enough to implement
+2. It demonstrates effective patterns for writing AI-friendly best practices
+
+Even when using custom best practices, we recommend regularly reviewing the auto best practices file to refine your custom rules.
+
+## Relevant configurations
+
+```toml
+[auto_best_practices]
+# Disable all auto best practices usage or generation
+enable_auto_best_practices = true  
+
+# Disable usage of auto best practices file in the 'improve' tool
+utilize_auto_best_practices = true 
+
+# Extra instructions to the auto best practices generation prompt
+extra_instructions = ""            
+
+# Max number of patterns to be detected
+max_patterns = 5                   
+```

docs/docs/core-abilities/fetching_ticket_context.md

@@ -1,16 +1,29 @@
 # Fetching Ticket Context for PRs
+`Supported Git Platforms: GitHub, GitLab, Bitbucket`
+
 ## Overview
 Qodo Merge PR Agent streamlines code review workflows by seamlessly connecting with multiple ticket management systems.
 This integration enriches the review process by automatically surfacing relevant ticket information and context alongside code changes.
 
+## Ticket systems supported
+- GitHub
+- Jira (💎)
+
+Ticket data fetched:
+
+1. Ticket Title
+2. Ticket Description
+3. Custom Fields (Acceptance criteria)
+4. Subtasks (linked tasks)
+5. Labels
+6. Attached Images/Screenshots
 
 ## Affected Tools
 
 Ticket Recognition Requirements:
 
-1. The PR description should contain a link to the ticket.
-2. For Jira tickets, you should follow the instructions in [Jira Integration](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/#jira-integration) in order to authenticate with Jira.
-
+- The PR description should contain a link to the ticket or if the branch name starts with the ticket id / number.
+- For Jira tickets, you should follow the instructions in [Jira Integration](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/#jira-integration) in order to authenticate with Jira.
 
 ### Describe tool
 Qodo Merge PR Agent will recognize the ticket and use the ticket content (title, description, labels) to provide additional context for the code changes.
@@ -49,12 +62,18 @@ Since Qodo Merge PR Agent is integrated with GitHub, it doesn't require any addi
 ### Jira Integration 💎
 
 We support both Jira Cloud and Jira Server/Data Center.
-To integrate with Jira, The PR Description should contain a link to the Jira ticket.
+To integrate with Jira, you can link your PR to a ticket using either of these methods:
 
-For Jira integration, include a ticket reference in your PR description using either the complete URL format `https://<JIRA_ORG>.atlassian.net/browse/ISSUE-123` or the shortened ticket ID `ISSUE-123`.
+**Method 1: Description Reference:**
+
+Include a ticket reference in your PR description using either the complete URL format https://<JIRA_ORG>.atlassian.net/browse/ISSUE-123 or the shortened ticket ID ISSUE-123.
+
+**Method 2: Branch Name Detection:**
+
+Name your branch with the ticket ID as a prefix (e.g., `ISSUE-123-feature-description` or `ISSUE-123/feature-description`).
 
 !!! note "Jira Base URL"
-    If using the shortened format, ensure your configuration file contains the Jira base URL under the [jira] section like this:
+    For shortened ticket IDs or branch detection (method 2), you must configure the Jira base URL in your configuration file under the [jira] section:
 
     ```toml
     [jira]
@@ -101,9 +120,45 @@ jira_api_email = "YOUR_EMAIL"
 ```
 
 
-#### Jira Server/Data Center 💎
+#### Jira Data Center/Server 💎
 
-Currently, we only support the Personal Access Token (PAT) Authentication method.
+##### Local App Authentication (For Qodo Merge On-Premise Customers)
+
+##### 1. Step 1: Set up an application link in Jira Data Center/Server
+* Go to Jira Administration > Applications > Application Links > Click on `Create link`
+
+![application links](https://www.qodo.ai/images/pr_agent/jira_app_links.png){width=384}
+* Choose `External application` and set the direction to `Incoming` and then click `Continue`
+
+![external application](https://www.qodo.ai/images/pr_agent/jira_create_link.png){width=256}
+* In the following screen, enter the following details:
+    * Name: `Qodo Merge`
+    * Redirect URL: Enter your Qodo Merge URL followed  `https://{QODO_MERGE_ENDPOINT}/register_ticket_provider`
+    * Permission: Select `Read`
+    * Click `Save`
+
+![external application details](https://www.qodo.ai/images/pr_agent/jira_fill_app_link.png){width=384}
+* Copy the `Client ID` and `Client secret` and set them in your `.secrets` file:
+
+![client id and secret](https://www.qodo.ai/images/pr_agent/jira_app_credentionals.png){width=256}
+```toml
+[jira]
+jira_app_secret = "..."
+jira_client_id = "..."
+```
+
+##### 2. Step 2: Authenticate with Jira Data Center/Server
+* Open this URL in your browser: `https://{QODO_MERGE_ENDPOINT}/jira_auth`
+* Click on link
+
+![jira auth success](https://www.qodo.ai/images/pr_agent/jira_auth_page.png){width=384}
+
+* You will be redirected to Jira Data Center/Server, click `Allow`
+* You will be redirected back to Qodo Merge PR Agent and you will see a success message.
+
+
+##### Personal Access Token (PAT) Authentication
+We also support Personal Access Token (PAT) Authentication method.
 
 1. Create a [Personal Access Token (PAT)](https://confluence.atlassian.com/enterprise/using-personal-access-tokens-1026032365.html) in your Jira account
 2. In your Configuration file/Environment variables/Secrets file, add the following lines:
@@ -112,4 +167,4 @@ Currently, we only support the Personal Access Token (PAT) Authentication method
 [jira]
 jira_base_url = "YOUR_JIRA_BASE_URL" # e.g. https://jira.example.com
 jira_api_token = "YOUR_API_TOKEN"
-```
+```

docs/docs/core-abilities/index.md

@@ -2,6 +2,7 @@
 Qodo Merge utilizes a variety of core abilities to provide a comprehensive and efficient code review experience. These abilities include:
 
 - [Fetching ticket context](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/)
+- [Auto best practices](https://qodo-merge-docs.qodo.ai/core-abilities/auto_best_practices/)
 - [Local and global metadata](https://qodo-merge-docs.qodo.ai/core-abilities/metadata/)
 - [Dynamic context](https://qodo-merge-docs.qodo.ai/core-abilities/dynamic_context/)
 - [Self-reflection](https://qodo-merge-docs.qodo.ai/core-abilities/self_reflection/)

docs/docs/core-abilities/metadata.md

@@ -32,14 +32,14 @@ For example, when generating code suggestions for different files, Qodo Merge ca
 
 @@ ... @@ def func1():
 __new hunk__
-11  unchanged code line0 in the PR
-12  unchanged code line1 in the PR
-13 +new code line2 added in the PR
-14  unchanged code line3 in the PR
+11  unchanged code line0
+12  unchanged code line1
+13 +new code line2 added
+14  unchanged code line3
 __old hunk__
  unchanged code line0
  unchanged code line1
--old code line2 removed in the PR
+-old code line2 removed
  unchanged code line3
 
 @@ ... @@ def func2():

docs/docs/core-abilities/static_code_analysis.md

@@ -61,7 +61,7 @@ Or be triggered interactively by using the `analyze` tool.
 
 ### Find Similar Code
 
-The [`similar code`](https://qodo-merge-docs.qodo.ai/tools/similar_code/) tool retrieves the most similar code components from inside the organization's codebase, or from open-source code.
+The [`similar code`](https://qodo-merge-docs.qodo.ai/tools/similar_code/) tool retrieves the most similar code components from inside the organization's codebase or from open-source code, including details about the license associated with each repository.
 
 For example:
 

docs/docs/faq/index.md

@@ -1,6 +1,6 @@
 # FAQ
 
-??? note "Question: Can Qodo Merge serve as a substitute for a human reviewer?"
+??? note "Q: Can Qodo Merge serve as a substitute for a human reviewer?"
     #### Answer:<span style="display:none;">1</span>
 
     Qodo Merge is designed to assist, not replace, human reviewers.
@@ -12,7 +12,7 @@
 
     1. Preserves user's original PR header
     2. Places user's description above the AI-generated PR description
-    3. Cannot approve PRs; approval remains reviewer's responsibility
+    3. Won't approve PRs; approval remains reviewer's responsibility
     4. The code suggestions are optional, and aim to:
         - Encourage self-review and self-reflection
         - Highlight potential bugs or oversights
@@ -22,15 +22,15 @@
 
 ___
 
-??? note "Question: I received an incorrect or irrelevant suggestion. Why?"
+??? note "Q: I received an incorrect or irrelevant suggestion. Why?"
 
     #### Answer:<span style="display:none;">2</span>
 
     - Modern AI models, like Claude 3.5 Sonnet and GPT-4, are improving rapidly but remain imperfect. Users should critically evaluate all suggestions rather than accepting them automatically.
-    - AI errors are rare, but possible. A main value from reviewing the code suggestions lies in their high probability of catching **mistakes or bugs made by the PR author**. We believe it's worth spending 30-60 seconds reviewing suggestions, even if some aren't relevant, as this practice can enhances code quality and prevent bugs in production.
+    - AI errors are rare, but possible. A main value from reviewing the code suggestions lies in their high probability of catching **mistakes or bugs made by the PR author**. We believe it's worth spending 30-60 seconds reviewing suggestions, even if some aren't relevant, as this practice can enhance code quality and prevent bugs in production.
 
 
-    - The hierarchical structure of the suggestions is designed to help the user to _quickly_ understand them, and to decide which ones are relevant and which are not:
+    - The hierarchical structure of the suggestions is designed to help the user _quickly_ understand them, and to decide which ones are relevant and which are not:
 
         - Only if the `Category` header is relevant, the user should move to the summarized suggestion description.
         - Only if the summarized suggestion description is relevant, the user should click on the collapsible, to read the full suggestion description with a code preview example.
@@ -40,14 +40,14 @@ ___
 
 ___
 
-??? note "Question: How can I get more tailored suggestions?"
+??? note "Q: How can I get more tailored suggestions?"
     #### Answer:<span style="display:none;">3</span>
 
     See [here](https://qodo-merge-docs.qodo.ai/tools/improve/#extra-instructions-and-best-practices) for more information on how to use the `extra_instructions` and `best_practices` configuration options, to guide the model to more tailored suggestions.
 
 ___
 
-??? note "Question: Will you store my code ? Are you using my code to train models?"
+??? note "Q: Will you store my code? Are you using my code to train models?"
     #### Answer:<span style="display:none;">4</span>
 
     No. Qodo Merge strict privacy policy ensures that your code is not stored or used for training purposes.
@@ -56,12 +56,35 @@ ___
 
 ___
 
-??? note "Question: Can I use my own LLM keys with Qodo Merge?"
+??? note "Q: Can I use my own LLM keys with Qodo Merge?"
     #### Answer:<span style="display:none;">5</span>
 
-    When you self-host, you use your own keys.
+    When you self-host the [open-source](https://github.com/Codium-ai/pr-agent) version, you use your own keys.
 
-    Qodo Merge Pro with SaaS deployment is a hosted version of Qodo Merge, where Qodo manages the infrastructure and the keys.
+    Qodo Merge with SaaS deployment is a hosted version of Qodo Merge, where Qodo manages the infrastructure and the keys.
     For enterprise customers, on-prem deployment is also available. [Contact us](https://www.codium.ai/contact/#pricing) for more information.
+___
+
+??? note "Q: Can Qodo Merge review draft/offline PRs?"
+    #### Answer:<span style="display:none;">5</span>
+
+    Yes. While Qodo Merge won't automatically review draft PRs, you can still get feedback by manually requesting it through [online commenting](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#online-usage).
+
+    For active PRs, you can customize the automatic feedback settings [here](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#qodo-merge-automatic-feedback) to match your team's workflow.
+___
+
+??? note "Q: Can the 'Review effort' feedback be calibrated or customized?"
+    #### Answer:<span style="display:none;">5</span>
+
+    Yes, you can customize review effort estimates using the `extra_instructions` configuration option (see [documentation](https://qodo-merge-docs.qodo.ai/tools/review/#configuration-options)).
+    
+    Example mapping:
+
+    - Effort 1: < 30 minutes review time
+    - Effort 2: 30-60 minutes review time
+    - Effort 3: 60-90 minutes review time
+    - ...
+    
+    Note: The effort levels (1-5) are primarily meant for _comparative_ purposes, helping teams prioritize reviewing smaller PRs first. The actual review duration may vary, as the focus is on providing consistent relative effort estimates.
 
 ___

docs/docs/index.md

@@ -1,15 +1,16 @@
 # Overview
 
-Qodo Merge is an open-source tool to help efficiently review and handle pull requests.
+[PR-Agent](https://github.com/Codium-ai/pr-agent) is an open-source tool to help efficiently review and handle pull requests. 
+Qodo Merge is a hosted version of PR-Agent, designed for companies and teams that require additional features and capabilities
 
 - See the [Installation Guide](./installation/index.md) for instructions on installing and running the tool on different git platforms.
 
-- See the [Usage Guide](./usage-guide/index.md) for instructions on running the Qodo Merge commands via different interfaces, including _CLI_, _online usage_, or by _automatically triggering_ them when a new PR is opened.
+- See the [Usage Guide](./usage-guide/index.md) for instructions on running commands via different interfaces, including _CLI_, _online usage_, or by _automatically triggering_ them when a new PR is opened.
 
 - See the [Tools Guide](./tools/index.md) for a detailed description of the different tools.
 
 
-## Qodo Merge Docs Smart Search
+## Docs Smart Search
 
 To search the documentation site using natural language:
 
@@ -18,43 +19,45 @@ To search the documentation site using natural language:
    - A pull request where Qodo Merge is installed
    - A [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat)
 
-2) Qodo Merge will respond with an [answer](https://github.com/Codium-ai/pr-agent/pull/1241#issuecomment-2365259334) that includes relevant documentation links.
+2) The bot will respond with an [answer](https://github.com/Codium-ai/pr-agent/pull/1241#issuecomment-2365259334) that includes relevant documentation links.
 
 
 ## Qodo Merge Features
 
-Qodo Merge offers extensive pull request functionalities across various git providers.
+Qodo Merge offers extensive pull request functionalities across various git providers:
 
 |       |                                                                                                                       | GitHub | Gitlab | Bitbucket | Azure DevOps |
 |-------|-----------------------------------------------------------------------------------------------------------------------|:------:|:------:|:---------:|:------------:|
-| TOOLS | Review                                                                                                                |   ✅    |   ✅    |   ✅       |      ✅       |
+| TOOLS | Review                                                                                                                |   ✅    |   ✅    |   ✅       |      ✅      |
 |       | ⮑ Incremental                                                                                                         |   ✅    |        |            |              |
-|       | Ask                                                                                                                   |   ✅    |   ✅    |   ✅        |      ✅       |
-|       | Describe                                                                                                              |   ✅    |   ✅    |   ✅        |      ✅       |
-|       | ⮑ [Inline file summary](https://qodo-merge-docs.qodo.ai/tools/describe/#inline-file-summary){:target="_blank"} 💎     |   ✅    |   ✅    |           |              |
-|       | Improve                                                                                                               |   ✅    |   ✅    |   ✅        |      ✅       |
-|       | ⮑ Extended                                                                                                            |   ✅    |   ✅    |   ✅        |      ✅       |
-|       | [Custom Prompt](./tools/custom_prompt.md){:target="_blank"} 💎                                                        |   ✅    |   ✅    |   ✅        |              |
-|       | Reflect and Review                                                                                                    |   ✅    |   ✅    |   ✅        |              |
+|       | Ask                                                                                                                   |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | Describe                                                                                                              |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | ⮑ [Inline file summary](https://qodo-merge-docs.qodo.ai/tools/describe/#inline-file-summary){:target="_blank"} 💎     |   ✅    |   ✅    |           |      ✅      |
+|       | Improve                                                                                                               |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | ⮑ Extended                                                                                                            |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | [Custom Prompt](./tools/custom_prompt.md){:target="_blank"} 💎                                                        |   ✅    |   ✅    |   ✅        |      ✅      |
+|       | Reflect and Review                                                                                                    |   ✅    |   ✅    |   ✅        |      ✅      |
 |       | Update CHANGELOG.md                                                                                                   |   ✅    |   ✅    |   ✅        |      ️       |
 |       | Find Similar Issue                                                                                                    |   ✅    |        |             |      ️       |
-|       | [Add PR Documentation](./tools/documentation.md){:target="_blank"} 💎                                                 |   ✅    |   ✅    |          |              |
-|       | [Generate Custom Labels](./tools/describe.md#handle-custom-labels-from-the-repos-labels-page-💎){:target="_blank"} 💎 |   ✅    |   ✅    |            |              |
-|       | [Analyze PR Components](./tools/analyze.md){:target="_blank"} 💎                                                      |   ✅    |   ✅    |       |              |
+|       | [Add PR Documentation](./tools/documentation.md){:target="_blank"} 💎                                                 |   ✅    |   ✅    |          |      ✅      |
+|       | [Generate Custom Labels](./tools/describe.md#handle-custom-labels-from-the-repos-labels-page-💎){:target="_blank"} 💎 |   ✅    |   ✅    |            |      ✅      |
+|       | [Analyze PR Components](./tools/analyze.md){:target="_blank"} 💎                                                      |   ✅    |   ✅    |       |      ✅      |
+|       | [Test](https://pr-agent-docs.codium.ai/tools/test/) 💎                                                                | ✅ |   ✅    |                    |              |
+|       | [Implement](https://pr-agent-docs.codium.ai/tools/implement/) 💎                                                      | ✅ |   ✅    |          ✅         |              |
 |       |                                                                                                                       |        |        |            |      ️       |
-| USAGE | CLI                                                                                                                   |   ✅    |   ✅    |   ✅       |      ✅       |
-|       | App / webhook                                                                                                         |   ✅    |   ✅    |    ✅        |      ✅       |
+| USAGE | CLI                                                                                                                   |   ✅    |   ✅    |   ✅       |      ✅      |
+|       | App / webhook                                                                                                         |   ✅    |   ✅    |    ✅        |      ✅      |
 |       | Actions                                                                                                               |   ✅    |        |            |      ️       |
 |       |                                                                                                                       |        |        |            |
-| CORE  | PR compression                                                                                                        |   ✅    |   ✅    |   ✅       |      ✅       |
-|       | Repo language prioritization                                                                                          |   ✅    |   ✅    |   ✅       |      ✅       |
-|       | Adaptive and token-aware file patch fitting                                                                           |   ✅    |   ✅    |   ✅     |      ✅       |
-|       | Multiple models support                                                                                               |   ✅    |   ✅    |   ✅       |      ✅       |
-|       | Incremental PR review                                                                                                 |   ✅    |        |            |              |
-|       | [Static code analysis](./tools/analyze.md/){:target="_blank"} 💎                                                      |   ✅    |   ✅     |    ✅    |              |
-|       | [Multiple configuration options](./usage-guide/configuration_options.md){:target="_blank"} 💎                         |   ✅    |   ✅     |    ✅    |              |
+| CORE  | PR compression                                                                                                        |   ✅    |   ✅    |   ✅       |   ✅        |
+|       | Repo language prioritization                                                                                          |   ✅    |   ✅    |   ✅       |   ✅        |
+|       | Adaptive and token-aware file patch fitting                                                                           |   ✅    |   ✅    |   ✅     |   ✅        |
+|       | Multiple models support                                                                                               |   ✅    |   ✅    |   ✅       |   ✅        |
+|       | Incremental PR review                                                                                                 |   ✅    |        |            |           |
+|       | [Static code analysis](./tools/analyze.md/){:target="_blank"} 💎                                                      |   ✅    |   ✅    |    ✅    |   ✅        |
+|       | [Multiple configuration options](./usage-guide/configuration_options.md){:target="_blank"} 💎                         |   ✅    |   ✅    |    ✅    |   ✅        |
 
-💎 marks a feature available only in [Qodo Merge Pro](https://www.codium.ai/pricing/){:target="_blank"}
+💎 marks a feature available only in [Qodo Merge](https://www.codium.ai/pricing/){:target="_blank"}, and not in the open-source version.
 
 
 ## Example Results
@@ -90,4 +93,4 @@ The following diagram illustrates Qodo Merge tools and their flow:
 
 ![Qodo Merge Tools](https://codium.ai/images/pr_agent/diagram-v0.9.png)
 
-Check out the [core abilities](core-abilities/index.md) page for a comprehensive overview of the variety of core abilities used by Qodo Merge.
+Check out the [PR Compression strategy](core-abilities/index.md) page for more details on how we convert a code diff to a manageable LLM prompt

docs/docs/installation/azure.md

@@ -1,5 +1,5 @@
 ## Azure DevOps Pipeline
-You can use a pre-built Action Docker image to run Qodo Merge as an Azure devops pipeline.
+You can use a pre-built Action Docker image to run PR-Agent as an Azure devops pipeline.
 add the following file to your repository under `azure-pipelines.yml`:
 ```yaml
 # Opt out of CI triggers
@@ -52,7 +52,7 @@ stages:
 This script will run Qodo Merge on every new merge request, with the `improve`, `review`, and `describe` commands.
 Note that you need to export the `azure_devops__pat` and `OPENAI_KEY` variables in the Azure DevOps pipeline settings (Pipelines -> Library -> + Variable group):
 
-![Qodo Merge Pro](https://codium.ai/images/pr_agent/azure_devops_pipeline_secrets.png){width=468}
+![Qodo Merge](https://codium.ai/images/pr_agent/azure_devops_pipeline_secrets.png){width=468}
 
 Make sure to give pipeline permissions to the `pr_agent` variable group.
 
@@ -80,7 +80,7 @@ org = "https://dev.azure.com/YOUR_ORGANIZATION/"
 # pat = "YOUR_PAT_TOKEN" needed only if using PAT for authentication
 ```
 
-### Azure DevOps Webhook
+## Azure DevOps Webhook
 
 To trigger from an Azure webhook, you need to manually [add a webhook](https://learn.microsoft.com/en-us/azure/devops/service-hooks/services/webhooks?view=azure-devops).
 Use the "Pull request created" type to trigger a review, or "Pull request commented on" to trigger any supported comment with /<command> <args> comment on the relevant PR. Note that for the "Pull request commented on" trigger, only API v2.0 is supported.

docs/docs/installation/bitbucket.md

@@ -27,10 +27,6 @@ You can get a Bitbucket token for your repository by following Repository Settin
 Note that comments on a PR are not supported in Bitbucket Pipeline.
 
 
-## Run using CodiumAI-hosted Bitbucket app 💎
-
-Please contact visit [Qodo Merge Pro](https://www.codium.ai/pricing/) if you're interested in a hosted BitBucket app solution that provides full functionality including PR reviews and comment handling. It's based on the [bitbucket_app.py](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/git_providers/bitbucket_provider.py) implementation.
-
 
 ## Bitbucket Server and Data Center
 

docs/docs/installation/github.md

@@ -1,6 +1,6 @@
 ## Run as a GitHub Action
 
-You can use our pre-built Github Action Docker image to run Qodo Merge 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`:
 
@@ -21,7 +21,7 @@ jobs:
     steps:
       - name: PR Agent action step
         id: pragent
-        uses: Codium-ai/pr-agent@main
+        uses: qodo-ai/pr-agent@main
         env:
           OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

docs/docs/installation/gitlab.md

@@ -1,5 +1,5 @@
 ## Run as a GitLab Pipeline
-You can use a pre-built Action Docker image to run Qodo Merge as a GitLab pipeline. This is a simple way to get started with Qodo Merge without setting up your own server.
+You can use a pre-built Action Docker image to run PR-Agent as a GitLab pipeline. This is a simple way to get started with Qodo Merge without setting up your own server.
 
 (1) Add the following file to your repository under `.gitlab-ci.yml`:
 ```yaml

docs/docs/installation/index.md

@@ -1,21 +1,17 @@
 # Installation
 
-## Self-hosted Qodo Merge
-If you choose to host your own Qodo Merge, you first need to acquire two tokens:
+## Self-hosted PR-Agent
 
-1. An OpenAI key from [here](https://platform.openai.com/api-keys), with access to GPT-4 (or a key for other [language models](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/), if you prefer).
-2. A GitHub\GitLab\BitBucket personal access token (classic), with the repo scope. [GitHub from [here](https://github.com/settings/tokens)]
-
-There are several ways to use self-hosted Qodo Merge:
+There are several ways to use self-hosted PR-Agent:
 
 - [Locally](./locally.md)
-- [GitHub](./github.md)
-- [GitLab](./gitlab.md)
-- [BitBucket](./bitbucket.md)
-- [Azure DevOps](./azure.md)
+- [GitHub integration](./github.md)
+- [GitLab integration](./gitlab.md)
+- [BitBucket integration](./bitbucket.md)
+- [Azure DevOps integration](./azure.md)
 
-## Qodo Merge Pro 💎
-Qodo Merge Pro, an app hosted by CodiumAI for GitHub\GitLab\BitBucket, is also available.
+## Qodo Merge 💎
+Qodo Merge, an app hosted by QodoAI for GitHub\GitLab\BitBucket, is also available.
 <br>
-With Qodo Merge Pro, installation is as simple as signing up and adding the Qodo Merge app to your relevant repo.
-See [here](https://qodo-merge-docs.qodo.ai/installation/pr_agent_pro/) for more details.
+With Qodo Merge, installation is as simple as adding the Qodo Merge app to your relevant repositories.
+See [here](https://qodo-merge-docs.qodo.ai/installation/qodo_merge/) for more details.

docs/docs/installation/locally.md

@@ -1,3 +1,77 @@
+To run PR-Agent locally, you first need to acquire two keys:
+
+1. An OpenAI key from [here](https://platform.openai.com/api-keys){:target="_blank"}, with access to GPT-4 (or a key for other [language models](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/), if you prefer).
+2. A personal access token from your Git platform (GitHub, GitLab, BitBucket) with repo scope. GitHub token, for example, can be issued from [here](https://github.com/settings/tokens){:target="_blank"}
+
+
+## Using Docker image
+
+A list of the relevant tools can be found in the [tools guide](../tools/ask.md).
+
+To invoke a tool (for example `review`), you can run PR-Agent 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
+    ```
+    If you are using GitHub enterprise server, you need to specify the custom url as variable.
+    For example, if your GitHub server is at `https://github.mycompany.com`, add the following to the command:
+    ```
+    -e GITHUB.BASE_URL=https://github.mycompany.com/api/v3
+    ```
+
+- 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
+    ```
+
+    If you have a dedicated GitLab instance, you need to specify the custom url as variable:
+    ```
+    -e GITLAB.URL=<your gitlab instance url>
+    ```
+
+- 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`](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/.secrets_template.toml) file for environment variables expected names and values.
+
+### Utilizing environment variables
+
+It is also possible to provide or override the configuration by setting the corresponding environment variables.
+You can define the corresponding environment variables by following this convention: `<TABLE>__<KEY>=<VALUE>` or `<TABLE>.<KEY>=<VALUE>`.
+The `<TABLE>` refers to a table/section in a configuration file and `<KEY>=<VALUE>` refers to the key/value pair of a setting in the configuration file.
+
+For example, suppose you want to run `pr_agent` that connects to a self-hosted GitLab instance similar to an example above.
+You can define the environment variables in a plain text file named `.env` with the following content:
+
+```
+CONFIG__GIT_PROVIDER="gitlab"
+GITLAB__URL="<your url>"
+GITLAB__PERSONAL_ACCESS_TOKEN="<your token>"
+OPENAI__KEY="<your key>"
+```
+
+Then, you can run `pr_agent` using Docker with the following command:
+
+```shell
+docker run --rm -it --env-file .env codiumai/pr-agent:latest <tool> <tool parameter>
+```
+
+---
+
+### I get an error when running the Docker image. What should I do?
+
+If you encounter an error when running the Docker image, it is almost always due to a misconfiguration of api keys or tokens.
+
+Note that litellm, which is used by pr-agent, sometimes returns non-informative error messages such as `APIError: OpenAIException - Connection error.`
+Carefully check the api keys and tokens you provided and make sure they are correct.
+Adjustments may be needed depending on your llm provider.
+
+For example, for Azure OpenAI, additional keys are [needed](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/#azure).
+Same goes for other providers, make sure to check the [documentation](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/#changing-a-model)
+
 ## Using pip package
 
 Install the package:
@@ -35,40 +109,6 @@ if __name__ == '__main__':
     main()
 ```
 
-## Using Docker image
-
-A list of the relevant tools can be found in the [tools guide](../tools/ask.md).
-
-To invoke a tool (for example `review`), you can run directly from the Docker image. Here's how:
-
-- For GitHub:
-    ```
-    docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
-    ```
-    If you are using GitHub enterprise server, you need to specify the custom url as variable.
-    For example, if your GitHub server is at `https://github.mycompany.com`, add the following to the command:
-    ```
-    -e GITHUB.BASE_URL=https://github.mycompany.com/api/v3
-    ```
-
-- 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
-    ```
-
-    If you have a dedicated GitLab instance, you need to specify the custom url as variable:
-    ```
-    -e GITLAB.URL=<your gitlab instance url>
-    ```
-
-- 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.
-
----
 
 ## Run from source
 

docs/docs/installation/pr_agent.md

@@ -0,0 +1,49 @@
+# PR-Agent Installation Guide
+
+PR-Agent can be deployed in various environments and platforms. Choose the installation method that best suits your needs:
+
+## 🖥️ Local Installation
+
+Learn how to run PR-Agent locally using:
+
+- Docker image
+- pip package
+- CLI from source code
+
+[View Local Installation Guide →](https://qodo-merge-docs.qodo.ai/installation/locally/)
+
+## 🐙 GitHub Integration
+
+Set up PR-Agent with GitHub as:
+
+- GitHub Action
+- Local GitHub App
+
+[View GitHub Integration Guide →](https://qodo-merge-docs.qodo.ai/installation/github/)
+
+## 🦊 GitLab Integration
+
+Deploy PR-Agent on GitLab as:
+
+- GitLab pipeline job
+- Local GitLab webhook server
+
+[View GitLab Integration Guide →](https://qodo-merge-docs.qodo.ai/installation/gitlab/)
+
+## 🟦 BitBucket Integration
+
+Implement PR-Agent in BitBucket as:
+
+- BitBucket pipeline job
+- Local BitBucket server
+
+[View BitBucket Integration Guide →](https://qodo-merge-docs.qodo.ai/installation/bitbucket/)
+
+## 🔷  Azure DevOps Integration
+
+Configure PR-Agent with Azure DevOps as:
+
+- Azure DevOps pipeline job
+- Local Azure DevOps webhook
+
+[View Azure DevOps Integration Guide →](https://qodo-merge-docs.qodo.ai/installation/azure/)

docs/docs/installation/pr_agent_pro.md

@@ -1,68 +0,0 @@
-
-## Getting Started with Qodo Merge Pro
-
-Qodo Merge Pro is a versatile application compatible with GitHub, GitLab, and BitBucket, hosted by CodiumAI.
-See [here](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) for more details about the benefits of using Qodo Merge Pro.
-
-Interested parties can subscribe to Qodo Merge Pro through the following [link](https://www.codium.ai/pricing/).
-After subscribing, you are granted the ability to easily install the application across any of your repositories.
-
-![Qodo Merge Pro](https://codium.ai/images/pr_agent/pr_agent_pro_install.png){width=468}
-
-Each user who wants to use Qodo Merge pro needs to buy a seat.
-Initially, CodiumAI offers a two-week trial period at no cost, after which continued access requires each user to secure a personal seat.
-Once a user acquires a seat, they gain the flexibility to use Qodo Merge Pro across any repository where it was enabled.
-
-Users without a purchased seat who interact with a repository featuring Qodo Merge Pro are entitled to receive up to five complimentary feedbacks.
-Beyond this limit, Qodo Merge Pro will cease to respond to their inquiries unless a seat is purchased.
-
-## Install Qodo Merge Pro for GitHub Enterprise Server
-
-To use Qodo Merge Pro application on your private GitHub Enterprise Server, you will need to contact us for starting an [Enterprise](https://www.codium.ai/pricing/) trial.
-
-
-## Install Qodo Merge Pro for GitLab (Teams & Enterprise)
-
-Since GitLab platform does not support apps, installing Qodo Merge Pro for GitLab is a bit more involved, and requires the following steps:
-
-### Step 1
-
-Acquire a personal, project or group level access token. Enable the “api” scope in order to allow Qodo Merge to read pull requests, comment and respond to requests.
-
-<figure markdown="1">
-![Step 1](https://www.codium.ai/images/pr_agent/gitlab_pro_pat.png){width=750}
-</figure>
-
-Store the token in a safe place, you won’t be able to access it again after it was generated.
-
-### Step 2
-
-Generate a shared secret and link it to the access token. Browse to [https://register.gitlab.pr-agent.codium.ai](https://register.gitlab.pr-agent.codium.ai).
-Fill in your generated GitLab token and your company or personal name in the appropriate fields and click "Submit".
-
-You should see "Success!" displayed above the Submit button, and a shared secret will be generated. Store it in a safe place, you won’t be able to access it again after it was generated.
-
-### Step 3
-
-Install a webhook for your repository or groups, by clicking “webhooks” on the settings menu. Click the “Add new webhook” button.
-
-<figure markdown="1">
-![Step 3.1](https://www.codium.ai/images/pr_agent/gitlab_pro_add_webhook.png)
-</figure>
-
-In the webhook definition form, fill in the following fields:
-URL: https://pro.gitlab.pr-agent.codium.ai/webhook
-
-Secret token: Your CodiumAI key
-Trigger: Check the ‘comments’ and ‘merge request events’ boxes.
-Enable SSL verification: Check the box.
-
-<figure markdown="1">
-![Step 3.2](https://www.codium.ai/images/pr_agent/gitlab_pro_webhooks.png){width=750}
-</figure>
-
-### Step 4
-
-You’re all set!
-
-Open a new merge request or add a MR comment with one of Qodo Merge’s commands such as /review, /describe or /improve.

docs/docs/installation/qodo_merge.md

@@ -0,0 +1,81 @@
+Qodo Merge is a versatile application compatible with GitHub, GitLab, and BitBucket, hosted by QodoAI.
+See [here](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) for more details about the benefits of using Qodo Merge.
+
+A complimentary two-week trial is provided to all new users. Following the trial period, user licenses (seats) are required for continued access.
+To purchase user licenses, please visit our [pricing page](https://www.qodo.ai/pricing/).
+Once subscribed, users can seamlessly deploy the application across any of their code repositories.
+
+## Install Qodo Merge for GitHub
+
+### GitHub Cloud
+
+Qodo Merge for GitHub cloud is available for installation through the [GitHub Marketplace](https://github.com/apps/qodo-merge-pro).
+
+![Qodo Merge](https://codium.ai/images/pr_agent/pr_agent_pro_install.png){width=468}
+
+### GitHub Enterprise Server
+
+To use Qodo Merge application on your private GitHub Enterprise Server, you will need to contact us for starting an [Enterprise](https://www.codium.ai/pricing/) trial.
+
+### GitHub Open Source Projects
+
+For open-source projects, Qodo Merge is available for free usage. To install Qodo Merge for your open-source repositories, use the following marketplace [link](https://github.com/apps/qodo-merge-pro-for-open-source).
+
+## Install Qodo Merge for Bitbucket
+
+###  Bitbucket Cloud
+
+Qodo Merge for Bitbucket Cloud is available for installation through the following [link](https://bitbucket.org/site/addons/authorize?addon_key=d6df813252c37258)
+
+![Qodo Merge](https://qodo.ai/images/pr_agent/pr_agent_pro_bitbucket_install.png){width=468}
+
+### Bitbucket Server
+
+To use Qodo Merge application on your private Bitbucket Server, you will need to contact us for starting an [Enterprise](https://www.qodo.ai/pricing/) trial.
+
+
+## Install Qodo Merge for GitLab (Teams & Enterprise)
+
+Since GitLab platform does not support apps, installing Qodo Merge for GitLab is a bit more involved, and requires the following steps:
+
+#### Step 1
+
+Acquire a personal, project or group level access token. Enable the “api” scope in order to allow Qodo Merge to read pull requests, comment and respond to requests.
+
+<figure markdown="1">
+![Step 1](https://www.codium.ai/images/pr_agent/gitlab_pro_pat.png){width=750}
+</figure>
+
+Store the token in a safe place, you won’t be able to access it again after it was generated.
+
+#### Step 2
+
+Generate a shared secret and link it to the access token. Browse to [https://register.gitlab.pr-agent.codium.ai](https://register.gitlab.pr-agent.codium.ai).
+Fill in your generated GitLab token and your company or personal name in the appropriate fields and click "Submit".
+
+You should see "Success!" displayed above the Submit button, and a shared secret will be generated. Store it in a safe place, you won’t be able to access it again after it was generated.
+
+#### Step 3
+
+Install a webhook for your repository or groups, by clicking “webhooks” on the settings menu. Click the “Add new webhook” button.
+
+<figure markdown="1">
+![Step 3.1](https://www.codium.ai/images/pr_agent/gitlab_pro_add_webhook.png)
+</figure>
+
+In the webhook definition form, fill in the following fields:
+URL: https://pro.gitlab.pr-agent.codium.ai/webhook
+
+Secret token: Your QodoAI key
+Trigger: Check the ‘comments’ and ‘merge request events’ boxes.
+Enable SSL verification: Check the box.
+
+<figure markdown="1">
+![Step 3.2](https://www.codium.ai/images/pr_agent/gitlab_pro_webhooks.png){width=750}
+</figure>
+
+#### Step 4
+
+You’re all set!
+
+Open a new merge request or add a MR comment with one of Qodo Merge’s commands such as /review, /describe or /improve.

docs/docs/overview/data_privacy.md

@@ -1,12 +1,12 @@
-## Self-hosted Qodo Merge
+## Self-hosted PR-Agent
 
-- If you self-host Qodo Merge with your OpenAI (or other LLM provider) API key, it is between you and the provider. We don't send your code data to Qodo Merge servers.
+- If you self-host PR-Agent with your OpenAI (or other LLM provider) API key, it is between you and the provider. We don't send your code data to Qodo servers.
 
-## Qodo Merge Pro 💎
+## Qodo Merge 💎
 
-- When using Qodo Merge Pro 💎, hosted by CodiumAI, we will not store any of your data, nor will we use it for training. You will also benefit from an OpenAI account with zero data retention.
+- When using Qodo Merge💎, hosted by Qodo, we will not store any of your data, nor will we use it for training. You will also benefit from an OpenAI account with zero data retention.
 
-- For certain clients, CodiumAI-hosted Qodo Merge Pro will use CodiumAI’s proprietary models. If this is the case, you will be notified.
+- For certain clients, Qodo Merge will use Qodo’s proprietary models. If this is the case, you will be notified.
 
 - No passive collection of Code and Pull Requests’ data — Qodo Merge will be active only when you invoke it, and it will then extract and analyze only data relevant to the executed command and queried pull request.
 

docs/docs/overview/index.md

@@ -1,93 +0,0 @@
-# Overview
-
-Qodo Merge is an open-source tool to help efficiently review and handle pull requests.
-
-- See the [Installation Guide](./installation/index.md) for instructions on installing and running the tool on different git platforms.
-
-- See the [Usage Guide](./usage-guide/index.md) for instructions on running the Qodo Merge commands via different interfaces, including _CLI_, _online usage_, or by _automatically triggering_ them when a new PR is opened.
-
-- See the [Tools Guide](./tools/index.md) for a detailed description of the different tools.
-
-
-## Qodo Merge Docs Smart Search
-
-To search the documentation site using natural language:
-
-1) Comment `/help "your question"` in either:
-
-   - A pull request where Qodo Merge is installed
-   - A [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat)
-
-2) Qodo Merge will respond with an [answer](https://github.com/Codium-ai/pr-agent/pull/1241#issuecomment-2365259334) that includes relevant documentation links.
-
-
-## Qodo Merge Features
-
-Qodo Merge offers extensive pull request functionalities across various git providers.
-
-|       |                                                                                                                       | GitHub | Gitlab | Bitbucket | Azure DevOps |
-|-------|-----------------------------------------------------------------------------------------------------------------------|:------:|:------:|:---------:|:------------:|
-| TOOLS | Review                                                                                                                |   ✅    |   ✅    |   ✅       |      ✅      |
-|       | ⮑ Incremental                                                                                                         |   ✅    |        |            |              |
-|       | Ask                                                                                                                   |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | Describe                                                                                                              |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | ⮑ [Inline file summary](https://qodo-merge-docs.qodo.ai/tools/describe/#inline-file-summary){:target="_blank"} 💎     |   ✅    |   ✅    |           |      ✅      |
-|       | Improve                                                                                                               |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | ⮑ Extended                                                                                                            |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | [Custom Prompt](./tools/custom_prompt.md){:target="_blank"} 💎                                                        |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | Reflect and Review                                                                                                    |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | Update CHANGELOG.md                                                                                                   |   ✅    |   ✅    |   ✅        |      ️       |
-|       | Find Similar Issue                                                                                                    |   ✅    |        |             |      ️       |
-|       | [Add PR Documentation](./tools/documentation.md){:target="_blank"} 💎                                                 |   ✅    |   ✅    |          |      ✅      |
-|       | [Generate Custom Labels](./tools/describe.md#handle-custom-labels-from-the-repos-labels-page-💎){:target="_blank"} 💎 |   ✅    |   ✅    |            |      ✅      |
-|       | [Analyze PR Components](./tools/analyze.md){:target="_blank"} 💎                                                      |   ✅    |   ✅    |       |      ✅      |
-|       |                                                                                                                       |        |        |            |      ️       |
-| USAGE | CLI                                                                                                                   |   ✅    |   ✅    |   ✅       |      ✅      |
-|       | App / webhook                                                                                                         |   ✅    |   ✅    |    ✅        |      ✅      |
-|       | Actions                                                                                                               |   ✅    |        |            |      ️       |
-|       |                                                                                                                       |        |        |            |
-| CORE  | PR compression                                                                                                        |   ✅    |   ✅    |   ✅       |   ✅        |
-|       | Repo language prioritization                                                                                          |   ✅    |   ✅    |   ✅       |   ✅        |
-|       | Adaptive and token-aware file patch fitting                                                                           |   ✅    |   ✅    |   ✅     |   ✅        |
-|       | Multiple models support                                                                                               |   ✅    |   ✅    |   ✅       |   ✅        |
-|       | Incremental PR review                                                                                                 |   ✅    |        |            |           |
-|       | [Static code analysis](./tools/analyze.md/){:target="_blank"} 💎                                                      |   ✅    |   ✅     |    ✅    |   ✅        |
-|       | [Multiple configuration options](./usage-guide/configuration_options.md){:target="_blank"} 💎                         |   ✅    |   ✅     |    ✅    |   ✅        |
-
-💎 marks a feature available only in [Qodo Merge Pro](https://www.codium.ai/pricing/){:target="_blank"}
-
-
-## Example Results
-<hr>
-
-#### [/describe](https://github.com/Codium-ai/pr-agent/pull/530)
-<figure markdown="1">
-![/describe](https://www.codium.ai/images/pr_agent/describe_new_short_main.png){width=512}
-</figure>
-<hr>
-
-#### [/review](https://github.com/Codium-ai/pr-agent/pull/732#issuecomment-1975099151)
-<figure markdown="1">
-![/review](https://www.codium.ai/images/pr_agent/review_new_short_main.png){width=512}
-</figure>
-<hr>
-
-#### [/improve](https://github.com/Codium-ai/pr-agent/pull/732#issuecomment-1975099159)
-<figure markdown="1">
-![/improve](https://www.codium.ai/images/pr_agent/improve_new_short_main.png){width=512}
-</figure>
-<hr>
-
-#### [/generate_labels](https://github.com/Codium-ai/pr-agent/pull/530)
-<figure markdown="1">
-![/generate_labels](https://www.codium.ai/images/pr_agent/geneare_custom_labels_main_short.png){width=300}
-</figure>
-<hr>
-
-## How it Works
-
-The following diagram illustrates Qodo Merge tools and their flow:
-
-![Qodo Merge Tools](https://codium.ai/images/pr_agent/diagram-v0.9.png)
-
-Check out the [PR Compression strategy](core-abilities/index.md) page for more details on how we convert a code diff to a manageable LLM prompt

docs/docs/overview/pr_agent_pro.md

@@ -1,21 +1,21 @@
 ### Overview
 
-[Qodo Merge Pro](https://www.codium.ai/pricing/) is a hosted version of Qodo Merge, provided by Qodo. A complimentary two-week trial is offered, followed by a monthly subscription fee.
-Qodo Merge Pro is designed for companies and teams that require additional features and capabilities. It provides the following benefits:
+[Qodo Merge](https://www.codium.ai/pricing/){:target="_blank"} is a hosted version of open-source [PR-Agent](https://github.com/Codium-ai/pr-agent){:target="_blank"}. A complimentary two-week trial is offered, followed by a monthly subscription fee.
+Qodo Merge is designed for companies and teams that require additional features and capabilities. It provides the following benefits:
 
 1. **Fully managed** - We take care of everything for you - hosting, models, regular updates, and more. Installation is as simple as signing up and adding the Qodo Merge app to your GitHub\GitLab\BitBucket repo.
 
-2. **Improved privacy** - No data will be stored or used to train models. Qodo Merge Pro will employ zero data retention, and will use an OpenAI and Claude accounts with zero data retention.
+2. **Improved privacy** - No data will be stored or used to train models. Qodo Merge will employ zero data retention, and will use an OpenAI and Claude accounts with zero data retention.
 
-3. **Improved support** - Qodo Merge Pro users will receive priority support, and will be able to request new features and capabilities.
+3. **Improved support** - Qodo Merge users will receive priority support, and will be able to request new features and capabilities.
 
-4. **Supporting self-hosted git servers** - Qodo Merge Pro can be installed on GitHub Enterprise Server, GitLab, and BitBucket. For more information, see the [installation guide](https://qodo-merge-docs.qodo.ai/installation/pr_agent_pro/).
+4. **Supporting self-hosted git servers** - Qodo Merge can be installed on GitHub Enterprise Server, GitLab, and BitBucket. For more information, see the [installation guide](https://qodo-merge-docs.qodo.ai/installation/pr_agent_pro/).
 
-5. **PR Chat** - Qodo Merge Pro allows you to engage in [private chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) about your pull requests on private repositories.
+5. **PR Chat** - Qodo Merge allows you to engage in [private chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) about your pull requests on private repositories.
 
 ### Additional features
 
-Here are some of the additional features and capabilities that Qodo Merge Pro offers:
+Here are some of the additional features and capabilities that Qodo Merge offers:
 
 | Feature                                                                                                              | Description                                                                                                                                                      |
 |----------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------|
@@ -24,28 +24,29 @@ Here are some of the additional features and capabilities that Qodo Merge Pro of
 | [**Apply suggestions**](https://qodo-merge-docs.qodo.ai/tools/improve/#overview)                                     | Generate committable code from the relevant suggestions interactively by clicking on a checkbox                                                                   |
 | [**Suggestions impact**](https://qodo-merge-docs.qodo.ai/tools/improve/#assessing-impact)                         | Automatically mark suggestions that were implemented by the user (either directly in GitHub, or indirectly in the IDE) to enable tracking of the impact of the suggestions |
 | [**CI feedback**](https://qodo-merge-docs.qodo.ai/tools/ci_feedback/) | Automatically analyze failed CI checks on GitHub and provide actionable feedback in the PR conversation, helping to resolve issues quickly |
-| [**Advanced usage statistics**](https://www.codium.ai/contact/#/)                                                    | Qodo Merge Pro offers detailed statistics at user, repository, and company levels, including metrics about Qodo Merge usage, and also general statistics and insights |
+| [**Advanced usage statistics**](https://www.codium.ai/contact/#/)                                                    | Qodo Merge offers detailed statistics at user, repository, and company levels, including metrics about Qodo Merge usage, and also general statistics and insights |
 | [**Incorporating companies' best practices**](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices)         | Use the companies' best practices as reference to increase the effectiveness and the relevance of the code suggestions                                           |
 | [**Interactive triggering**](https://qodo-merge-docs.qodo.ai/tools/analyze/#example-usage)                           | Interactively apply different tools via the `analyze` command                                                                                                    |
-| [**Custom labels**](https://qodo-merge-docs.qodo.ai/tools/describe/#handle-custom-labels-from-the-repos-labels-page) | Define custom labels for Qodo Merge to assign to the PR                                                                                                            |
+| [**Custom labels**](https://qodo-merge-docs.qodo.ai/tools/describe/#handle-custom-labels-from-the-repos-labels-page) | Define custom labels for Qodo Merge to assign to the PR                                                                                                           |
 
 ### Additional tools
 
-Here are additional tools that are available only for Qodo Merge Pro users:
+Here are additional tools that are available only for Qodo Merge users:
 
-| Feature | Description |
-|---------|-------------|
+| Feature                                                                               | Description |
+|---------------------------------------------------------------------------------------|-------------|
 | [**Custom Prompt Suggestions**](https://qodo-merge-docs.qodo.ai/tools/custom_prompt/) | Generate code suggestions based on custom prompts from the user |
-| [**Analyze PR components**](https://qodo-merge-docs.qodo.ai/tools/analyze/) | Identify the components that changed in the PR, and enable to interactively apply different tools to them |
-| [**Tests**](https://qodo-merge-docs.qodo.ai/tools/test/) | Generate tests for code components that changed in the PR |
-| [**PR documentation**](https://qodo-merge-docs.qodo.ai/tools/documentation/) | Generate docstring for code components that changed in the PR |
-| [**Improve Component**](https://qodo-merge-docs.qodo.ai/tools/improve_component/) | Generate code suggestions for code components that changed in the PR |
-| [**Similar code search**](https://qodo-merge-docs.qodo.ai/tools/similar_code/) | Search for similar code in the repository, organization, or entire GitHub |
+| [**Analyze PR components**](https://qodo-merge-docs.qodo.ai/tools/analyze/)           | Identify the components that changed in the PR, and enable to interactively apply different tools to them |
+| [**Tests**](https://qodo-merge-docs.qodo.ai/tools/test/)                              | Generate tests for code components that changed in the PR |
+| [**PR documentation**](https://qodo-merge-docs.qodo.ai/tools/documentation/)          | Generate docstring for code components that changed in the PR |
+| [**Improve Component**](https://qodo-merge-docs.qodo.ai/tools/improve_component/)     | Generate code suggestions for code components that changed in the PR |
+| [**Similar code search**](https://qodo-merge-docs.qodo.ai/tools/similar_code/)        | Search for similar code in the repository, organization, or entire GitHub |
+| [**Code implementation**](https://qodo-merge-docs.qodo.ai/tools/implement/)        | Generates implementation code from review suggestions |
 
 
 ### Supported languages
 
-Qodo Merge Pro leverages the world's leading code models - Claude 3.5 Sonnet and GPT-4.
+Qodo Merge leverages the world's leading code models - Claude 3.5 Sonnet and GPT-4.
 As a result, its primary tools such as `describe`, `review`, and `improve`, as well as the PR-chat feature, support virtually all programming languages.
 
-For specialized commands that require static code analysis, Qodo Merge Pro offers support for specific languages. For more details about features that require static code analysis, please refer to the [documentation](https://qodo-merge-docs.qodo.ai/tools/analyze/#overview).
+For specialized commands that require static code analysis, Qodo Merge offers support for specific languages. For more details about features that require static code analysis, please refer to the [documentation](https://qodo-merge-docs.qodo.ai/tools/analyze/#overview).

docs/docs/tools/custom_labels.md

@@ -28,7 +28,7 @@ When working from CLI, you need to apply the [configuration changes](#configurat
 To enable custom labels, you need to apply the [configuration changes](#configuration-options) to the local `.pr_agent.toml` file in your repository.
 
 #### 3. Handle custom labels from the Repo's labels page 💎
-> This feature is available only in Qodo Merge Pro
+> This feature is available only in Qodo Merge
 
 * GitHub : `https://github.com/{owner}/{repo}/labels`, or click on the "Labels" tab in the issues or PRs page.
 * GitLab : `https://gitlab.com/{owner}/{repo}/-/labels`, or click on "Manage" -> "Labels" on the left menu.

docs/docs/tools/help.md

@@ -1,6 +1,6 @@
 ## Overview
 The `help` tool provides a list of all the available tools and their descriptions.
-For Qodo Merge Pro users, it also enables to trigger each tool by checking the relevant box.
+For Qodo Merge users, it also enables to trigger each tool by checking the relevant box.
 
 It can be invoked manually by commenting on any PR:
 ```

docs/docs/tools/implement.md

@@ -0,0 +1,50 @@
+## Overview
+
+The `implement` tool converts human code review discussions and feedback into ready-to-commit code changes.
+It leverages LLM technology to transform PR comments and review suggestions into concrete implementation code, helping developers quickly turn feedback into working solutions.
+
+## Usage Scenarios
+
+
+### For Reviewers
+
+Reviewers can request code changes by: <br>
+1. Selecting the code block to be modified. <br>
+2. Adding a comment with the syntax: 
+```
+/implement <code-change-description>
+```
+
+![implement1](https://codium.ai/images/pr_agent/implement1.png){width=640}
+
+
+### For PR Authors
+
+PR authors can implement suggested changes by replying to a review comment using either: <br>
+1. Add specific implementation details as described above
+```
+/implement <code-change-description>
+```
+2. Use the original review comment as instructions
+```
+/implement
+```
+
+![implement2](https://codium.ai/images/pr_agent/implement2.png){width=640}
+
+### For Referencing Comments
+
+You can reference and implement changes from any comment by:
+```
+/implement <link-to-review-comment>
+```
+
+![implement3](https://codium.ai/images/pr_agent/implement3.png){width=640}
+
+Note that the implementation will occur within the review discussion thread.
+
+
+**Configuration options** <br>
+- Use `/implement` to implement code change within and based on the review discussion. <br>
+- Use `/implement <code-change-description>` inside a review discussion to implement specific instructions. <br>
+- Use `/implement <link-to-review-comment>` to indirectly call the tool from any comment. <br>

docs/docs/tools/improve.md

@@ -9,7 +9,7 @@ The tool can be triggered automatically every time a new PR is [opened](../usage
 
 ![code_suggestions_as_comment_open.png](https://codium.ai/images/pr_agent/code_suggestions_as_comment_open.png){width=512}
 
-Note that the `Apply this suggestion` checkbox, which interactively converts a suggestion into a commitable code comment, is available only for Qodo Merge Pro 💎 users.
+Note that the `Apply this suggestion` checkbox, which interactively converts a suggestion into a commitable code comment, is available only for Qodo Merge💎 users.
 
 
 ## Example usage
@@ -54,7 +54,7 @@ num_code_suggestions_per_chunk = ...
 
 ### Assessing Impact 💎
 
-Note that Qodo Merge pro tracks two types of implementations:
+Note that Qodo Merge tracks two types of implementations:
 
 - Direct implementation - when the user directly applies the suggestion by clicking the `Apply` checkbox.
 - Indirect implementation - when the user implements the suggestion in their IDE environment. In this case, Qodo Merge will utilize, after each commit, a dedicated logic to identify if a suggestion was implemented, and will mark it as implemented.
@@ -70,7 +70,7 @@ In post-process, Qodo Merge counts the number of suggestions that were implement
 ## Suggestion tracking 💎
 `Platforms supported: GitHub, GitLab`
 
-Qodo Merge employs an novel detection system to automatically [identify](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/) AI code suggestions that PR authors have accepted and implemented.
+Qodo Merge employs a novel detection system to automatically [identify](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/) AI code suggestions that PR authors have accepted and implemented.
 
 Accepted suggestions are also automatically documented in a dedicated wiki page called `.pr_agent_accepted_suggestions`, allowing users to track historical changes, assess the tool's effectiveness, and learn from previously implemented recommendations in the repository.
 An example [result](https://github.com/Codium-ai/pr-agent/wiki/.pr_agent_accepted_suggestions):
@@ -95,6 +95,148 @@ This feature is controlled by a boolean configuration parameter: `pr_code_sugges
 
     Instead, we leverage a dedicated private page, within your repository wiki, to track suggestions. This approach offers convenient secure suggestion tracking while avoiding pull requests or any noise to the main repository.
 
+## `Extra instructions` and `best practices`
+
+The `improve` tool can be further customized by providing additional instructions and best practices to the AI model.
+
+### Extra instructions
+
+>`Platforms supported: GitHub, GitLab, Bitbucket, Azure DevOps`
+
+You can use the `extra_instructions` configuration option to give the AI model additional instructions for the `improve` tool.
+Be specific, clear, and concise in the instructions. With extra instructions, you are the prompter.
+
+Examples for possible instructions:
+```toml
+[pr_code_suggestions]
+extra_instructions="""\
+(1) Answer in japanese
+(2) Don't suggest to add try-except block
+(3) Ignore changes in toml files
+...
+"""
+```
+Use triple quotes to write multi-line instructions. Use bullet points or numbers to make the instructions more readable.
+
+### Best practices 💎
+
+>`Platforms supported: GitHub, GitLab, Bitbucket`
+
+Another option to give additional guidance to the AI model is by creating a `best_practices.md` file, either in your repository's root directory or as a [**wiki page**](https://github.com/Codium-ai/pr-agent/wiki) (we recommend the wiki page, as editing and maintaining it over time is easier).
+This page can contain a list of best practices, coding standards, and guidelines that are specific to your repo/organization.
+
+The AI model will use this wiki page as a reference, and in case the PR code violates any of the guidelines, it will create additional suggestions, with a dedicated label: `Organization
+best practice`.
+
+Example for a python `best_practices.md` content:
+```markdown
+## Project best practices
+- Make sure that I/O operations are encapsulated in a try-except block
+- Use the `logging` module for logging instead of `print` statements
+- Use `is` and `is not` to compare with `None`
+- Use `if __name__ == '__main__':` to run the code only when the script is executed
+- Use `with` statement to open files
+...
+```
+
+Tips for writing an effective `best_practices.md` file:
+
+- Write clearly and concisely
+- Include brief code examples when helpful
+- Focus on project-specific guidelines, that will result in relevant suggestions you actually want to get
+- Keep the file relatively short, under 800 lines, since:
+    - AI models may not process effectively very long documents
+    - Long files tend to contain generic guidelines already known to AI
+
+#### Local and global best practices
+By default, Qodo Merge will look for a local `best_practices.md` wiki file in the root of the relevant local repo.
+
+If you want to enable also a global `best_practices.md` wiki file, set first in the global configuration file:
+
+```toml
+[best_practices]
+enable_global_best_practices = true
+```
+
+Then, create a `best_practices.md` wiki file in the root of [global](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#global-configuration-file) configuration repository,  `pr-agent-settings`.
+
+#### Best practices for multiple languages
+For a git organization working with multiple programming languages, you can maintain a centralized global `best_practices.md` file containing language-specific guidelines. 
+When reviewing pull requests, Qodo Merge automatically identifies the programming language and applies the relevant best practices from this file.
+
+To do this, structure your `best_practices.md` file using the following format:
+
+```
+# [Python]
+...
+# [Java]
+...
+# [JavaScript]
+...
+```
+
+#### Dedicated label for best practices suggestions
+Best practice suggestions are labeled as `Organization best practice` by default. 
+To customize this label, modify it in your configuration file:
+
+```toml
+[best_practices]
+organization_name = "..."
+```
+
+And the label will be: `{organization_name} best practice`.
+
+
+#### Example results
+
+![best_practice](https://codium.ai/images/pr_agent/org_best_practice.png){width=512}
+
+### Auto best practices 💎
+
+>`Platforms supported: GitHub`
+
+'Auto best practices' is a novel Qodo Merge capability that:
+
+1. Identifies recurring patterns from accepted suggestions
+2. **Automatically** generates [best practices page](https://github.com/qodo-ai/pr-agent/wiki/.pr_agent_auto_best_practices) based on what your team consistently values
+3. Applies these learned patterns to future code reviews
+
+This creates an automatic feedback loop where the system continuously learns from your team's choices to provide increasingly relevant suggestions. 
+The system maintains two analysis phases:
+
+- Open exploration for new issues
+- Targeted checking against established best practices
+
+Note that when a [custom best practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) exist, Qodo Merge will still generate an 'auto best practices' wiki file, though it won't use it in the `improve` tool.
+Learn more about utilizing 'auto best practices' in our [detailed guide](https://qodo-merge-docs.qodo.ai/core-abilities/auto_best_practices/).
+
+#### Relevant configurations
+
+```toml
+[auto_best_practices]
+# Disable all auto best practices usage or generation
+enable_auto_best_practices = true  
+
+# Disable usage of auto best practices file in the 'improve' tool
+utilize_auto_best_practices = true 
+
+# Extra instructions to the auto best practices generation prompt
+extra_instructions = ""            
+
+# Max number of patterns to be detected
+max_patterns = 5                   
+```
+
+
+### Combining `extra instructions` and `best practices` 💎
+
+The `extra instructions` configuration is more related to the `improve` tool prompt. It can be used, for example, to avoid specific suggestions ("Don't suggest to add try-except block", "Ignore changes in toml files", ...) or to emphasize specific aspects or formats ("Answer in Japanese", "Give only short suggestions", ...)
+
+In contrast, the `best_practices.md` file is a general guideline for the way code should be written in the repo.
+
+Using a combination of both can help the AI model to provide relevant and tailored suggestions.
+
+
 ## Usage Tips
 
 ### Implementing the proposed code suggestions
@@ -191,99 +333,6 @@ This approach has two main benefits:
 Note: Chunking is primarily relevant for large PRs. For most PRs (up to 500 lines of code), Qodo Merge will be able to process the entire code in a single call.
 
 
-### 'Extra instructions' and 'best practices'
-
-#### Extra instructions
-
->`Platforms supported: GitHub, GitLab, Bitbucket`
-
-You can use the `extra_instructions` configuration option to give the AI model additional instructions for the `improve` tool.
-Be specific, clear, and concise in the instructions. With extra instructions, you are the prompter. Specify relevant aspects that you want the model to focus on.
-
-Examples for possible instructions:
-```toml
-[pr_code_suggestions]
-extra_instructions="""\
-(1) Answer in japanese
-(2) Don't suggest to add try-excpet block
-(3) Ignore changes in toml files
-...
-"""
-```
-Use triple quotes to write multi-line instructions. Use bullet points or numbers to make the instructions more readable.
-
-#### Best practices 💎
-
->`Platforms supported: GitHub, GitLab`
-
-Another option to give additional guidance to the AI model is by creating a dedicated [**wiki page**](https://github.com/Codium-ai/pr-agent/wiki) called `best_practices.md`.
-This page can contain a list of best practices, coding standards, and guidelines that are specific to your repo/organization.
-
-The AI model will use this wiki page as a reference, and in case the PR code violates any of the guidelines, it will suggest improvements accordingly, with a dedicated label: `Organization
-best practice`.
-
-Example for a `best_practices.md` content can be found [here](https://github.com/Codium-ai/pr-agent/blob/main/docs/docs/usage-guide/EXAMPLE_BEST_PRACTICE.md) (adapted from Google's [pyguide](https://google.github.io/styleguide/pyguide.html)).
-This file is only an example. Since it is used as a prompt for an AI model, we want to emphasize the following:
-
-- It should be written in a clear and concise manner
-- If needed, it should give short relevant code snippets as examples
-- Recommended to limit the text to 800 lines or fewer. Here’s why:
-
-     1) Extremely long best practices documents may not be fully processed by the AI model.
-
-     2) A lengthy file probably represent a more "**generic**" set of guidelines, which the AI model is already familiar with. The objective is to focus on a more targeted set of guidelines tailored to the specific needs of this project.
-
-##### Local and global best practices
-By default, Qodo Merge will look for a local `best_practices.md` wiki file in the root of the relevant local repo.
-
-If you want to enable also a global `best_practices.md` wiki file, set first in the global configuration file:
-
-```toml
-[best_practices]
-enable_global_best_practices = true
-```
-
-Then, create a `best_practices.md` wiki file in the root of [global](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#global-configuration-file) configuration repository,  `pr-agent-settings`.
-
-##### Best practices for multiple languages
-For a git organization working with multiple programming languages, you can maintain a centralized global `best_practices.md` file containing language-specific guidelines. 
-When reviewing pull requests, Qodo Merge automatically identifies the programming language and applies the relevant best practices from this file.
-Structure your `best_practices.md` file using the following format:
-
-```
-# [Python]
-...
-# [Java]
-...
-# [JavaScript]
-...
-```
-
-##### Dedicated label for best practices suggestions
-Best practice suggestions are labeled as `Organization best practice` by default. 
-To customize this label, modify it in your configuration file:
-
-```toml
-[best_practices]
-organization_name = ""
-```
-
-And the label will be: `{organization_name} best practice`.
-
-
-##### Example results
-
-![best_practice](https://codium.ai/images/pr_agent/org_best_practice.png){width=512}
-
-
-#### How to combine `extra instructions` and `best practices`
-
-The `extra instructions` configuration is more related to the `improve` tool prompt. It can be used, for example, to avoid specific suggestions ("Don't suggest to add try-except block", "Ignore changes in toml files", ...) or to emphasize specific aspects or formats ("Answer in Japanese", "Give only short suggestions", ...)
-
-In contrast, the `best_practices.md` file is a general guideline for the way code should be written in the repo.
-
-Using a combination of both can help the AI model to provide relevant and tailored suggestions.
-
 ## Configuration options
 
 ??? example "General options"
@@ -329,6 +378,10 @@ Using a combination of both can help the AI model to provide relevant and tailor
         <td><b>wiki_page_accepted_suggestions</b></td>
         <td>If set to true, the tool will automatically track accepted suggestions in a dedicated wiki page called `.pr_agent_accepted_suggestions`. Default is true.</td>
       </tr>
+      <tr>
+        <td><b>allow_thumbs_up_down</b></td>
+        <td>If set to true, all code suggestions will have thumbs up and thumbs down buttons, to encourage users to provide feedback on the suggestions. Default is false.</td>
+      </tr>
     </table>
 
 ??? example "Params for number of suggestions and AI calls"
@@ -346,10 +399,6 @@ Using a combination of both can help the AI model to provide relevant and tailor
         <td><b>max_number_of_calls</b></td>
         <td>Maximum number of chunks. Default is 3.</td>
       </tr>
-      <tr>
-        <td><b>rank_extended_suggestions</b></td>
-        <td>If set to true, the tool will rank the suggestions, based on importance. Default is true.</td>
-      </tr>
     </table>
 
 ## A note on code suggestions quality

docs/docs/tools/index.md

@@ -2,21 +2,22 @@
 
 Here is a list of Qodo Merge tools, each with a dedicated page that explains how to use it:
 
-| Tool                                                                                     | Description                                                                                                                                 |
-|------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------|
-| **[PR Description (`/describe`](./describe.md))**                                        | Automatically generating PR description - title, type, summary, code walkthrough and labels                                                 |
-| **[PR Review (`/review`](./review.md))**                                                 | Adjustable feedback about the PR, possible issues, security concerns, review effort and more                                                |
-| **[Code Suggestions (`/improve`](./improve.md))**                                        | Code suggestions for improving the PR                                                                                                       |
-| **[Question Answering (`/ask ...`](./ask.md))**                                          | Answering free-text questions about the PR, or on specific code lines                                                                       |
-| **[Update Changelog (`/update_changelog`](./update_changelog.md))**                      | Automatically updating the CHANGELOG.md file with the PR changes                                                                            |
-| **[Find Similar Issue (`/similar_issue`](./similar_issues.md))**                         | Automatically retrieves and presents similar issues                                                                                         |
-| **[Help (`/help`](./help.md))**                                                          | Provides a list of all the available tools. Also enables to trigger them interactively (💎)                                                 |
-| **💎 [Add Documentation (`/add_docs`](./documentation.md))**                             | Generates documentation to methods/functions/classes that changed in the PR                                                                 |
-| **💎 [Generate Custom Labels (`/generate_labels`](./custom_labels.md))**                 | Generates custom labels for the PR, based on specific guidelines defined by the user                                                        |
-| **💎 [Analyze (`/analyze`](./analyze.md))**                                              | Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component |
-| **💎 [Custom Prompt (`/custom_prompt`](./custom_prompt.md))**                            | Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user                      |
-| **💎 [Generate Tests (`/test component_name`](./test.md))**                              | Automatically generates unit tests for a selected component, based on the PR code changes                                                   |
-| **💎 [Improve Component (`/improve_component component_name`](./improve_component.md))** | Generates code suggestions for a specific code component that changed in the PR                                                             |
-| **💎 [CI Feedback (`/checks ci_job`](./ci_feedback.md))**                                | Automatically generates feedback and analysis for a failed CI job                                                                           |
-
-Note that the tools marked with 💎 are available only for Qodo Merge Pro users.
+| Tool                                                                                     | Description                                                                                                                                |
+|------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
+| **[PR Description (`/describe`](./describe.md))**                                        | Automatically generating PR description - title, type, summary, code walkthrough and labels                                                |
+| **[PR Review (`/review`](./review.md))**                                                 | Adjustable feedback about the PR, possible issues, security concerns, review effort and more                                               |
+| **[Code Suggestions (`/improve`](./improve.md))**                                        | Code suggestions for improving the PR                                                                                                      |
+| **[Question Answering (`/ask ...`](./ask.md))**                                          | Answering free-text questions about the PR, or on specific code lines                                                                      |
+| **[Update Changelog (`/update_changelog`](./update_changelog.md))**                      | Automatically updating the CHANGELOG.md file with the PR changes                                                                           |
+| **[Find Similar Issue (`/similar_issue`](./similar_issues.md))**                         | Automatically retrieves and presents similar issues                                                                                        |
+| **[Help (`/help`](./help.md))**                                                          | Provides a list of all the available tools. Also enables to trigger them interactively (💎)                                                |
+| **💎 [Add Documentation (`/add_docs`](./documentation.md))**                             | Generates documentation to methods/functions/classes that changed in the PR                                                                |
+| **💎 [Generate Custom Labels (`/generate_labels`](./custom_labels.md))**                 | Generates custom labels for the PR, based on specific guidelines defined by the user                                                       |
+| **💎 [Analyze (`/analyze`](./analyze.md))**                                              | Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component|
+| **💎 [Test (`/test`](./test.md))**                                                       | generate tests for a selected component, based on the PR code changes                                                                      |
+| **💎 [Custom Prompt (`/custom_prompt`](./custom_prompt.md))**                            | Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user                     |
+| **💎 [Generate Tests (`/test component_name`](./test.md))**                              | Automatically generates unit tests for a selected component, based on the PR code changes                                                  |
+| **💎 [Improve Component (`/improve_component component_name`](./improve_component.md))** | Generates code suggestions for a specific code component that changed in the PR                                                            |
+| **💎 [CI Feedback (`/checks ci_job`](./ci_feedback.md))**                                | Automatically generates feedback and analysis for a failed CI job                                                                          |
+| **💎 [Implement (`/implement`](./implement.md))**                                        | Generates implementation code from review suggestions                                                                                      |
+Note that the tools marked with 💎 are available only for Qodo Merge users.

docs/docs/tools/review.md

@@ -39,72 +39,27 @@ pr_commands = [
 ]
 
 [pr_reviewer]
-num_code_suggestions = ...
+extra_instructions = "..."
 ...
 ```
 
 - The `pr_commands` lists commands that will be executed automatically when a PR is opened.
 - The `[pr_reviewer]` section contains the configurations for the `review` tool you want to edit (if any).
 
-[//]: # ()
-[//]: # (### Incremental Mode)
-
-[//]: # (Incremental review only considers changes since the last Qodo Merge review. This can be useful when working on the PR in an iterative manner, and you want to focus on the changes since the last review instead of reviewing the entire PR again.)
-
-[//]: # (For invoking the incremental mode, the following command can be used:)
-
-[//]: # (```)
-
-[//]: # (/review -i)
-
-[//]: # (```)
-
-[//]: # (Note that the incremental mode is only available for GitHub.)
-
-[//]: # ()
-[//]: # (![incremental review](https://codium.ai/images/pr_agent/incremental_review_2.png){width=512})
-
-[//]: # (### PR Reflection)
-
-[//]: # ()
-[//]: # (By invoking:)
-
-[//]: # (```)
-
-[//]: # (/reflect_and_review)
-
-[//]: # (```)
-
-[//]: # (The tool will first ask the author questions about the PR, and will guide the review based on their answers.)
-
-[//]: # ()
-[//]: # (![reflection questions](https://codium.ai/images/pr_agent/reflection_questions.png){width=512})
-
-[//]: # ()
-[//]: # (![reflection answers](https://codium.ai/images/pr_agent/reflection_answers.png){width=512})
-
-[//]: # ()
-[//]: # (![reflection insights](https://codium.ai/images/pr_agent/reflection_insights.png){width=512})
-
-
 
 ## Configuration options
 
 !!! example "General options"
 
 <table>
-  <tr>
-    <td><b>num_code_suggestions</b></td>
-    <td>Number of code suggestions provided by the 'review' tool. Default is 0, meaning no code suggestions will be provided by the `review` tool.</td>
-  </tr>
-  <tr>
-    <td><b>inline_code_comments</b></td>
-    <td>If set to true, the tool will publish the code suggestions as comments on the code diff. Default is false. Note that you need to set `num_code_suggestions`>0 to get code suggestions </td>
-  </tr>
   <tr>
     <td><b>persistent_comment</b></td>
     <td>If set to true, the review comment will be persistent, meaning that every new review request will edit the previous one. Default is true.</td>
   </tr>
+  <tr>
+  <td><b>final_update_message</b></td>
+  <td>When set to true, updating a persistent review comment during online commenting will automatically add a short comment with a link to the updated review in the pull request .Default is true.</td>
+  </tr>
   <tr>
     <td><b>extra_instructions</b></td>
     <td>Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".</td>
@@ -168,10 +123,6 @@ If enabled, the `review` tool can approve a PR when a specific comment, `/review
     <td><b>enable_auto_approval</b></td>
     <td>If set to true, the tool will approve the PR when invoked with the 'auto_approve' command. Default is false. This flag can be changed only from a configuration file.</td>
   </tr>
-  <tr>
-    <td><b>maximal_review_effort</b></td>
-    <td>Maximal effort level for auto-approval. If the PR's estimated review effort is above this threshold, the auto-approval will not run. Default is 5.</td>
-  </tr>
 </table>
 
 ## Usage Tips
@@ -189,9 +140,9 @@ If enabled, the `review` tool can approve a PR when a specific comment, `/review
 !!! tip "Automation"
     When you first install Qodo Merge app, the [default mode](../usage-guide/automations_and_usage.md#github-app-automatic-tools-when-a-new-pr-is-opened) for the `review` tool is:
     ```
-    pr_commands = ["/review --pr_reviewer.num_code_suggestions=0", ...]
+    pr_commands = ["/review", ...]
     ```
-    Meaning the `review` tool will run automatically on every PR, without providing code suggestions.
+    Meaning the `review` tool will run automatically on every PR, without any additional configurations.
     Edit this field to enable/disable the tool, or to change the configurations used.
 
 !!! tip "Possible labels from the review tool"
@@ -243,18 +194,8 @@ If enabled, the `review` tool can approve a PR when a specific comment, `/review
     Qodo Merge will automatically approve the PR, and add a comment with the approval.
 
 
-    You can also enable auto-approval only if the PR meets certain requirements, such as that the `estimated_review_effort` label is equal or below a certain threshold, by adjusting the flag:
-    ```
-    [pr_reviewer]
-    maximal_review_effort = 5
-    ```
+!!! tip  "Code suggestions"
 
-[//]: # (!!! tip  "Code suggestions")
+    The `review` tool previously included a legacy feature for providing code suggestions (controlled by `--pr_reviewer.num_code_suggestion`). This functionality has been deprecated and replaced by the [`improve`](./improve.md) tool, which offers higher quality and more actionable code suggestions.
 
-[//]: # ()
-[//]: # (    If you set `num_code_suggestions`>0 , the `review` tool will also provide code suggestions.)
-
-[//]: # (    )
-[//]: # (    Notice If you are interested **only** in the code suggestions, it is recommended to use the [`improve`]&#40;./improve.md&#41; feature instead, since it is a dedicated only to code suggestions, and usually gives better results.)
-
-[//]: # (    Use the `review` tool if you want to get more comprehensive feedback, which includes code suggestions as well.)
+    

docs/docs/tools/similar_code.md

@@ -49,9 +49,10 @@ It can be invoked automatically from the analyze table, can be accessed by:
 /analyze
 ```
 Choose the components you want to find similar code for, and click on the `similar` checkbox.
+
 ![analyze similar](https://codium.ai/images/pr_agent/analyze_similar.png){width=768}
 
-If you are looking to search for similar code in the organization's codebase, you can click on the `Organization` checkbox, and it will invoke a new search command just for the organization's codebase.
+You can search for similar code either within the organization's codebase or globally, which includes open-source repositories. Each result will include the relevant code components along with their associated license details.
 
 ![similar code global](https://codium.ai/images/pr_agent/similar_code_global.png){width=768}
 

docs/docs/tools/test.md

@@ -17,8 +17,8 @@ The tool will generate tests for the selected component (if no component is stat
 
 (Example taken from [here](https://github.com/Codium-ai/pr-agent/pull/598#issuecomment-1913679429)):
 
-**Notes**
-- Language that are currently supported by the tool: Python, Java, C++, JavaScript, TypeScript, C#.
+**Notes** <br>
+- The following languages are currently supported: Python, Java, C++, JavaScript, TypeScript, C#. <br>
 - This tool can also be triggered interactively by using the [`analyze`](./analyze.md) tool.
 
 

docs/docs/tools/update_changelog.md

@@ -17,3 +17,4 @@ Under the section `pr_update_changelog`, the [configuration file](https://github
 
 - `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 ...
+- `add_pr_link`: whether the model should try to add a link to the PR in the changelog. Default is true.

docs/docs/usage-guide/PR_agent_pro_models.md

@@ -1,17 +1,17 @@
-## Qodo Merge Pro Models
+## Qodo Merge Models
 
-The default models used by Qodo Merge Pro are a combination of Claude-3.5-sonnet and  OpenAI's GPT-4 models.
+The default models used by Qodo Merge are a combination of Claude-3.5-sonnet and  OpenAI's GPT-4 models.
 
-Users can configure Qodo Merge Pro to use solely a specific model by editing the [configuration](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/) file.
+Users can configure Qodo Merge to use solely a specific model by editing the [configuration](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/) file.
 
-For example, to restrict Qodo Merge Pro to using only `Claude-3.5-sonnet`, add this setting:
+For example, to restrict Qodo Merge to using only `Claude-3.5-sonnet`, add this setting:
 
 ```
 [config]
 model="claude-3-5-sonnet"
 ```
 
-Or to restrict Qodo Merge Pro to using only `GPT-4o`, add this setting:
+Or to restrict Qodo Merge to using only `GPT-4o`, add this setting:
 ```
 [config]
 model="gpt-4o"

docs/docs/usage-guide/additional_configurations.md

@@ -1,5 +1,5 @@
 ## Show possible configurations
-The possible configurations of Qodo Merge are stored in [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml).
+The possible configurations of Qodo Merge are stored in [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml){:target="_blank"}.
 In the [tools](https://qodo-merge-docs.qodo.ai/tools/) page you can find explanations on how to use these configurations for each tool.
 
 To print all the available configurations as a comment on your PR, you can use the following command:
@@ -138,7 +138,17 @@ LANGSMITH_BASE_URL=<url>
 
 ## Ignoring automatic commands in PRs
 
-In some cases, you may want to automatically ignore specific PRs . Qodo Merge enables you to ignore PR with a specific title, or from/to specific branches (regex matching).
+Qodo Merge allows you to automatically ignore certain PRs based on various criteria:
+
+- PRs with specific titles (using regex matching)
+- PRs between specific branches (using regex matching)
+- PRs that don't include changes from specific folders (using regex matching)
+- PRs containing specific labels
+- PRs opened by specific users
+
+### Example usage
+
+#### Ignoring PRs with specific titles
 
 To ignore PRs with a specific title such as "[Bump]: ...", you can add the following to your `configuration.toml` file:
 
@@ -149,6 +159,7 @@ ignore_pr_title = ["\\[Bump\\]"]
 
 Where the `ignore_pr_title` is a list of regex patterns to match the PR title you want to ignore. Default is `ignore_pr_title = ["^\\[Auto\\]", "^Auto"]`.
 
+#### Ignoring PRs between specific branches
 
 To ignore PRs from specific source or target branches, you can add the following to your `configuration.toml` file:
 
@@ -161,6 +172,7 @@ ignore_pr_target_branches = ["qa"]
 Where the `ignore_pr_source_branches` and `ignore_pr_target_branches` are lists of regex patterns to match the source and target branches you want to ignore.
 They are not mutually exclusive, you can use them together or separately.
 
+#### Ignoring PRs that don't include changes from specific folders
 
 To allow only specific folders (often needed in large monorepos), set:
 
@@ -170,3 +182,35 @@ allow_only_specific_folders=['folder1','folder2']
 ```
 
 For the configuration above, automatic feedback will only be triggered when the PR changes include files from 'folder1' or 'folder2'
+
+#### Ignoring PRs containg specific labels
+
+To ignore PRs containg specific labels, you can add the following to your `configuration.toml` file:
+
+``` 
+[config]
+ignore_pr_labels = ["do-not-merge"]
+```
+
+Where the `ignore_pr_labels` is a list of labels that when present in the PR, the PR will be ignored.
+
+#### Ignoring PRs from specific users
+
+Qodo Merge automatically identifies and ignores pull requests created by bots using:
+
+- GitHub's native bot detection system
+- Name-based pattern matching
+
+While this detection is robust, it may not catch all cases, particularly when:
+
+- Bots are registered as regular user accounts
+- Bot names don't match common patterns
+
+To supplement the automatic bot detection, you can manually specify users to ignore. Add the following to your `configuration.toml` file to ignore PRs from specific users:
+```
+[config]
+ignore_pr_authors = ["my-special-bot-user", ...]
+```
+
+Where the `ignore_pr_authors` is a list of usernames that you want to ignore.
+

docs/docs/usage-guide/automations_and_usage.md

@@ -1,4 +1,5 @@
 ## Local repo (CLI)
+
 When running from your locally cloned Qodo Merge repo (CLI), your local configuration file will be used.
 Examples of invoking the different tools via the CLI:
 
@@ -35,9 +36,29 @@ This is useful for debugging or experimenting with different tools.
 
 Default is "github".
 
+### CLI Health Check
+To verify that Qodo Merge has been configured correctly, you can run this health check command from the repository root:
 
+```bash
+python -m tests.health_test.main
+```
 
-### Online usage
+If the health check passes, you will see the following output:
+
+```
+========
+Health test passed successfully
+========
+```
+
+At the end of the run.
+
+Before running the health check, ensure you have:
+
+- Configured your [LLM provider](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/)
+- Added a valid GitHub token to your configuration file
+
+## Online usage
 
 Online usage means invoking Qodo Merge 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:
@@ -58,50 +79,70 @@ For example, if you want to edit the `review` tool configurations, you can run:
 Any configuration value in [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) file can be similarly edited. Comment `/config` to see the list of available configurations.
 
 
-## GitHub App
+## Qodo Merge Automatic Feedback
 
-!!! note "Configurations for Qodo Merge Pro"
-    Qodo Merge Pro for GitHub is an App, hosted by CodiumAI. So all the instructions below are relevant also for Qodo Merge Pro users.
+
+### Disabling all automatic feedback
+
+To easily disable all automatic feedback from Qodo Merge (GitHub App, GitLab Webhook, BitBucket App, Azure DevOps Webhook), set in a configuration file:
+
+```toml
+[config]
+disable_auto_feedback = true
+```
+
+When this parameter is set to `true`, Qodo Merge will not run any automatic tools (like `describe`, `review`, `improve`) when a new PR is opened, or when new code is pushed to an open PR.
+
+### GitHub App
+
+!!! note "Configurations for Qodo Merge"
+    Qodo Merge for GitHub is an App, hosted by Qodo. So all the instructions below are relevant also for Qodo Merge users.
     Same goes for [GitLab webhook](#gitlab-webhook) and [BitBucket App](#bitbucket-app) sections.
 
-### GitHub app automatic tools when a new PR is opened
+#### GitHub app automatic tools when a new PR is opened
 
-The [github_app](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L108) section defines GitHub app specific configurations.
+The [github_app](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L220) section defines GitHub app specific configurations.
 
-The configuration parameter `pr_commands` defines the list of tools that will be **run automatically** when a new PR is opened.
-```
+The configuration parameter `pr_commands` defines the list of tools that will be **run automatically** when a new PR is opened:
+```toml
 [github_app]
 pr_commands = [
     "/describe",
     "/review",
-    "/improve --pr_code_suggestions.suggestions_score_threshold=5",
+    "/improve",
 ]
 ```
 
 This means that when a new PR is opened/reopened or marked as ready for review, Qodo Merge will run the `describe`, `review` and `improve` tools.  
-For the `improve` tool, for example, the `suggestions_score_threshold` parameter will be set to 5 (suggestions below a score of 5 won't be presented)
 
 You can override the default tool parameters by using one the three options for a [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/): **wiki**, **local**, or **global**.
-For example, if your local `.pr_agent.toml` file contains:
-```
+For example, if your configuration file contains:
+
+```toml
 [pr_description]
 generate_ai_title = true
 ```
-Every time you run the `describe` tool, including automatic runs, the PR title will be generated by the AI.
 
-To cancel the automatic run of all the tools, set:
-```
+Every time you run the `describe` tool (including automatic runs) the PR title will be generated by the AI.
+
+You can customize configurations specifically for automated runs by using the `--config_path=<value>` parameter.
+For instance, to modify the `review` tool settings only for newly opened PRs, use:
+```toml
 [github_app]
-pr_commands = []
+pr_commands = [
+    "/describe",
+    "/review --pr_reviewer.extra_instructions='focus on the file: ...'",
+    "/improve",
+]
 ```
 
-### GitHub app automatic tools for push actions (commits to an open PR)
+#### GitHub app automatic tools for push actions (commits to an open PR)
 
 In addition to running automatic tools when a PR is opened, the GitHub app can also respond to new code that is pushed to an open PR.
 
 The configuration toggle `handle_push_trigger` can be used to enable this feature.
 The configuration parameter `push_commands` defines the list of tools that will be **run automatically** when new code is pushed to the PR.
-```
+```toml
 [github_app]
 handle_push_trigger = true
 push_commands = [
@@ -111,7 +152,7 @@ push_commands = [
 ```
 This means that when new code is pushed to the PR, the Qodo Merge will run the `describe` and `review` tools, with the specified parameters.
 
-## GitHub Action
+### GitHub Action
 `GitHub Action` is a different way to trigger Qodo Merge tools, and uses a different configuration mechanism than `GitHub App`.<br>
 You can configure settings for `GitHub Action` by adding environment variables under the env section in `.github/workflows/pr_agent.yml` file.
 Specifically, start by setting the following environment variables:
@@ -122,7 +163,7 @@ Specifically, start by setting the following environment variables:
         github_action_config.auto_review: "true" # enable\disable auto review
         github_action_config.auto_describe: "true" # enable\disable auto describe
         github_action_config.auto_improve: "true" # enable\disable auto improve
-        github_action_config.pr_actions: ["opened", "reopened", "ready_for_review", "review_requested"]
+        github_action_config.pr_actions: '["opened", "reopened", "ready_for_review", "review_requested"]'
 ```
 `github_action_config.auto_review`, `github_action_config.auto_describe` and `github_action_config.auto_improve` are used to enable/disable automatic tools that run when a new PR is opened.
 If not set, the default configuration is for all three tools to run automatically when a new PR is opened.
@@ -137,15 +178,18 @@ The JSON structure is equivalent to the yaml data structure defined in [pr_revie
 Note that you can give additional config parameters by adding environment variables to `.github/workflows/pr_agent.yml`, or by using a `.pr_agent.toml` [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#global-configuration-file) in the root of your repo
 
 For example, you can set an environment variable: `pr_description.publish_labels=false`, or add a `.pr_agent.toml` file with the following content:
-```
+
+```toml
 [pr_description]
 publish_labels = false
 ```
+
 to prevent Qodo Merge from publishing labels when running the `describe` tool.
 
-## GitLab Webhook
+### GitLab Webhook
 After setting up a GitLab webhook, to control which commands will run automatically when a new MR is opened, you can set the `pr_commands` parameter in the configuration file, similar to the GitHub App:
-```
+
+```toml
 [gitlab]
 pr_commands = [
     "/describe",
@@ -157,7 +201,7 @@ pr_commands = [
 the GitLab webhook can also respond to new code that is pushed to an open MR.
 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 MR.
-```
+```toml
 [gitlab]
 handle_push_trigger = true
 push_commands = [
@@ -168,13 +212,13 @@ push_commands = [
 
 Note that to use the 'handle_push_trigger' feature, you need to give the gitlab webhook also the "Push events" scope.
 
-## BitBucket App
+### BitBucket App
 Similar to GitHub app, when running Qodo Merge from BitBucket App, the default [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) from a pre-built docker will be initially loaded.
 
 By uploading a local `.pr_agent.toml` file to the root of the repo's main branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
 
 For example, if your local `.pr_agent.toml` file contains:
-```
+```toml
 [pr_reviewer]
 extra_instructions = "Answer in japanese"
 ```
@@ -187,12 +231,12 @@ If you experience a lack of responses from Qodo Merge, you might want to set: `b
 This will prevent Qodo Merge from acquiring the full file content, and will only use the diff content. This will reduce the number of requests made to BitBucket, at the cost of small decrease in accuracy, as dynamic context will not be applicable.
 
 
-### BitBucket Self-Hosted App automatic tools
+#### BitBucket Self-Hosted App automatic tools
 
 To control which commands will run automatically when a new PR is opened, you can set the `pr_commands` parameter in the configuration file:
 Specifically, set the following values:
 
-```
+```toml
 [bitbucket_app]
 pr_commands = [
     "/review",
@@ -203,7 +247,7 @@ Note that we set specifically for bitbucket, we recommend using: `--pr_code_sugg
 Since this platform only supports inline code suggestions, we want to limit the number of suggestions, and only present a limited number.
 
 To enable BitBucket app to respond to each **push** to the PR, set (for example):
-```
+```toml
 [bitbucket_app]
 handle_push_trigger = true
 push_commands = [
@@ -212,10 +256,10 @@ push_commands = [
 ]
 ```
 
-## Azure DevOps provider
+### Azure DevOps provider
 
 To use Azure DevOps provider use the following settings in configuration.toml:
-```
+```toml
 [config]
 git_provider="azure"
 ```
@@ -234,14 +278,14 @@ org = "https://dev.azure.com/YOUR_ORGANIZATION/"
 # pat = "YOUR_PAT_TOKEN" needed only if using PAT for authentication
 ```
 
-### Azure DevOps Webhook
+#### Azure DevOps Webhook
 
 To control which commands will run automatically when a new PR is opened, you can set the `pr_commands` parameter in the configuration file, similar to the GitHub App:
-```
+```toml
 [azure_devops_server]
 pr_commands = [
     "/describe",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
     "/improve",
 ]
 ```

docs/docs/usage-guide/changing_a_model.md

@@ -1,11 +1,10 @@
-## Changing a model
+## Changing a model in PR-Agent
 
 See [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/algo/__init__.py) for a list of available models.
 To use a different model than the default (GPT-4), you need to edit in the [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L2) the fields:
 ```
 [config]
 model = "..."
-model_turbo = "..."
 fallback_models = ["..."]
 ```
 
@@ -27,57 +26,43 @@ deployment_id = ""  # The deployment name you chose when you deployed the engine
 and set in your configuration file:
 ```
 [config]
-model="" # the OpenAI model you've deployed on Azure (e.g. gpt-3.5-turbo)
-model_turbo="" # the OpenAI model you've deployed on Azure (e.g. gpt-3.5-turbo)
-fallback_models=["..."] # the OpenAI model you've deployed on Azure (e.g. gpt-3.5-turbo)
+model="" # the OpenAI model you've deployed on Azure (e.g. gpt-4o)
+fallback_models=["..."]
 ```
 
+### Ollama
+
+You can run 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 model locally via Ollama, set in `.secrets.toml` or in a configuration file:
+```
+[config]
+model = "ollama/qwen2.5-coder:32b"
+fallback_models=["ollama/qwen2.5-coder:32b"]
+custom_model_max_tokens=128000 # set the maximal input tokens for the model
+duplicate_examples=true # will duplicate the examples in the prompt, to help the model to generate structured output
+
+[ollama]
+api_base = "http://localhost:11434" # or whatever port you're running Ollama on
+```
+
+!!! note "Local models vs commercial models"
+    Qodo Merge is compatible with almost any AI model, but analyzing complex code repositories and pull requests requires a model specifically optimized for code analysis.
+    
+    Commercial models such as GPT-4, Claude Sonnet, and Gemini have demonstrated robust capabilities in generating structured output for code analysis tasks with large input. In contrast, most open-source models currently available (as of January 2025) face challenges with these complex tasks.
+
+    Based on our testing, local open-source models are suitable for experimentation and learning purposes, but they are not suitable for production-level code analysis tasks.
+    
+    Hence, for production workflows and real-world usage, we recommend using commercial models.
+
 ### Hugging Face
 
-**Local**
-You can run Hugging Face 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 Hugging Face model locally via Ollama, set:
-```
-[__init__.py]
-MAX_TOKENS = {
-    "model-name-on-ollama": <max_tokens>
-}
-e.g.
-MAX_TOKENS={
-    ...,
-    "ollama/llama2": 4096
-}
-
-
-[config] # in configuration.toml
-model = "ollama/llama2"
-model_turbo = "ollama/llama2"
-fallback_models=["ollama/llama2"]
-
-[ollama] # in .secrets.toml
-api_base = ... # the base url for your Hugging Face inference endpoint
-# e.g. if running Ollama locally, you may use:
-api_base = "http://localhost:11434/"
-```
-
-### Inference Endpoints
-
 To use a new model with Hugging Face Inference Endpoints, for example, set:
 ```
-[__init__.py]
-MAX_TOKENS = {
-    "model-name-on-huggingface": <max_tokens>
-}
-e.g.
-MAX_TOKENS={
-    ...,
-    "meta-llama/Llama-2-7b-chat-hf": 4096
-}
 [config] # in configuration.toml
 model = "huggingface/meta-llama/Llama-2-7b-chat-hf"
-model_turbo = "huggingface/meta-llama/Llama-2-7b-chat-hf"
 fallback_models=["huggingface/meta-llama/Llama-2-7b-chat-hf"]
+custom_model_max_tokens=... # set the maximal input tokens for the model
 
 [huggingface] # in .secrets.toml
 key = ... # your Hugging Face api key
@@ -91,7 +76,6 @@ To use Llama2 model with Replicate, for example, set:
 ```
 [config] # in configuration.toml
 model = "replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"
-model_turbo = "replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"
 fallback_models=["replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"]
 [replicate] # in .secrets.toml
 key = ...
@@ -107,7 +91,6 @@ To use Llama3 model with Groq, for example, set:
 ```
 [config] # in configuration.toml
 model = "llama3-70b-8192"
-model_turbo = "llama3-70b-8192"
 fallback_models = ["groq/llama3-70b-8192"]
 [groq] # in .secrets.toml
 key = ... # your Groq api key
@@ -121,7 +104,6 @@ To use Google's Vertex AI platform and its associated models (chat-bison/codecha
 ```
 [config] # in configuration.toml
 model = "vertex_ai/codechat-bison"
-model_turbo = "vertex_ai/codechat-bison"
 fallback_models="vertex_ai/codechat-bison"
 
 [vertexai] # in .secrets.toml
@@ -140,7 +122,6 @@ To use [Google AI Studio](https://aistudio.google.com/) models, set the relevant
 ```toml
 [config] # in configuration.toml
 model="google_ai_studio/gemini-1.5-flash"
-model_turbo="google_ai_studio/gemini-1.5-flash"
 fallback_models=["google_ai_studio/gemini-1.5-flash"]
 
 [google_ai_studio] # in .secrets.toml
@@ -156,7 +137,6 @@ To use Anthropic models, set the relevant models in the configuration section of
 ```
 [config]
 model="anthropic/claude-3-opus-20240229"
-model_turbo="anthropic/claude-3-opus-20240229"
 fallback_models=["anthropic/claude-3-opus-20240229"]
 ```
 
@@ -173,7 +153,6 @@ To use Amazon Bedrock and its foundational models, add the below configuration:
 ```
 [config] # in configuration.toml
 model="bedrock/anthropic.claude-3-sonnet-20240229-v1:0"
-model_turbo="bedrock/anthropic.claude-3-sonnet-20240229-v1:0"
 fallback_models=["bedrock/anthropic.claude-v2:1"]
 ```
 
@@ -187,6 +166,25 @@ drop_params = true
 
 AWS session is automatically authenticated from your environment, but you can also explicitly set `AWS_ACCESS_KEY_ID`, `AWS_SECRET_ACCESS_KEY` and `AWS_REGION_NAME` environment variables. Please refer to [this document](https://litellm.vercel.app/docs/providers/bedrock) for more details.
 
+### DeepSeek
+
+To use deepseek-chat model with DeepSeek, for example, set:
+
+```toml
+[config] # in configuration.toml
+model = "deepseek/deepseek-chat"
+fallback_models=["deepseek/deepseek-chat"]
+```
+
+and fill up your key
+
+```toml
+[deepseek] # in .secrets.toml
+key = ...
+```
+
+(you can obtain a deepseek-chat key from [here](https://platform.deepseek.com))
+
 ### Custom models
 
 If the relevant model doesn't appear [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/algo/__init__.py), you can still use it as a custom model:
@@ -195,7 +193,6 @@ If the relevant model doesn't appear [here](https://github.com/Codium-ai/pr-agen
 ```
 [config]
 model="custom_model_name"
-model_turbo="custom_model_name"
 fallback_models=["custom_model_name"]
 ```
 (2) Set the maximal tokens for the model:

docs/docs/usage-guide/configuration_options.md

@@ -20,7 +20,7 @@ In terms of precedence, wiki configurations will override local configurations,
 
 `Platforms supported: GitHub, GitLab, Bitbucket`
 
-With Qodo Merge Pro, you can set configurations by creating a page called `.pr_agent.toml` in the [wiki](https://github.com/Codium-ai/pr-agent/wiki/pr_agent.toml) of the repo.
+With Qodo Merge, you can set configurations by creating a page called `.pr_agent.toml` in the [wiki](https://github.com/Codium-ai/pr-agent/wiki/pr_agent.toml) of the repo.
 The advantage of this method is that it allows to set configurations without needing to commit new content to the repo - just edit the wiki page and **save**.
 
 

docs/docs/usage-guide/enabling_a_wiki.md

@@ -0,0 +1,33 @@
+`Supported Git Platforms: GitHub, GitLab, Bitbucket`
+
+
+For optimal functionality of Qodo Merge, we recommend enabling a wiki for each repository where Qodo Merge is installed. The wiki serves several important purposes:
+
+**Key Wiki Features: 💎**
+
+- Storing a [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#wiki-configuration-file)
+- Defining a [`best_practices.md`](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) file
+- Track [accepted suggestions](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking)
+- Facilitates learning over time by creating an [auto_best_practices.md](https://qodo-merge-docs.qodo.ai/core-abilities/auto_best_practices) file
+
+
+**Setup Instructions (GitHub):**
+
+To enable a wiki for your repository:
+
+1. Navigate to your repository's main page on GitHub
+2. Select "Settings" from the top navigation bar
+3. Locate the "Features" section
+4. Enable the "Wikis" option by checking the corresponding box
+5. Return to your repository's main page
+6. Look for the newly added "Wiki" tab in the top navigation
+7. Initialize your wiki by clicking "Create the first page" and saving (this step is important - without creating an initial page, the wiki will not be fully functional)
+
+### Why Wiki?
+
+- Your code (and its derivatives, including accepted code suggestions) is yours. Qodo Merge will never store it on external servers.
+- Repository changes typically require pull requests, which create overhead and are time-consuming. This process is too cumbersome for auto data aggregation, and is not very convenient even for managing frequently updated content like configuration files and best practices.
+- A repository wiki page provides an ideal balance:
+    - It lives within your repository, making it suitable for code-related documentation
+    - It enables quick updates without the overhead of pull requests
+    - It maintains full Git version control, allowing you to track changes over time.

docs/docs/usage-guide/index.md

@@ -5,6 +5,7 @@ It includes information on how to adjust Qodo Merge configurations, define which
 
 
 - [Introduction](./introduction.md)
+- [Enabling a Wiki](./enabling_a_wiki)
 - [Configuration File](./configuration_options.md)
 - [Usage and Automation](./automations_and_usage.md)
     - [Local Repo (CLI)](./automations_and_usage.md#local-repo-cli)
@@ -23,4 +24,4 @@ It includes information on how to adjust Qodo Merge configurations, define which
     - [Changing a model](./additional_configurations.md#changing-a-model)
     - [Patch Extra Lines](./additional_configurations.md#patch-extra-lines)
     - [Editing the prompts](./additional_configurations.md#editing-the-prompts)
-- [Qodo Merge Pro Models](./PR_agent_pro_models.md)
+- [Qodo Merge Models](./PR_agent_pro_models.md)

docs/docs/usage-guide/introduction.md

@@ -2,7 +2,7 @@
 After [installation](https://qodo-merge-docs.qodo.ai/installation/), there are three basic ways to invoke Qodo Merge:
 
 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
+2. Online usage - by [commenting](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021901){:target="_blank"} on a PR
 3. Enabling Qodo Merge tools to run automatically when a new PR is opened
 
 

docs/mkdocs.yml

@@ -1,29 +1,26 @@
-site_name: Qodo Merge (formerly known as PR-Agent)
+site_name: Qodo Merge (and open-source PR-Agent)
 repo_url: https://github.com/Codium-ai/pr-agent
 repo_name: Codium-ai/pr-agent
 
 nav:
   - Overview:
     - 'index.md'
-    - 💎 Qodo Merge Pro: 'overview/pr_agent_pro.md'
+    - 💎 Qodo Merge: 'overview/pr_agent_pro.md'
     - Data Privacy: 'overview/data_privacy.md'
   - Installation:
     - 'installation/index.md'
-    - Locally: 'installation/locally.md'
-    - GitHub: 'installation/github.md'
-    - GitLab: 'installation/gitlab.md'
-    - BitBucket: 'installation/bitbucket.md'
-    - Azure DevOps: 'installation/azure.md'
-    - 💎 Qodo Merge Pro: 'installation/pr_agent_pro.md'
+    - PR-Agent: 'installation/pr_agent.md'
+    - 💎 Qodo Merge: 'installation/qodo_merge.md'
   - Usage Guide:
     - 'usage-guide/index.md'
     - Introduction: 'usage-guide/introduction.md'
+    - Enabling a Wiki: 'usage-guide/enabling_a_wiki.md'
     - Configuration File: 'usage-guide/configuration_options.md'
     - Usage and Automation: 'usage-guide/automations_and_usage.md'
     - Managing Mail Notifications: 'usage-guide/mail_notifications.md'
     - Changing a Model: 'usage-guide/changing_a_model.md'
     - Additional Configurations: 'usage-guide/additional_configurations.md'
-    - 💎 Qodo Merge Pro Models: 'usage-guide/PR_agent_pro_models'
+    - 💎 Qodo Merge Models: 'usage-guide/PR_agent_pro_models'
   - Tools:
     - 'tools/index.md'
     - Describe: 'tools/describe.md'
@@ -41,9 +38,11 @@ nav:
     - 💎 Custom Prompt: 'tools/custom_prompt.md'
     - 💎 CI Feedback: 'tools/ci_feedback.md'
     - 💎 Similar Code: 'tools/similar_code.md'
+    - 💎 Implement: 'tools/implement.md'
   - Core Abilities:
       - 'core-abilities/index.md'
       - Fetching ticket context: 'core-abilities/fetching_ticket_context.md'
+      - Auto best practices: 'core-abilities/auto_best_practices.md'
       - Local and global metadata: 'core-abilities/metadata.md'
       - Dynamic context: 'core-abilities/dynamic_context.md'
       - Self-reflection: 'core-abilities/self_reflection.md'

pr_agent/agent/pr_agent.py

@@ -13,7 +13,6 @@ 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_help_message import PRHelpMessage
-from pr_agent.tools.pr_information_from_user import PRInformationFromUser
 from pr_agent.tools.pr_line_questions import PR_LineQuestions
 from pr_agent.tools.pr_questions import PRQuestions
 from pr_agent.tools.pr_reviewer import PRReviewer
@@ -25,8 +24,6 @@ command2class = {
     "answer": PRReviewer,
     "review": PRReviewer,
     "review_pr": PRReviewer,
-    "reflect": PRInformationFromUser,
-    "reflect_and_review": PRInformationFromUser,
     "describe": PRDescription,
     "describe_pr": PRDescription,
     "improve": PRCodeSuggestions,
@@ -49,7 +46,6 @@ commands = list(command2class.keys())
 class PRAgent:
     def __init__(self, ai_handler: partial[BaseAiHandler,] = LiteLLMAIHandler):
         self.ai_handler = ai_handler  # will be initialized in run_action
-        self.forbidden_cli_args = ['enable_auto_approval']
 
     async def handle_request(self, pr_url, request, notify=None) -> bool:
         # First, apply repo specific settings if exists
@@ -64,24 +60,33 @@ class PRAgent:
         else:
             action, *args = request
 
+        forbidden_cli_args = ['enable_auto_approval', 'approve_pr_on_self_review', 'base_url', 'url', 'app_name', 'secret_provider',
+                              'git_provider', 'skip_keys', 'openai.key', 'ANALYTICS_FOLDER', 'uri', 'app_id', 'webhook_secret',
+                              'bearer_token', 'PERSONAL_ACCESS_TOKEN', 'override_deployment_type', 'private_key',
+                              'local_cache_path', 'enable_local_cache', 'jira_base_url', 'api_base', 'api_type', 'api_version',
+                              'skip_keys']
         if args:
-            for forbidden_arg in self.forbidden_cli_args:
-                for arg in args:
-                    if forbidden_arg in arg:
-                        get_logger().error(
-                            f"CLI argument for param '{forbidden_arg}' is forbidden. Use instead a configuration file."
-                        )
-                        return False
+            for arg in args:
+                if arg.startswith('--'):
+                    arg_word = arg.lower()
+                    arg_word = arg_word.replace('__', '.')  # replace double underscore with dot, e.g. --openai__key -> --openai.key
+                    for forbidden_arg in forbidden_cli_args:
+                        forbidden_arg_word = forbidden_arg.lower()
+                        if '.' not in forbidden_arg_word:
+                            forbidden_arg_word = '.' + forbidden_arg_word
+                        if forbidden_arg_word in arg_word:
+                            get_logger().error(
+                                f"CLI argument for param '{forbidden_arg}' is forbidden. Use instead a configuration file."
+                            )
+                            return False
         args = update_settings_from_args(args)
 
         action = action.lstrip("/").lower()
         if action not in command2class:
-            get_logger().debug(f"Unknown command: {action}")
+            get_logger().error(f"Unknown command: {action}")
             return False
         with get_logger().contextualize(command=action, pr_url=pr_url):
             get_logger().info("PR-Agent request handler started", analytics=True)
-            if action == "reflect_and_review":
-                get_settings().pr_reviewer.ask_and_reflect = True
             if action == "answer":
                 if notify:
                     notify()

pr_agent/algo/__init__.py

@@ -24,9 +24,13 @@ MAX_TOKENS = {
     'o1-mini-2024-09-12': 128000,  # 128K, but may be limited by config.max_model_tokens
     'o1-preview': 128000,  # 128K, but may be limited by config.max_model_tokens
     'o1-preview-2024-09-12': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'o1-2024-12-17': 204800,  # 200K, but may be limited by config.max_model_tokens
+    'o1': 204800,  # 200K, but may be limited by config.max_model_tokens
     'claude-instant-1': 100000,
     'claude-2': 100000,
     'command-nightly': 4096,
+    'deepseek/deepseek-chat': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'deepseek/deepseek-reasoner': 64000,  # 64K, but may be limited by config.max_model_tokens
     'replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1': 4096,
     'meta-llama/Llama-2-7b-chat-hf': 4096,
     'vertex_ai/codechat-bison': 6144,
@@ -39,9 +43,11 @@ MAX_TOKENS = {
     'vertex_ai/claude-3-5-sonnet-v2@20241022': 100000,
     'vertex_ai/gemini-1.5-pro': 1048576,
     'vertex_ai/gemini-1.5-flash': 1048576,
+    'vertex_ai/gemini-2.0-flash-exp': 1048576,
     'vertex_ai/gemma2': 8200,
     'gemini/gemini-1.5-pro': 1048576,
     'gemini/gemini-1.5-flash': 1048576,
+    'gemini/gemini-2.0-flash-exp': 1048576,
     'codechat-bison': 6144,
     'codechat-bison-32k': 32000,
     'anthropic.claude-instant-v1': 100000,
@@ -59,13 +65,14 @@ MAX_TOKENS = {
     'bedrock/anthropic.claude-3-5-haiku-20241022-v1:0': 100000,
     'bedrock/anthropic.claude-3-5-sonnet-20240620-v1:0': 100000,
     'bedrock/anthropic.claude-3-5-sonnet-20241022-v2:0': 100000,
+    "bedrock/us.anthropic.claude-3-5-sonnet-20241022-v2:0": 100000,
     'claude-3-5-sonnet': 100000,
     'groq/llama3-8b-8192': 8192,
     'groq/llama3-70b-8192': 8192,
+    'groq/llama-3.1-8b-instant': 8192,
+    'groq/llama-3.3-70b-versatile': 128000,
     'groq/mixtral-8x7b-32768': 32768,
-    'groq/llama-3.1-8b-instant': 131072,
-    'groq/llama-3.1-70b-versatile': 131072,
-    'groq/llama-3.1-405b-reasoning': 131072,
+    'groq/gemma2-9b-it': 8192,
     'ollama/llama3': 4096,
     'watsonx/meta-llama/llama-3-8b-instruct': 4096,
     "watsonx/meta-llama/llama-3-70b-instruct": 4096,

pr_agent/algo/ai_handlers/litellm_ai_handler.py

@@ -7,6 +7,7 @@ from litellm import acompletion
 from tenacity import retry, retry_if_exception_type, stop_after_attempt
 
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
+from pr_agent.algo.utils import get_version
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 
@@ -89,6 +90,10 @@ class LiteLLMAIHandler(BaseAiHandler):
         if get_settings().get("GOOGLE_AI_STUDIO.GEMINI_API_KEY", None):
           os.environ["GEMINI_API_KEY"] = get_settings().google_ai_studio.gemini_api_key
 
+        # Support deepseek models
+        if get_settings().get("DEEPSEEK.KEY", None):
+            os.environ['DEEPSEEK_API_KEY'] = get_settings().get("DEEPSEEK.KEY")
+
     def prepare_logs(self, response, system, user, resp, finish_reason):
         response_log = response.dict().copy()
         response_log['system'] = system
@@ -132,7 +137,7 @@ class LiteLLMAIHandler(BaseAiHandler):
         if "langfuse" in callbacks:
             metadata.update({
                 "trace_name": command,
-                "tags": [git_provider, command],
+                "tags": [git_provider, command, f'version:{get_version()}'],
                 "trace_metadata": {
                     "command": command,
                     "pr_url": pr_url,
@@ -141,7 +146,7 @@ class LiteLLMAIHandler(BaseAiHandler):
         if "langsmith" in callbacks:
             metadata.update({
                 "run_name": command,
-                "tags": [git_provider, command],
+                "tags": [git_provider, command, f'version:{get_version()}'],
                 "extra": {
                     "metadata": {
                         "command": command,
@@ -192,13 +197,13 @@ class LiteLLMAIHandler(BaseAiHandler):
                 messages[1]["content"] = [{"type": "text", "text": messages[1]["content"]},
                                           {"type": "image_url", "image_url": {"url": img_path}}]
 
-            # Currently O1 does not support separate system and user prompts
-            O1_MODEL_PREFIX = 'o1-'
+            # Currently, model OpenAI o1 series does not support a separate system and user prompts
+            O1_MODEL_PREFIX = 'o1'
             model_type = model.split('/')[-1] if '/' in model else model
-            if model_type.startswith(O1_MODEL_PREFIX):
+            if (model_type.startswith(O1_MODEL_PREFIX)) or ("deepseek-reasoner" in model):
                 user = f"{system}\n\n\n{user}"
                 system = ""
-                get_logger().info(f"Using O1 model, combining system and user prompts")
+                get_logger().info(f"Using model {model}, combining system and user prompts")
                 messages = [{"role": "user", "content": user}]
                 kwargs = {
                     "model": model,

pr_agent/algo/git_patch_processing.py

@@ -364,48 +364,51 @@ __old hunk__
 
 
 def extract_hunk_lines_from_patch(patch: str, file_name, line_start, line_end, side) -> tuple[str, str]:
+    try:
+        patch_with_lines_str = f"\n\n## File: '{file_name.strip()}'\n\n"
+        selected_lines = ""
+        patch_lines = patch.splitlines()
+        RE_HUNK_HEADER = re.compile(
+            r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
+        match = None
+        start1, size1, start2, size2 = -1, -1, -1, -1
+        skip_hunk = False
+        selected_lines_num = 0
+        for line in patch_lines:
+            if 'no newline at end of file' in line.lower():
+                continue
 
-    patch_with_lines_str = f"\n\n## File: '{file_name.strip()}'\n\n"
-    selected_lines = ""
-    patch_lines = patch.splitlines()
-    RE_HUNK_HEADER = re.compile(
-        r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
-    match = None
-    start1, size1, start2, size2 = -1, -1, -1, -1
-    skip_hunk = False
-    selected_lines_num = 0
-    for line in patch_lines:
-        if 'no newline at end of file' in line.lower():
-            continue
+            if line.startswith('@@'):
+                skip_hunk = False
+                selected_lines_num = 0
+                header_line = line
 
-        if line.startswith('@@'):
-            skip_hunk = False
-            selected_lines_num = 0
-            header_line = line
+                match = RE_HUNK_HEADER.match(line)
 
-            match = RE_HUNK_HEADER.match(line)
+                section_header, size1, size2, start1, start2 = extract_hunk_headers(match)
 
-            section_header, size1, size2, start1, start2 = extract_hunk_headers(match)
-
-            # check if line range is in this hunk
-            if side.lower() == 'left':
                 # check if line range is in this hunk
-                if not (start1 <= line_start <= start1 + size1):
-                    skip_hunk = True
-                    continue
-            elif side.lower() == 'right':
-                if not (start2 <= line_start <= start2 + size2):
-                    skip_hunk = True
-                    continue
-            patch_with_lines_str += f'\n{header_line}\n'
+                if side.lower() == 'left':
+                    # check if line range is in this hunk
+                    if not (start1 <= line_start <= start1 + size1):
+                        skip_hunk = True
+                        continue
+                elif side.lower() == 'right':
+                    if not (start2 <= line_start <= start2 + size2):
+                        skip_hunk = True
+                        continue
+                patch_with_lines_str += f'\n{header_line}\n'
 
-        elif not skip_hunk:
-            if side.lower() == 'right' and line_start <= start2 + selected_lines_num <= line_end:
-                selected_lines += line + '\n'
-            if side.lower() == 'left' and start1 <= selected_lines_num + start1 <= line_end:
-                selected_lines += line + '\n'
-            patch_with_lines_str += line + '\n'
-            if not line.startswith('-'): # currently we don't support /ask line for deleted lines
-                selected_lines_num += 1
+            elif not skip_hunk:
+                if side.lower() == 'right' and line_start <= start2 + selected_lines_num <= line_end:
+                    selected_lines += line + '\n'
+                if side.lower() == 'left' and start1 <= selected_lines_num + start1 <= line_end:
+                    selected_lines += line + '\n'
+                patch_with_lines_str += line + '\n'
+                if not line.startswith('-'): # currently we don't support /ask line for deleted lines
+                    selected_lines_num += 1
+    except Exception as e:
+        get_logger().error(f"Failed to extract hunk lines from patch: {e}", artifact={"traceback": traceback.format_exc()})
+        return "", ""
 
     return patch_with_lines_str.rstrip(), selected_lines.rstrip()

pr_agent/algo/pr_processing.py

@@ -11,7 +11,7 @@ from pr_agent.algo.git_patch_processing import (
 from pr_agent.algo.language_handler import sort_files_by_main_languages
 from pr_agent.algo.token_handler import TokenHandler
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
-from pr_agent.algo.utils import ModelType, clip_tokens, get_max_tokens
+from pr_agent.algo.utils import ModelType, clip_tokens, get_max_tokens, get_weak_model
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.git_provider import GitProvider
 from pr_agent.log import get_logger
@@ -205,10 +205,11 @@ def pr_generate_extended_diff(pr_languages: list,
             if not extended_patch:
                 get_logger().warning(f"Failed to extend patch for file: {file.filename}")
                 continue
-            full_extended_patch = f"\n\n## {file.filename}\n{extended_patch.rstrip()}\n"
 
             if add_line_numbers_to_hunks:
                 full_extended_patch = convert_to_hunks_with_lines_numbers(extended_patch, file)
+            else:
+                full_extended_patch = f"\n\n## File: '{file.filename.strip()}'\n{extended_patch.rstrip()}\n"
 
             # add AI-summary metadata to the patch
             if file.ai_file_summary and  get_settings().get("config.enable_ai_metadata", False):
@@ -316,13 +317,13 @@ def generate_full_patch(convert_hunks_to_line_numbers, file_dict, max_tokens_mod
             # 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:
-                get_logger().warning(f"Patch too large, skipping it, {filename}")
+                get_logger().warning(f"Patch too large, skipping it: '{filename}'")
             remaining_files_list_new.append(filename)
             continue
 
         if patch:
             if not convert_hunks_to_line_numbers:
-                patch_final = f"\n\n## File: '{filename.strip()}\n\n{patch.strip()}\n'"
+                patch_final = f"\n\n## File: '{filename.strip()}'\n\n{patch.strip()}\n"
             else:
                 patch_final = "\n\n" + patch.strip()
             patches.append(patch_final)
@@ -354,8 +355,8 @@ async def retry_with_fallback_models(f: Callable, model_type: ModelType = ModelT
 
 
 def _get_all_models(model_type: ModelType = ModelType.REGULAR) -> List[str]:
-    if model_type == ModelType.TURBO:
-        model = get_settings().config.model_turbo
+    if model_type == ModelType.WEAK:
+        model = get_weak_model()
     else:
         model = get_settings().config.model
     fallback_models = get_settings().config.fallback_models

pr_agent/algo/types.py

@@ -1,5 +1,6 @@
 from dataclasses import dataclass
 from enum import Enum
+from typing import Optional
 
 
 class EDIT_TYPE(Enum):
@@ -21,4 +22,5 @@ class FilePatchInfo:
     old_filename: str = None
     num_plus_lines: int = -1
     num_minus_lines: int = -1
+    language: Optional[str] = None
     ai_file_summary: str = None

pr_agent/algo/utils.py

@@ -7,11 +7,13 @@ import html
 import json
 import os
 import re
+import sys
 import textwrap
 import time
 import traceback
 from datetime import datetime
 from enum import Enum
+from importlib.metadata import PackageNotFoundError, version
 from typing import Any, List, Tuple
 
 import html2text
@@ -21,12 +23,19 @@ from pydantic import BaseModel
 from starlette_context import context
 
 from pr_agent.algo import MAX_TOKENS
+from pr_agent.algo.git_patch_processing import extract_hunk_lines_from_patch
 from pr_agent.algo.token_handler import TokenEncoder
 from pr_agent.algo.types import FilePatchInfo
 from pr_agent.config_loader import get_settings, global_settings
 from pr_agent.log import get_logger
 
 
+def get_weak_model() -> str:
+    if get_settings().get("config.model_weak"):
+        return get_settings().config.model_weak
+    return get_settings().config.model
+
+
 class Range(BaseModel):
     line_start: int  # should be 0-indexed
     line_end: int
@@ -35,8 +44,7 @@ class Range(BaseModel):
 
 class ModelType(str, Enum):
     REGULAR = "regular"
-    TURBO = "turbo"
-
+    WEAK = "weak"
 
 class PRReviewHeader(str, Enum):
     REGULAR = "## PR Reviewer Guide"
@@ -97,7 +105,8 @@ def unique_strings(input_list: List[str]) -> List[str]:
 def convert_to_markdown_v2(output_data: dict,
                            gfm_supported: bool = True,
                            incremental_review=None,
-                           git_provider=None) -> str:
+                           git_provider=None,
+                           files=None) -> str:
     """
     Convert a dictionary of data into markdown format.
     Args:
@@ -221,9 +230,13 @@ def convert_to_markdown_v2(output_data: dict,
                             continue
                         relevant_file = issue.get('relevant_file', '').strip()
                         issue_header = issue.get('issue_header', '').strip()
+                        if issue_header.lower() == 'possible bug':
+                            issue_header = 'Possible Issue'  # Make the header less frightening
                         issue_content = issue.get('issue_content', '').strip()
                         start_line = int(str(issue.get('start_line', 0)).strip())
                         end_line = int(str(issue.get('end_line', 0)).strip())
+
+                        relevant_lines_str = extract_relevant_lines_str(end_line, files, relevant_file, start_line, dedent=True)
                         if git_provider:
                             reference_link = git_provider.get_line_link(relevant_file, start_line, end_line)
                         else:
@@ -231,7 +244,10 @@ def convert_to_markdown_v2(output_data: dict,
 
                         if gfm_supported:
                             if reference_link is not None and len(reference_link) > 0:
-                                issue_str = f"<a href='{reference_link}'><strong>{issue_header}</strong></a><br>{issue_content}"
+                                if relevant_lines_str:
+                                    issue_str = f"<details><summary><a href='{reference_link}'><strong>{issue_header}</strong></a>\n\n{issue_content}</summary>\n\n{relevant_lines_str}\n\n</details>"
+                                else:
+                                    issue_str = f"<a href='{reference_link}'><strong>{issue_header}</strong></a><br>{issue_content}"
                             else:
                                 issue_str = f"<strong>{issue_header}</strong><br>{issue_content}"
                         else:
@@ -255,68 +271,143 @@ def convert_to_markdown_v2(output_data: dict,
     if gfm_supported:
         markdown_text += "</table>\n"
 
-    if 'code_feedback' in output_data:
-        if gfm_supported:
-            markdown_text += f"\n\n"
-            markdown_text += f"<details><summary> <strong>Code feedback:</strong></summary>\n\n"
-            markdown_text += "<hr>"
-        else:
-            markdown_text += f"\n\n### Code feedback:\n\n"
-        for i, value in enumerate(output_data['code_feedback']):
-            if value is None or value == '' or value == {} or value == []:
-                continue
-            markdown_text += parse_code_suggestion(value, i, gfm_supported)+"\n\n"
-        if markdown_text.endswith('<hr>'):
-            markdown_text= markdown_text[:-4]
-        if gfm_supported:
-            markdown_text += f"</details>"
-
     return markdown_text
 
 
+def extract_relevant_lines_str(end_line, files, relevant_file, start_line, dedent=False) -> str:
+    """
+    Finds 'relevant_file' in 'files', and extracts the lines from 'start_line' to 'end_line' string from the file content.
+    """
+    try:
+        relevant_lines_str = ""
+        if files:
+            files = set_file_languages(files)
+            for file in files:
+                if file.filename.strip() == relevant_file:
+                    if not file.head_file:
+                        # as a fallback, extract relevant lines directly from patch
+                        patch = file.patch
+                        get_logger().info(f"No content found in file: '{file.filename}' for 'extract_relevant_lines_str'. Using patch instead")
+                        _, selected_lines = extract_hunk_lines_from_patch(patch, file.filename, start_line, end_line,side='right')
+                        if not selected_lines:
+                            get_logger().error(f"Failed to extract relevant lines from patch: {file.filename}")
+                            return ""
+                        # filter out '-' lines
+                        relevant_lines_str = ""
+                        for line in selected_lines.splitlines():
+                            if line.startswith('-'):
+                                continue
+                            relevant_lines_str += line[1:] + '\n'
+                    else:
+                        relevant_file_lines = file.head_file.splitlines()
+                        relevant_lines_str = "\n".join(relevant_file_lines[start_line - 1:end_line])
+
+                    if dedent and relevant_lines_str:
+                        # Remove the longest leading string of spaces and tabs common to all lines.
+                        relevant_lines_str = textwrap.dedent(relevant_lines_str)
+                    relevant_lines_str = f"```{file.language}\n{relevant_lines_str}\n```"
+                    break
+
+        return relevant_lines_str
+    except Exception as e:
+        get_logger().exception(f"Failed to extract relevant lines: {e}")
+        return ""
+
+
 def ticket_markdown_logic(emoji, markdown_text, value, gfm_supported) -> str:
     ticket_compliance_str = ""
-    final_compliance_level = -1
+    compliance_emoji = ''
+    # Track compliance levels across all tickets
+    all_compliance_levels = []
+
     if isinstance(value, list):
-        for v in value:
-            ticket_url = v.get('ticket_url', '').strip()
-            compliance_level = v.get('overall_compliance_level', '').strip()
-            # add emojis, if 'Fully compliant' ✅, 'Partially compliant' 🔶, or 'Not compliant' ❌
-            if compliance_level.lower() == 'fully compliant':
-                # compliance_level = '✅ Fully compliant'
-                final_compliance_level = 2 if final_compliance_level == -1 else 1
-            elif compliance_level.lower() == 'partially compliant':
-                # compliance_level = '🔶 Partially compliant'
-                final_compliance_level = 1
-            elif compliance_level.lower() == 'not compliant':
-                # compliance_level = '❌ Not compliant'
-                final_compliance_level = 0 if final_compliance_level < 1 else 1
+        for ticket_analysis in value:
+            try:
+                ticket_url = ticket_analysis.get('ticket_url', '').strip()
+                explanation = ''
+                ticket_compliance_level = ''  # Individual ticket compliance
+                fully_compliant_str = ticket_analysis.get('fully_compliant_requirements', '').strip()
+                not_compliant_str = ticket_analysis.get('not_compliant_requirements', '').strip()
+                requires_further_human_verification = ticket_analysis.get('requires_further_human_verification',
+                                                                          '').strip()
 
-            # explanation = v.get('compliance_analysis', '').strip()
-            explanation = ''
-            fully_compliant_str = v.get('fully_compliant_requirements', '').strip()
-            not_compliant_str = v.get('not_compliant_requirements', '').strip()
-            if fully_compliant_str:
-                explanation += f"Fully compliant requirements:\n{fully_compliant_str}\n\n"
-            if not_compliant_str:
-                explanation += f"Not compliant requirements:\n{not_compliant_str}\n\n"
+                if not fully_compliant_str and not not_compliant_str:
+                    get_logger().debug(f"Ticket compliance has no requirements",
+                                       artifact={'ticket_url': ticket_url})
+                    continue
 
-            ticket_compliance_str += f"\n\n**[{ticket_url.split('/')[-1]}]({ticket_url}) - {compliance_level}**\n\n{explanation}\n\n"
-        if final_compliance_level == 2:
-            compliance_level = '✅'
-        elif final_compliance_level == 1:
-            compliance_level = '🔶'
-        else:
-            compliance_level = '❌'
+                # Calculate individual ticket compliance level
+                if fully_compliant_str:
+                    if not_compliant_str:
+                        ticket_compliance_level = 'Partially compliant'
+                    else:
+                        if not requires_further_human_verification:
+                            ticket_compliance_level = 'Fully compliant'
+                        else:
+                            ticket_compliance_level = 'PR Code Verified'
+                elif not_compliant_str:
+                    ticket_compliance_level = 'Not compliant'
 
+                # Store the compliance level for aggregation
+                if ticket_compliance_level:
+                    all_compliance_levels.append(ticket_compliance_level)
+
+                # build compliance string
+                if fully_compliant_str:
+                    explanation += f"Compliant requirements:\n\n{fully_compliant_str}\n\n"
+                if not_compliant_str:
+                    explanation += f"Non-compliant requirements:\n\n{not_compliant_str}\n\n"
+                if requires_further_human_verification:
+                    explanation += f"Requires further human verification:\n\n{requires_further_human_verification}\n\n"
+                ticket_compliance_str += f"\n\n**[{ticket_url.split('/')[-1]}]({ticket_url}) - {ticket_compliance_level}**\n\n{explanation}\n\n"
+
+                # for debugging
+                if requires_further_human_verification:
+                    get_logger().debug(f"Ticket compliance requires further human verification",
+                                       artifact={'ticket_url': ticket_url,
+                                                 'requires_further_human_verification': requires_further_human_verification,
+                                                 'compliance_level': ticket_compliance_level})
+
+            except Exception as e:
+                get_logger().exception(f"Failed to process ticket compliance: {e}")
+                continue
+
+        # Calculate overall compliance level and emoji
+        if all_compliance_levels:
+            if all(level == 'Fully compliant' for level in all_compliance_levels):
+                compliance_level = 'Fully compliant'
+                compliance_emoji = '✅'
+            elif all(level == 'PR Code Verified' for level in all_compliance_levels):
+                compliance_level = 'PR Code Verified'
+                compliance_emoji = '✅'
+            elif any(level == 'Not compliant' for level in all_compliance_levels):
+                # If there's a mix of compliant and non-compliant tickets
+                if any(level in ['Fully compliant', 'PR Code Verified'] for level in all_compliance_levels):
+                    compliance_level = 'Partially compliant'
+                    compliance_emoji = '🔶'
+                else:
+                    compliance_level = 'Not compliant'
+                    compliance_emoji = '❌'
+            elif any(level == 'Partially compliant' for level in all_compliance_levels):
+                compliance_level = 'Partially compliant'
+                compliance_emoji = '🔶'
+            else:
+                compliance_level = 'PR Code Verified'
+                compliance_emoji = '✅'
+
+            # Set extra statistics outside the ticket loop
+            get_settings().set('config.extra_statistics', {'compliance_level': compliance_level})
+
+        # editing table row for ticket compliance analysis
         if gfm_supported:
             markdown_text += f"<tr><td>\n\n"
-            markdown_text += f"**{emoji} Ticket compliance analysis {compliance_level}**\n\n"
+            markdown_text += f"**{emoji} Ticket compliance analysis {compliance_emoji}**\n\n"
             markdown_text += ticket_compliance_str
             markdown_text += f"</td></tr>\n"
         else:
-            markdown_text += f"### {emoji} Ticket compliance analysis {compliance_level}\n\n"
-            markdown_text += ticket_compliance_str+"\n\n"
+            markdown_text += f"### {emoji} Ticket compliance analysis {compliance_emoji}\n\n"
+            markdown_text += ticket_compliance_str + "\n\n"
+
     return markdown_text
 
 
@@ -543,27 +634,22 @@ def load_large_diff(filename, new_file_content_str: str, original_file_content_s
     """
     Generate a patch for a modified file by comparing the original content of the file with the new content provided as
     input.
-
-    Args:
-        new_file_content_str: The new content of the file as a string.
-        original_file_content_str: The original content of the file as a string.
-
-    Returns:
-        The generated or provided patch string.
-
-    Raises:
-        None.
     """
-    patch = ""
+    if not original_file_content_str and not new_file_content_str:
+        return ""
+
     try:
+        original_file_content_str = (original_file_content_str or "").rstrip() + "\n"
+        new_file_content_str = (new_file_content_str or "").rstrip() + "\n"
         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 and show_warning:
-            get_logger().warning(f"File was modified, but no patch was found. Manually creating patch: {filename}.")
+            get_logger().info(f"File was modified, but no patch was found. Manually creating patch: {filename}.")
         patch = ''.join(diff)
-    except Exception:
-        pass
-    return patch
+        return patch
+    except Exception as e:
+        get_logger().exception(f"Failed to generate patch for file: {filename}")
+        return ""
 
 
 def update_settings_from_args(args: List[str]) -> List[str]:
@@ -1106,3 +1192,48 @@ def process_description(description_full: str) -> Tuple[str, List]:
         get_logger().exception(f"Failed to process description: {e}")
 
     return base_description_str, files
+
+def get_version() -> str:
+    # First check pyproject.toml if running directly out of repository
+    if os.path.exists("pyproject.toml"):
+        if sys.version_info >= (3, 11):
+            import tomllib
+            with open("pyproject.toml", "rb") as f:
+                data = tomllib.load(f)
+                if "project" in data and "version" in data["project"]:
+                    return data["project"]["version"]
+                else:
+                    get_logger().warning("Version not found in pyproject.toml")
+        else:
+            get_logger().warning("Unable to determine local version from pyproject.toml")
+
+    # Otherwise get the installed pip package version
+    try:
+        return version('pr-agent')
+    except PackageNotFoundError:
+        get_logger().warning("Unable to find package named 'pr-agent'")
+        return "unknown"
+
+
+def set_file_languages(diff_files) -> List[FilePatchInfo]:
+    try:
+        # if the language is already set, do not change it
+        if hasattr(diff_files[0], 'language') and diff_files[0].language:
+            return diff_files
+
+        # map file extensions to programming languages
+        language_extension_map_org = get_settings().language_extension_map_org
+        extension_to_language = {}
+        for language, extensions in language_extension_map_org.items():
+            for ext in extensions:
+                extension_to_language[ext] = language
+        for file in diff_files:
+            extension_s = '.' + file.filename.rsplit('.')[-1]
+            language_name = "txt"
+            if extension_s and (extension_s in extension_to_language):
+                language_name = extension_to_language[extension_s]
+            file.language = language_name.lower()
+    except Exception as e:
+        get_logger().exception(f"Failed to set file languages: {e}")
+
+    return diff_files

pr_agent/cli.py

@@ -3,6 +3,7 @@ import asyncio
 import os
 
 from pr_agent.agent.pr_agent import PRAgent, commands
+from pr_agent.algo.utils import get_version
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger, setup_logger
 
@@ -45,6 +46,7 @@ def set_parser():
     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('--version', action='version', version=f'pr-agent {get_version()}')
     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')

pr_agent/config_loader.py

@@ -12,7 +12,6 @@ global_settings = Dynaconf(
     envvar_prefix=False,
     merge_enabled=True,
     settings_files=[join(current_dir, f) for f in [
-        "settings/.secrets.toml",
         "settings/configuration.toml",
         "settings/ignore.toml",
         "settings/language_extensions.toml",
@@ -29,6 +28,7 @@ global_settings = Dynaconf(
         "settings/pr_add_docs.toml",
         "settings/custom_labels.toml",
         "settings/pr_help_prompts.toml",
+        "settings/.secrets.toml",
         "settings_prod/.secrets.toml",
     ]]
 )

pr_agent/git_providers/azuredevops_provider.py

@@ -326,13 +326,13 @@ class AzureDevopsProvider(GitProvider):
                     edit_type = EDIT_TYPE.ADDED
                 elif diff_types[file] == "delete":
                     edit_type = EDIT_TYPE.DELETED
-                elif diff_types[file] == "rename":
+                elif "rename" in diff_types[file]: # diff_type can be `rename` | `edit, rename`
                     edit_type = EDIT_TYPE.RENAMED
 
                 version = GitVersionDescriptor(
                     version=base_sha.commit_id, version_type="commit"
                 )
-                if edit_type == EDIT_TYPE.ADDED:
+                if edit_type == EDIT_TYPE.ADDED or edit_type == EDIT_TYPE.RENAMED:
                     original_file_content_str = ""
                 else:
                     try:

pr_agent/git_providers/bitbucket_server_provider.py

@@ -234,7 +234,7 @@ class BitbucketServerProvider(GitProvider):
                     new_file_content_str = self.get_file(file_path, head_sha)
                     new_file_content_str = decode_if_bytes(new_file_content_str)
 
-            patch = load_large_diff(file_path, new_file_content_str, original_file_content_str)
+            patch = load_large_diff(file_path, new_file_content_str, original_file_content_str, show_warning=False)
 
             diff_files.append(
                 FilePatchInfo(
@@ -402,10 +402,21 @@ class BitbucketServerProvider(GitProvider):
 
         try:
             projects_index = path_parts.index("projects")
-        except ValueError as e:
+        except ValueError:
+            projects_index = -1
+
+        try:
+            users_index = path_parts.index("users")
+        except ValueError:
+            users_index = -1
+
+        if projects_index == -1 and users_index == -1:
             raise ValueError(f"The provided URL '{pr_url}' does not appear to be a Bitbucket PR URL")
 
-        path_parts = path_parts[projects_index:]
+        if projects_index != -1:
+            path_parts = path_parts[projects_index:]
+        else:
+            path_parts = path_parts[users_index:]
 
         if len(path_parts) < 6 or path_parts[2] != "repos" or path_parts[4] != "pull-requests":
             raise ValueError(
@@ -413,6 +424,8 @@ class BitbucketServerProvider(GitProvider):
             )
 
         workspace_slug = path_parts[1]
+        if users_index != -1:
+            workspace_slug = f"~{workspace_slug}"
         repo_slug = path_parts[3]
         try:
             pr_number = int(path_parts[5])

pr_agent/git_providers/github_provider.py

@@ -19,7 +19,7 @@ from ..algo.language_handler import is_valid_file
 from ..algo.types import EDIT_TYPE
 from ..algo.utils import (PRReviewHeader, Range, clip_tokens,
                           find_line_number_of_relevant_line_in_file,
-                          load_large_diff)
+                          load_large_diff, set_file_languages)
 from ..config_loader import get_settings
 from ..log import get_logger
 from ..servers.utils import RateLimitExceeded
@@ -174,6 +174,24 @@ class GithubProvider(GitProvider):
 
             diff_files = []
             invalid_files_names = []
+            is_close_to_rate_limit = False
+
+            # The base.sha will point to the current state of the base branch (including parallel merges), not the original base commit when the PR was created
+            # We can fix this by finding the merge base commit between the PR head and base branches
+            # Note that The pr.head.sha is actually correct as is - it points to the latest commit in your PR branch.
+            # This SHA isn't affected by parallel merges to the base branch since it's specific to your PR's branch.
+            repo = self.repo_obj
+            pr = self.pr
+            try:
+                compare = repo.compare(pr.base.sha, pr.head.sha) # communication with GitHub
+                merge_base_commit = compare.merge_base_commit
+            except Exception as e:
+                get_logger().error(f"Failed to get merge base commit: {e}")
+                merge_base_commit = pr.base
+            if merge_base_commit.sha != pr.base.sha:
+                get_logger().info(
+                    f"Using merge base commit {merge_base_commit.sha} instead of base commit ")
+
             counter_valid = 0
             for file in files:
                 if not is_valid_file(file.filename):
@@ -181,48 +199,36 @@ class GithubProvider(GitProvider):
                     continue
 
                 patch = file.patch
-
-                # allow only a limited number of files to be fully loaded. We can manage the rest with diffs only
-                counter_valid += 1
-                avoid_load = False
-                if counter_valid >= MAX_FILES_ALLOWED_FULL and patch and not self.incremental.is_incremental:
-                    avoid_load = True
-                    if counter_valid == MAX_FILES_ALLOWED_FULL:
-                        get_logger().info(f"Too many files in PR, will avoid loading full content for rest of files")
-
-                if avoid_load:
+                if is_close_to_rate_limit:
                     new_file_content_str = ""
+                    original_file_content_str = ""
                 else:
-                    new_file_content_str = self._get_pr_file_content(file, self.pr.head.sha)  # communication with GitHub
+                    # allow only a limited number of files to be fully loaded. We can manage the rest with diffs only
+                    counter_valid += 1
+                    avoid_load = False
+                    if counter_valid >= MAX_FILES_ALLOWED_FULL and patch and not self.incremental.is_incremental:
+                        avoid_load = True
+                        if counter_valid == MAX_FILES_ALLOWED_FULL:
+                            get_logger().info(f"Too many files in PR, will avoid loading full content for rest of files")
 
-                if self.incremental.is_incremental and self.unreviewed_files_set:
-                    original_file_content_str = self._get_pr_file_content(file, self.incremental.last_seen_commit_sha)
-                    patch = load_large_diff(file.filename, new_file_content_str, original_file_content_str)
-                    self.unreviewed_files_set[file.filename] = patch
-                else:
                     if avoid_load:
-                        original_file_content_str = ""
+                        new_file_content_str = ""
                     else:
-                        # The base.sha will point to the current state of the base branch (including parallel merges), not the original base commit when the PR was created
-                        # We can fix this by finding the merge base commit between the PR head and base branches
-                        # Note that The pr.head.sha is actually correct as is - it points to the latest commit in your PR branch.
-                        # This SHA isn't affected by parallel merges to the base branch since it's specific to your PR's branch.
-                        repo = self.repo_obj
-                        pr = self.pr
-                        try:
-                            compare = repo.compare(pr.base.sha, pr.head.sha)
-                            merge_base_commit = compare.merge_base_commit
-                        except Exception as e:
-                            get_logger().error(f"Failed to get merge base commit: {e}")
-                            merge_base_commit = pr.base
-                        if merge_base_commit.sha != pr.base.sha:
-                            get_logger().info(
-                                f"Using merge base commit {merge_base_commit.sha} instead of base commit "
-                                f"{pr.base.sha} for {file.filename}")
-                        original_file_content_str = self._get_pr_file_content(file, merge_base_commit.sha)
+                        new_file_content_str = self._get_pr_file_content(file, self.pr.head.sha)  # communication with GitHub
 
-                    if not patch:
+                    if self.incremental.is_incremental and self.unreviewed_files_set:
+                        original_file_content_str = self._get_pr_file_content(file, self.incremental.last_seen_commit_sha)
                         patch = load_large_diff(file.filename, new_file_content_str, original_file_content_str)
+                        self.unreviewed_files_set[file.filename] = patch
+                    else:
+                        if avoid_load:
+                            original_file_content_str = ""
+                        else:
+                            original_file_content_str = self._get_pr_file_content(file, merge_base_commit.sha)
+                            # original_file_content_str = self._get_pr_file_content(file, self.pr.base.sha)
+                        if not patch:
+                            patch = load_large_diff(file.filename, new_file_content_str, original_file_content_str)
+
 
                 if file.status == 'added':
                     edit_type = EDIT_TYPE.ADDED
@@ -237,9 +243,14 @@ class GithubProvider(GitProvider):
                     edit_type = EDIT_TYPE.UNKNOWN
 
                 # count number of lines added and removed
-                patch_lines = patch.splitlines(keepends=True)
-                num_plus_lines = len([line for line in patch_lines if line.startswith('+')])
-                num_minus_lines = len([line for line in patch_lines if line.startswith('-')])
+                if hasattr(file, 'additions') and hasattr(file, 'deletions'):
+                    num_plus_lines = file.additions
+                    num_minus_lines = file.deletions
+                else:
+                    patch_lines = patch.splitlines(keepends=True)
+                    num_plus_lines = len([line for line in patch_lines if line.startswith('+')])
+                    num_minus_lines = len([line for line in patch_lines if line.startswith('-')])
+
                 file_patch_canonical_structure = FilePatchInfo(original_file_content_str, new_file_content_str, patch,
                                                                file.filename, edit_type=edit_type,
                                                                num_plus_lines=num_plus_lines,
@@ -889,18 +900,7 @@ class GithubProvider(GitProvider):
         RE_HUNK_HEADER = re.compile(
             r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
 
-        # map file extensions to programming languages
-        language_extension_map_org = get_settings().language_extension_map_org
-        extension_to_language = {}
-        for language, extensions in language_extension_map_org.items():
-            for ext in extensions:
-                extension_to_language[ext] = language
-        for file in diff_files:
-            extension_s = '.' + file.filename.rsplit('.')[-1]
-            language_name = "txt"
-            if extension_s and (extension_s in extension_to_language):
-                language_name = extension_to_language[extension_s]
-            file.language = language_name.lower()
+        diff_files = set_file_languages(diff_files)
 
         for suggestion in code_suggestions_copy:
             try:

pr_agent/git_providers/local_git_provider.py

@@ -141,6 +141,18 @@ class LocalGitProvider(GitProvider):
     def remove_comment(self, comment):
         pass  # Not applicable to the local git provider, but required by the interface
 
+    def add_eyes_reaction(self, comment):
+        pass  # Not applicable to the local git provider, but required by the interface
+
+    def get_commit_messages(self):
+        pass  # Not applicable to the local git provider, but required by the interface
+
+    def get_repo_settings(self):
+        pass  # Not applicable to the local git provider, but required by the interface
+
+    def remove_reaction(self, comment):
+        pass  # Not applicable to the local git provider, but required by the interface
+
     def get_languages(self):
         """
         Calculate percentage of languages in repository. Used for hunk prioritisation.

pr_agent/git_providers/utils.py

@@ -99,5 +99,5 @@ def set_claude_model():
     """
     model_claude = "bedrock/anthropic.claude-3-5-sonnet-20240620-v1:0"
     get_settings().set('config.model', model_claude)
-    get_settings().set('config.model_turbo', model_claude)
+    get_settings().set('config.model_weak', model_claude)
     get_settings().set('config.fallback_models', [model_claude])

pr_agent/servers/azuredevops_server_webhook.py

@@ -64,6 +64,9 @@ def authorize(credentials: HTTPBasicCredentials = Depends(security)):
 
 async def _perform_commands_azure(commands_conf: str, agent: PRAgent, api_url: str, log_context: dict):
     apply_repo_settings(api_url)
+    if commands_conf == "pr_commands" and get_settings().config.disable_auto_feedback:  # auto commands for PR, and auto feedback is disabled
+        get_logger().info(f"Auto feedback is disabled, skipping auto commands for PR {api_url=}", **log_context)
+        return
     commands = get_settings().get(f"azure_devops_server.{commands_conf}")
     get_settings().set("config.is_auto_command", True)
     for command in commands:

pr_agent/servers/bitbucket_app.py

@@ -24,10 +24,6 @@ from pr_agent.identity_providers import get_identity_provider
 from pr_agent.identity_providers.identity_provider import Eligibility
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.secret_providers import get_secret_provider
-from pr_agent.servers.github_action_runner import get_setting_or_env, is_true
-from pr_agent.tools.pr_code_suggestions import PRCodeSuggestions
-from pr_agent.tools.pr_description import PRDescription
-from pr_agent.tools.pr_reviewer import PRReviewer
 
 setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
 router = APIRouter()
@@ -75,8 +71,23 @@ async def handle_manifest(request: Request, response: Response):
     return JSONResponse(manifest_obj)
 
 
+def _get_username(data):
+    actor = data.get("data", {}).get("actor", {})
+    if actor:
+        if "username" in actor:
+            return actor["username"]
+        elif "display_name" in actor:
+            return actor["display_name"]
+        elif "nickname" in actor:
+            return actor["nickname"]
+    return ""
+
+
 async def _perform_commands_bitbucket(commands_conf: str, agent: PRAgent, api_url: str, log_context: dict, data: dict):
     apply_repo_settings(api_url)
+    if commands_conf == "pr_commands" and get_settings().config.disable_auto_feedback:  # auto commands for PR, and auto feedback is disabled
+        get_logger().info(f"Auto feedback is disabled, skipping auto commands for PR {api_url=}")
+        return
     if data.get("event", "") == "pullrequest:created":
         if not should_process_pr_logic(data):
             return
@@ -115,6 +126,14 @@ def should_process_pr_logic(data) -> bool:
         title = pr_data.get("title", "")
         source_branch = pr_data.get("source", {}).get("branch", {}).get("name", "")
         target_branch = pr_data.get("destination", {}).get("branch", {}).get("name", "")
+        sender = _get_username(data)
+
+        # logic to ignore PRs from specific users
+        ignore_pr_users = get_settings().get("CONFIG.IGNORE_PR_AUTHORS", [])
+        if ignore_pr_users and sender:
+            if sender in ignore_pr_users:
+                get_logger().info(f"Ignoring PR from user '{sender}' due to 'config.ignore_pr_authors' setting")
+                return False
 
         # logic to ignore PRs with specific titles
         if title:
@@ -164,16 +183,7 @@ async def handle_github_webhooks(background_tasks: BackgroundTasks, request: Req
                     return "OK"
 
             # Get the username of the sender
-            actor = data.get("data", {}).get("actor", {})
-            if actor:
-                try:
-                    username = actor["username"]
-                except KeyError:
-                    try:
-                        username = actor["display_name"]
-                    except KeyError:
-                        username = actor["nickname"]
-                log_context["sender"] = username
+            log_context["sender"] = _get_username(data)
 
             sender_id = data.get("data", {}).get("actor", {}).get("account_id", "")
             log_context["sender_id"] = sender_id

pr_agent/servers/bitbucket_server_webhook.py

@@ -72,6 +72,11 @@ async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
     commands_to_run = []
 
     if data["eventKey"] == "pr:opened":
+        apply_repo_settings(pr_url)
+        if get_settings().config.disable_auto_feedback:  # auto commands for PR, and auto feedback is disabled
+            get_logger().info(f"Auto feedback is disabled, skipping auto commands for PR {pr_url}", **log_context)
+            return
+        get_settings().set("config.is_auto_command", True)
         commands_to_run.extend(_get_commands_list_from_settings('BITBUCKET_SERVER.PR_COMMANDS'))
     elif data["eventKey"] == "pr:comment:added":
         commands_to_run.append(data["comment"]["text"])

pr_agent/servers/github_app.py

@@ -257,6 +257,14 @@ def should_process_pr_logic(body) -> bool:
         pr_labels = pull_request.get("labels", [])
         source_branch = pull_request.get("head", {}).get("ref", "")
         target_branch = pull_request.get("base", {}).get("ref", "")
+        sender = body.get("sender", {}).get("login")
+
+        # logic to ignore PRs from specific users
+        ignore_pr_users = get_settings().get("CONFIG.IGNORE_PR_AUTHORS", [])
+        if ignore_pr_users and sender:
+            if sender in ignore_pr_users:
+                get_logger().info(f"Ignoring PR from user '{sender}' due to 'config.ignore_pr_authors' setting")
+                return False
 
         # logic to ignore PRs with specific titles
         if title:
@@ -276,6 +284,7 @@ def should_process_pr_logic(body) -> bool:
                 get_logger().info(f"Ignoring PR with labels '{labels_str}' due to config.ignore_pr_labels settings")
                 return False
 
+        # logic to ignore PRs with specific source or target branches
         ignore_pr_source_branches = get_settings().get("CONFIG.IGNORE_PR_SOURCE_BRANCHES", [])
         ignore_pr_target_branches = get_settings().get("CONFIG.IGNORE_PR_TARGET_BRANCHES", [])
         if pull_request and (ignore_pr_source_branches or ignore_pr_target_branches):
@@ -374,6 +383,9 @@ def _check_pull_request_event(action: str, body: dict, log_context: dict) -> Tup
 async def _perform_auto_commands_github(commands_conf: str, agent: PRAgent, body: dict, api_url: str,
                                         log_context: dict):
     apply_repo_settings(api_url)
+    if commands_conf == "pr_commands" and get_settings().config.disable_auto_feedback:  # auto commands for PR, and auto feedback is disabled
+        get_logger().info(f"Auto feedback is disabled, skipping auto commands for PR {api_url=}")
+        return
     if not should_process_pr_logic(body): # Here we already updated the configuration with the repo settings
         return {}
     commands = get_settings().get(f"github_app.{commands_conf}")

pr_agent/servers/github_polling.py

@@ -84,6 +84,7 @@ async def is_valid_notification(notification, headers, handled_ids, session, use
                     return False, handled_ids
                 async with session.get(latest_comment, headers=headers) as comment_response:
                     check_prev_comments = False
+                    user_tag = "@" + user_id
                     if comment_response.status == 200:
                         comment = await comment_response.json()
                         if 'id' in comment:
@@ -101,7 +102,6 @@ async def is_valid_notification(notification, headers, handled_ids, session, use
                             get_logger().debug(f"no comment_body")
                             check_prev_comments = True
                         else:
-                            user_tag = "@" + user_id
                             if user_tag not in comment_body:
                                 get_logger().debug(f"user_tag not in comment_body")
                                 check_prev_comments = True

pr_agent/servers/gitlab_webhook.py

@@ -61,6 +61,9 @@ async def handle_request(api_url: str, body: str, log_context: dict, sender_id:
 async def _perform_commands_gitlab(commands_conf: str, agent: PRAgent, api_url: str,
                                    log_context: dict, data: dict):
     apply_repo_settings(api_url)
+    if commands_conf == "pr_commands" and get_settings().config.disable_auto_feedback:  # auto commands for PR, and auto feedback is disabled
+        get_logger().info(f"Auto feedback is disabled, skipping auto commands for PR {api_url=}", **log_context)
+        return
     if not should_process_pr_logic(data): # Here we already updated the configurations
         return
     commands = get_settings().get(f"gitlab.{commands_conf}", {})
@@ -97,6 +100,14 @@ def should_process_pr_logic(data) -> bool:
         if not data.get('object_attributes', {}):
             return False
         title = data['object_attributes'].get('title')
+        sender = data.get("user", {}).get("username", "")
+
+        # logic to ignore PRs from specific users
+        ignore_pr_users = get_settings().get("CONFIG.IGNORE_PR_AUTHORS", [])
+        if ignore_pr_users and sender:
+            if sender in ignore_pr_users:
+                get_logger().info(f"Ignoring PR from user '{sender}' due to 'config.ignore_pr_authors' settings")
+                return False
 
         # logic to ignore MRs for titles, labels and source, target branches.
         ignore_mr_title = get_settings().get("CONFIG.IGNORE_PR_TITLE", [])

pr_agent/settings/.secrets_template.toml

@@ -91,3 +91,6 @@ pat = ""
 # Optional, uncomment if you want to use Azure devops webhooks. Value assinged when you create the webhook
 # webhook_username = "<basic auth user>"
 # webhook_password = "<basic auth password>"
+
+[deepseek]
+key = ""

pr_agent/settings/configuration.toml

@@ -1,8 +1,8 @@
 [config]
 # models
-model="gpt-4-turbo-2024-04-09"
-model_turbo="gpt-4o-2024-11-20"
+model="gpt-4o-2024-11-20"
 fallback_models=["gpt-4o-2024-08-06"]
+#model_weak="gpt-4o-mini-2024-07-18" # optional, a weaker model to use for some easier tasks
 # CLI
 git_provider="github"
 publish_output=true
@@ -14,6 +14,7 @@ use_extra_bad_extensions=false
 use_wiki_settings_file=true
 use_repo_settings_file=true
 use_global_settings_file=true
+disable_auto_feedback = false
 ai_timeout=120 # 2minutes
 skip_keys = []
 # token limits
@@ -33,6 +34,7 @@ ai_disclaimer_title=""  # Pro feature, title for a collapsible disclaimer to AI
 ai_disclaimer=""  # Pro feature, full text for the AI disclaimer
 output_relevant_configurations=false
 large_patch_policy = "clip" # "clip", "skip"
+duplicate_prompt_examples = false
 # seed
 seed=-1 # set positive value to fix the seed (and ensure temperature=0)
 temperature=0.2
@@ -41,6 +43,7 @@ ignore_pr_title = ["^\\[Auto\\]", "^Auto"] # a list of regular expressions to ma
 ignore_pr_target_branches = [] # a list of regular expressions of target branches to ignore from PR agent when an PR is created
 ignore_pr_source_branches = [] # a list of regular expressions of source branches to ignore from PR agent when an PR is created
 ignore_pr_labels = [] # labels to ignore from PR agent when an PR is created
+ignore_pr_authors = [] # authors to ignore from PR agent when an PR is created
 #
 is_auto_command = false # will be auto-set to true if the command is triggered by an automation
 enable_ai_metadata = false # will enable adding ai metadata
@@ -54,10 +57,6 @@ require_can_be_split_review=false
 require_security_review=true
 require_ticket_analysis_review=true
 # general options
-num_code_suggestions=0
-inline_code_comments = false
-ask_and_reflect=false
-#automatic_review=true
 persistent_comment=true
 extra_instructions = ""
 final_update_message = true
@@ -72,7 +71,6 @@ enable_intro_text=true
 enable_help_text=false # Determines whether to include help text in the PR review. Enabled by default.
 # auto approval
 enable_auto_approval=false
-maximal_review_effort=5
 
 
 [pr_description] # /describe #
@@ -91,6 +89,7 @@ publish_description_as_comment_persistent=true
 ## changes walkthrough section
 enable_semantic_files_types=true
 collapsible_file_list='adaptive' # true, false, 'adaptive'
+collapsible_file_list_threshold=8
 inline_file_summary=false # false, true, 'table'
 # markers
 use_description_markers=false
@@ -99,7 +98,6 @@ include_generated_by_header=true
 enable_large_pr_handling=true
 max_ai_calls=4
 async_ai_calls=true
-mention_extra_files=true
 #custom_labels = ['Bug fix', 'Tests', 'Bug fix with tests', 'Enhancement', 'Documentation', 'Other']
 
 [pr_questions] # /ask #
@@ -114,7 +112,6 @@ dual_publishing_score_threshold=-1 # -1 to disable, [0-10] to set the threshold
 focus_only_on_problems=true
 #
 extra_instructions = ""
-rank_suggestions = false
 enable_help_text=false
 enable_chat_text=false
 enable_intro_text=true
@@ -129,7 +126,7 @@ auto_extended_mode=true
 num_code_suggestions_per_chunk=4
 max_number_of_calls = 3
 parallel_calls = true
-rank_extended_suggestions = false
+
 final_clip_factor = 0.8
 # self-review checkbox
 demand_code_suggestions_self_review=false # add a checkbox for the author to self-review the code suggestions
@@ -139,6 +136,7 @@ fold_suggestions_on_self_review=true # Pro feature. if true, the code suggestion
 # Suggestion impact 💎
 publish_post_process_suggestion_impact=true
 wiki_page_accepted_suggestions=true
+allow_thumbs_up_down=false
 
 [pr_custom_prompt] # /custom_prompt #
 prompt = """\
@@ -162,6 +160,7 @@ class_name = ""        # in case there are several methods with the same name in
 [pr_update_changelog] # /update_changelog #
 push_changelog_changes=false
 extra_instructions = ""
+add_pr_link=true
 
 [pr_analyze] # /analyze #
 enable_help_text=true
@@ -218,7 +217,7 @@ override_deployment_type = true
 handle_pr_actions = ['opened', 'reopened', 'ready_for_review']
 pr_commands = [
     "/describe --pr_description.final_update_message=false",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
     "/improve",
 ]
 # settings for "pull_request" event with "synchronize" action - used to detect and handle push triggers for new commits
@@ -230,27 +229,27 @@ push_trigger_pending_tasks_backlog = true
 push_trigger_pending_tasks_ttl = 300
 push_commands = [
     "/describe",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
 ]
 
 [gitlab]
 url = "https://gitlab.com"
 pr_commands = [
     "/describe --pr_description.final_update_message=false",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
     "/improve",
 ]
 handle_push_trigger = false
 push_commands = [
     "/describe",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
 ]
 
 [bitbucket_app]
 pr_commands = [
     "/describe --pr_description.final_update_message=false",
-    "/review --pr_reviewer.num_code_suggestions=0",
-    "/improve --pr_code_suggestions.commitable_code_suggestions=true --pr_code_suggestions.suggestions_score_threshold=7",
+    "/review",
+    "/improve --pr_code_suggestions.commitable_code_suggestions=true",
 ]
 avoid_full_files = false
 
@@ -275,8 +274,8 @@ avoid_full_files = false
 url = ""
 pr_commands = [
     "/describe --pr_description.final_update_message=false",
-    "/review --pr_reviewer.num_code_suggestions=0",
-    "/improve --pr_code_suggestions.commitable_code_suggestions=true --pr_code_suggestions.suggestions_score_threshold=7",
+    "/review",
+    "/improve --pr_code_suggestions.commitable_code_suggestions=true",
 ]
 
 [litellm]
@@ -308,7 +307,16 @@ number_of_results = 5
 
 [lancedb]
 uri = "./lancedb"
+
 [best_practices]
 content = ""
+organization_name = ""
 max_lines_allowed = 800
 enable_global_best_practices = false
+
+[auto_best_practices]
+enable_auto_best_practices = true # public - general flag to disable all auto best practices usage
+utilize_auto_best_practices = true # public - disable usage of auto best practices in the 'improve' tool
+extra_instructions = "" # public - extra instructions to the auto best practices generation prompt
+content = ""
+max_patterns = 5 # max number of patterns to be detected

pr_agent/settings/pr_code_suggestions_prompts.toml

@@ -17,30 +17,36 @@ The PR code diff will be in the following structured format:
 
 @@ ... @@ def func1():
 __new hunk__
- unchanged code line0 in the PR
- unchanged code line1 in the PR
-+new code line2 added in the PR
- unchanged code line3 in the PR
+ unchanged code line0
+ unchanged code line1
++new code line2 added
+ unchanged code line3
 __old hunk__
  unchanged code line0
  unchanged code line1
--old code line2 removed in the PR
+-old code line2 removed
  unchanged code line3
 
 @@ ... @@ def func2():
 __new hunk__
  unchanged code line4
-+new code line5 removed in the PR
++new code line5 added
  unchanged code line6
 
 ## File: 'src/file2.py'
 ...
 ======
 
-- In the format above, the diff is organized into separate '__new hunk__' and '__old hunk__' sections for each code chunk. '__new hunk__' contains the updated code, while '__old hunk__' shows the removed code. If no code was removed in a specific chunk, the __old hunk__ section will be omitted.
-- Code lines are prefixed with symbols: '+' for new code added in the PR, '-' for code removed, and ' ' for unchanged code.
+Important notes about the structured diff format above:
+1. Each PR code chunk is decoupled into separate '__new hunk__' and '__old hunk__' sections:
+  - The '__new hunk__' section shows the code chunk AFTER the PR changes.
+  - The '__old hunk__' section shows the code chunk BEFORE the PR changes. If no code was removed from the chunk, the '__old hunk__' section will be omitted.
+2. The diff uses line prefixes to show changes:
+  '+' → new line code added (will appear only in '__new hunk__')
+  '-' → line code removed (will appear only in '__old hunk__')
+  ' ' → unchanged context lines (will appear in both sections)
 {%- if is_ai_metadata %}
-- When available, an AI-generated summary will precede each file's diff, with a high-level overview of the changes. Note that this summary may not be fully accurate or complete.
+3. When available, an AI-generated summary will precede each file's diff, with a high-level overview of the changes. Note that this summary may not be fully accurate or complete.
 {%- endif %}
 
 
@@ -50,16 +56,17 @@ Specific guidelines for generating code suggestions:
 {%- else %}
 - Provide up to {{ num_code_suggestions }} distinct and insightful code suggestions. Return less suggestions if no pertinent ones are applicable.
 {%- endif %}
-- Focus solely on enhancing new code introduced in the PR, identified by '+' prefixes in '__new hunk__' sections.
+- DO NOT suggest implementing changes that are already present in the '+' lines compared to the '-' lines.
+- Focus your suggestions ONLY on new code introduced in the PR ('+' lines in '__new hunk__' sections).
 {%- if not focus_only_on_problems %}
 - Prioritize suggestions that address potential issues, critical problems, and bugs in the PR code. Avoid repeating changes already implemented in the PR. If no pertinent suggestions are applicable, return an empty list.
+- Don't suggest to add docstring, type hints, or comments, to remove unused imports, or to use more specific exception types.
 {%- else %}
 - Only give suggestions that address critical problems and bugs in the PR code. If no relevant suggestions are applicable, return an empty list.
+- Do not suggest to change packages version, add missing import statement, or declare undefined variable.
 {%- endif %}
-- Don't suggest to add docstring, type hints, or comments, to remove unused imports, or to use more specific exception types.
-- When referencing variables or names from the code, enclose them in backticks (`). Example: "ensure that `variable_name` is..."
-- Be mindful you are viewing a partial PR code diff, not the full codebase. Avoid suggestions that might conflict with unseen code or alerting variables not declared in the visible scope, as the context is incomplete.
-
+- When mentioning code elements (variables, names, or files) in your response, surround them with backticks (`). For example: "verify that `user_id` is..."
+- Note that you only see changed code segments (diff hunks in a PR), not the entire codebase. Avoid suggestions that might duplicate existing functionality or questioning code elements (like variables declarations or import statements) that may be defined elsewhere in the codebase.
 
 {%- if extra_instructions %}
 
@@ -77,9 +84,9 @@ class CodeSuggestion(BaseModel):
     relevant_file: str = Field(description="Full path of the relevant file")
     language: str = Field(description="Programming language used by the relevant file")
     suggestion_content: str = Field(description="An actionable suggestion to enhance, improve or fix the new code introduced in the PR. Don't present here actual code snippets, just the suggestion. Be short and concise")
-    existing_code: str = Field(description="A short code snippet from a '__new hunk__' section that the suggestion aims to enhance or fix. Include only complete code lines. Use ellipsis (...) for brevity if needed. This snippet should represent the specific PR code targeted for improvement.")
+    existing_code: str = Field(description="A short code snippet, from a '__new hunk__' section after the PR changes, that the suggestion aims to enhance or fix. Include only complete code lines. Use ellipsis (...) for brevity if needed. This snippet should represent the specific PR code targeted for improvement.")
     improved_code: str = Field(description="A refined code snippet that replaces the 'existing_code' snippet after implementing the suggestion.")
-    one_sentence_summary: str = Field(description="A concise, single-sentence overview of the suggested improvement. Focus on the 'what'. Be general, and avoid method or variable names.")
+    one_sentence_summary: str = Field(description="A concise, single-sentence overview (up to 6 words) of the suggested improvement. Focus on the 'what'. Be general, and avoid method or variable names.")
 {%- if not focus_only_on_problems %}
     label: str = Field(description="A single, descriptive label that best characterizes the suggestion type. Possible labels include 'security', 'possible bug', 'possible issue', 'performance', 'enhancement', 'best practice', 'maintainability', 'typo'. Other relevant labels are also acceptable.")
 {%- else %}
@@ -111,7 +118,6 @@ code_suggestions:
     ...
 ```
 
-
 Each YAML output MUST be after a newline, indented, with block scalar indicator ('|').
 """
 
@@ -119,12 +125,40 @@ user="""--PR Info--
 
 Title: '{{title}}'
 
+{%- if date %}
+
+Today's Date: {{date}}
+{%- endif %}
 
 The PR Diff:
 ======
 {{ diff_no_line_numbers|trim }}
 ======
 
+{%- if duplicate_prompt_examples %}
+
+
+Example output:
+```yaml
+code_suggestions:
+- relevant_file: |
+    src/file1.py
+  language: |
+    python
+  suggestion_content: |
+    ...
+  existing_code: |
+    ...
+  improved_code: |
+    ...
+  one_sentence_summary: |
+    ...
+  label: |
+    ...
+```
+(replace '...' with actual content)
+{%- endif %}
+
 
 Response (should be a valid YAML, and nothing else):
 ```yaml

pr_agent/settings/pr_code_suggestions_reflect_prompts.toml

@@ -49,14 +49,14 @@ The PR code diff will be presented in the following structured format:
 
 @@ ... @@ def func1():
 __new hunk__
-11  unchanged code line0 in the PR
-12  unchanged code line1 in the PR
-13 +new code line2 added in the PR
-14  unchanged code line3 in the PR
+11  unchanged code line0
+12  unchanged code line1
+13 +new code line2 added
+14  unchanged code line3
 __old hunk__
  unchanged code line0
  unchanged code line1
--old code line2 removed in the PR
+-old code line2 removed
  unchanged code line3
 
 @@ ... @@ def func2():
@@ -122,6 +122,25 @@ Below are {{ num_code_suggestions }} AI-generated code suggestions for enhancing
 ======
 
 
+{%- if duplicate_prompt_examples %}
+
+
+Example output:
+```yaml
+code_suggestions:
+- suggestion_summary: |
+    ...
+  relevant_file: "..."
+  relevant_lines_start: ...
+  relevant_lines_end: ...
+  suggestion_score: ...
+  why: |
+    ...
+- ...
+```
+(replace '...' with actual content)
+{%- endif %}
+
 Response (should be a valid YAML, and nothing else):
 ```yaml
 """

pr_agent/settings/pr_description_prompts.toml

@@ -1,15 +1,11 @@
 [pr_description_prompt]
 system="""You are PR-Reviewer, a language model designed to review a Git Pull Request (PR).
-{%- if enable_custom_labels %}
-Your task is to provide a full description for the PR content - files walkthrough, title, type, description and labels.
-{%- else %}
-Your task is to provide a full description for the PR content - files walkthrough, title, type, and description.
-{%- endif %}
-- Focus on the new PR code (lines starting with '+').
+Your task is to provide a full description for the PR content - type, description, title and files walkthrough.
+- Focus on the new PR code (lines starting with '+' in the 'PR Git Diff' section).
 - Keep in mind that the 'Previous title', 'Previous description' and 'Commit messages' sections may be partial, simplistic, non-informative or out of date. Hence, compare them to the PR diff code, and use them only as a reference.
 - The generated title and description should prioritize the most significant changes.
-- If needed, each YAML output should be in block scalar indicator ('|-')
-- When quoting variables or names from the code, use backticks (`) instead of single quote (').
+- If needed, each YAML output should be in block scalar indicator ('|')
+- When quoting variables, names or file paths from the code, use backticks (`) instead of single quote (').
 
 {%- if extra_instructions %}
 
@@ -38,22 +34,20 @@ class PRType(str, Enum):
 {%- if enable_semantic_files_types %}
 
 class FileDescription(BaseModel):
-    filename: str = Field(description="The full file path of the relevant file.")
-    language: str = Field(description="The programming language of the relevant file.")
+    filename: str = Field(description="The full file path of the relevant file")
+{%- if include_file_summary_changes %}
     changes_summary: str = Field(description="concise summary of the changes in the relevant file, in bullet points (1-4 bullet points).")
-    changes_title: str = Field(description="an informative title for the changes in the files, describing its main theme (5-10 words).")
+{%- endif %}
+    changes_title: str = Field(description="one-line summary (5-10 words) capturing the main theme of changes in the file")
     label: str = Field(description="a single semantic label that represents a type of code changes that occurred in the File. Possible values (partial list): 'bug fix', 'tests', 'enhancement', 'documentation', 'error handling', 'configuration changes', 'dependencies', 'formatting', 'miscellaneous', ...")
 {%- endif %}
 
 class PRDescription(BaseModel):
     type: List[PRType] = Field(description="one or more types that describe the PR content. Return the label member value (e.g. 'Bug fix', not 'bug_fix')")
+    description: str = Field(description="summarize the PR changes in up to four bullet points, each up to 8 words. For large PRs, add sub-bullets if needed. Order bullets by importance, with each bullet highlighting a key change group.")
+    title: str = Field(description="a concise and descriptive title that captures the PR's main theme")
 {%- if enable_semantic_files_types %}
-    pr_files: List[FileDescription] = Field(max_items=15, description="a list of the files in the PR, and summary of their changes")
-{%- endif %}
-    description: str = Field(description="an informative and concise description of the PR. Use bullet points. Display first the most significant changes.")
-    title: str = Field(description="an informative title for the PR, describing its main theme")
-{%- if enable_custom_labels %}
-    labels: List[Label] =  Field(min_items=0, description="choose the relevant custom labels that describe the PR content, and return their keys. Use the value field of the Label object to better understand the label meaning.")
+    pr_files: List[FileDescription] = Field(max_items=20, description="a list of all the files that were changed in the PR, and summary of their changes. Each file must be analyzed regardless of change size.")
 {%- endif %}
 =====
 
@@ -64,30 +58,23 @@ Example output:
 type:
 - ...
 - ...
-{%- if enable_semantic_files_types %}
-pr_files:
-- filename: |
-    ...
-  language: |
-    ...
-  changes_summary: |
-    ...
-  changes_title: |
-    ...
-  label: |
-    ...
-...
-{%- endif %}
 description: |
   ...
 title: |
   ...
-{%- if enable_custom_labels %}
-labels:
-- |
-  ...
-- |
-  ...
+{%- if enable_semantic_files_types %}
+pr_files:
+- filename: |
+    ...
+{%- if include_file_summary_changes %}
+  changes_summary: |
+    ...
+{%- endif %}
+  changes_title: |
+    ...
+  label: |
+    label_key_1
+...
 {%- endif %}
 ```
 
@@ -136,13 +123,44 @@ Commit messages:
 {%- endif %}
 
 
-The PR Diff:
+The PR Git Diff:
 =====
 {{ diff|trim }}
 =====
 
 Note that lines in the diff body are prefixed with a symbol that represents the type of change: '-' for deletions, '+' for additions, and ' ' (a space) for unchanged lines.
 
+{%- if duplicate_prompt_examples %}
+
+
+Example output:
+```yaml
+type:
+- Bug fix
+- Refactoring
+- ...
+description: |
+  ...
+title: |
+  ...
+{%- if enable_semantic_files_types %}
+pr_files:
+- filename: |
+    ...
+{%- if include_file_summary_changes %}
+  changes_summary: |
+    ...
+{%- endif %}
+  changes_title: |
+    ...
+  label: |
+    label_key_1
+...
+{%- endif %}
+```
+(replace '...' with the actual values)
+{%- endif %}
+
 
 Response (should be a valid YAML, and nothing else):
 ```yaml

pr_agent/settings/pr_reviewer_prompts.toml

@@ -1,10 +1,6 @@
 [pr_review_prompt]
 system="""You are PR-Reviewer, a language model designed to review a Git Pull Request (PR).
-{%- if num_code_suggestions > 0 %}
-Your task is to provide constructive and concise feedback for the PR, and also provide meaningful code suggestions.
-{%- else %}
 Your task is to provide constructive and concise feedback for the PR.
-{%- endif %}
 The review should focus on new code added in the PR code diff (lines starting with '+')
 
 
@@ -20,20 +16,20 @@ The format we will use to present the PR code diff:
 
 @@ ... @@ def func1():
 __new hunk__
-11  unchanged code line0 in the PR
-12  unchanged code line1 in the PR
-13 +new code line2 added in the PR
-14  unchanged code line3 in the PR
+11  unchanged code line0
+12  unchanged code line1
+13 +new code line2 added
+14  unchanged code line3
 __old hunk__
  unchanged code line0
  unchanged code line1
--old code line2 removed in the PR
+-old code line2 removed
  unchanged code line3
 
 @@ ... @@ def func2():
 __new hunk__
  unchanged code line4
-+new code line5 removed in the PR
++new code line5 removed
  unchanged code line6
 
 ## File: 'src/file2.py'
@@ -47,18 +43,8 @@ __new hunk__
 {%- if is_ai_metadata %}
 - If available, an AI-generated summary will appear and provide a high-level overview of the file changes. Note that this summary may not be fully accurate or complete.
 {%- endif %}
-- When quoting variables or names from the code, use backticks (`) instead of single quote (').
+- When quoting variables, names or file paths from the code, use backticks (`) instead of single quote (').
 
-{%- if num_code_suggestions > 0 %}
-
-
-Code suggestions guidelines:
-- Provide up to {{ num_code_suggestions }} code suggestions. Try to provide diverse and insightful suggestions.
-- Focus on important suggestions like fixing code problems, issues and bugs. As a second priority, provide suggestions for meaningful code improvements, like performance, vulnerability, modularity, and best practices.
-- Avoid making suggestions that have already been implemented in the PR code. For example, if you want to add logs, or change a variable to const, or anything else, make sure it isn't already in the PR code.
-- Don't suggest to add docstring, type hints, or comments.
-- Suggestions should address the new code added in the PR diff (lines starting with '+')
-{%- endif %}
 
 {%- if extra_instructions %}
 
@@ -80,8 +66,8 @@ class SubPR(BaseModel):
 
 class KeyIssuesComponentLink(BaseModel):
     relevant_file: str = Field(description="The full file path of the relevant file")
-    issue_header: str = Field(description="One or two word title for the the issue. For example: 'Possible Bug', 'Performance Issue', 'Code Smell', etc.")
-    issue_content: str = Field(description="A short and concise summary of what should be further inspected and validated during the PR review process for this issue. Don't state line numbers here")
+    issue_header: str = Field(description="One or two word title for the the issue. For example: 'Possible Bug', etc.")
+    issue_content: str = Field(description="A short and concise summary of what should be further inspected and validated during the PR review process for this issue. Do not reference line numbers in this field.")
     start_line: int = Field(description="The start line that corresponds to this issue in the relevant file")
     end_line: int = Field(description="The end line that corresponds to this issue in the relevant file")
 
@@ -89,10 +75,10 @@ class KeyIssuesComponentLink(BaseModel):
 
 class TicketCompliance(BaseModel):
     ticket_url: str = Field(description="Ticket URL or ID")
-    ticket_requirements: str = Field(description="Repeat, in your own words, all ticket requirements, in bullet points")
-    fully_compliant_requirements: str = Field(description="A list, in bullet points, of which requirements are met by the PR code. Don't explain how the requirements are met, just list them shortly. Can be empty")
-    not_compliant_requirements: str = Field(description="A list, in bullet points, of which requirements are not met by the PR code. Don't explain how the requirements are not met, just list them shortly. Can be empty")
-    overall_compliance_level: str = Field(description="Overall give this PR one of these three values in relation to the ticket: 'Fully compliant', 'Partially compliant', or 'Not compliant'")
+    ticket_requirements: str = Field(description="Repeat, in your own words (in bullet points), all the requirements, sub-tasks, DoD, and acceptance criteria raised by the ticket")
+    fully_compliant_requirements: str = Field(description="Bullet-point list of items from the  'ticket_requirements' section above that are fulfilled by the PR code. Don't explain how the requirements are met, just list them shortly. Can be empty")
+    not_compliant_requirements: str = Field(description="Bullet-point list of items from the 'ticket_requirements' section above that are not fulfilled by the PR code. Don't explain how the requirements are not met, just list them shortly. Can be empty")
+    requires_further_human_verification: str = Field(description="Bullet-point list of items from the 'ticket_requirements' section above that cannot be assessed through code review alone, are unclear, or need further human review (e.g., browser testing, UI checks). Leave empty if all 'ticket_requirements' were marked as fully compliant or not compliant")
 {%- endif %}
 
 class Review(BaseModel):
@@ -111,32 +97,16 @@ class Review(BaseModel):
 {%- if question_str %}
     insights_from_user_answers: str = Field(description="shortly summarize the insights you gained from the user's answers to the questions")
 {%- endif %}
-    key_issues_to_review: List[KeyIssuesComponentLink] = Field("A diverse list of bugs, issue or major performance concerns introduced in this PR, which the PR reviewer should further investigate")
+    key_issues_to_review: List[KeyIssuesComponentLink] = Field("A short and diverse list (0-3 issues) of high-priority bugs, problems or performance concerns introduced in the PR code, which the PR reviewer should further focus on and validate during the review process.")
 {%- if require_security_review %}
     security_concerns: str = Field(description="Does this PR code introduce possible vulnerabilities such as exposure of sensitive information (e.g., API keys, secrets, passwords), or security concerns like SQL injection, XSS, CSRF, and others ? Answer 'No' (without explaining why) if there are no possible issues. If there are security concerns or issues, start your answer with a short header, such as: 'Sensitive information exposure: ...', 'SQL injection: ...' etc. Explain your answer. Be specific and give examples if possible")
 {%- endif %}
 {%- if require_can_be_split_review %}
     can_be_split: List[SubPR] = Field(min_items=0, max_items=3, description="Can this PR, which contains {{ num_pr_files }} changed files in total, be divided into smaller sub-PRs with distinct tasks that can be reviewed and merged independently, regardless of the order ? Make sure that the sub-PRs are indeed independent, with no code dependencies between them, and that each sub-PR represent a meaningful independent task. Output an empty list if the PR code does not need to be split.")
 {%- endif %}
-{%- if num_code_suggestions > 0 %}
-
-class CodeSuggestion(BaseModel):
-    relevant_file: str = Field(description="The full file path of the relevant file")
-    language: str = Field(description="The programming language of the relevant file")
-    suggestion: str = Field(description="a concrete suggestion for meaningfully improving the new PR code. Also describe how, specifically, the suggestion can be applied to new PR code. Add tags with importance measure that matches each suggestion ('important' or 'medium'). Do not make suggestions for updating or adding docstrings, renaming PR title and description, or linter like.")
-    relevant_line: str = Field(description="a single code line taken from the relevant file, to which the suggestion applies. The code line should start with a '+'. Make sure to output the line exactly as it appears in the relevant file")
-{%- endif %}
-{%- if num_code_suggestions > 0 %}
 
 class PRReview(BaseModel):
     review: Review
-    code_feedback: List[CodeSuggestion]
-{%- else %}
-
-
-class PRReview(BaseModel):
-    review: Review
-{%- endif %}
 =====
 
 
@@ -185,18 +155,6 @@ review:
     title: ...
   - ...
 {%- endif %}
-
-{%- if num_code_suggestions > 0 %}
-code_feedback:
-- relevant_file: |
-    directory/xxx.py
-  language: |
-    python
-  suggestion: |
-    xxx [important]
-  relevant_line: |
-    xxx
-{%- endif %}
 ```
 
 Answer should be a valid YAML, and nothing else. Each YAML output MUST be after a newline, with proper indent, and block scalar indicator ('|')
@@ -263,6 +221,59 @@ The PR code diff:
 ======
 
 
+{%- if duplicate_prompt_examples %}
+
+
+Example output:
+```yaml
+review:
+{%- if related_tickets %}
+  ticket_compliance_check:
+    - ticket_url: |
+        ...
+      ticket_requirements: |
+        ...
+      fully_compliant_requirements: |
+        ...
+      not_compliant_requirements: |
+        ...
+      overall_compliance_level: |
+        ...
+{%- endif %}
+{%- if require_estimate_effort_to_review %}
+  estimated_effort_to_review_[1-5]: |
+    3
+{%- endif %}
+{%- if require_score %}
+  score: 89
+{%- endif %}
+  relevant_tests: |
+    No
+  key_issues_to_review:
+    - relevant_file: |
+        ...
+      issue_header: |
+        ...
+      issue_content: |
+        ...
+      start_line: ...
+      end_line: ...
+    - ...
+  security_concerns: |
+    No
+{%- if require_can_be_split_review %}
+  can_be_split:
+  - relevant_files:
+    - ...
+    - ...
+    title: ...
+  - ...
+{%- endif %}
+```
+(replace '...' with the actual values)
+{%- endif %}
+
+
 Response (should be a valid YAML, and nothing else):
 ```yaml
 """

pr_agent/settings/pr_update_changelog_prompts.toml

@@ -1,9 +1,14 @@
 [pr_update_changelog_prompt]
 system="""You are a language model called PR-Changelog-Updater.
-Your task is to update the CHANGELOG.md file of the project, to shortly summarize important changes introduced in this PR (the '+' lines).
-- The output should match the existing CHANGELOG.md format, style and conventions, so it will look like a natural part of the file. For example, if previous changes were summarized in a single line, you should do the same.
-- Don't repeat previous changes. Generate only new content, that is not already in the CHANGELOG.md file.
-- Be general, and avoid specific details, files, etc. The output should be minimal, no more than 3-4 short lines. Ignore non-relevant subsections.
+Your task is to add a brief summary of this PR's changes to CHANGELOG.md file of the project:
+- Follow the file's existing format and style conventions like dates, section titles, etc.
+- Only add new changes (don't repeat existing entries)
+- Be general, and avoid specific details, files, etc. The output should be minimal, no more than 3-4 short lines.
+- Write only the new content to be added to CHANGELOG.md, without any introduction or summary. The content should appear as if it's a natural part of the existing file.
+{%- if pr_link %}
+- If relevant, convert the changelog main header into a clickable link using the PR URL '{{ pr_link }}'. Format: header [*][pr_link]
+{%- endif %}
+
 
 {%- if extra_instructions %}
 
@@ -47,16 +52,19 @@ The PR Git Diff:
 {{ diff|trim }}
 ======
 
+
 Current date:
 ```
 {{today}}
 ```
 
-The current CHANGELOG.md:
+
+The current 'CHANGELOG.md' file
 ======
 {{ changelog_file_str }}
 ======
 
 
 Response:
+```markdown
 """

pr_agent/tools/pr_code_suggestions.py

@@ -4,6 +4,7 @@ import difflib
 import re
 import textwrap
 import traceback
+from datetime import datetime
 from functools import partial
 from typing import Dict, List
 
@@ -21,7 +22,7 @@ from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import (AzureDevopsProvider, GithubProvider,
                                     GitLabProvider, get_git_provider,
                                     get_git_provider_with_context)
-from pr_agent.git_providers.git_provider import get_main_pr_language
+from pr_agent.git_providers.git_provider import get_main_pr_language, GitProvider
 from pr_agent.log import get_logger
 from pr_agent.servers.help import HelpMessage
 from pr_agent.tools.pr_description import insert_br_after_x_chars
@@ -81,6 +82,8 @@ class PRCodeSuggestions:
             "relevant_best_practices": "",
             "is_ai_metadata": get_settings().get("config.enable_ai_metadata", False),
             "focus_only_on_problems": get_settings().get("pr_code_suggestions.focus_only_on_problems", False),
+            "date": datetime.now().strftime('%Y-%m-%d'),
+            'duplicate_prompt_examples': get_settings().config.get('duplicate_prompt_examples', False),
         }
         self.pr_code_suggestions_prompt_system = get_settings().pr_code_suggestions_prompt.system
 
@@ -103,6 +106,8 @@ class PRCodeSuggestions:
             relevant_configs = {'pr_code_suggestions': dict(get_settings().pr_code_suggestions),
                                 'config': dict(get_settings().config)}
             get_logger().debug("Relevant configs", artifacts=relevant_configs)
+
+            # publish "Preparing suggestions..." comments
             if (get_settings().config.publish_output and get_settings().config.publish_output_progress and
                     not get_settings().config.get('is_auto_command', False)):
                 if self.git_provider.is_supported("gfm_markdown"):
@@ -110,33 +115,26 @@ class PRCodeSuggestions:
                 else:
                     self.git_provider.publish_comment("Preparing suggestions...", is_temporary=True)
 
+            # call the model to get the suggestions, and self-reflect on them
             if not self.is_extended:
-                data = await retry_with_fallback_models(self._prepare_prediction)
+                data = await retry_with_fallback_models(self._prepare_prediction, model_type=ModelType.REGULAR)
             else:
-                data = await retry_with_fallback_models(self._prepare_prediction_extended)
+                data = await retry_with_fallback_models(self._prepare_prediction_extended, model_type=ModelType.REGULAR)
             if not data:
                 data = {"code_suggestions": []}
+            self.data = data
 
+            # Handle the case where the PR has no suggestions
             if (data is None or 'code_suggestions' not in data or not data['code_suggestions']):
-                pr_body = "## PR Code Suggestions ✨\n\nNo code suggestions found for the PR."
-                get_logger().warning('No code suggestions found for the PR.')
-                if get_settings().config.publish_output and get_settings().config.publish_output_no_suggestions:
-                    get_logger().debug(f"PR output", artifact=pr_body)
-                    if self.progress_response:
-                        self.git_provider.edit_comment(self.progress_response, body=pr_body)
-                    else:
-                        self.git_provider.publish_comment(pr_body)
-                else:
-                    get_settings().data = {"artifact": ""}
+                await self.publish_no_suggestions()
                 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'])
-
+            # publish the suggestions
             if get_settings().config.publish_output:
+                # If a temporary comment was published, remove it
                 self.git_provider.remove_initial_comment()
+
+                # Publish table summarized suggestions
                 if ((not get_settings().pr_code_suggestions.commitable_code_suggestions) and
                         self.git_provider.is_supported("gfm_markdown")):
 
@@ -146,10 +144,7 @@ class PRCodeSuggestions:
 
                     # require self-review
                     if get_settings().pr_code_suggestions.demand_code_suggestions_self_review:
-                        text = get_settings().pr_code_suggestions.code_suggestions_self_review_text
-                        pr_body += f"\n\n- [ ]  {text}"
-                        if get_settings().pr_code_suggestions.approve_pr_on_self_review:
-                            pr_body += ' <!-- approve pr self-review -->'
+                        pr_body = await self.add_self_review_text(pr_body)
 
                     # add usage guide
                     if (get_settings().pr_code_suggestions.enable_chat_text and get_settings().config.is_auto_command
@@ -165,13 +160,13 @@ class PRCodeSuggestions:
                         pr_body += show_relevant_configurations(relevant_section='pr_code_suggestions')
 
                     # publish the PR comment
-                    if get_settings().pr_code_suggestions.persistent_comment:
-                        final_update_message = False
-                        self.publish_persistent_comment_with_history(pr_body,
+                    if get_settings().pr_code_suggestions.persistent_comment: # true by default
+                        self.publish_persistent_comment_with_history(self.git_provider,
+                                                                     pr_body,
                                                                      initial_header="## PR Code Suggestions ✨",
                                                                      update_header=True,
                                                                      name="suggestions",
-                                                                     final_update_message=final_update_message,
+                                                                     final_update_message=False,
                                                                      max_previous_comments=get_settings().pr_code_suggestions.max_history_len,
                                                                      progress_response=self.progress_response)
                     else:
@@ -182,29 +177,15 @@ class PRCodeSuggestions:
 
                     # dual publishing mode
                     if int(get_settings().pr_code_suggestions.dual_publishing_score_threshold) > 0:
-                        data_above_threshold = {'code_suggestions': []}
-                        try:
-                            for suggestion in data['code_suggestions']:
-                                if int(suggestion.get('score', 0)) >= int(get_settings().pr_code_suggestions.dual_publishing_score_threshold) \
-                                        and suggestion.get('improved_code'):
-                                    data_above_threshold['code_suggestions'].append(suggestion)
-                                    if not data_above_threshold['code_suggestions'][-1]['existing_code']:
-                                        get_logger().info(f'Identical existing and improved code for dual publishing found')
-                                        data_above_threshold['code_suggestions'][-1]['existing_code'] = suggestion[
-                                            'improved_code']
-                            if data_above_threshold['code_suggestions']:
-                                get_logger().info(
-                                    f"Publishing {len(data_above_threshold['code_suggestions'])} suggestions in dual publishing mode")
-                                self.push_inline_code_suggestions(data_above_threshold)
-                        except Exception as e:
-                            get_logger().error(f"Failed to publish dual publishing suggestions, error: {e}")
+                        await self.dual_publishing(data)
                 else:
-                    self.push_inline_code_suggestions(data)
+                    await self.push_inline_code_suggestions(data)
                     if self.progress_response:
                         self.git_provider.remove_comment(self.progress_response)
             else:
                 get_logger().info('Code suggestions generated for PR, but not published since publish_output is False.')
-                get_settings().data = {"artifact": data}
+                pr_body = self.generate_summarized_suggestions(data)
+                get_settings().data = {"artifact": pr_body}
                 return
         except Exception as e:
             get_logger().error(f"Failed to generate code suggestions for PR, error: {e}",
@@ -217,47 +198,108 @@ class PRCodeSuggestions:
                         self.git_provider.remove_initial_comment()
                         self.git_provider.publish_comment(f"Failed to generate code suggestions for PR")
                     except Exception as e:
-                        pass
+                        get_logger().exception(f"Failed to update persistent review, error: {e}")
 
-    def publish_persistent_comment_with_history(self, pr_comment: str,
+    async def add_self_review_text(self, pr_body):
+        text = get_settings().pr_code_suggestions.code_suggestions_self_review_text
+        pr_body += f"\n\n- [ ]  {text}"
+        approve_pr_on_self_review = get_settings().pr_code_suggestions.approve_pr_on_self_review
+        fold_suggestions_on_self_review = get_settings().pr_code_suggestions.fold_suggestions_on_self_review
+        if approve_pr_on_self_review and not fold_suggestions_on_self_review:
+            pr_body += ' <!-- approve pr self-review -->'
+        elif fold_suggestions_on_self_review and not approve_pr_on_self_review:
+            pr_body += ' <!-- fold suggestions self-review -->'
+        else:
+            pr_body += ' <!-- approve and fold suggestions self-review -->'
+        return pr_body
+
+    async def publish_no_suggestions(self):
+        pr_body = "## PR Code Suggestions ✨\n\nNo code suggestions found for the PR."
+        if get_settings().config.publish_output and get_settings().config.publish_output_no_suggestions:
+            get_logger().warning('No code suggestions found for the PR.')
+            get_logger().debug(f"PR output", artifact=pr_body)
+            if self.progress_response:
+                self.git_provider.edit_comment(self.progress_response, body=pr_body)
+            else:
+                self.git_provider.publish_comment(pr_body)
+        else:
+            get_settings().data = {"artifact": ""}
+
+    async def dual_publishing(self, data):
+        data_above_threshold = {'code_suggestions': []}
+        try:
+            for suggestion in data['code_suggestions']:
+                if int(suggestion.get('score', 0)) >= int(
+                        get_settings().pr_code_suggestions.dual_publishing_score_threshold) \
+                        and suggestion.get('improved_code'):
+                    data_above_threshold['code_suggestions'].append(suggestion)
+                    if not data_above_threshold['code_suggestions'][-1]['existing_code']:
+                        get_logger().info(f'Identical existing and improved code for dual publishing found')
+                        data_above_threshold['code_suggestions'][-1]['existing_code'] = suggestion[
+                            'improved_code']
+            if data_above_threshold['code_suggestions']:
+                get_logger().info(
+                    f"Publishing {len(data_above_threshold['code_suggestions'])} suggestions in dual publishing mode")
+                await self.push_inline_code_suggestions(data_above_threshold)
+        except Exception as e:
+            get_logger().error(f"Failed to publish dual publishing suggestions, error: {e}")
+
+    @staticmethod
+    def publish_persistent_comment_with_history(git_provider: GitProvider,
+                                                pr_comment: str,
                                                 initial_header: str,
                                                 update_header: bool = True,
                                                 name='review',
                                                 final_update_message=True,
                                                 max_previous_comments=4,
-                                                progress_response=None):
+                                                progress_response=None,
+                                                only_fold=False):
 
-        if isinstance(self.git_provider, AzureDevopsProvider): # get_latest_commit_url is not supported yet
+        def _extract_link(comment_text: str):
+            r = re.compile(r"<!--.*?-->")
+            match = r.search(comment_text)
+
+            up_to_commit_txt = ""
+            if match:
+                up_to_commit_txt = f" up to commit {match.group(0)[4:-3].strip()}"
+            return up_to_commit_txt
+
+        if isinstance(git_provider, AzureDevopsProvider): # get_latest_commit_url is not supported yet
             if progress_response:
-                self.git_provider.edit_comment(progress_response, pr_comment)
+                git_provider.edit_comment(progress_response, pr_comment)
+                new_comment = progress_response
             else:
-                self.git_provider.publish_comment(pr_comment)
-            return
+                new_comment = git_provider.publish_comment(pr_comment)
+            return new_comment
 
         history_header = f"#### Previous suggestions\n"
-        last_commit_num = self.git_provider.get_latest_commit_url().split('/')[-1][:7]
-        latest_suggestion_header = f"Latest suggestions up to {last_commit_num}"
+        last_commit_num = git_provider.get_latest_commit_url().split('/')[-1][:7]
+        if only_fold: # A user clicked on the 'self-review' checkbox
+            text = get_settings().pr_code_suggestions.code_suggestions_self_review_text
+            latest_suggestion_header = f"\n\n- [x]  {text}"
+        else:
+            latest_suggestion_header = f"Latest suggestions up to {last_commit_num}"
         latest_commit_html_comment = f"<!-- {last_commit_num} -->"
         found_comment = None
 
         if max_previous_comments > 0:
             try:
-                prev_comments = list(self.git_provider.get_issue_comments())
+                prev_comments = list(git_provider.get_issue_comments())
                 for comment in prev_comments:
                     if comment.body.startswith(initial_header):
                         prev_suggestions = comment.body
                         found_comment = comment
-                        comment_url = self.git_provider.get_comment_url(comment)
+                        comment_url = git_provider.get_comment_url(comment)
 
                         if history_header.strip() not in comment.body:
                             # no history section
                             # extract everything between <table> and </table> in comment.body including <table> and </table>
                             table_index = comment.body.find("<table>")
                             if table_index == -1:
-                                self.git_provider.edit_comment(comment, pr_comment)
+                                git_provider.edit_comment(comment, pr_comment)
                                 continue
                             # find http link from comment.body[:table_index]
-                            up_to_commit_txt = self.extract_link(comment.body[:table_index])
+                            up_to_commit_txt = _extract_link(comment.body[:table_index])
                             prev_suggestion_table = comment.body[
                                                     table_index:comment.body.rfind("</table>") + len("</table>")]
 
@@ -278,7 +320,7 @@ class PRCodeSuggestions:
 
                             # get text after the latest_suggestion_header in comment.body
                             table_ind = latest_table.find("<table>")
-                            up_to_commit_txt = self.extract_link(latest_table[:table_ind])
+                            up_to_commit_txt = _extract_link(latest_table[:table_ind])
 
                             latest_table = latest_table[table_ind:latest_table.rfind("</table>") + len("</table>")]
                             # enforce max_previous_comments
@@ -305,11 +347,12 @@ class PRCodeSuggestions:
 
                         get_logger().info(f"Persistent mode - updating comment {comment_url} to latest {name} message")
                         if progress_response:  # publish to 'progress_response' comment, because it refreshes immediately
-                            self.git_provider.edit_comment(progress_response, pr_comment_updated)
-                            self.git_provider.remove_comment(comment)
+                            git_provider.edit_comment(progress_response, pr_comment_updated)
+                            git_provider.remove_comment(comment)
+                            comment = progress_response
                         else:
-                            self.git_provider.edit_comment(comment, pr_comment_updated)
-                        return
+                            git_provider.edit_comment(comment, pr_comment_updated)
+                        return comment
             except Exception as e:
                 get_logger().exception(f"Failed to update persistent review, error: {e}")
                 pass
@@ -318,9 +361,12 @@ class PRCodeSuggestions:
         body = pr_comment.replace(initial_header, "").strip()
         pr_comment = f"{initial_header}\n\n{latest_commit_html_comment}\n\n{body}\n\n"
         if progress_response:
-            self.git_provider.edit_comment(progress_response, pr_comment)
+            git_provider.edit_comment(progress_response, pr_comment)
+            new_comment = progress_response
         else:
-            self.git_provider.publish_comment(pr_comment)
+            new_comment = git_provider.publish_comment(pr_comment)
+        return new_comment
+
 
     def extract_link(self, s):
         r = re.compile(r"<!--.*?-->")
@@ -371,50 +417,7 @@ class PRCodeSuggestions:
         response_reflect = await self.self_reflect_on_suggestions(data["code_suggestions"],
                                                                   patches_diff, model=model_reflection)
         if response_reflect:
-            response_reflect_yaml = load_yaml(response_reflect)
-            code_suggestions_feedback = response_reflect_yaml["code_suggestions"]
-            if len(code_suggestions_feedback) == len(data["code_suggestions"]):
-                for i, suggestion in enumerate(data["code_suggestions"]):
-                    try:
-                        suggestion["score"] = code_suggestions_feedback[i]["suggestion_score"]
-                        suggestion["score_why"] = code_suggestions_feedback[i]["why"]
-
-                        if 'relevant_lines_start' not in suggestion:
-                            relevant_lines_start = code_suggestions_feedback[i].get('relevant_lines_start', -1)
-                            relevant_lines_end = code_suggestions_feedback[i].get('relevant_lines_end', -1)
-                            suggestion['relevant_lines_start'] = relevant_lines_start
-                            suggestion['relevant_lines_end'] = relevant_lines_end
-                            if relevant_lines_start < 0 or relevant_lines_end < 0:
-                                suggestion["score"] = 0
-
-                        try:
-                            if get_settings().config.publish_output:
-                                suggestion_statistics_dict = {'score': int(suggestion["score"]),
-                                                              'label': suggestion["label"].lower().strip()}
-                                get_logger().info(f"PR-Agent suggestions statistics",
-                                                  statistics=suggestion_statistics_dict, analytics=True)
-                        except Exception as e:
-                            get_logger().error(f"Failed to log suggestion statistics, error: {e}")
-                            pass
-
-                    except Exception as e:  #
-                        get_logger().error(f"Error processing suggestion score {i}",
-                                           artifact={"suggestion": suggestion,
-                                                     "code_suggestions_feedback": code_suggestions_feedback[i]})
-                        suggestion["score"] = 7
-                        suggestion["score_why"] = ""
-
-                    # if the before and after code is the same, clear one of them
-                    try:
-                        if suggestion['existing_code'] == suggestion['improved_code']:
-                            get_logger().debug(
-                                f"edited improved suggestion {i + 1}, because equal to existing code: {suggestion['existing_code']}")
-                            if get_settings().pr_code_suggestions.commitable_code_suggestions:
-                                suggestion['improved_code'] = ""  # we need 'existing_code' to locate the code in the PR
-                            else:
-                                suggestion['existing_code'] = ""
-                    except Exception as e:
-                        get_logger().error(f"Error processing suggestion {i + 1}, error: {e}")
+            await self.analyze_self_reflection_response(data, response_reflect)
         else:
             # get_logger().error(f"Could not self-reflect on suggestions. using default score 7")
             for i, suggestion in enumerate(data["code_suggestions"]):
@@ -423,6 +426,58 @@ class PRCodeSuggestions:
 
         return data
 
+    async def analyze_self_reflection_response(self, data, response_reflect):
+        response_reflect_yaml = load_yaml(response_reflect)
+        code_suggestions_feedback = response_reflect_yaml.get("code_suggestions", [])
+        if code_suggestions_feedback and len(code_suggestions_feedback) == len(data["code_suggestions"]):
+            for i, suggestion in enumerate(data["code_suggestions"]):
+                try:
+                    suggestion["score"] = code_suggestions_feedback[i]["suggestion_score"]
+                    suggestion["score_why"] = code_suggestions_feedback[i]["why"]
+
+                    if 'relevant_lines_start' not in suggestion:
+                        relevant_lines_start = code_suggestions_feedback[i].get('relevant_lines_start', -1)
+                        relevant_lines_end = code_suggestions_feedback[i].get('relevant_lines_end', -1)
+                        suggestion['relevant_lines_start'] = relevant_lines_start
+                        suggestion['relevant_lines_end'] = relevant_lines_end
+                        if relevant_lines_start < 0 or relevant_lines_end < 0:
+                            suggestion["score"] = 0
+
+                    try:
+                        if get_settings().config.publish_output:
+                            if not suggestion["score"]:
+                                score = -1
+                            else:
+                                score = int(suggestion["score"])
+                            label = suggestion["label"].lower().strip()
+                            label = label.replace('<br>', ' ')
+                            suggestion_statistics_dict = {'score': score,
+                                                          'label': label}
+                            get_logger().info(f"PR-Agent suggestions statistics",
+                                              statistics=suggestion_statistics_dict, analytics=True)
+                    except Exception as e:
+                        get_logger().error(f"Failed to log suggestion statistics, error: {e}")
+                        pass
+
+                except Exception as e:  #
+                    get_logger().error(f"Error processing suggestion score {i}",
+                                       artifact={"suggestion": suggestion,
+                                                 "code_suggestions_feedback": code_suggestions_feedback[i]})
+                    suggestion["score"] = 7
+                    suggestion["score_why"] = ""
+
+                # if the before and after code is the same, clear one of them
+                try:
+                    if suggestion['existing_code'] == suggestion['improved_code']:
+                        get_logger().debug(
+                            f"edited improved suggestion {i + 1}, because equal to existing code: {suggestion['existing_code']}")
+                        if get_settings().pr_code_suggestions.commitable_code_suggestions:
+                            suggestion['improved_code'] = ""  # we need 'existing_code' to locate the code in the PR
+                        else:
+                            suggestion['existing_code'] = ""
+                except Exception as e:
+                    get_logger().error(f"Error processing suggestion {i + 1}, error: {e}")
+
     @staticmethod
     def _truncate_if_needed(suggestion):
         max_code_suggestion_length = get_settings().get("PR_CODE_SUGGESTIONS.MAX_CODE_SUGGESTION_LENGTH", 0)
@@ -486,7 +541,7 @@ class PRCodeSuggestions:
 
         return data
 
-    def push_inline_code_suggestions(self, data):
+    async def push_inline_code_suggestions(self, data):
         code_suggestions = []
 
         if not data['code_suggestions']:
@@ -584,7 +639,9 @@ class PRCodeSuggestions:
                 patches_diff_lines = patches_diff.splitlines()
                 for i, line in enumerate(patches_diff_lines):
                     if line.strip():
-                        if line[0].isdigit():
+                        if line.isnumeric():
+                            patches_diff_lines[i] = ''
+                        elif line[0].isdigit():
                             # find the first letter in the line that starts with a valid letter
                             for j, char in enumerate(line):
                                 if not char.isdigit():
@@ -642,62 +699,6 @@ class PRCodeSuggestions:
             self.data = data = None
         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 = []
-        if not data:
-            return suggestion_list
-        for suggestion in data:
-            suggestion_list.append(suggestion)
-        data_sorted = [[]] * len(suggestion_list)
-
-        if len(suggestion_list) == 1:
-            return 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)
-            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:
-                max_len = max(
-                    len(data_sorted),
-                    int(get_settings().pr_code_suggestions.num_code_suggestions_per_chunk),
-                )
-                new_len = int(0.5 + max_len * get_settings().pr_code_suggestions.final_clip_factor)
-                if new_len < len(data_sorted):
-                    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
-
     def generate_summarized_suggestions(self, data: Dict) -> str:
         try:
             pr_body = "## PR Code Suggestions ✨\n\n"
@@ -813,7 +814,12 @@ class PRCodeSuggestions:
             get_logger().info(f"Failed to publish summarized code suggestions, error: {e}")
             return ""
 
-    async def self_reflect_on_suggestions(self, suggestion_list: List, patches_diff: str, model: str) -> str:
+    async def self_reflect_on_suggestions(self,
+                                          suggestion_list: List,
+                                          patches_diff: str,
+                                          model: str,
+                                          prev_suggestions_str: str = "",
+                                          dedicated_prompt: str = "") -> str:
         if not suggestion_list:
             return ""
 
@@ -826,13 +832,22 @@ class PRCodeSuggestions:
                          'suggestion_str': suggestion_str,
                          "diff": patches_diff,
                          'num_code_suggestions': len(suggestion_list),
-                         "is_ai_metadata": get_settings().get("config.enable_ai_metadata", False)}
+                         'prev_suggestions_str': prev_suggestions_str,
+                         "is_ai_metadata": get_settings().get("config.enable_ai_metadata", False),
+                         'duplicate_prompt_examples': get_settings().config.get('duplicate_prompt_examples', False)}
             environment = Environment(undefined=StrictUndefined)
-            system_prompt_reflect = environment.from_string(
-                get_settings().pr_code_suggestions_reflect_prompt.system).render(
-                variables)
-            user_prompt_reflect = environment.from_string(
-                get_settings().pr_code_suggestions_reflect_prompt.user).render(variables)
+
+            if dedicated_prompt:
+                system_prompt_reflect = environment.from_string(
+                    get_settings().get(dedicated_prompt).system).render(variables)
+                user_prompt_reflect = environment.from_string(
+                    get_settings().get(dedicated_prompt).user).render(variables)
+            else:
+                system_prompt_reflect = environment.from_string(
+                    get_settings().pr_code_suggestions_reflect_prompt.system).render(variables)
+                user_prompt_reflect = environment.from_string(
+                    get_settings().pr_code_suggestions_reflect_prompt.user).render(variables)
+
             with get_logger().contextualize(command="self_reflect_on_suggestions"):
                 response_reflect, finish_reason_reflect = await self.ai_handler.chat_completion(model=model,
                                                                                                 system=system_prompt_reflect,
@@ -840,4 +855,4 @@ class PRCodeSuggestions:
         except Exception as e:
             get_logger().info(f"Could not reflect on suggestions, error: {e}")
             return ""
-        return response_reflect
+        return response_reflect

pr_agent/tools/pr_config.py

@@ -38,12 +38,15 @@ class PRConfig:
             if (header.lower().startswith("pr_") or header.lower().startswith("config")) and header.lower() in configuration_headers
         }
 
-        skip_keys = ['ai_disclaimer', 'ai_disclaimer_title', 'ANALYTICS_FOLDER', 'secret_provider', "skip_keys",
-                          'trial_prefix_message', 'no_eligible_message', 'identity_provider', 'ALLOWED_REPOS',
-                          'APP_NAME']
+        skip_keys = ['ai_disclaimer', 'ai_disclaimer_title', 'ANALYTICS_FOLDER', 'secret_provider', "skip_keys", "app_id", "redirect",
+                     'trial_prefix_message', 'no_eligible_message', 'identity_provider', 'ALLOWED_REPOS',
+                     'APP_NAME', 'PERSONAL_ACCESS_TOKEN', 'shared_secret', 'key', 'AWS_ACCESS_KEY_ID', 'AWS_SECRET_ACCESS_KEY', 'user_token',
+                     'private_key', 'private_key_id', 'client_id', 'client_secret', 'token', 'bearer_token']
         extra_skip_keys = get_settings().config.get('config.skip_keys', [])
         if extra_skip_keys:
             skip_keys.extend(extra_skip_keys)
+        skip_keys_lower = [key.lower() for key in skip_keys]
+
 
         markdown_text = "<details> <summary><strong>🛠️ PR-Agent Configurations:</strong></summary> \n\n"
         markdown_text += f"\n\n```yaml\n\n"
@@ -52,7 +55,7 @@ class PRConfig:
                 markdown_text += "\n\n"
                 markdown_text += f"==================== {header} ===================="
             for key, value in configs.items():
-                if key in skip_keys:
+                if key.lower() in skip_keys_lower:
                     continue
                 markdown_text += f"\n{header.lower()}.{key.lower()} = {repr(value) if isinstance(value, str) else value}"
                 markdown_text += "  "

pr_agent/tools/pr_description.py

@@ -1,6 +1,7 @@
 import asyncio
 import copy
 import re
+import traceback
 from functools import partial
 from typing import List, Tuple
 
@@ -57,6 +58,7 @@ class PRDescription:
         self.ai_handler.main_pr_language = self.main_pr_language
 
         # Initialize the variables dictionary
+        self.COLLAPSIBLE_FILE_LIST_THRESHOLD = get_settings().pr_description.get("collapsible_file_list_threshold", 8)
         self.vars = {
             "title": self.git_provider.pr.title,
             "branch": self.git_provider.get_pr_branch(),
@@ -69,6 +71,8 @@ class PRDescription:
             "custom_labels_class": "",  # will be filled if necessary in 'set_custom_labels' function
             "enable_semantic_files_types": get_settings().pr_description.enable_semantic_files_types,
             "related_tickets": "",
+            "include_file_summary_changes": len(self.git_provider.get_diff_files()) <= self.COLLAPSIBLE_FILE_LIST_THRESHOLD,
+            'duplicate_prompt_examples': get_settings().config.get('duplicate_prompt_examples', False),
         }
 
         self.user_description = self.git_provider.get_user_description()
@@ -85,7 +89,6 @@ class PRDescription:
         self.patches_diff = None
         self.prediction = None
         self.file_label_dict = None
-        self.COLLAPSIBLE_FILE_LIST_THRESHOLD = 8
 
     async def run(self):
         try:
@@ -99,7 +102,7 @@ class PRDescription:
             # ticket extraction if exists
             await extract_and_cache_pr_tickets(self.git_provider, self.vars)
 
-            await retry_with_fallback_models(self._prepare_prediction, ModelType.TURBO)
+            await retry_with_fallback_models(self._prepare_prediction, ModelType.WEAK)
 
             if self.prediction:
                 self._prepare_data()
@@ -114,6 +117,8 @@ class PRDescription:
             pr_labels, pr_file_changes = [], []
             if get_settings().pr_description.publish_labels:
                 pr_labels = self._prepare_labels()
+            else:
+                get_logger().debug(f"Publishing labels disabled")
 
             if get_settings().pr_description.use_description_markers:
                 pr_title, pr_body, changes_walkthrough, pr_file_changes = self._prepare_pr_answer_with_markers()
@@ -129,14 +134,25 @@ class PRDescription:
                 pr_body += "<hr>\n\n<details> <summary><strong>✨ Describe tool usage guide:</strong></summary><hr> \n\n"
                 pr_body += HelpMessage.get_describe_usage_guide()
                 pr_body += "\n</details>\n"
-            elif get_settings().pr_description.enable_help_comment:
-                pr_body += '\n\n___\n\n> 💡 **PR-Agent usage**: Comment `/help "your question"` on any pull request to receive relevant information'
+            elif get_settings().pr_description.enable_help_comment and self.git_provider.is_supported("gfm_markdown"):
+                if isinstance(self.git_provider, GithubProvider):
+                    pr_body += ('\n\n___\n\n> <details> <summary>  Need help?</summary><li>Type <code>/help how to ...</code> '
+                                'in the comments thread for any questions about PR-Agent usage.</li><li>Check out the '
+                                '<a href="https://qodo-merge-docs.qodo.ai/usage-guide/">documentation</a> '
+                                'for more information.</li></details>')
+                else: # gitlab
+                    pr_body += ("\n\n___\n\n<details><summary>Need help?</summary>- Type <code>/help how to ...</code> in the comments "
+                                "thread for any questions about PR-Agent usage.<br>- Check out the "
+                                "<a href='https://qodo-merge-docs.qodo.ai/usage-guide/'>documentation</a> for more information.</details>")
+            # elif get_settings().pr_description.enable_help_comment:
+            #     pr_body += '\n\n___\n\n> 💡 **PR-Agent usage**: Comment `/help "your question"` on any pull request to receive relevant information'
 
             # Output the relevant configurations if enabled
             if get_settings().get('config', {}).get('output_relevant_configurations', False):
                 pr_body += show_relevant_configurations(relevant_section='pr_description')
 
             if get_settings().config.publish_output:
+
                 # publish labels
                 if get_settings().pr_description.publish_labels and pr_labels and self.git_provider.is_supported("get_labels"):
                     original_labels = self.git_provider.get_pr_labels(update=True)
@@ -164,43 +180,49 @@ class PRDescription:
                     self.git_provider.publish_description(pr_title, pr_body)
 
                     # publish final update message
-                    if (get_settings().pr_description.final_update_message):
+                    if (get_settings().pr_description.final_update_message and not get_settings().config.get('is_auto_command', False)):
                         latest_commit_url = self.git_provider.get_latest_commit_url()
                         if latest_commit_url:
                             pr_url = self.git_provider.get_pr_url()
                             update_comment = f"**[PR Description]({pr_url})** updated to latest commit ({latest_commit_url})"
                             self.git_provider.publish_comment(update_comment)
                 self.git_provider.remove_initial_comment()
+            else:
+                get_logger().info('PR description, but not published since publish_output is False.')
+                get_settings().data = {"artifact": pr_body}
+                return
         except Exception as e:
-            get_logger().error(f"Error generating PR description {self.pr_id}: {e}")
+            get_logger().error(f"Error generating PR description {self.pr_id}: {e}",
+                               artifact={"traceback": traceback.format_exc()})
 
         return ""
 
     async def _prepare_prediction(self, model: str) -> None:
         if get_settings().pr_description.use_description_markers and 'pr_agent:' not in self.user_description:
-            get_logger().info(
-                "Markers were enabled, but user description does not contain markers. skipping AI prediction")
+            get_logger().info("Markers were enabled, but user description does not contain markers. skipping AI prediction")
             return None
 
         large_pr_handling = get_settings().pr_description.enable_large_pr_handling and "pr_description_only_files_prompts" in get_settings()
-        output = get_pr_diff(self.git_provider, self.token_handler, model, large_pr_handling=large_pr_handling,
-                             return_remaining_files=True)
+        output = get_pr_diff(self.git_provider, self.token_handler, model, large_pr_handling=large_pr_handling, return_remaining_files=True)
         if isinstance(output, tuple):
             patches_diff, remaining_files_list = output
         else:
             patches_diff = output
             remaining_files_list = []
+
         if not large_pr_handling or patches_diff:
             self.patches_diff = patches_diff
             if patches_diff:
+                # generate the prediction
                 get_logger().debug(f"PR diff", artifact=self.patches_diff)
                 self.prediction = await self._get_prediction(model, patches_diff, prompt="pr_description_prompt")
-                if (remaining_files_list and 'pr_files' in self.prediction and 'label:' in self.prediction and
-                        get_settings().pr_description.mention_extra_files):
-                    get_logger().debug(f"Extending additional files, {len(remaining_files_list)} files")
-                    self.prediction = await self.extend_additional_files(remaining_files_list)
+
+                # extend the prediction with additional files not shown
+                if get_settings().pr_description.enable_semantic_files_types:
+                    self.prediction = await self.extend_uncovered_files(self.prediction)
             else:
-                get_logger().error(f"Error getting PR diff {self.pr_id}")
+                get_logger().error(f"Error getting PR diff {self.pr_id}",
+                                   artifact={"traceback": traceback.format_exc()})
                 self.prediction = None
         else:
             # get the diff in multiple patches, with the token handler only for the files prompt
@@ -285,43 +307,81 @@ class PRDescription:
                                                             prompt="pr_description_only_description_prompts")
             prediction_headers = prediction_headers.strip().removeprefix('```yaml').strip('`').strip()
 
-            # manually add extra files to final prediction
-            MAX_EXTRA_FILES_TO_OUTPUT = 100
-            if get_settings().pr_description.mention_extra_files:
-                for i, file in enumerate(remaining_files_list):
-                    extra_file_yaml = f"""\
-- filename: |
-    {file}
-  changes_summary: |
-    ...
-  changes_title: |
-    ...
-  label: |
-    additional files (token-limit)
-"""
-                    files_walkthrough = files_walkthrough.strip() + "\n" + extra_file_yaml.strip()
-                    if i >= MAX_EXTRA_FILES_TO_OUTPUT:
-                        files_walkthrough += f"""\
-extra_file_yaml =
-- filename: |
-    Additional {len(remaining_files_list) - MAX_EXTRA_FILES_TO_OUTPUT} files not shown
-  changes_summary: |
-    ...
-  changes_title: |
-    ...
-  label: |
-    additional files (token-limit)
-"""
-                        break
+            # extend the tables with the files not shown
+            files_walkthrough_extended = await self.extend_uncovered_files(files_walkthrough)
 
             # final processing
-            self.prediction = prediction_headers + "\n" + "pr_files:\n" + files_walkthrough
+            self.prediction = prediction_headers + "\n" + "pr_files:\n" + files_walkthrough_extended
             if not load_yaml(self.prediction, keys_fix_yaml=self.keys_fix):
                 get_logger().error(f"Error getting valid YAML in large PR handling for describe {self.pr_id}")
                 if load_yaml(prediction_headers, keys_fix_yaml=self.keys_fix):
                     get_logger().debug(f"Using only headers for describe {self.pr_id}")
                     self.prediction = prediction_headers
 
+    async def extend_uncovered_files(self, original_prediction: str) -> str:
+        try:
+            prediction = original_prediction
+
+            # get the original prediction filenames
+            original_prediction_loaded = load_yaml(original_prediction, keys_fix_yaml=self.keys_fix)
+            if isinstance(original_prediction_loaded, list):
+                original_prediction_dict = {"pr_files": original_prediction_loaded}
+            else:
+                original_prediction_dict = original_prediction_loaded
+            filenames_predicted = [file['filename'].strip() for file in original_prediction_dict.get('pr_files', [])]
+
+            # extend the prediction with additional files not included in the original prediction
+            pr_files = self.git_provider.get_diff_files()
+            prediction_extra = "pr_files:"
+            MAX_EXTRA_FILES_TO_OUTPUT = 100
+            counter_extra_files = 0
+            for file in pr_files:
+                if file.filename in filenames_predicted:
+                    continue
+
+                # add up to MAX_EXTRA_FILES_TO_OUTPUT files
+                counter_extra_files += 1
+                if counter_extra_files > MAX_EXTRA_FILES_TO_OUTPUT:
+                    extra_file_yaml = f"""\
+- filename: |
+    Additional files not shown
+  changes_title: |
+    ...
+  label: |
+    additional files
+"""
+                    prediction_extra = prediction_extra + "\n" + extra_file_yaml.strip()
+                    get_logger().debug(f"Too many remaining files, clipping to {MAX_EXTRA_FILES_TO_OUTPUT}")
+                    break
+
+                extra_file_yaml = f"""\
+- filename: |
+    {file.filename}
+  changes_title: |
+    ...
+  label: |
+    additional files
+"""
+                prediction_extra = prediction_extra + "\n" + extra_file_yaml.strip()
+
+            # merge the two dictionaries
+            if counter_extra_files > 0:
+                get_logger().info(f"Adding {counter_extra_files} unprocessed extra files to table prediction")
+                prediction_extra_dict = load_yaml(prediction_extra, keys_fix_yaml=self.keys_fix)
+                if isinstance(original_prediction_dict, dict) and isinstance(prediction_extra_dict, dict):
+                    original_prediction_dict["pr_files"].extend(prediction_extra_dict["pr_files"])
+                    new_yaml = yaml.dump(original_prediction_dict)
+                    if load_yaml(new_yaml, keys_fix_yaml=self.keys_fix):
+                        prediction = new_yaml
+                if isinstance(original_prediction, list):
+                    prediction = yaml.dump(original_prediction_dict["pr_files"])
+
+            return prediction
+        except Exception as e:
+            get_logger().error(f"Error extending uncovered files {self.pr_id}: {e}")
+            return original_prediction
+
+
     async def extend_additional_files(self, remaining_files_list) -> str:
         prediction = self.prediction
         try:
@@ -393,35 +453,44 @@ extra_file_yaml =
             self.data['pr_files'] = self.data.pop('pr_files')
 
     def _prepare_labels(self) -> List[str]:
-        pr_types = []
+        pr_labels = []
 
         # If the 'PR Type' key is present in the dictionary, split its value by comma and assign it to 'pr_types'
-        if 'labels' in self.data:
+        if 'labels' in self.data and self.data['labels']:
             if type(self.data['labels']) == list:
-                pr_types = self.data['labels']
+                pr_labels = self.data['labels']
             elif type(self.data['labels']) == str:
-                pr_types = self.data['labels'].split(',')
-        elif 'type' in self.data:
+                pr_labels = self.data['labels'].split(',')
+        elif 'type' in self.data and self.data['type'] and get_settings().pr_description.publish_labels:
             if type(self.data['type']) == list:
-                pr_types = self.data['type']
+                pr_labels = self.data['type']
             elif type(self.data['type']) == str:
-                pr_types = self.data['type'].split(',')
-        pr_types = [label.strip() for label in pr_types]
+                pr_labels = self.data['type'].split(',')
+        pr_labels = [label.strip() for label in pr_labels]
 
         # convert lowercase labels to original case
         try:
             if "labels_minimal_to_labels_dict" in self.variables:
                 d: dict = self.variables["labels_minimal_to_labels_dict"]
-                for i, label_i in enumerate(pr_types):
+                for i, label_i in enumerate(pr_labels):
                     if label_i in d:
-                        pr_types[i] = d[label_i]
+                        pr_labels[i] = d[label_i]
         except Exception as e:
             get_logger().error(f"Error converting labels to original case {self.pr_id}: {e}")
-        return pr_types
+        return pr_labels
 
     def _prepare_pr_answer_with_markers(self) -> Tuple[str, str, str, List[dict]]:
         get_logger().info(f"Using description marker replacements {self.pr_id}")
-        title = self.vars["title"]
+
+        # Remove the 'PR Title' key from the dictionary
+        ai_title = self.data.pop('title', self.vars["title"])
+        if (not get_settings().pr_description.generate_ai_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
+      
         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"
@@ -430,7 +499,11 @@ extra_file_yaml =
 
         ai_type = self.data.get('type')
         if ai_type and not re.search(r'<!--\s*pr_agent:type\s*-->', body):
-            pr_type = f"{ai_header}{ai_type}"
+            if isinstance(ai_type, list):
+                pr_types = [f"{ai_header}{t}" for t in ai_type]
+                pr_type = ','.join(pr_types)
+            else:
+                pr_type = f"{ai_header}{ai_type}"
             body = body.replace('pr_agent:type', pr_type)
 
         ai_summary = self.data.get('description')
@@ -507,6 +580,11 @@ extra_file_yaml =
             elif 'pr_files' in key.lower() and get_settings().pr_description.enable_semantic_files_types:
                 changes_walkthrough, pr_file_changes = self.process_pr_files_prediction(changes_walkthrough, value)
                 changes_walkthrough = f"{PRDescriptionHeader.CHANGES_WALKTHROUGH.value}\n{changes_walkthrough}"
+            elif key.lower().strip() == 'description':
+                if isinstance(value, list):
+                    value = ', '.join(v.rstrip() for v in value)
+                value = value.replace('\n-', '\n\n-').strip() # makes the bullet points more readable by adding double space
+                pr_body += f"{value}\n"
             else:
                 # if the value is a list, join its items by comma
                 if isinstance(value, list):
@@ -524,14 +602,18 @@ extra_file_yaml =
             return file_label_dict
         for file in self.data['pr_files']:
             try:
-                required_fields = ['changes_summary', 'changes_title', 'filename', 'label']
+                required_fields = ['changes_title', 'filename', 'label']
                 if not all(field in file for field in required_fields):
                     # can happen for example if a YAML generation was interrupted in the middle (no more tokens)
                     get_logger().warning(f"Missing required fields in file label dict {self.pr_id}, skipping file",
                                          artifact={"file": file})
                     continue
+                if not file.get('changes_title'):
+                    get_logger().warning(f"Empty changes title or summary in file label dict {self.pr_id}, skipping file",
+                                         artifact={"file": file})
+                    continue
                 filename = file['filename'].replace("'", "`").replace('"', '`')
-                changes_summary = file['changes_summary']
+                changes_summary = file.get('changes_summary', "").strip()
                 changes_title = file['changes_title'].strip()
                 label = file.get('label').strip().lower()
                 if label not in file_label_dict:
@@ -574,12 +656,14 @@ extra_file_yaml =
                 for filename, file_changes_title, file_change_description in list_tuples:
                     filename = filename.replace("'", "`").rstrip()
                     filename_publish = filename.split("/")[-1]
-
-                    file_changes_title_code = f"<code>{file_changes_title}</code>"
-                    file_changes_title_code_br = insert_br_after_x_chars(file_changes_title_code, x=(delta - 5)).strip()
-                    if len(file_changes_title_code_br) < (delta - 5):
-                        file_changes_title_code_br += "&nbsp; " * ((delta - 5) - len(file_changes_title_code_br))
-                    filename_publish = f"<strong>{filename_publish}</strong><dd>{file_changes_title_code_br}</dd>"
+                    if file_changes_title and file_changes_title.strip() != "...":
+                        file_changes_title_code = f"<code>{file_changes_title}</code>"
+                        file_changes_title_code_br = insert_br_after_x_chars(file_changes_title_code, x=(delta - 5)).strip()
+                        if len(file_changes_title_code_br) < (delta - 5):
+                            file_changes_title_code_br += "&nbsp; " * ((delta - 5) - len(file_changes_title_code_br))
+                        filename_publish = f"<strong>{filename_publish}</strong><dd>{file_changes_title_code_br}</dd>"
+                    else:
+                        filename_publish = f"<strong>{filename_publish}</strong>"
                     diff_plus_minus = ""
                     delta_nbsp = ""
                     diff_files = self.git_provider.get_diff_files()
@@ -588,6 +672,8 @@ extra_file_yaml =
                             num_plus_lines = f.num_plus_lines
                             num_minus_lines = f.num_minus_lines
                             diff_plus_minus += f"+{num_plus_lines}/-{num_minus_lines}"
+                            if len(diff_plus_minus) > 12 or diff_plus_minus == "+0/-0":
+                                diff_plus_minus = "[link]"
                             delta_nbsp = "&nbsp; " * max(0, (8 - len(diff_plus_minus)))
                             break
 
@@ -596,9 +682,40 @@ extra_file_yaml =
                     if hasattr(self.git_provider, 'get_line_link'):
                         filename = filename.strip()
                         link = self.git_provider.get_line_link(filename, relevant_line_start=-1)
+                    if (not link or not diff_plus_minus) and ('additional files' not in filename.lower()):
+                        get_logger().warning(f"Error getting line link for '{filename}'")
+                        continue
 
+                    # Add file data to the PR body
                     file_change_description_br = insert_br_after_x_chars(file_change_description, x=(delta - 5))
-                    pr_body += f"""
+                    pr_body = self.add_file_data(delta_nbsp, diff_plus_minus, file_change_description_br, filename,
+                                                 filename_publish, link, pr_body)
+
+                # Close the collapsible file list
+                if use_collapsible_file_list:
+                    pr_body += """</table></details></td></tr>"""
+                else:
+                    pr_body += """</table></td></tr>"""
+            pr_body += """</tr></tbody></table>"""
+
+        except Exception as e:
+            get_logger().error(f"Error processing pr files to markdown {self.pr_id}: {str(e)}")
+            pass
+        return pr_body, pr_comments
+
+    def add_file_data(self, delta_nbsp, diff_plus_minus, file_change_description_br, filename, filename_publish, link,
+                      pr_body) -> str:
+
+        if not file_change_description_br:
+            pr_body += f"""
+<tr>
+  <td>{filename_publish}</td>
+  <td><a href="{link}">{diff_plus_minus}</a>{delta_nbsp}</td>
+
+</tr>
+"""
+        else:
+            pr_body += f"""
 <tr>
   <td>
     <details>
@@ -618,17 +735,7 @@ extra_file_yaml =
 
 </tr>
 """
-                if use_collapsible_file_list:
-                    pr_body += """</table></details></td></tr>"""
-                else:
-                    pr_body += """</table></td></tr>"""
-            pr_body += """</tr></tbody></table>"""
-
-        except Exception as e:
-            get_logger().error(f"Error processing pr files to markdown {self.pr_id}: {e}")
-            pass
-        return pr_body, pr_comments
-
+        return pr_body
 
 def count_chars_without_html(string):
     if '<' not in string:
@@ -637,11 +744,14 @@ def count_chars_without_html(string):
     return len(no_html_string)
 
 
-def insert_br_after_x_chars(text, x=70):
+def insert_br_after_x_chars(text: str, x=70):
     """
     Insert <br> into a string after a word that increases its length above x characters.
     Use proper HTML tags for code and new lines.
     """
+
+    if not text:
+        return ""
     if count_chars_without_html(text) < x:
         return text
 

pr_agent/tools/pr_help_message.py

@@ -114,7 +114,7 @@ class PRHelpMessage:
                 self.vars['snippets'] = docs_prompt.strip()
 
                 # run the AI model
-                response = await retry_with_fallback_models(self._prepare_prediction, model_type=ModelType.REGULAR)
+                response = await retry_with_fallback_models(self._prepare_prediction, model_type=ModelType.WEAK)
                 response_yaml = load_yaml(response)
                 response_str = response_yaml.get('response')
                 relevant_sections = response_yaml.get('relevant_sections')
@@ -174,10 +174,11 @@ class PRHelpMessage:
                 tool_names.append(f"[IMPROVE COMPONENT]({base_path}/improve_component/) 💎")
                 tool_names.append(f"[ANALYZE]({base_path}/analyze/) 💎")
                 tool_names.append(f"[ASK]({base_path}/ask/)")
+                tool_names.append(f"[SIMILAR ISSUE]({base_path}/similar_issues/)")
                 tool_names.append(f"[GENERATE CUSTOM LABELS]({base_path}/custom_labels/) 💎")
                 tool_names.append(f"[CI FEEDBACK]({base_path}/ci_feedback/) 💎")
                 tool_names.append(f"[CUSTOM PROMPT]({base_path}/custom_prompt/) 💎")
-                tool_names.append(f"[SIMILAR ISSUE]({base_path}/similar_issues/)")
+                tool_names.append(f"[IMPLEMENT]({base_path}/implement/) 💎")
 
                 descriptions = []
                 descriptions.append("Generates PR description - title, type, summary, code walkthrough and labels")
@@ -189,10 +190,11 @@ class PRHelpMessage:
                 descriptions.append("Code suggestions for a specific component that changed in the PR")
                 descriptions.append("Identifies code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component")
                 descriptions.append("Answering free-text questions about the PR")
+                descriptions.append("Automatically retrieves and presents similar issues")
                 descriptions.append("Generates custom labels for the PR, based on specific guidelines defined by the user")
                 descriptions.append("Generates feedback and analysis for a failed CI job")
                 descriptions.append("Generates custom suggestions for improving the PR code, derived only from a specific guidelines prompt defined by the user")
-                descriptions.append("Automatically retrieves and presents similar issues")
+                descriptions.append("Generates implementation code from review suggestions")
 
                 commands  =[]
                 commands.append("`/describe`")
@@ -204,10 +206,11 @@ class PRHelpMessage:
                 commands.append("`/improve_component`")
                 commands.append("`/analyze`")
                 commands.append("`/ask`")
+                commands.append("`/similar_issue`")
                 commands.append("`/generate_labels`")
                 commands.append("`/checks`")
                 commands.append("`/custom_prompt`")
-                commands.append("`/similar_issue`")
+                commands.append("`/implement`")
 
                 checkbox_list = []
                 checkbox_list.append(" - [ ] Run <!-- /describe -->")
@@ -226,13 +229,14 @@ class PRHelpMessage:
                 checkbox_list.append("[*]")
                 checkbox_list.append("[*]")
                 checkbox_list.append("[*]")
+                checkbox_list.append("[*]")
 
                 if isinstance(self.git_provider, GithubProvider) and not get_settings().config.get('disable_checkboxes', False):
                     pr_comment += f"<table><tr align='left'><th align='left'>Tool</th><th align='left'>Description</th><th align='left'>Trigger Interactively :gem:</th></tr>"
                     for i in range(len(tool_names)):
                         pr_comment += f"\n<tr><td align='left'>\n\n<strong>{tool_names[i]}</strong></td>\n<td>{descriptions[i]}</td>\n<td>\n\n{checkbox_list[i]}\n</td></tr>"
                     pr_comment += "</table>\n\n"
-                    pr_comment += f"""\n\n(1) Note that each tool be [triggered automatically](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#github-app-automatic-tools-when-a-new-pr-is-opened) when a new PR is opened, or called manually by [commenting on a PR](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#online-usage)."""
+                    pr_comment += f"""\n\n(1) Note that each tool can be [triggered automatically](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#github-app-automatic-tools-when-a-new-pr-is-opened) when a new PR is opened, or called manually by [commenting on a PR](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#online-usage)."""
                     pr_comment += f"""\n\n(2) Tools marked with [*] require additional parameters to be passed. For example, to invoke the `/ask` tool, you need to comment on a PR: `/ask "<question content>"`. See the relevant documentation for each tool for more details."""
                 elif isinstance(self.git_provider, BitbucketServerProvider):
                     # only support basic commands in BBDC
@@ -242,7 +246,7 @@ class PRHelpMessage:
                     for i in range(len(tool_names)):
                         pr_comment += f"\n<tr><td align='left'>\n\n<strong>{tool_names[i]}</strong></td><td>{commands[i]}</td><td>{descriptions[i]}</td></tr>"
                     pr_comment += "</table>\n\n"
-                    pr_comment += f"""\n\nNote that each tool be [invoked automatically](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/) when a new PR is opened, or called manually by [commenting on a PR](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#online-usage)."""
+                    pr_comment += f"""\n\nNote that each tool can be [invoked automatically](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/) when a new PR is opened, or called manually by [commenting on a PR](https://pr-agent-docs.codium.ai/usage-guide/automations_and_usage/#online-usage)."""
 
                 if get_settings().config.publish_output:
                     self.git_provider.publish_comment(pr_comment)

pr_agent/tools/pr_information_from_user.py

@@ -1,79 +0,0 @@
-import copy
-from functools import partial
-
-from jinja2 import Environment, StrictUndefined
-
-from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
-from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
-from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
-from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.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:
-    def __init__(self, pr_url: str, args: list = None,
-                 ai_handler: partial[BaseAiHandler,] = LiteLLMAIHandler):
-        self.git_provider = get_git_provider()(pr_url)
-        self.main_pr_language = get_main_pr_language(
-            self.git_provider.get_languages(), self.git_provider.get_files()
-        )
-        self.ai_handler = ai_handler()
-        self.ai_handler.main_pr_language = self.main_pr_language
-
-        self.vars = {
-            "title": self.git_provider.pr.title,
-            "branch": self.git_provider.get_pr_branch(),
-            "description": self.git_provider.get_pr_description(),
-            "language": self.main_pr_language,
-            "diff": "",  # empty diff for initial calculation
-            "commit_messages_str": self.git_provider.get_commit_messages(),
-        }
-        self.token_handler = TokenHandler(self.git_provider.pr,
-                                          self.vars,
-                                          get_settings().pr_information_from_user_prompt.system,
-                                          get_settings().pr_information_from_user_prompt.user)
-        self.patches_diff = None
-        self.prediction = None
-
-    async def run(self):
-        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)
-        get_logger().info('Preparing questions...')
-        pr_comment = self._prepare_pr_answer()
-        if get_settings().config.publish_output:
-            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):
-        get_logger().info('Getting PR diff...')
-        self.patches_diff = get_pr_diff(self.git_provider, self.token_handler, model)
-        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_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:
-            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=get_settings().config.temperature, system=system_prompt, user=user_prompt)
-        return response
-
-    def _prepare_pr_answer(self) -> str:
-        model_output = self.prediction.strip()
-        if get_settings().config.verbosity_level >= 2:
-            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_line_questions.py

@@ -79,13 +79,17 @@ class PR_LineQuestions:
                                                                                                line_end=line_end,
                                                                                                side=side)
         if self.patch_with_lines:
-            response = await retry_with_fallback_models(self._get_prediction, model_type=ModelType.TURBO)
+            model_answer = await retry_with_fallback_models(self._get_prediction, model_type=ModelType.WEAK)
+            # sanitize the answer so that no line will start with "/"
+            model_answer_sanitized = model_answer.strip().replace("\n/", "\n /")
+            if model_answer_sanitized.startswith("/"):
+                model_answer_sanitized = " " + model_answer_sanitized
 
             get_logger().info('Preparing answer...')
             if comment_id:
-                self.git_provider.reply_to_comment_from_comment_id(comment_id, response)
+                self.git_provider.reply_to_comment_from_comment_id(comment_id, model_answer_sanitized)
             else:
-                self.git_provider.publish_comment(response)
+                self.git_provider.publish_comment(model_answer_sanitized)
 
         return ""
 

pr_agent/tools/pr_questions.py

@@ -63,7 +63,7 @@ class PRQuestions:
         if img_path:
             get_logger().debug(f"Image path identified", artifact=img_path)
 
-        await retry_with_fallback_models(self._prepare_prediction, model_type=ModelType.TURBO)
+        await retry_with_fallback_models(self._prepare_prediction, model_type=ModelType.WEAK)
 
         pr_comment = self._prepare_pr_answer()
         get_logger().debug(f"PR output", artifact=pr_comment)
@@ -117,6 +117,16 @@ class PRQuestions:
         return response
 
     def _prepare_pr_answer(self) -> str:
+        model_answer = self.prediction.strip()
+        # sanitize the answer so that no line will start with "/"
+        model_answer_sanitized = model_answer.replace("\n/", "\n /")
+        if model_answer_sanitized.startswith("/"):
+            model_answer_sanitized = " " + model_answer_sanitized
+        if model_answer_sanitized != model_answer:
+            get_logger().debug(f"Sanitized model answer",
+                               artifact={"model_answer": model_answer, "sanitized_answer": model_answer_sanitized})
+
+
         answer_str = f"### **Ask**❓\n{self.question_str}\n\n"
-        answer_str += f"### **Answer:**\n{self.prediction.strip()}\n\n"
+        answer_str += f"### **Answer:**\n{model_answer_sanitized}\n\n"
         return answer_str

pr_agent/tools/pr_reviewer.py

@@ -86,7 +86,6 @@ class PRReviewer:
             "require_estimate_effort_to_review": get_settings().pr_reviewer.require_estimate_effort_to_review,
             'require_can_be_split_review': get_settings().pr_reviewer.require_can_be_split_review,
             'require_security_review': get_settings().pr_reviewer.require_security_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,
@@ -95,6 +94,7 @@ class PRReviewer:
             "enable_custom_labels": get_settings().config.enable_custom_labels,
             "is_ai_metadata":  get_settings().get("config.enable_ai_metadata", False),
             "related_tickets": get_settings().get('related_tickets', []),
+            'duplicate_prompt_examples': get_settings().config.get('duplicate_prompt_examples', False),
         }
 
         self.token_handler = TokenHandler(
@@ -148,7 +148,7 @@ class PRReviewer:
             if get_settings().config.publish_output and not get_settings().config.get('is_auto_command', False):
                 self.git_provider.publish_comment("Preparing review...", is_temporary=True)
 
-            await retry_with_fallback_models(self._prepare_prediction)
+            await retry_with_fallback_models(self._prepare_prediction, model_type=ModelType.REGULAR)
             if not self.prediction:
                 self.git_provider.remove_initial_comment()
                 return None
@@ -168,8 +168,10 @@ class PRReviewer:
                     self.git_provider.publish_comment(pr_review)
 
                 self.git_provider.remove_initial_comment()
-                if get_settings().pr_reviewer.inline_code_comments:
-                    self._publish_inline_code_comments()
+            else:
+                get_logger().info("Review output is not published")
+                get_settings().data = {"artifact": pr_review}
+                return
         except Exception as e:
             get_logger().error(f"Failed to review PR: {e}")
 
@@ -231,33 +233,6 @@ class PRReviewer:
             key_issues_to_review = data['review'].pop('key_issues_to_review')
             data['review']['key_issues_to_review'] = key_issues_to_review
 
-        if 'code_feedback' in data:
-            code_feedback = data['code_feedback']
-
-            # Filter out code suggestions that can be submitted as inline comments
-            if get_settings().pr_reviewer.inline_code_comments:
-                del data['code_feedback']
-            else:
-                for suggestion in code_feedback:
-                    if ('relevant_file' in suggestion) and (not suggestion['relevant_file'].startswith('``')):
-                        suggestion['relevant_file'] = f"``{suggestion['relevant_file']}``"
-
-                    if 'relevant_line' not in suggestion:
-                        suggestion['relevant_line'] = ''
-
-                    relevant_line_str = suggestion['relevant_line'].split('\n')[0]
-
-                    # removing '+'
-                    suggestion['relevant_line'] = relevant_line_str.lstrip('+').strip()
-
-                    # try to add line numbers link to code suggestions
-                    if hasattr(self.git_provider, 'generate_link_to_relevant_line_number'):
-                        link = self.git_provider.generate_link_to_relevant_line_number(suggestion)
-                        if link:
-                            suggestion['relevant_line'] = f"[{suggestion['relevant_line']}]({link})"
-                    else:
-                        pass
-
         incremental_review_markdown_text = None
         # Add incremental review section
         if self.incremental.is_incremental:
@@ -266,7 +241,9 @@ class PRReviewer:
             incremental_review_markdown_text = f"Starting from commit {last_commit_url}"
 
         markdown_text = convert_to_markdown_v2(data, self.git_provider.is_supported("gfm_markdown"),
-                                            incremental_review_markdown_text, git_provider=self.git_provider)
+                                            incremental_review_markdown_text,
+                                               git_provider=self.git_provider,
+                                               files=self.git_provider.get_diff_files())
 
         # Add help text if gfm_markdown is supported
         if self.git_provider.is_supported("gfm_markdown") and get_settings().pr_reviewer.enable_help_text:
@@ -286,38 +263,6 @@ class PRReviewer:
 
         return markdown_text
 
-    def _publish_inline_code_comments(self) -> None:
-        """
-        Publishes inline comments on a pull request with code suggestions generated by the AI model.
-        """
-        if get_settings().pr_reviewer.num_code_suggestions == 0:
-            return
-
-        first_key = 'review'
-        last_key = 'security_concerns'
-        data = load_yaml(self.prediction.strip(),
-                         keys_fix_yaml=["ticket_compliance_check", "estimated_effort_to_review_[1-5]:", "security_concerns:", "key_issues_to_review:",
-                                        "relevant_file:", "relevant_line:", "suggestion:"],
-                         first_key=first_key, last_key=last_key)
-        comments: List[str] = []
-        for suggestion in data.get('code_feedback', []):
-            relevant_file = suggestion.get('relevant_file', '').strip()
-            relevant_line_in_file = suggestion.get('relevant_line', '').strip()
-            content = suggestion.get('suggestion', '')
-            if not relevant_file or not relevant_line_in_file or not content:
-                get_logger().info("Skipping inline comment with missing file/line/content")
-                continue
-
-            if self.git_provider.is_supported("create_inline_comment"):
-                comment = self.git_provider.create_inline_comment(content, relevant_file, relevant_line_in_file)
-                if comment:
-                    comments.append(comment)
-            else:
-                self.git_provider.publish_inline_comment(content, relevant_file, relevant_line_in_file, suggestion)
-
-        if comments:
-            self.git_provider.publish_inline_comments(comments)
-
     def _get_user_answers(self) -> Tuple[str, str]:
         """
         Retrieves the question and answer strings from the discussion messages related to a pull request.
@@ -439,7 +384,7 @@ class PRReviewer:
                 get_logger().debug(f"Current labels:\n{current_labels}")
                 if current_labels:
                     current_labels_filtered = [label for label in current_labels if
-                                               not label.lower().startswith('review effort [1-5]:') and not label.lower().startswith(
+                                               not label.lower().startswith('review effort') and not label.lower().startswith(
                                                    'possible security concern')]
                 else:
                     current_labels_filtered = []
@@ -457,20 +402,6 @@ class PRReviewer:
         Auto-approve a pull request if it meets the conditions for auto-approval.
         """
         if get_settings().pr_reviewer.enable_auto_approval:
-            maximal_review_effort = get_settings().pr_reviewer.maximal_review_effort
-            if maximal_review_effort < 5:
-                current_labels = self.git_provider.get_pr_labels()
-                for label in current_labels:
-                    if label.lower().startswith('review effort [1-5]:'):
-                        effort = int(label.split(':')[1].strip())
-                        if effort > maximal_review_effort:
-                            get_logger().info(
-                                f"Auto-approve error: PR review effort ({effort}) is higher than the maximal review effort "
-                                f"({maximal_review_effort}) allowed")
-                            self.git_provider.publish_comment(
-                                f"Auto-approve error: PR review effort ({effort}) is higher than the maximal review effort "
-                                f"({maximal_review_effort}) allowed")
-                            return
             is_auto_approved = self.git_provider.auto_approve()
             if is_auto_approved:
                 get_logger().info("Auto-approved PR")

pr_agent/tools/pr_update_changelog.py

@@ -41,6 +41,7 @@ class PRUpdateChangelog:
             "description": self.git_provider.get_pr_description(),
             "language": self.main_language,
             "diff": "",  # empty diff for initial calculation
+            "pr_link": "",
             "changelog_file_str": self.changelog_file_str,
             "today": date.today(),
             "extra_instructions": get_settings().pr_update_changelog.extra_instructions,
@@ -73,7 +74,7 @@ class PRUpdateChangelog:
         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, model_type=ModelType.TURBO)
+        await retry_with_fallback_models(self._prepare_prediction, model_type=ModelType.WEAK)
 
         new_file_content, answer = self._prepare_changelog_update()
 
@@ -102,12 +103,23 @@ class PRUpdateChangelog:
     async def _get_prediction(self, model: str):
         variables = copy.deepcopy(self.vars)
         variables["diff"] = self.patches_diff  # update diff
+        if get_settings().pr_update_changelog.add_pr_link:
+            variables["pr_link"] = self.git_provider.get_pr_url()
         environment = Environment(undefined=StrictUndefined)
         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)
         response, finish_reason = await self.ai_handler.chat_completion(
             model=model, system=system_prompt, user=user_prompt, temperature=get_settings().config.temperature)
 
+        # post-process the response
+        response = response.strip()
+        if not response:
+            return ""
+        if response.startswith("```"):
+            response_lines = response.splitlines()
+            response_lines = response_lines[1:]
+            response = "\n".join(response_lines)
+        response = response.strip("`")
         return response
 
     def _prepare_changelog_update(self) -> Tuple[str, str]:

pr_agent/tools/ticket_pr_compliance_check.py

@@ -51,6 +51,11 @@ def extract_ticket_links_from_pr_description(pr_description, repo_path, base_url
                 issue_number = match[5][1:]  # remove #
                 if issue_number.isdigit() and len(issue_number) < 5 and repo_path:
                     github_tickets.add(f'{base_url_html.strip("/")}/{repo_path}/issues/{issue_number}')
+
+        if len(github_tickets) > 3:
+            get_logger().info(f"Too many tickets found in PR description: {len(github_tickets)}")
+            # Limit the number of tickets to 3
+            github_tickets = set(list(github_tickets)[:3])
     except Exception as e:
         get_logger().error(f"Error extracting tickets error= {e}",
                            artifact={"traceback": traceback.format_exc()})

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pr-agent"
-version = "0.2.4"
+version = "0.2.5"
 
 authors = [{ name = "CodiumAI", email = "tal.r@codium.ai" }]
 
@@ -31,7 +31,7 @@ dynamic = ["dependencies"]
 dependencies = { file = ["requirements.txt"] }
 
 [project.urls]
-"Homepage" = "https://github.com/Codium-ai/pr-agent"
+"Homepage" = "https://github.com/qodo-ai/pr-agent"
 "Documentation" = "https://pr-agent-docs.codium.ai/"
 
 [tool.setuptools]

setup.py

@@ -3,3 +3,4 @@
 from setuptools import setup
 
 setup()
+print("aaa")

tests/health_test/main.py

@@ -0,0 +1,70 @@
+import argparse
+import asyncio
+import copy
+import os
+from pathlib import Path
+
+from starlette_context import request_cycle_context, context
+
+from pr_agent.cli import run_command
+from pr_agent.config_loader import get_settings, global_settings
+
+from pr_agent.agent.pr_agent import PRAgent, commands
+from pr_agent.log import get_logger, setup_logger
+from tests.e2e_tests import e2e_utils
+
+log_level = os.environ.get("LOG_LEVEL", "INFO")
+setup_logger(log_level)
+
+
+async def run_async():
+    pr_url = os.getenv('TEST_PR_URL', 'https://github.com/Codium-ai/pr-agent/pull/1385')
+
+    get_settings().set("config.git_provider", "github")
+    get_settings().set("config.publish_output", False)
+    get_settings().set("config.fallback_models", [])
+
+    agent = PRAgent()
+    try:
+        # Run the 'describe' command
+        get_logger().info(f"\nSanity check for the 'describe' command...")
+        original_settings = copy.deepcopy(get_settings())
+        await agent.handle_request(pr_url, ['describe'])
+        pr_header_body = dict(get_settings().data)['artifact']
+        assert pr_header_body.startswith('###') and 'PR Type' in pr_header_body and 'Description' in pr_header_body
+        context['settings'] = copy.deepcopy(original_settings) # Restore settings state after each test to prevent test interference
+        get_logger().info("PR description generated successfully\n")
+
+        # Run the 'review' command
+        get_logger().info(f"\nSanity check for the 'review' command...")
+        original_settings = copy.deepcopy(get_settings())
+        await agent.handle_request(pr_url, ['review'])
+        pr_review_body = dict(get_settings().data)['artifact']
+        assert pr_review_body.startswith('##') and 'PR Reviewer Guide' in pr_review_body
+        context['settings'] = copy.deepcopy(original_settings)  # Restore settings state after each test to prevent test interference
+        get_logger().info("PR review generated successfully\n")
+
+        # Run the 'improve' command
+        get_logger().info(f"\nSanity check for the 'improve' command...")
+        original_settings = copy.deepcopy(get_settings())
+        await agent.handle_request(pr_url, ['improve'])
+        pr_improve_body = dict(get_settings().data)['artifact']
+        assert pr_improve_body.startswith('##') and 'PR Code Suggestions' in pr_improve_body
+        context['settings'] = copy.deepcopy(original_settings)  # Restore settings state after each test to prevent test interference
+        get_logger().info("PR improvements generated successfully\n")
+
+        get_logger().info(f"\n\n========\nHealth test passed successfully\n========")
+
+    except Exception as e:
+        get_logger().exception(f"\n\n========\nHealth test failed\n========")
+        raise e
+
+
+def run():
+    with request_cycle_context({}):
+        context['settings'] = copy.deepcopy(global_settings)
+        asyncio.run(run_async())
+
+
+if __name__ == '__main__':
+    run()

tests/unittest/test_bitbucket_provider.py

@@ -24,6 +24,13 @@ class TestBitbucketServerProvider:
         assert repo_slug == "my-repo"
         assert pr_number == 1
 
+    def test_parse_pr_url_with_users(self):
+        url = "https://bitbucket.company-server.url/users/username/repos/my-repo/pull-requests/1"
+        workspace_slug, repo_slug, pr_number = BitbucketServerProvider._parse_pr_url(url)
+        assert workspace_slug == "~username"
+        assert repo_slug == "my-repo"
+        assert pr_number == 1
+
     def mock_get_content_of_file(self, project_key, repository_slug, filename, at=None, markup=None):
         content_map = {
             '9c1cffdd9f276074bfb6fb3b70fbee62d298b058': 'file\nwith\nsome\nlines\nto\nemulate\na\nreal\nfile\n',
@@ -244,7 +251,7 @@ class TestBitbucketServerProvider:
             FilePatchInfo(
                 'file\nwith\nmultiple\nlines\nto\nemulate\na\nreal\nfile',
                 'readme\nwithout\nsome\nlines\nto\nsimulate\na\nreal\nfile',
-                '--- \n+++ \n@@ -1,9 +1,9 @@\n-file\n-with\n-multiple\n+readme\n+without\n+some\n lines\n to\n-emulate\n+simulate\n a\n real\n file',
+                '--- \n+++ \n@@ -1,9 +1,9 @@\n-file\n-with\n-multiple\n+readme\n+without\n+some\n lines\n to\n-emulate\n+simulate\n a\n real\n file\n',
                 'Readme.md',
                 edit_type=EDIT_TYPE.MODIFIED,
             )
@@ -266,7 +273,7 @@ class TestBitbucketServerProvider:
             FilePatchInfo(
                 'file\nwith\nsome\nlines\nto\nemulate\na\nreal\nfile',
                 'readme\nwithout\nsome\nlines\nto\nsimulate\na\nreal\nfile',
-                '--- \n+++ \n@@ -1,9 +1,9 @@\n-file\n-with\n+readme\n+without\n some\n lines\n to\n-emulate\n+simulate\n a\n real\n file',
+                '--- \n+++ \n@@ -1,9 +1,9 @@\n-file\n-with\n+readme\n+without\n some\n lines\n to\n-emulate\n+simulate\n a\n real\n file\n',
                 'Readme.md',
                 edit_type=EDIT_TYPE.MODIFIED,
             )
@@ -288,7 +295,7 @@ class TestBitbucketServerProvider:
             FilePatchInfo(
                 'file\nwith\nsome\nlines\nto\nemulate\na\nreal\nfile',
                 'readme\nwithout\nsome\nlines\nto\nsimulate\na\nreal\nfile',
-                '--- \n+++ \n@@ -1,9 +1,9 @@\n-file\n-with\n+readme\n+without\n some\n lines\n to\n-emulate\n+simulate\n a\n real\n file',
+                '--- \n+++ \n@@ -1,9 +1,9 @@\n-file\n-with\n+readme\n+without\n some\n lines\n to\n-emulate\n+simulate\n a\n real\n file\n',
                 'Readme.md',
                 edit_type=EDIT_TYPE.MODIFIED,
             )

tests/unittest/test_convert_to_markdown.py

@@ -47,13 +47,10 @@ class TestConvertToMarkdown:
     def test_simple_dictionary_input(self):
         input_data = {'review': {
             'estimated_effort_to_review_[1-5]': '1, because the changes are minimal and straightforward, focusing on a single functionality addition.\n',
-            'relevant_tests': 'No\n', 'possible_issues': 'No\n', 'security_concerns': 'No\n'}, 'code_feedback': [
-            {'relevant_file': '``pr_agent/git_providers/git_provider.py\n``', 'language': 'python\n',
-             'suggestion': "Consider raising an exception or logging a warning when 'pr_url' attribute is not found. This can help in debugging issues related to the absence of 'pr_url' in instances where it's expected. [important]\n",
-             'relevant_line': '[return ""](https://github.com/Codium-ai/pr-agent-pro/pull/102/files#diff-52d45f12b836f77ed1aef86e972e65404634ea4e2a6083fb71a9b0f9bb9e062fR199)'}]}
+            'relevant_tests': 'No\n', 'possible_issues': 'No\n', 'security_concerns': 'No\n'}}
 
 
-        expected_output = f'{PRReviewHeader.REGULAR.value} 🔍\n\nHere are some key observations to aid the review process:\n\n<table>\n<tr><td>⏱️&nbsp;<strong>Estimated effort to review</strong>: 1 🔵⚪⚪⚪⚪</td></tr>\n<tr><td>🧪&nbsp;<strong>No relevant tests</strong></td></tr>\n<tr><td>&nbsp;<strong>Possible issues</strong>: No\n</td></tr>\n<tr><td>🔒&nbsp;<strong>No security concerns identified</strong></td></tr>\n</table>\n\n\n<details><summary> <strong>Code feedback:</strong></summary>\n\n<hr><table><tr><td>relevant file</td><td>pr_agent/git_providers/git_provider.py\n</td></tr><tr><td>suggestion &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</td><td>\n\n<strong>\n\nConsider raising an exception or logging a warning when \'pr_url\' attribute is not found. This can help in debugging issues related to the absence of \'pr_url\' in instances where it\'s expected. [important]\n\n</strong>\n</td></tr><tr><td>relevant line</td><td><a href=\'https://github.com/Codium-ai/pr-agent-pro/pull/102/files#diff-52d45f12b836f77ed1aef86e972e65404634ea4e2a6083fb71a9b0f9bb9e062fR199\'>return ""</a></td></tr></table><hr>\n\n</details>'
+        expected_output = f'{PRReviewHeader.REGULAR.value} 🔍\n\nHere are some key observations to aid the review process:\n\n<table>\n<tr><td>⏱️&nbsp;<strong>Estimated effort to review</strong>: 1 🔵⚪⚪⚪⚪</td></tr>\n<tr><td>🧪&nbsp;<strong>No relevant tests</strong></td></tr>\n<tr><td>&nbsp;<strong>Possible issues</strong>: No\n</td></tr>\n<tr><td>🔒&nbsp;<strong>No security concerns identified</strong></td></tr>\n</table>'
 
         assert convert_to_markdown_v2(input_data).strip() == expected_output.strip()
 
@@ -67,7 +64,7 @@ class TestConvertToMarkdown:
         assert convert_to_markdown_v2(input_data).strip() == expected_output.strip()
 
     def test_dictionary_with_empty_dictionaries(self):
-        input_data = {'review': {}, 'code_feedback': [{}]}
+        input_data = {'review': {}}
 
         expected_output = ''
 

tests/unittest/test_extend_patch.py

@@ -3,6 +3,7 @@ import pytest
 from pr_agent.algo.git_patch_processing import extend_patch
 from pr_agent.algo.pr_processing import pr_generate_extended_diff
 from pr_agent.algo.token_handler import TokenHandler
+from pr_agent.algo.utils import load_large_diff
 from pr_agent.config_loader import get_settings
 
 
@@ -145,8 +146,8 @@ class TestExtendedPatchMoreLines:
         # Check that with no extra lines, the patches are the same as the original patches
         p0 = patches_extended_no_extra_lines[0].strip()
         p1 = patches_extended_no_extra_lines[1].strip()
-        assert p0 == '## file1\n' + pr_languages[0]['files'][0].patch.strip()
-        assert p1 == '## file2\n' + pr_languages[0]['files'][1].patch.strip()
+        assert p0 == "## File: 'file1'\n" + pr_languages[0]['files'][0].patch.strip()
+        assert p1 == "## File: 'file2'\n" + pr_languages[0]['files'][1].patch.strip()
 
         patches_extended_with_extra_lines, total_tokens, patches_extended_tokens = pr_generate_extended_diff(
             pr_languages, token_handler, add_line_numbers_to_hunks=False,
@@ -154,5 +155,37 @@ class TestExtendedPatchMoreLines:
             patch_extra_lines_after=1
         )
 
+
         p0_extended = patches_extended_with_extra_lines[0].strip()
-        assert p0_extended == '## file1\n\n@@ -3,8 +3,8 @@ \n line0\n line1\n-original content\n+modified content\n line2\n line3\n line4\n line5\n line6'
+        assert p0_extended == "## File: 'file1'\n\n@@ -3,8 +3,8 @@ \n line0\n line1\n-original content\n+modified content\n line2\n line3\n line4\n line5\n line6"
+
+
+class TestLoadLargeDiff:
+    def test_no_newline(self):
+        patch = load_large_diff("test.py",
+                                """\
+                                old content 1
+                                some new content
+                                another line
+                                """,
+                                """
+                                old content 1
+                                old content 2""")
+
+        patch_expected="""\
+--- 
++++ 
+@@ -1,3 +1,3 @@
+-
+                                 old content 1
+-                                old content 2
++                                some new content
++                                another line
+"""
+        assert patch == patch_expected
+
+    def test_empty_inputs(self):
+        assert load_large_diff("test.py", "", "") == ""
+        assert load_large_diff("test.py", None, None) == ""
+        assert (load_large_diff("test.py", "content\n", "") ==
+                '--- \n+++ \n@@ -1 +1 @@\n-\n+content\n')