Merge pull request #1421 from dceoy/main

Update Groq models and tokens

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

@@ -37,5 +37,3 @@ jobs:
         name: Test dev docker
         run: |
           docker run --rm codiumai/pr-agent:test pytest -v tests/unittest
-        
-          

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

@@ -30,6 +30,3 @@ jobs:
           GITHUB_ACTION_CONFIG.AUTO_DESCRIBE: true
           GITHUB_ACTION_CONFIG.AUTO_REVIEW: true
           GITHUB_ACTION_CONFIG.AUTO_IMPROVE: true
-
-
-

.github/workflows/pre-commit.yml

@@ -0,0 +1,17 @@
+# disabled. We might run it manually if needed.
+name: pre-commit
+
+on:
+  workflow_dispatch:
+#  pull_request:
+#  push:
+#    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v5
+      # SEE https://github.com/pre-commit/action
+      - uses: pre-commit/action@v3.0.1

.gitignore

@@ -1,6 +1,7 @@
 .idea/
 .lsp/
 .vscode/
+.env
 venv/
 pr_agent/settings/.secrets.toml
 __pycache__

.pre-commit-config.yaml

@@ -0,0 +1,46 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+default_language_version:
+  python: python3
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  # - repo: https://github.com/rhysd/actionlint
+  #   rev: v1.7.3
+  #   hooks:
+  #     - id: actionlint
+  - repo: https://github.com/pycqa/isort
+    # rev must match what's in dev-requirements.txt
+    rev: 5.13.2
+    hooks:
+      - id: isort
+  # - repo: https://github.com/PyCQA/bandit
+  #   rev: 1.7.10
+  #   hooks:
+  #     - id: bandit
+  #       args: [
+  #         "-c", "pyproject.toml",
+  #       ]
+  # - repo: https://github.com/astral-sh/ruff-pre-commit
+  #   rev: v0.7.1
+  #   hooks:
+  #     - id: ruff
+  #       args:
+  #         - --fix
+  #     - id: ruff-format
+  # -   repo: https://github.com/PyCQA/autoflake
+  #     rev: v2.3.1
+  #     hooks:
+  #     -   id: autoflake
+  #         args:
+  #           - --in-place
+  #           - --remove-all-unused-imports
+  #           - --remove-unused-variables

README.md

@@ -13,15 +13,13 @@
 Qode Merge 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/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)
+<a href="https://github.com/Codium-ai/pr-agent/commits/main">
-[![Cheat Sheet](https://img.shields.io/badge/Cheat-Sheet-red)](https://www.codium.ai/images/pr_agent/cheat_sheet.pdf)
+<img alt="GitHub" src="https://img.shields.io/github/last-commit/Codium-ai/pr-agent/main?style=for-the-badge" height="20">
-    <a href="https://github.com/Codium-ai/pr-agent/commits/main">
+</a>
-    <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/)
@@ -43,50 +41,44 @@ Qode Merge PR-Agent aims to help efficiently review and handle pull requests, by
 
 ## News and Updates
 
-### November 3, 2024
+### December 25, 2024
 
-Meaningful improvement to the quality of code suggestions by separating the code suggestion generation from [line number detection](https://github.com/Codium-ai/pr-agent/pull/1338)
+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.
 
-<kbd>![image](https://github.com/user-attachments/assets/093c185c-31ca-47a1-a4fe-be7d9335ea66)</kbd>
+### December 2, 2024
+
+Open-source repositories can now freely use Qodo Merge Pro, 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 Pro for private repositories.
 
 
-### October 27, 2024
+### November 18, 2024
 
-Qodo Merge PR Agent will now automatically document accepted code suggestions in a dedicated wiki page (`.pr_agent_accepted_suggestions`), enabling users to track historical changes, assess the tool's effectiveness, and learn from previously implemented recommendations in the repository.
+A new mode was enabled by default for code suggestions - `--pr_code_suggestions.focus_only_on_problems=true`:
 
-This dedicated wiki page will also serve as a foundation for future AI model improvements, allowing it to learn from historically implemented suggestions and generate more targeted, contextually relevant recommendations.
+- This option reduces the number of code suggestions received
-Read more about this novel feature [here](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking).
+- The suggestions will focus more on identifying and fixing code problems, rather than style considerations like best practices, maintainability, or readability.
+- The suggestions will be categorized into just two groups: "Possible Issues" and "General".
 
-<kbd><img href="https://qodo.ai/images/pr_agent/pr_agent_accepted_suggestions1.png" src="https://qodo.ai/images/pr_agent/pr_agent_accepted_suggestions1.png" width="768"></kbd>
+Still, if you prefer the previous mode, you can set `--pr_code_suggestions.focus_only_on_problems=false` in the [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/).
+
+**Example results:**
+
+Original mode
+
+<kbd><img src="https://qodo.ai/images/pr_agent/code_suggestions_original_mode.png" width="512"></kbd>
+
+Focused mode
+
+<kbd><img src="https://qodo.ai/images/pr_agent/code_suggestions_focused_mode.png" width="512"></kbd>
 
 
+### November 4, 2024
 
-### October 21, 2024
+Qodo Merge PR Agent will now leverage context from Jira or GitHub tickets to enhance the PR Feedback. Read more about this feature
-**Disable publishing labels by default:** 
+[here](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/)
-
-The default setting for `pr_description.publish_labels` has been updated to `false`. This means that labels generated by the `/describe` tool will no longer be published, unless this configuration is explicitly set to `true`.
-
-We constantly strive to balance informative AI analysis with reducing unnecessary noise. User feedback indicated that in many cases, the original PR title alone provides sufficient information, making the generated labels (`enhancement`, `documentation`, `bug fix`, ...) redundant.
-The [`review_effort`](https://qodo-merge-docs.qodo.ai/tools/review/#configuration-options) label, generated by the `review` tool, will still be published by default, as it provides valuable information enabling reviewers to prioritize small PRs first.
-
-However, every user has different preferences. To still publish the `describe` labels, set `pr_description.publish_labels=true` in the [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/).
-For more tailored and relevant labeling, we recommend using the [`custom_labels 💎`](https://qodo-merge-docs.qodo.ai/tools/custom_labels/) tool, that allows generating labels specific to your project's needs.
-
-<kbd>![image](https://github.com/user-attachments/assets/8f38d222-53b1-4742-b2ec-7ea0a30c9076)</kbd>
-
-→
-
-<kbd>![image](https://github.com/user-attachments/assets/8285bd90-0dda-4c7e-9237-bbfde5e21880)</kbd>
-
-
-
-### October 14, 2024
-Improved support for GitHub enterprise server with [GitHub Actions](https://qodo-merge-docs.qodo.ai/installation/github/#action-for-github-enterprise-server)
-
-### October 10, 2024
-New ability for the `review` tool - **ticket compliance feedback**. If the PR contains a ticket number, PR-Agent will check if the PR code actually [complies](https://github.com/Codium-ai/pr-agent/pull/1279#issuecomment-2404042130) with the ticket requirements.
-
-<kbd><img src="https://github.com/user-attachments/assets/4a2a728b-5f47-40fa-80cc-16efd296938c" width="768"></kbd>
 
 
 ## Overview
@@ -94,39 +86,41 @@ New ability for the `review` tool - **ticket compliance feedback**. If the PR co
 
 Supported commands per platform:
 
-|       |                                                                                                         | GitHub             | Gitlab             | Bitbucket          | Azure DevOps |
+|       |                                                                                                         | GitHub             | GitLab             | Bitbucket          | Azure DevOps |
 |-------|---------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:--------------------:|:------------:|
-| TOOLS | Review                                                                                                  | ✅ | ✅ | ✅ |      ✅       |
+| TOOLS | [Review](https://qodo-merge-docs.qodo.ai/tools/review/)                                                                                                  | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ Incremental                                                                                           | ✅ |                    |                    |              |
+|       | [Describe](https://qodo-merge-docs.qodo.ai/tools/describe/)                                                                                                | ✅ | ✅ | ✅ |      ✅       |
-|       | Describe                                                                                                | ✅ | ✅ | ✅ |      ✅       |
+|       | [Improve](https://qodo-merge-docs.qodo.ai/tools/improve/)                                                                                                 | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ [Inline File Summary](https://pr-agent-docs.codium.ai/tools/describe#inline-file-summary) 💎          | ✅ |                    |                    |              |
+|       | [Ask](https://qodo-merge-docs.qodo.ai/tools/ask/)                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | 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/) 💎                                | ✅ | ✅ | ✅ |              |
+|       | [Update CHANGELOG](https://qodo-merge-docs.qodo.ai/tools/update_changelog/)                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | [Test](https://pr-agent-docs.codium.ai/tools/test/) 💎                                                  | ✅ | ✅ |                    |              |
+|       | [Ticket Context](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/) 💎  | ✅ | ✅ |  ✅                  |   |
-|       | Reflect and Review                                                                                      | ✅ | ✅ | ✅ |      ✅       |
+|       | [Utilizing Best Practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) 💎  | ✅ | ✅ |  ✅                  |   |
-|       | Update CHANGELOG.md                                                                                     | ✅ | ✅ | ✅ |      ✅       |
+|       | [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) 💎  | ✅ |  |                    |   |
-|       | Find Similar Issue                                                                                      | ✅ |                    |                    |              |
+|       | [Suggestion Tracking](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking) 💎  | ✅ | ✅ |                    |   |
-|       | [Add PR Documentation](https://pr-agent-docs.codium.ai/tools/documentation/) 💎                         | ✅ | ✅ |                   |              |
+|       | [CI Feedback](https://pr-agent-docs.codium.ai/tools/ci_feedback/) 💎                                    | ✅ |                    |                    |              |
+|       | [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/) 💎                                  | ✅ |                    |                    |              |
+|       | [Custom Prompt](https://pr-agent-docs.codium.ai/tools/custom_prompt/) 💎                                | ✅ | ✅ | ✅ |              |
+|       | [Test](https://pr-agent-docs.codium.ai/tools/test/) 💎                                                  | ✅ | ✅ |                    |              |
 |       |                                                                                                         |                    |                    |                    |              |
-| USAGE | CLI                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
+| USAGE | [CLI](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#local-repo-cli)                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | App / webhook                                                                                           | ✅ | ✅ | ✅ |      ✅       |
+|       | [App / webhook](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#github-app)                                                                                           | ✅ | ✅ | ✅ |      ✅       |
-|       | Tagging bot                                                                                             | ✅ |                    |                    |              |
+|       | [Tagging bot](https://github.com/Codium-ai/pr-agent#try-it-now)                                                                                             | ✅ |                    |                    |              |
-|       | Actions                                                                                                 | ✅ |✅| ✅ |✅|
+|       | [Actions](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-action)                                                                                                 | ✅ |✅| ✅ |✅|
 |       |                                                                                                         |                    |                    |                    |              |
-| CORE  | PR compression                                                                                          | ✅ | ✅ | ✅ |      ✅       |
+| CORE  | [PR compression](https://qodo-merge-docs.qodo.ai/core-abilities/compression_strategy/)                                                                  | ✅ | ✅ | ✅ |      ✅       |
-|       | Repo language prioritization                                                                            | ✅ | ✅ | ✅ |      ✅       |
 |       | Adaptive and token-aware file patch fitting                                                             | ✅ | ✅ | ✅ |      ✅       |
-|       | Multiple models support                                                                                 | ✅ | ✅ | ✅ |      ✅       |
+|       | [Multiple models support](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/)                                                                                 | ✅ | ✅ | ✅ |      ✅       |
-|       | [Static code analysis](https://pr-agent-docs.codium.ai/core-abilities/#static-code-analysis) 💎         | ✅ | ✅ | ✅ |              |
+|       | [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://pr-agent-docs.codium.ai/usage-guide/configuration_options/) 💎 | ✅ | ✅ | ✅ |              |
 |       | [PR interactive actions](https://www.codium.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 [PR-Agent Pro](https://www.codium.ai/pricing/)
 
 [//]: # (- Support for additional git providers is described in [here]&#40;./docs/Full_environments.md&#41;)
@@ -187,50 +181,8 @@ ___
 </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">
 
 

docs/docs/chrome-extension/data_privacy.md

@@ -2,4 +2,3 @@ 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.
-

docs/docs/chrome-extension/index.md

@@ -4,7 +4,7 @@ With a single-click installation you will gain access to a context-aware chat on
 
 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 private repositories, you will need to install [Qodo Merge Pro](https://github.com/apps/qodo-merge-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).
 
 <img src="https://codium.ai/images/pr_agent/PR-AgentChat.gif" width="768">

docs/docs/core-abilities/fetching_ticket_context.md

@@ -0,0 +1,134 @@
+# 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:
+
+- 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.
+By understanding the reasoning and intent behind modifications, the LLM can offer more insightful and relevant code analysis.
+
+### Review tool
+Similarly to the `describe` tool, the `review` tool will use the ticket content to provide additional context for the code changes.
+
+In addition, this feature will evaluate how well a Pull Request (PR) adheres to its original purpose/intent as defined by the associated ticket or issue mentioned in the PR description.
+Each ticket will be assigned a label (Compliance/Alignment level), Indicates the degree to which the PR fulfills its original purpose, Options: Fully compliant, Partially compliant or Not compliant.
+
+
+![Ticket Compliance](https://www.qodo.ai/images/pr_agent/ticket_compliance_review.png){width=768}
+
+By default, the tool will automatically validate if the PR complies with the referenced ticket.
+If you want to disable this feedback, add the following line to your configuration file:
+
+```toml
+[pr_reviewer]
+require_ticket_analysis_review=false
+```
+
+## Providers
+
+### Github Issues Integration
+
+Qodo Merge PR Agent will automatically recognize Github issues mentioned in the PR description and fetch the issue content.
+Examples of valid GitHub issue references:
+
+- `https://github.com/<ORG_NAME>/<REPO_NAME>/issues/<ISSUE_NUMBER>`
+- `#<ISSUE_NUMBER>`
+- `<ORG_NAME>/<REPO_NAME>#<ISSUE_NUMBER>`
+
+Since Qodo Merge PR Agent is integrated with GitHub, it doesn't require any additional configuration to fetch GitHub issues.
+
+### Jira Integration 💎
+
+We support both Jira Cloud and Jira Server/Data Center.
+To integrate with Jira, you can link your PR to a ticket using either of these methods:
+
+**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"
+    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]
+    jira_base_url = "https://<JIRA_ORG>.atlassian.net"
+    ```
+
+#### Jira Cloud 💎
+There are two ways to authenticate with Jira Cloud:
+
+**1) Jira App Authentication**
+
+The recommended way to authenticate with Jira Cloud is to install the Qodo Merge app in your Jira Cloud instance. This will allow Qodo Merge to access Jira data on your behalf.
+
+Installation steps:
+
+1. Click [here](https://auth.atlassian.com/authorize?audience=api.atlassian.com&client_id=8krKmA4gMD8mM8z24aRCgPCSepZNP1xf&scope=read%3Ajira-work%20offline_access&redirect_uri=https%3A%2F%2Fregister.jira.pr-agent.codium.ai&state=qodomerge&response_type=code&prompt=consent) to install the Qodo Merge app in your Jira Cloud instance, click the `accept` button.<br>
+![Jira Cloud App Installation](https://www.qodo.ai/images/pr_agent/jira_app_installation1.png){width=384}
+
+2. After installing the app, you will be redirected to the Qodo Merge registration page. and you will see a success message.<br>
+![Jira Cloud App success message](https://www.qodo.ai/images/pr_agent/jira_app_success.png){width=384}
+
+3. Now you can use the Jira integration in Qodo Merge PR Agent.
+
+**2) Email/Token Authentication**
+
+You can create an API token from your Atlassian account:
+
+1. Log in to https://id.atlassian.com/manage-profile/security/api-tokens.
+
+2. Click Create API token.
+
+3. From the dialog that appears, enter a name for your new token and click Create.
+
+4. Click Copy to clipboard.
+
+![Jira Cloud API Token](https://images.ctfassets.net/zsv3d0ugroxu/1RYvh9lqgeZjjNe5S3Hbfb/155e846a1cb38f30bf17512b6dfd2229/screenshot_NewAPIToken){width=384}
+
+5. In your [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/) add the following lines:
+
+```toml
+[jira]
+jira_api_token = "YOUR_API_TOKEN"
+jira_api_email = "YOUR_EMAIL"
+```
+
+
+#### Jira Server/Data Center 💎
+
+Currently, we only support the 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:
+
+```toml
+[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

@@ -1,6 +1,7 @@
 # Core Abilities
 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/)
 - [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/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/index.md

@@ -25,36 +25,43 @@ To search the documentation site using natural language:
 
 Qodo Merge offers extensive pull request functionalities across various git providers.
 
-|       |                                                                                                                       | GitHub | Gitlab | Bitbucket | Azure DevOps |
+|       |                                                                                                         | GitHub             | GitLab             | Bitbucket          | Azure DevOps |
-|-------|-----------------------------------------------------------------------------------------------------------------------|:------:|:------:|:---------:|:------------:|
+|-------|---------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:--------------------:|:------------:|
-| TOOLS | Review                                                                                                                |   ✅    |   ✅    |   ✅       |      ✅       |
+| TOOLS | [Review](https://qodo-merge-docs.qodo.ai/tools/review/)                                                                                                  | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ Incremental                                                                                                         |   ✅    |        |            |              |
+|       | [Describe](https://qodo-merge-docs.qodo.ai/tools/describe/)                                                                                                | ✅ | ✅ | ✅ |      ✅       |
-|       | Ask                                                                                                                   |   ✅    |   ✅    |   ✅        |      ✅       |
+|       | [Improve](https://qodo-merge-docs.qodo.ai/tools/improve/)                                                                                                 | ✅ | ✅ | ✅ |      ✅       |
-|       | Describe                                                                                                              |   ✅    |   ✅    |   ✅        |      ✅       |
+|       | [Ask](https://qodo-merge-docs.qodo.ai/tools/ask/)                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ [Inline file summary](https://qodo-merge-docs.qodo.ai/tools/describe/#inline-file-summary){:target="_blank"} 💎     |   ✅    |   ✅    |           |              |
+|       | ⮑ [Ask on code lines](https://pr-agent-docs.codium.ai/tools/ask#ask-lines)                              | ✅ | ✅ |                    |              |
-|       | Improve                                                                                                               |   ✅    |   ✅    |   ✅        |      ✅       |
+|       | [Update CHANGELOG](https://qodo-merge-docs.qodo.ai/tools/update_changelog/)                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ Extended                                                                                                            |   ✅    |   ✅    |   ✅        |      ✅       |
+|       | [Ticket Context](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/) 💎  | ✅ | ✅ |  ✅                  |   |
-|       | [Custom Prompt](./tools/custom_prompt.md){:target="_blank"} 💎                                                        |   ✅    |   ✅    |   ✅        |              |
+|       | [Utilizing Best Practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) 💎  | ✅ | ✅ |  ✅                  |   |
-|       | Reflect and Review                                                                                                    |   ✅    |   ✅    |   ✅        |              |
+|       | [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) 💎  | ✅ |  |                    |   |
-|       | Update CHANGELOG.md                                                                                                   |   ✅    |   ✅    |   ✅        |      ️       |
+|       | [Suggestion Tracking](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking) 💎  | ✅ | ✅ |                    |   |
-|       | Find Similar Issue                                                                                                    |   ✅    |        |             |      ️       |
+|       | [CI Feedback](https://pr-agent-docs.codium.ai/tools/ci_feedback/) 💎                                    | ✅ |                    |                    |              |
-|       | [Add PR Documentation](./tools/documentation.md){:target="_blank"} 💎                                                 |   ✅    |   ✅    |          |              |
+|       | [PR Documentation](https://pr-agent-docs.codium.ai/tools/documentation/) 💎                         | ✅ | ✅ |                   |              |
-|       | [Generate Custom Labels](./tools/describe.md#handle-custom-labels-from-the-repos-labels-page-💎){:target="_blank"} 💎 |   ✅    |   ✅    |            |              |
+|       | [Custom Labels](https://pr-agent-docs.codium.ai/tools/custom_labels/) 💎                                | ✅ | ✅ |                    |              |
-|       | [Analyze PR Components](./tools/analyze.md){:target="_blank"} 💎                                                      |   ✅    |   ✅    |       |              |
+|       | [Analyze](https://pr-agent-docs.codium.ai/tools/analyze/) 💎                                            | ✅ | ✅ |                    |              |
-|       |                                                                                                                       |        |        |            |      ️       |
+|       | [Similar Code](https://pr-agent-docs.codium.ai/tools/similar_code/) 💎                                  | ✅ |                    |                    |              |
-| USAGE | CLI                                                                                                                   |   ✅    |   ✅    |   ✅       |      ✅       |
+|       | [Custom Prompt](https://pr-agent-docs.codium.ai/tools/custom_prompt/) 💎                                | ✅ | ✅ | ✅ |              |
-|       | App / webhook                                                                                                         |   ✅    |   ✅    |    ✅        |      ✅       |
+|       | [Test](https://pr-agent-docs.codium.ai/tools/test/) 💎                                                  | ✅ | ✅ |                    |              |
-|       | Actions                                                                                                               |   ✅    |        |            |      ️       |
+|       |                                                                                                         |                    |                    |                    |              |
-|       |                                                                                                                       |        |        |            |
+| USAGE | [CLI](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#local-repo-cli)                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-| CORE  | PR compression                                                                                                        |   ✅    |   ✅    |   ✅       |      ✅       |
+|       | [App / webhook](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#github-app)                                                                                           | ✅ | ✅ | ✅ |      ✅       |
-|       | Repo language prioritization                                                                                          |   ✅    |   ✅    |   ✅       |      ✅       |
+|       | [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](https://qodo-merge-docs.qodo.ai/core-abilities/compression_strategy/)                                                                  | ✅ | ✅ | ✅ |      ✅       |
 |       | Adaptive and token-aware file patch fitting                                                             | ✅ | ✅ | ✅ |      ✅       |
-|       | Multiple models support                                                                                               |   ✅    |   ✅    |   ✅       |      ✅       |
+|       | [Multiple models support](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/)                                                                                 | ✅ | ✅ | ✅ |      ✅       |
-|       | Incremental PR review                                                                                                 |   ✅    |        |            |              |
+|       | [Local and global metadata](https://qodo-merge-docs.qodo.ai/core-abilities/metadata/)          | ✅ | ✅ | ✅ | ✅             |
-|       | [Static code analysis](./tools/analyze.md/){:target="_blank"} 💎                                                      |   ✅    |   ✅     |    ✅    |              |
+|       | [Dynamic context](https://qodo-merge-docs.qodo.ai/core-abilities/dynamic_context/)          | ✅ | ✅ | ✅ | ✅             |
-|       | [Multiple configuration options](./usage-guide/configuration_options.md){:target="_blank"} 💎                         |   ✅    |   ✅     |    ✅    |              |
+|       | [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://pr-agent-docs.codium.ai/usage-guide/configuration_options/) 💎 | ✅ | ✅ | ✅ |              |
+|       | [PR interactive actions](https://www.codium.ai/images/pr_agent/pr-actions.mp4) 💎                       | ✅ |        ✅           |                    |              |
+|       | [Impact Evaluation](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/) 💎  | ✅ | ✅ |                    |   |
 
-💎 marks a feature available only in [Qodo Merge Pro](https://www.codium.ai/pricing/){:target="_blank"}
+💎 marks a feature available only in [Qodo Merge Pro](https://www.qodo.ai/pricing/){:target="_blank"}
 
 
 ## Example Results

docs/docs/installation/azure.md

@@ -51,10 +51,12 @@ 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}
 
 Make sure to give pipeline permissions to the `pr_agent` variable group.
 
+> Note that Azure Pipelines lacks support for triggering workflows from PR comments. If you find a viable solution, please contribute it to our [issue tracker](https://github.com/Codium-ai/pr-agent/issues)
 
 ## Azure DevOps from CLI
 

docs/docs/installation/gitlab.md

@@ -38,6 +38,7 @@ You can also modify the `script` section to run different Qodo Merge commands, o
 
 Note that if your base branches are not protected, don't set the variables as `protected`, since the pipeline will not have access to them.
 
+> **Note**: The `$CI_SERVER_FQDN` variable is available starting from GitLab version 16.10. If you're using an earlier version, this variable will not be available. However, you can combine `$CI_SERVER_HOST` and `$CI_SERVER_PORT` to achieve the same result. Please ensure you're using a compatible version or adjust your configuration.
 
 
 ## Run a GitLab webhook server

docs/docs/installation/locally.md

@@ -66,7 +66,30 @@ To invoke a tool (for example `review`), you can run directly from the Docker im
     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.
+For other git providers, update `CONFIG.GIT_PROVIDER` accordingly and check the `pr_agent/settings/.secrets_template.toml` file for environment variables expected names and values.
+The `pr_agent` uses [Dynaconf](https://www.dynaconf.com/) to load settings from configuration files.
+
+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:
+
+> Warning: Never commit the `.env` file to version control system as it might contains sensitive credentials!
+
+```
+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>
+```
 
 ---
 

docs/docs/installation/pr_agent_pro.md

@@ -1,31 +1,44 @@
-
+Qodo Merge Pro is a versatile application compatible with GitHub, GitLab, and BitBucket, hosted by QodoAI.
-## 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/). 
+A complimentary two-week trial is provided to all new users. Following the trial period, user licenses (seats) are required for continued access.
-After subscribing, you are granted the ability to easily install the application across any of your repositories.
+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 Pro for GitHub
+
+### GitHub Cloud
+
+Qodo Merge Pro for GitHub cloud is available for installation through the [GitHub Marketplace](https://github.com/apps/qodo-merge-pro).
 
 ![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. 
+### GitHub Enterprise Server
-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.
 
+### GitHub Open Source Projects
+
+For open-source projects, Qodo Merge Pro is available for free usage. To install Qodo Merge Pro for your open-source repositories, use the following marketplace [link](https://github.com/apps/qodo-merge-pro-for-open-source).
+
+## Install Qodo Merge Pro for Bitbucket
+
+###  Bitbucket Cloud
+
+Qodo Merge Pro for Bitbucket Cloud is available for installation through the following [link](https://bitbucket.org/site/addons/authorize?addon_key=d6df813252c37258)
+
+![Qodo Merge Pro](https://qodo.ai/images/pr_agent/pr_agent_pro_bitbucket_install.png){width=468}
+
+### Bitbucket Server
+
+To use Qodo Merge Pro application on your private Bitbucket 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
+#### 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.
 
@@ -35,14 +48,14 @@ Acquire a personal, project or group level access token. Enable the “api” sc
 
 Store the token in a safe place, you won’t be able to access it again after it was generated.
 
-### Step 2
+#### 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
+#### Step 3
 
 Install a webhook for your repository or groups, by clicking “webhooks” on the settings menu. Click the “Add new webhook” button.
 
@@ -53,7 +66,7 @@ Install a webhook for your repository or groups, by clicking “webhooks” on t
 In the webhook definition form, fill in the following fields:
 URL: https://pro.gitlab.pr-agent.codium.ai/webhook
 
-Secret token: Your CodiumAI key
+Secret token: Your QodoAI key
 Trigger: Check the ‘comments’ and ‘merge request events’ boxes.
 Enable SSL verification: Check the box.
 
@@ -61,7 +74,7 @@ Enable SSL verification: Check the box.
 ![Step 3.2](https://www.codium.ai/images/pr_agent/gitlab_pro_webhooks.png){width=750}
 </figure>
 
-### Step 4
+#### Step 4
 
 You’re all set!
 

docs/docs/overview/pr_agent_pro.md

@@ -1,6 +1,6 @@
 ### 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](https://www.codium.ai/pricing/) is a hosted version of open-source [Qodo Merge (PR-Agent)](https://github.com/Codium-ai/pr-agent). 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:
 
 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.

docs/docs/tools/improve.md

@@ -95,6 +95,112 @@ 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 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 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}
+
+
+### 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.
+
+
 ## Usage Tips
 
 ### Implementing the proposed code suggestions
@@ -191,73 +297,6 @@ 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`.
-
-##### 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"
@@ -275,6 +314,10 @@ Using a combination of both can help the AI model to provide relevant and tailor
         <td><b>dual_publishing_score_threshold</b></td>
         <td>Minimum score threshold for suggestions to be presented as commitable PR comments in addition to the table. Default is -1 (disabled).</td>
       </tr>
+      <tr>
+        <td><b>focus_only_on_problems</b></td>
+        <td>If set to true, suggestions will focus primarily on identifying and fixing code problems, and less on style considerations like best practices, maintainability, or readability. Default is true.</td> 
+      </tr>
       <tr>
         <td><b>persistent_comment</b></td>
         <td>If set to true, the improve comment will be persistent, meaning that every new improve request will edit the previous one. Default is false.</td>
@@ -299,6 +342,10 @@ 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"
@@ -316,10 +363,6 @@ 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/review.md

@@ -39,68 +39,19 @@ 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>
@@ -140,7 +91,7 @@ num_code_suggestions = ...
   </tr>
   <tr>
     <td><b>require_ticket_analysis_review</b></td>
-    <td>If set to true, and the PR contains a GitHub ticket number, the tool will add a section that checks if the PR in fact fulfilled the ticket requirements. Default is true.</td>
+    <td>If set to true, and the PR contains a GitHub or Jira ticket link, the tool will add a section that checks if the PR in fact fulfilled the ticket requirements. Default is true.</td>
   </tr>
 </table>
 
@@ -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"
@@ -249,13 +200,8 @@ If enabled, the `review` tool can approve a PR when a specific comment, `/review
     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/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/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:
@@ -58,59 +79,80 @@ 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
+
+
+### 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 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.
     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 --pr_description.final_update_message=false",
+    "/describe",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
     "/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 `review` tool, for example, the `num_code_suggestions` parameter will be set to 0.
 
 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 = [
     "/describe",
-    "/review  --pr_reviewer.num_code_suggestions=0 --pr_reviewer.final_update_message=false",
+    "/review",
 ]
 ```
 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:
@@ -121,7 +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.
@@ -136,19 +178,22 @@ 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",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
     "/improve",
 ]
 ```
@@ -156,24 +201,24 @@ 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 = [
     "/describe",
-    "/review  --pr_reviewer.num_code_suggestions=0 --pr_reviewer.final_update_message=false",
+    "/review",
 ]
 ```
 
 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"
 ```
@@ -182,29 +227,39 @@ Each time you invoke a `/review` tool, it will use the extra instructions you se
 
 
 Note that among other limitations, BitBucket provides relatively low rate-limits for applications (up to 1000 requests per hour), and does not provide an API to track the actual rate-limit usage.
-If you experience lack of responses from Qodo Merge, you might want to set: `bitbucket_app.avoid_full_files=true` in your configuration file.
+If you experience a lack of responses from Qodo Merge, you might want to set: `bitbucket_app.avoid_full_files=true` in your configuration file.
 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 --pr_reviewer.num_code_suggestions=0",
+    "/review",
     "/improve --pr_code_suggestions.commitable_code_suggestions=true --pr_code_suggestions.suggestions_score_threshold=7",
 ]
 ```
 Note that we set specifically for bitbucket, we recommend using: `--pr_code_suggestions.suggestions_score_threshold=7` and that is the default value we set for bitbucket.
 Since this platform only supports inline code suggestions, we want to limit the number of suggestions, and only present a limited number.
 
-## Azure DevOps provider
+To enable BitBucket app to respond to each **push** to the PR, set (for example):
+```toml
+[bitbucket_app]
+handle_push_trigger = true
+push_commands = [
+    "/describe",
+    "/review",
+]
+```
+
+### Azure DevOps provider
 
 To use Azure DevOps provider use the following settings in configuration.toml:
-```
+```toml
 [config]
 git_provider="azure"
 ```
@@ -223,14 +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

@@ -5,7 +5,6 @@ To use a different model than the default (GPT-4), you need to edit in the [conf
 ```
 [config]
 model = "..."
-model_turbo = "..."
 fallback_models = ["..."]
 ```
 
@@ -27,9 +26,8 @@ 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="" # the OpenAI model you've deployed on Azure (e.g. gpt-4o)
-model_turbo="" # the OpenAI model you've deployed on Azure (e.g. gpt-3.5-turbo)
+fallback_models=["..."]
-fallback_models=["..."] # the OpenAI model you've deployed on Azure (e.g. gpt-3.5-turbo)
 ```
 
 ### Hugging Face
@@ -52,7 +50,6 @@ MAX_TOKENS={
 
 [config] # in configuration.toml
 model = "ollama/llama2"
-model_turbo = "ollama/llama2"
 fallback_models=["ollama/llama2"]
 
 [ollama] # in .secrets.toml
@@ -76,7 +73,6 @@ MAX_TOKENS={
 }
 [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"]
 
 [huggingface] # in .secrets.toml
@@ -91,7 +87,6 @@ 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 +102,6 @@ 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 +115,6 @@ 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 +133,6 @@ 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 +148,6 @@ 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 +164,6 @@ 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"]
 ```
 
@@ -195,7 +185,6 @@ 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/introduction.md

@@ -10,4 +10,3 @@ Specifically, CLI commands can be issued by invoking a pre-built [docker image](
 
 For online usage, you will need to setup either a [GitHub App](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-app) or a [GitHub Action](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-action) (GitHub), a [GitLab webhook](https://qodo-merge-docs.qodo.ai/installation/gitlab/#run-a-gitlab-webhook-server) (GitLab), or a [BitBucket App](https://qodo-merge-docs.qodo.ai/installation/bitbucket/#run-using-codiumai-hosted-bitbucket-app) (BitBucket).
 These platforms also enable to run Qodo Merge specific tools automatically when a new PR is opened, or on each push to a branch.
-

docs/mkdocs.yml

@@ -43,6 +43,7 @@ nav:
     - 💎 Similar Code: 'tools/similar_code.md'
   - Core Abilities:
       - 'core-abilities/index.md'
+      - Fetching ticket context: 'core-abilities/fetching_ticket_context.md'
       - Local and global metadata: 'core-abilities/metadata.md'
       - Dynamic context: 'core-abilities/dynamic_context.md'
       - Self-reflection: 'core-abilities/self_reflection.md'

docs/overrides/partials/integrations/analytics/custom.html

@@ -3,5 +3,5 @@
     new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],
     j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src=
     'https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);
-    })(window,document,'script','dataLayer','GTM-5C9KZBM3');</script>
+    })(window,document,'script','dataLayer','GTM-M6PJSFV');</script>
     <!-- End Google Tag Manager -->

pr_agent/__init__.py

@@ -1 +0,0 @@
-

pr_agent/agent/pr_agent.py

@@ -3,7 +3,6 @@ from functools import partial
 
 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.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.utils import apply_repo_settings
@@ -14,7 +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
@@ -26,8 +24,6 @@ command2class = {
     "answer": PRReviewer,
     "review": PRReviewer,
     "review_pr": PRReviewer,
-    "reflect": PRInformationFromUser,
-    "reflect_and_review": PRInformationFromUser,
     "describe": PRDescription,
     "describe_pr": PRDescription,
     "improve": PRCodeSuggestions,
@@ -50,7 +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
@@ -65,10 +60,13 @@ class PRAgent:
         else:
             action, *args = request
 
+        forbidden_cli_args = ['enable_auto_approval', 'base_url', 'url', 'app_name', 'secret_provider',
+                              'git_provider', 'skip_keys', 'key', 'ANALYTICS_FOLDER', 'uri', 'app_id', 'webhook_secret',
+                              'bearer_token', 'PERSONAL_ACCESS_TOKEN', 'override_deployment_type', 'private_key', 'api_base', 'api_type', 'api_version']
         if args:
-            for forbidden_arg in self.forbidden_cli_args:
+            for forbidden_arg in forbidden_cli_args:
                 for arg in args:
-                    if forbidden_arg in arg:
+                    if forbidden_arg.lower() in arg.lower():
                         get_logger().error(
                             f"CLI argument for param '{forbidden_arg}' is forbidden. Use instead a configuration file."
                         )
@@ -77,12 +75,10 @@ class PRAgent:
 
         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

@@ -19,10 +19,13 @@ MAX_TOKENS = {
     'gpt-4o-mini': 128000,  # 128K, but may be limited by config.max_model_tokens
     'gpt-4o-mini-2024-07-18': 128000,  # 128K, but may be limited by config.max_model_tokens
     'gpt-4o-2024-08-06': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'gpt-4o-2024-11-20': 128000,  # 128K, but may be limited by config.max_model_tokens
     'o1-mini': 128000,  # 128K, but may be limited by config.max_model_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,
@@ -31,6 +34,7 @@ MAX_TOKENS = {
     'vertex_ai/codechat-bison': 6144,
     'vertex_ai/codechat-bison-32k': 32000,
     'vertex_ai/claude-3-haiku@20240307': 100000,
+    'vertex_ai/claude-3-5-haiku@20241022': 100000,
     'vertex_ai/claude-3-sonnet@20240229': 100000,
     'vertex_ai/claude-3-opus@20240229': 100000,
     'vertex_ai/claude-3-5-sonnet@20240620': 100000,
@@ -40,6 +44,7 @@ MAX_TOKENS = {
     '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,
@@ -48,20 +53,23 @@ MAX_TOKENS = {
     'anthropic/claude-3-opus-20240229': 100000,
     'anthropic/claude-3-5-sonnet-20240620': 100000,
     'anthropic/claude-3-5-sonnet-20241022': 100000,
+    'anthropic/claude-3-5-haiku-20241022': 100000,
     'bedrock/anthropic.claude-instant-v1': 100000,
     'bedrock/anthropic.claude-v2': 100000,
     'bedrock/anthropic.claude-v2:1': 100000,
     'bedrock/anthropic.claude-3-sonnet-20240229-v1:0': 100000,
     'bedrock/anthropic.claude-3-haiku-20240307-v1:0': 100000,
+    '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/gemma2-9b-it': 8192,
-    'groq/llama-3.1-70b-versatile': 131072,
-    'groq/llama-3.1-405b-reasoning': 131072,
     'ollama/llama3': 4096,
     'watsonx/meta-llama/llama-3-8b-instruct': 4096,
     "watsonx/meta-llama/llama-3-70b-instruct": 4096,

pr_agent/algo/ai_handlers/langchain_ai_handler.py

@@ -1,17 +1,18 @@
 try:
-    from langchain_openai import ChatOpenAI, AzureChatOpenAI
+    from langchain_core.messages import HumanMessage, SystemMessage
-    from langchain_core.messages import SystemMessage, HumanMessage
+    from langchain_openai import AzureChatOpenAI, ChatOpenAI
 except:  # we don't enforce langchain as a dependency, so if it's not installed, just move on
     pass
 
+import functools
+
+from openai import APIError, RateLimitError, Timeout
+from retry import retry
+
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 
-from openai import APIError, RateLimitError, Timeout
-from retry import retry
-import functools
-
 OPENAI_RETRIES = 5
 
 
@@ -73,4 +74,3 @@ class LangChainOpenAIHandler(BaseAiHandler):
                 raise ValueError(f"OpenAI {e.name} is required") from e
             else:
                 raise e
-

pr_agent/algo/ai_handlers/litellm_ai_handler.py

@@ -1,11 +1,13 @@
 import os
-import requests
+
 import litellm
 import openai
+import requests
 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
 
@@ -131,7 +133,7 @@ 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,
@@ -140,7 +142,7 @@ 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,
@@ -191,8 +193,8 @@ 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
+            # Currently, model OpenAI o1 series does not support a separate system and user prompts
-            O1_MODEL_PREFIX = 'o1-'
+            O1_MODEL_PREFIX = 'o1'
             model_type = model.split('/')[-1] if '/' in model else model
             if model_type.startswith(O1_MODEL_PREFIX):
                 user = f"{system}\n\n\n{user}"

pr_agent/algo/ai_handlers/openai_ai_handler.py

@@ -4,6 +4,7 @@ import openai
 from openai import APIError, AsyncOpenAI, RateLimitError, Timeout
 from retry import retry
 
+from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 
@@ -41,7 +42,6 @@ class OpenAIHandler(BaseAiHandler):
            tries=OPENAI_RETRIES, delay=2, backoff=2, jitter=(1, 3))
     async def chat_completion(self, model: str, system: str, user: str, temperature: float = 0.2):
         try:
-            deployment_id = self.deployment_id
             get_logger().info("System: ", system)
             get_logger().info("User: ", user)
             messages = [{"role": "system", "content": system}, {"role": "user", "content": user}]

pr_agent/algo/git_patch_processing.py

@@ -3,8 +3,8 @@ from __future__ import annotations
 import re
 import traceback
 
-from pr_agent.config_loader import get_settings
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 
 
@@ -31,7 +31,7 @@ def extend_patch(original_file_str, patch_str, patch_extra_lines_before=0,
 
 
 def decode_if_bytes(original_file_str):
-    if isinstance(original_file_str, bytes):
+    if isinstance(original_file_str, (bytes, bytearray)):
         try:
             return original_file_str.decode('utf-8')
         except UnicodeDecodeError:
@@ -61,23 +61,26 @@ def process_patch_lines(patch_str, original_file_str, patch_extra_lines_before,
     patch_lines = patch_str.splitlines()
     extended_patch_lines = []
 
+    is_valid_hunk = True
     start1, size1, start2, size2 = -1, -1, -1, -1
     RE_HUNK_HEADER = re.compile(
         r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
     try:
-        for line in patch_lines:
+        for i,line in enumerate(patch_lines):
             if line.startswith('@@'):
                 match = RE_HUNK_HEADER.match(line)
                 # identify hunk header
                 if match:
                     # finish processing previous hunk
-                    if start1 != -1 and patch_extra_lines_after > 0:
+                    if is_valid_hunk and (start1 != -1 and patch_extra_lines_after > 0):
                         delta_lines = [f' {line}' for line in original_lines[start1 + size1 - 1:start1 + size1 - 1 + patch_extra_lines_after]]
                         extended_patch_lines.extend(delta_lines)
 
                     section_header, size1, size2, start1, start2 = extract_hunk_headers(match)
 
-                    if patch_extra_lines_before > 0 or patch_extra_lines_after > 0:
+                    is_valid_hunk = check_if_hunk_lines_matches_to_file(i, original_lines, patch_lines, start1)
+
+                    if is_valid_hunk and (patch_extra_lines_before > 0 or patch_extra_lines_after > 0):
                         def _calc_context_limits(patch_lines_before):
                             extended_start1 = max(1, start1 - patch_lines_before)
                             extended_size1 = size1 + (start1 - extended_start1) + patch_extra_lines_after
@@ -138,7 +141,7 @@ def process_patch_lines(patch_str, original_file_str, patch_extra_lines_before,
         return patch_str
 
     # finish processing last hunk
-    if start1 != -1 and patch_extra_lines_after > 0:
+    if start1 != -1 and patch_extra_lines_after > 0 and is_valid_hunk:
         delta_lines = original_lines[start1 + size1 - 1:start1 + size1 - 1 + patch_extra_lines_after]
         # add space at the beginning of each extra line
         delta_lines = [f' {line}' for line in delta_lines]
@@ -148,6 +151,23 @@ def process_patch_lines(patch_str, original_file_str, patch_extra_lines_before,
     return extended_patch_str
 
 
+def check_if_hunk_lines_matches_to_file(i, original_lines, patch_lines, start1):
+    """
+    Check if the hunk lines match the original file content. We saw cases where the hunk header line doesn't match the original file content, and then
+    extending the hunk with extra lines before the hunk header can cause the hunk to be invalid.
+    """
+    is_valid_hunk = True
+    try:
+        if i + 1 < len(patch_lines) and patch_lines[i + 1][0] == ' ': # an existing line in the file
+            if patch_lines[i + 1].strip() != original_lines[start1 - 1].strip():
+                is_valid_hunk = False
+                get_logger().error(
+                    f"Invalid hunk in PR, line {start1} in hunk header doesn't match the original file content")
+    except:
+        pass
+    return is_valid_hunk
+
+
 def extract_hunk_headers(match):
     res = list(match.groups())
     for i in range(len(res)):
@@ -344,7 +364,7 @@ __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()
@@ -387,5 +407,8 @@ def extract_hunk_lines_from_patch(patch: str, file_name, line_start, line_end, s
                 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/language_handler.py

@@ -4,8 +4,6 @@ from typing import Dict
 from pr_agent.config_loader import get_settings
 
 
-
-
 def filter_bad_extensions(files):
     # Bad Extensions, source: https://github.com/EleutherAI/github-downloader/blob/345e7c4cbb9e0dc8a0615fd995a08bf9d73b3fe6/download_repo_text.py  # noqa: E501
     bad_extensions = get_settings().bad_extensions.default

pr_agent/algo/pr_processing.py

@@ -5,14 +5,15 @@ from typing import Callable, List, Tuple
 
 from github import RateLimitExceededException
 
-from pr_agent.algo.git_patch_processing import convert_to_hunks_with_lines_numbers, extend_patch, handle_patch_deletions
-from pr_agent.algo.language_handler import sort_files_by_main_languages
 from pr_agent.algo.file_filter import filter_ignored
+from pr_agent.algo.git_patch_processing import (
+    convert_to_hunks_with_lines_numbers, extend_patch, handle_patch_deletions)
+from pr_agent.algo.language_handler import sort_files_by_main_languages
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import get_max_tokens, clip_tokens, ModelType
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+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.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.log import get_logger
 
 DELETED_FILES_ = "Deleted files:\n"
@@ -315,13 +316,13 @@ 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)
@@ -353,8 +354,8 @@ 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:
+    if model_type == ModelType.WEAK:
-        model = get_settings().config.model_turbo
+        model = get_weak_model()
     else:
         model = get_settings().config.model
     fallback_models = get_settings().config.fallback_models

pr_agent/algo/token_handler.py

@@ -1,8 +1,9 @@
-from jinja2 import Environment, StrictUndefined
-from tiktoken import encoding_for_model, get_encoding
-from pr_agent.config_loader import get_settings
 from threading import Lock
 
+from jinja2 import Environment, StrictUndefined
+from tiktoken import encoding_for_model, get_encoding
+
+from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
 
 

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

@@ -7,14 +7,15 @@ 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
 import requests
 import yaml
@@ -22,11 +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.config_loader import get_settings, global_settings
 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:
@@ -173,7 +182,7 @@ def convert_to_markdown_v2(output_data: dict,
                 if is_value_no(value):
                     markdown_text += f'### {emoji} No relevant tests\n\n'
                 else:
-                    markdown_text += f"### PR contains tests\n\n"
+                    markdown_text += f"### {emoji} PR contains tests\n\n"
         elif 'ticket compliance check' in key_nice.lower():
             markdown_text = ticket_markdown_logic(emoji, markdown_text, value, gfm_supported)
         elif 'security concerns' in key_nice.lower():
@@ -221,15 +230,31 @@ 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:
+                            reference_link = None
 
                         if gfm_supported:
+                            if reference_link is not None and len(reference_link) > 0:
+                                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:
+                            if reference_link is not None and len(reference_link) > 0:
                                 issue_str = f"[**{issue_header}**]({reference_link})\n\n{issue_content}\n\n"
+                            else:
+                                issue_str = f"**{issue_header}**\n\n{issue_content}\n\n"
                         markdown_text += f"{issue_str}\n\n"
                     except Exception as e:
                         get_logger().exception(f"Failed to process 'Recommended focus areas for review': {e}")
@@ -246,25 +271,49 @@ 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
@@ -534,27 +583,20 @@ 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:
         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
+    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]:
@@ -1097,3 +1139,48 @@ 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

@@ -3,8 +3,9 @@ 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 setup_logger, get_logger
+from pr_agent.log import get_logger, setup_logger
 
 log_level = os.environ.get("LOG_LEVEL", "INFO")
 setup_logger(log_level)
@@ -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/git_providers/__init__.py

@@ -1,14 +1,16 @@
+from starlette_context import context
+
 from pr_agent.config_loader import get_settings
+from pr_agent.git_providers.azuredevops_provider import AzureDevopsProvider
 from pr_agent.git_providers.bitbucket_provider import BitbucketProvider
-from pr_agent.git_providers.bitbucket_server_provider import BitbucketServerProvider
+from pr_agent.git_providers.bitbucket_server_provider import \
+    BitbucketServerProvider
 from pr_agent.git_providers.codecommit_provider import CodeCommitProvider
+from pr_agent.git_providers.gerrit_provider import GerritProvider
 from pr_agent.git_providers.git_provider import GitProvider
 from pr_agent.git_providers.github_provider import GithubProvider
 from pr_agent.git_providers.gitlab_provider import GitLabProvider
 from pr_agent.git_providers.local_git_provider import LocalGitProvider
-from pr_agent.git_providers.azuredevops_provider import AzureDevopsProvider
-from pr_agent.git_providers.gerrit_provider import GerritProvider
-from starlette_context import context
 
 _GIT_PROVIDERS = {
     'github': GithubProvider,

pr_agent/git_providers/azuredevops_provider.py

@@ -2,33 +2,33 @@ import os
 from typing import Optional, Tuple
 from urllib.parse import urlparse
 
-from ..algo.file_filter import filter_ignored
-from ..log import get_logger
-from ..algo.language_handler import is_valid_file
-from ..algo.utils import clip_tokens, find_line_number_of_relevant_line_in_file, load_large_diff, PRDescriptionHeader
-from ..config_loader import get_settings
-from .git_provider import GitProvider
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 
+from ..algo.file_filter import filter_ignored
+from ..algo.language_handler import is_valid_file
+from ..algo.utils import (PRDescriptionHeader, clip_tokens,
+                          find_line_number_of_relevant_line_in_file,
+                          load_large_diff)
+from ..config_loader import get_settings
+from ..log import get_logger
+from .git_provider import GitProvider
+
 AZURE_DEVOPS_AVAILABLE = True
 ADO_APP_CLIENT_DEFAULT_ID = "499b84ac-1321-427f-aa17-267ca6975798/.default"
 MAX_PR_DESCRIPTION_AZURE_LENGTH = 4000-1
 
 try:
     # noinspection PyUnresolvedReferences
-    from msrest.authentication import BasicAuthentication
     # noinspection PyUnresolvedReferences
     from azure.devops.connection import Connection
     # noinspection PyUnresolvedReferences
-    from azure.identity import DefaultAzureCredential
+    from azure.devops.v7_1.git.models import (Comment, CommentThread,
-    # noinspection PyUnresolvedReferences
-    from azure.devops.v7_1.git.models import (
-        Comment,
-        CommentThread,
-        GitVersionDescriptor,
                                               GitPullRequest,
                                               GitPullRequestIterationChanges,
-    )
+                                              GitVersionDescriptor)
+    # noinspection PyUnresolvedReferences
+    from azure.identity import DefaultAzureCredential
+    from msrest.authentication import BasicAuthentication
 except ImportError:
     AZURE_DEVOPS_AVAILABLE = False
 
@@ -67,14 +67,12 @@ class AzureDevopsProvider(GitProvider):
             relevant_lines_end = suggestion['relevant_lines_end']
 
             if not relevant_lines_start or relevant_lines_start == -1:
-                if get_settings().config.verbosity_level >= 2:
+                get_logger().warning(
-                    get_logger().exception(
                     f"Failed to publish code suggestion, relevant_lines_start is {relevant_lines_start}")
                 continue
 
             if relevant_lines_end < relevant_lines_start:
-                if get_settings().config.verbosity_level >= 2:
+                get_logger().warning(f"Failed to publish code suggestion, "
-                    get_logger().exception(f"Failed to publish code suggestion, "
                                        f"relevant_lines_end is {relevant_lines_end} and "
                                        f"relevant_lines_start is {relevant_lines_start}")
                 continue
@@ -95,9 +93,11 @@ class AzureDevopsProvider(GitProvider):
                     "side": "RIGHT",
                 }
             post_parameters_list.append(post_parameters)
+        if not post_parameters_list:
+            return False
 
-        try:
         for post_parameters in post_parameters_list:
+            try:
                 comment = Comment(content=post_parameters["body"], comment_type=1)
                 thread = CommentThread(comments=[comment],
                                        thread_context={
@@ -117,15 +117,11 @@ class AzureDevopsProvider(GitProvider):
                     repository_id=self.repo_slug,
                     pull_request_id=self.pr_num
                 )
-                if get_settings().config.verbosity_level >= 2:
-                    get_logger().info(
-                        f"Published code suggestion on {self.pr_num} at {post_parameters['path']}"
-                    )
-            return True
             except Exception as e:
-            if get_settings().config.verbosity_level >= 2:
+                get_logger().warning(f"Azure failed to publish code suggestion, error: {e}")
-                get_logger().error(f"Failed to publish code suggestion, error: {e}")
+        return True
-            return False
+
+
 
     def get_pr_description_full(self) -> str:
         return self.pr.description
@@ -382,6 +378,9 @@ class AzureDevopsProvider(GitProvider):
             return []
 
     def publish_comment(self, pr_comment: str, is_temporary: bool = False, thread_context=None):
+        if is_temporary and not get_settings().config.publish_output_progress:
+            get_logger().debug(f"Skipping publish_comment for temporary comment: {pr_comment}")
+            return None
         comment = Comment(content=pr_comment)
         thread = CommentThread(comments=[comment], thread_context=thread_context, status=5)
         thread_response = self.azure_devops_client.create_thread(
@@ -620,4 +619,3 @@ class AzureDevopsProvider(GitProvider):
 
     def publish_file_comments(self, file_comments: list) -> bool:
         pass
-

pr_agent/git_providers/bitbucket_provider.py

@@ -1,4 +1,6 @@
+import difflib
 import json
+import re
 from typing import Optional, Tuple
 from urllib.parse import urlparse
 
@@ -6,13 +8,14 @@ import requests
 from atlassian.bitbucket import Cloud
 from starlette_context import context
 
-from pr_agent.algo.types import FilePatchInfo, EDIT_TYPE
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+
 from ..algo.file_filter import filter_ignored
 from ..algo.language_handler import is_valid_file
 from ..algo.utils import find_line_number_of_relevant_line_in_file
 from ..config_loader import get_settings
 from ..log import get_logger
-from .git_provider import GitProvider, MAX_FILES_ALLOWED_FULL
+from .git_provider import MAX_FILES_ALLOWED_FULL, GitProvider
 
 
 def _gef_filename(diff):
@@ -71,19 +74,33 @@ class BitbucketProvider(GitProvider):
         post_parameters_list = []
         for suggestion in code_suggestions:
             body = suggestion["body"]
+            original_suggestion = suggestion.get('original_suggestion', None)  # needed for diff code
+            if original_suggestion:
+                try:
+                    existing_code = original_suggestion['existing_code'].rstrip() + "\n"
+                    improved_code = original_suggestion['improved_code'].rstrip() + "\n"
+                    diff = difflib.unified_diff(existing_code.split('\n'),
+                                                improved_code.split('\n'), n=999)
+                    patch_orig = "\n".join(diff)
+                    patch = "\n".join(patch_orig.splitlines()[5:]).strip('\n')
+                    diff_code = f"\n\n```diff\n{patch.rstrip()}\n```"
+                    # replace ```suggestion ... ``` with diff_code, using regex:
+                    body = re.sub(r'```suggestion.*?```', diff_code, body, flags=re.DOTALL)
+                except Exception as e:
+                    get_logger().exception(f"Bitbucket failed to get diff code for publishing, error: {e}")
+                    continue
+
             relevant_file = suggestion["relevant_file"]
             relevant_lines_start = suggestion["relevant_lines_start"]
             relevant_lines_end = suggestion["relevant_lines_end"]
 
             if not relevant_lines_start or relevant_lines_start == -1:
-                if get_settings().config.verbosity_level >= 2:
                 get_logger().exception(
                     f"Failed to publish code suggestion, relevant_lines_start is {relevant_lines_start}"
                 )
                 continue
 
             if relevant_lines_end < relevant_lines_start:
-                if get_settings().config.verbosity_level >= 2:
                 get_logger().exception(
                     f"Failed to publish code suggestion, "
                     f"relevant_lines_end is {relevant_lines_end} and "
@@ -112,8 +129,7 @@ class BitbucketProvider(GitProvider):
             self.publish_inline_comments(post_parameters_list)
             return True
         except Exception as e:
-            if get_settings().config.verbosity_level >= 2:
+            get_logger().error(f"Bitbucket failed to publish code suggestion, error: {e}")
-                get_logger().error(f"Failed to publish code suggestion, error: {e}")
             return False
 
     def publish_file_comments(self, file_comments: list) -> bool:
@@ -309,6 +325,9 @@ class BitbucketProvider(GitProvider):
         self.publish_comment(pr_comment)
 
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
+        if is_temporary and not get_settings().config.publish_output_progress:
+            get_logger().debug(f"Skipping publish_comment for temporary comment: {pr_comment}")
+            return None
         pr_comment = self.limit_output_characters(pr_comment, self.max_comment_length)
         comment = self.pr.comment(pr_comment)
         if is_temporary:

pr_agent/git_providers/bitbucket_server_provider.py

@@ -1,16 +1,21 @@
-from distutils.version import LooseVersion
+import difflib
-from requests.exceptions import HTTPError
+import re
+
+from packaging.version import parse as parse_version
 from typing import Optional, Tuple
 from urllib.parse import quote_plus, urlparse
 
 from atlassian.bitbucket import Bitbucket
+from requests.exceptions import HTTPError
 
-from .git_provider import GitProvider
+from ..algo.git_patch_processing import decode_if_bytes
-from ..algo.types import EDIT_TYPE, FilePatchInfo
 from ..algo.language_handler import is_valid_file
-from ..algo.utils import load_large_diff, find_line_number_of_relevant_line_in_file
+from ..algo.types import EDIT_TYPE, FilePatchInfo
+from ..algo.utils import (find_line_number_of_relevant_line_in_file,
+                          load_large_diff)
 from ..config_loader import get_settings
 from ..log import get_logger
+from .git_provider import GitProvider
 
 
 class BitbucketServerProvider(GitProvider):
@@ -35,7 +40,7 @@ class BitbucketServerProvider(GitProvider):
                                                               token=get_settings().get("BITBUCKET_SERVER.BEARER_TOKEN",
                                                                                        None))
         try:
-            self.bitbucket_api_version = LooseVersion(self.bitbucket_client.get("rest/api/1.0/application-properties").get('version'))
+            self.bitbucket_api_version = parse_version(self.bitbucket_client.get("rest/api/1.0/application-properties").get('version'))
         except Exception:
             self.bitbucket_api_version = None
 
@@ -65,20 +70,33 @@ class BitbucketServerProvider(GitProvider):
         post_parameters_list = []
         for suggestion in code_suggestions:
             body = suggestion["body"]
+            original_suggestion = suggestion.get('original_suggestion', None)  # needed for diff code
+            if original_suggestion:
+                try:
+                    existing_code = original_suggestion['existing_code'].rstrip() + "\n"
+                    improved_code = original_suggestion['improved_code'].rstrip() + "\n"
+                    diff = difflib.unified_diff(existing_code.split('\n'),
+                                                improved_code.split('\n'), n=999)
+                    patch_orig = "\n".join(diff)
+                    patch = "\n".join(patch_orig.splitlines()[5:]).strip('\n')
+                    diff_code = f"\n\n```diff\n{patch.rstrip()}\n```"
+                    # replace ```suggestion ... ``` with diff_code, using regex:
+                    body = re.sub(r'```suggestion.*?```', diff_code, body, flags=re.DOTALL)
+                except Exception as e:
+                    get_logger().exception(f"Bitbucket failed to get diff code for publishing, error: {e}")
+                    continue
             relevant_file = suggestion["relevant_file"]
             relevant_lines_start = suggestion["relevant_lines_start"]
             relevant_lines_end = suggestion["relevant_lines_end"]
 
             if not relevant_lines_start or relevant_lines_start == -1:
-                if get_settings().config.verbosity_level >= 2:
+                get_logger().warning(
-                    get_logger().exception(
                     f"Failed to publish code suggestion, relevant_lines_start is {relevant_lines_start}"
                 )
                 continue
 
             if relevant_lines_end < relevant_lines_start:
-                if get_settings().config.verbosity_level >= 2:
+                get_logger().warning(
-                    get_logger().exception(
                     f"Failed to publish code suggestion, "
                     f"relevant_lines_end is {relevant_lines_end} and "
                     f"relevant_lines_start is {relevant_lines_start}"
@@ -159,7 +177,7 @@ class BitbucketServerProvider(GitProvider):
         head_sha = self.pr.fromRef['latestCommit']
 
         # if Bitbucket api version is >= 8.16 then use the merge-base api for 2-way diff calculation
-        if self.bitbucket_api_version is not None and self.bitbucket_api_version >= LooseVersion("8.16"):
+        if self.bitbucket_api_version is not None and self.bitbucket_api_version >= parse_version("8.16"):
             try:
                 base_sha = self.bitbucket_client.get(self._get_merge_base())['id']
             except Exception as e:
@@ -174,7 +192,7 @@ class BitbucketServerProvider(GitProvider):
             # if Bitbucket api version is None or < 7.0 then do a simple diff with a guaranteed common ancestor
             base_sha = source_commits_list[-1]['parents'][0]['id']
             # if Bitbucket api version is 7.0-8.15 then use 2-way diff functionality for the base_sha
-            if self.bitbucket_api_version is not None and self.bitbucket_api_version >= LooseVersion("7.0"):
+            if self.bitbucket_api_version is not None and self.bitbucket_api_version >= parse_version("7.0"):
                 try:
                     destination_commits = list(
                         self.bitbucket_client.get_commits(self.workspace_slug, self.repo_slug, base_sha,
@@ -200,25 +218,21 @@ class BitbucketServerProvider(GitProvider):
                 case 'ADD':
                     edit_type = EDIT_TYPE.ADDED
                     new_file_content_str = self.get_file(file_path, head_sha)
-                    if isinstance(new_file_content_str, (bytes, bytearray)):
+                    new_file_content_str = decode_if_bytes(new_file_content_str)
-                        new_file_content_str = new_file_content_str.decode("utf-8")
                     original_file_content_str = ""
                 case 'DELETE':
                     edit_type = EDIT_TYPE.DELETED
                     new_file_content_str = ""
                     original_file_content_str = self.get_file(file_path, base_sha)
-                    if isinstance(original_file_content_str, (bytes, bytearray)):
+                    original_file_content_str = decode_if_bytes(original_file_content_str)
-                        original_file_content_str = original_file_content_str.decode("utf-8")
                 case 'RENAME':
                     edit_type = EDIT_TYPE.RENAMED
                 case _:
                     edit_type = EDIT_TYPE.MODIFIED
                     original_file_content_str = self.get_file(file_path, base_sha)
-                    if isinstance(original_file_content_str, (bytes, bytearray)):
+                    original_file_content_str = decode_if_bytes(original_file_content_str)
-                        original_file_content_str = original_file_content_str.decode("utf-8")
                     new_file_content_str = self.get_file(file_path, head_sha)
-                    if isinstance(new_file_content_str, (bytes, bytearray)):
+                    new_file_content_str = decode_if_bytes(new_file_content_str)
-                        new_file_content_str = new_file_content_str.decode("utf-8")
 
             patch = load_large_diff(file_path, new_file_content_str, original_file_content_str)
 

pr_agent/git_providers/codecommit_provider.py

@@ -4,13 +4,15 @@ from collections import Counter
 from typing import List, Optional, Tuple
 from urllib.parse import urlparse
 
-from pr_agent.git_providers.codecommit_client import CodeCommitClient
+from pr_agent.algo.language_handler import is_valid_file
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+from pr_agent.git_providers.codecommit_client import CodeCommitClient
+
 from ..algo.utils import load_large_diff
-from .git_provider import GitProvider
 from ..config_loader import get_settings
 from ..log import get_logger
-from pr_agent.algo.language_handler import is_valid_file
+from .git_provider import GitProvider
+
 
 class PullRequestCCMimic:
     """

pr_agent/git_providers/gerrit_provider.py

@@ -12,9 +12,9 @@ import requests
 import urllib3.util
 from git import Repo
 
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.git_provider import GitProvider
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.git_providers.local_git_provider import PullRequestMimic
 from pr_agent.log import get_logger
 

pr_agent/git_providers/git_provider.py

@@ -1,12 +1,12 @@
 from abc import ABC, abstractmethod
-
 # enum EDIT_TYPE (ADDED, DELETED, MODIFIED, RENAMED)
 from typing import Optional
 
+from pr_agent.algo.types import FilePatchInfo
 from pr_agent.algo.utils import Range, process_description
 from pr_agent.config_loader import get_settings
-from pr_agent.algo.types import FilePatchInfo
 from pr_agent.log import get_logger
+
 MAX_FILES_ALLOWED_FULL = 50
 
 class GitProvider(ABC):
@@ -62,8 +62,8 @@ class GitProvider(ABC):
         pass
 
     def get_pr_description(self, full: bool = True, split_changes_walkthrough=False) -> str or tuple:
-        from pr_agent.config_loader import get_settings
         from pr_agent.algo.utils import clip_tokens
+        from pr_agent.config_loader import get_settings
         max_tokens_description = get_settings().get("CONFIG.MAX_DESCRIPTION_TOKENS", None)
         description = self.get_pr_description_full() if full else self.get_user_description()
         if split_changes_walkthrough:

pr_agent/git_providers/github_provider.py

@@ -1,22 +1,30 @@
-import itertools
+import copy
-import time
+import difflib
 import hashlib
+import itertools
+import re
+import time
 import traceback
 from datetime import datetime
 from typing import Optional, Tuple
 from urllib.parse import urlparse
+
 from github import AppAuthentication, Auth, Github
 from retry import retry
 from starlette_context import context
 
 from ..algo.file_filter import filter_ignored
+from ..algo.git_patch_processing import extract_hunk_headers
 from ..algo.language_handler import is_valid_file
 from ..algo.types import EDIT_TYPE
-from ..algo.utils import PRReviewHeader, load_large_diff, clip_tokens, find_line_number_of_relevant_line_in_file, Range
+from ..algo.utils import (PRReviewHeader, Range, clip_tokens,
+                          find_line_number_of_relevant_line_in_file,
+                          load_large_diff, set_file_languages)
 from ..config_loader import get_settings
 from ..log import get_logger
 from ..servers.utils import RateLimitExceeded
-from .git_provider import FilePatchInfo, GitProvider, IncrementalPR, MAX_FILES_ALLOWED_FULL
+from .git_provider import (MAX_FILES_ALLOWED_FULL, FilePatchInfo, GitProvider,
+                           IncrementalPR)
 
 
 class GithubProvider(GitProvider):
@@ -166,6 +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):
@@ -173,7 +199,10 @@ class GithubProvider(GitProvider):
                     continue
 
                 patch = file.patch
-
+                if is_close_to_rate_limit:
+                    new_file_content_str = ""
+                    original_file_content_str = ""
+                else:
                     # 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
@@ -195,10 +224,12 @@ class GithubProvider(GitProvider):
                         if avoid_load:
                             original_file_content_str = ""
                         else:
-                        original_file_content_str = self._get_pr_file_content(file, self.pr.base.sha)
+                            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
                 elif file.status == 'removed':
@@ -212,9 +243,14 @@ class GithubProvider(GitProvider):
                     edit_type = EDIT_TYPE.UNKNOWN
 
                 # count number of lines added and removed
+                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,
@@ -279,7 +315,6 @@ class GithubProvider(GitProvider):
                                                                                 relevant_line_in_file,
                                                                                 absolute_position)
         if position == -1:
-            if get_settings().config.verbosity_level >= 2:
             get_logger().info(f"Could not find position for {relevant_file} {relevant_line_in_file}")
             subject_type = "FILE"
         else:
@@ -292,11 +327,9 @@ class GithubProvider(GitProvider):
             # publish all comments in a single message
             self.pr.create_review(commit=self.last_commit_id, comments=comments)
         except Exception as e:
-            if get_settings().config.verbosity_level >= 2:
+            get_logger().info(f"Initially failed to publish inline comments as committable")
-                get_logger().error(f"Failed to publish inline comments")
 
-            if (getattr(e, "status", None) == 422
+            if (getattr(e, "status", None) == 422 and not disable_fallback):
-                    and get_settings().github.publish_inline_comments_fallback_with_verification and not disable_fallback):
                 pass  # continue to try _publish_inline_comments_fallback_with_verification
             else:
                 raise e # will end up with publishing the comments one by one
@@ -304,7 +337,6 @@ class GithubProvider(GitProvider):
             try:
                 self._publish_inline_comments_fallback_with_verification(comments)
             except Exception as e:
-                if get_settings().config.verbosity_level >= 2:
                 get_logger().error(f"Failed to publish inline code comments fallback, error: {e}")
                 raise e
 
@@ -330,10 +362,8 @@ class GithubProvider(GitProvider):
             for comment in fixed_comments_as_one_liner:
                 try:
                     self.publish_inline_comments([comment], disable_fallback=True)
-                    if get_settings().config.verbosity_level >= 2:
                     get_logger().info(f"Published invalid comment as a single line comment: {comment}")
                 except:
-                    if get_settings().config.verbosity_level >= 2:
                     get_logger().error(f"Failed to publish invalid comment as a single line comment: {comment}")
 
     def _verify_code_comment(self, comment: dict):
@@ -392,7 +422,6 @@ class GithubProvider(GitProvider):
                 if fixed_comment != comment:
                     fixed_comments.append(fixed_comment)
             except Exception as e:
-                if get_settings().config.verbosity_level >= 2:
                 get_logger().error(f"Failed to fix inline comment, error: {e}")
         return fixed_comments
 
@@ -401,20 +430,21 @@ class GithubProvider(GitProvider):
         Publishes code suggestions as comments on the PR.
         """
         post_parameters_list = []
-        for suggestion in code_suggestions:
+
+        code_suggestions_validated = self.validate_comments_inside_hunks(code_suggestions)
+
+        for suggestion in code_suggestions_validated:
             body = suggestion['body']
             relevant_file = suggestion['relevant_file']
             relevant_lines_start = suggestion['relevant_lines_start']
             relevant_lines_end = suggestion['relevant_lines_end']
 
             if not relevant_lines_start or relevant_lines_start == -1:
-                if get_settings().config.verbosity_level >= 2:
                 get_logger().exception(
                     f"Failed to publish code suggestion, relevant_lines_start is {relevant_lines_start}")
                 continue
 
             if relevant_lines_end < relevant_lines_start:
-                if get_settings().config.verbosity_level >= 2:
                 get_logger().exception(f"Failed to publish code suggestion, "
                                   f"relevant_lines_end is {relevant_lines_end} and "
                                   f"relevant_lines_start is {relevant_lines_start}")
@@ -441,7 +471,6 @@ class GithubProvider(GitProvider):
             self.publish_inline_comments(post_parameters_list)
             return True
         except Exception as e:
-            if get_settings().config.verbosity_level >= 2:
             get_logger().error(f"Failed to publish code suggestion, error: {e}")
             return False
 
@@ -501,6 +530,7 @@ class GithubProvider(GitProvider):
                     elif self.deployment_type == 'user':
                         same_comment_creator = self.github_user_id == existing_comment['user']['login']
                     if existing_comment['subject_type'] == 'file' and comment['path'] == existing_comment['path'] and same_comment_creator:
+
                         headers, data_patch = self.pr._requester.requestJsonAndCheck(
                             "PATCH", f"{self.base_url}/repos/{self.repo}/pulls/comments/{existing_comment['id']}", input={"body":comment['body']}
                         )
@@ -512,7 +542,6 @@ class GithubProvider(GitProvider):
                     )
             return True
         except Exception as e:
-            if get_settings().config.verbosity_level >= 2:
             get_logger().error(f"Failed to publish diffview file summary, error: {e}")
             return False
 
@@ -801,7 +830,6 @@ class GithubProvider(GitProvider):
                 link = f"{self.base_url_html}/{self.repo}/pull/{self.pr_num}/files#diff-{sha_file}R{absolute_position}"
                 return link
         except Exception as e:
-            if get_settings().config.verbosity_level >= 2:
             get_logger().info(f"Failed adding line link, error: {e}")
 
         return ""
@@ -862,3 +890,89 @@ class GithubProvider(GitProvider):
 
     def calc_pr_statistics(self, pull_request_data: dict):
             return {}
+
+    def validate_comments_inside_hunks(self, code_suggestions):
+        """
+        validate that all committable comments are inside PR hunks - this is a must for committable comments in GitHub
+        """
+        code_suggestions_copy = copy.deepcopy(code_suggestions)
+        diff_files = self.get_diff_files()
+        RE_HUNK_HEADER = re.compile(
+            r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
+
+        diff_files = set_file_languages(diff_files)
+
+        for suggestion in code_suggestions_copy:
+            try:
+                relevant_file_path = suggestion['relevant_file']
+                for file in diff_files:
+                    if file.filename == relevant_file_path:
+
+                        # generate on-demand the patches range for the relevant file
+                        patch_str = file.patch
+                        if not hasattr(file, 'patches_range'):
+                            file.patches_range = []
+                            patch_lines = patch_str.splitlines()
+                            for i, line in enumerate(patch_lines):
+                                if line.startswith('@@'):
+                                    match = RE_HUNK_HEADER.match(line)
+                                    # identify hunk header
+                                    if match:
+                                        section_header, size1, size2, start1, start2 = extract_hunk_headers(match)
+                                        file.patches_range.append({'start': start2, 'end': start2 + size2 - 1})
+
+                        patches_range = file.patches_range
+                        comment_start_line = suggestion.get('relevant_lines_start', None)
+                        comment_end_line = suggestion.get('relevant_lines_end', None)
+                        original_suggestion = suggestion.get('original_suggestion', None) # needed for diff code
+                        if not comment_start_line or not comment_end_line or not original_suggestion:
+                            continue
+
+                        # check if the comment is inside a valid hunk
+                        is_valid_hunk = False
+                        min_distance = float('inf')
+                        patch_range_min = None
+                        # find the hunk that contains the comment, or the closest one
+                        for i, patch_range in enumerate(patches_range):
+                            d1 = comment_start_line - patch_range['start']
+                            d2 = patch_range['end'] - comment_end_line
+                            if d1 >= 0 and d2 >= 0:  # found a valid hunk
+                                is_valid_hunk = True
+                                min_distance = 0
+                                patch_range_min = patch_range
+                                break
+                            elif d1 * d2 <= 0:  # comment is possibly inside the hunk
+                                d1_clip = abs(min(0, d1))
+                                d2_clip = abs(min(0, d2))
+                                d = max(d1_clip, d2_clip)
+                                if d < min_distance:
+                                    patch_range_min = patch_range
+                                    min_distance = min(min_distance, d)
+                        if not is_valid_hunk:
+                            if min_distance < 10:  # 10 lines - a reasonable distance to consider the comment inside the hunk
+                                # make the suggestion non-committable, yet multi line
+                                suggestion['relevant_lines_start'] = max(suggestion['relevant_lines_start'], patch_range_min['start'])
+                                suggestion['relevant_lines_end'] = min(suggestion['relevant_lines_end'], patch_range_min['end'])
+                                body = suggestion['body'].strip()
+
+                                # present new diff code in collapsible
+                                existing_code = original_suggestion['existing_code'].rstrip() + "\n"
+                                improved_code = original_suggestion['improved_code'].rstrip() + "\n"
+                                diff = difflib.unified_diff(existing_code.split('\n'),
+                                                            improved_code.split('\n'), n=999)
+                                patch_orig = "\n".join(diff)
+                                patch = "\n".join(patch_orig.splitlines()[5:]).strip('\n')
+                                diff_code = f"\n\n<details><summary>New proposed code:</summary>\n\n```diff\n{patch.rstrip()}\n```"
+                                # replace ```suggestion ... ``` with diff_code, using regex:
+                                body = re.sub(r'```suggestion.*?```', diff_code, body, flags=re.DOTALL)
+                                body += "\n\n</details>"
+                                suggestion['body'] = body
+                                get_logger().info(f"Comment was moved to a valid hunk, "
+                                                  f"start_line={suggestion['relevant_lines_start']}, end_line={suggestion['relevant_lines_end']}, file={file.filename}")
+                            else:
+                                get_logger().error(f"Comment is not inside a valid hunk, "
+                                                   f"start_line={suggestion['relevant_lines_start']}, end_line={suggestion['relevant_lines_end']}, file={file.filename}")
+            except Exception as e:
+                get_logger().error(f"Failed to process patch for committable comment, error: {e}")
+        return code_suggestions_copy
+

pr_agent/git_providers/gitlab_provider.py

@@ -1,3 +1,4 @@
+import difflib
 import hashlib
 import re
 from typing import Optional, Tuple
@@ -7,13 +8,16 @@ import gitlab
 import requests
 from gitlab import GitlabGetError
 
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+
 from ..algo.file_filter import filter_ignored
 from ..algo.language_handler import is_valid_file
-from ..algo.utils import load_large_diff, clip_tokens, find_line_number_of_relevant_line_in_file
+from ..algo.utils import (clip_tokens,
+                          find_line_number_of_relevant_line_in_file,
+                          load_large_diff)
 from ..config_loader import get_settings
-from .git_provider import GitProvider, MAX_FILES_ALLOWED_FULL
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from ..log import get_logger
+from .git_provider import MAX_FILES_ALLOWED_FULL, GitProvider
 
 
 class DiffNotFoundError(Exception):
@@ -190,6 +194,9 @@ class GitLabProvider(GitProvider):
         self.publish_persistent_comment_full(pr_comment, initial_header, update_header, name, final_update_message)
 
     def publish_comment(self, mr_comment: str, is_temporary: bool = False):
+        if is_temporary and not get_settings().config.publish_output_progress:
+            get_logger().debug(f"Skipping publish_comment for temporary comment: {mr_comment}")
+            return None
         mr_comment = self.limit_output_characters(mr_comment, self.max_comment_chars)
         comment = self.mr.notes.create({'body': mr_comment})
         if is_temporary:
@@ -275,20 +282,23 @@ class GitLabProvider(GitProvider):
                         new_code_snippet = original_suggestion['improved_code']
                         content = original_suggestion['suggestion_content']
                         label = original_suggestion['label']
-                        if 'score' in original_suggestion:
+                        score = original_suggestion.get('score', 7)
-                            score = original_suggestion['score']
-                        else:
-                            score = 7
 
                     if hasattr(self, 'main_language'):
                         language = self.main_language
                     else:
                         language = ''
                     link = self.get_line_link(relevant_file, line_start, line_end)
-                    body_fallback =f"**Suggestion:** {content} [{label}, importance: {score}]\n___\n"
+                    body_fallback =f"**Suggestion:** {content} [{label}, importance: {score}]\n\n"
-                    body_fallback +=f"\n\nReplace  lines ([{line_start}-{line_end}]({link}))\n\n```{language}\n{old_code_snippet}\n````\n\n"
+                    body_fallback +=f"\n\n<details><summary>[{target_file.filename} [{line_start}-{line_end}]]({link}):</summary>\n\n"
-                    body_fallback +=f"with\n\n```{language}\n{new_code_snippet}\n````"
+                    body_fallback += f"\n\n___\n\n`(Cannot implement directly - GitLab API allows committable suggestions strictly on MR diff lines)`"
-                    body_fallback += f"\n\n___\n\n`(Cannot implement this suggestion directly, as gitlab API does not enable committing to a non -+ line in a PR)`"
+                    body_fallback+="</details>\n\n"
+                    diff_patch = difflib.unified_diff(old_code_snippet.split('\n'),
+                                                new_code_snippet.split('\n'), n=999)
+                    patch_orig = "\n".join(diff_patch)
+                    patch = "\n".join(patch_orig.splitlines()[5:]).strip('\n')
+                    diff_code = f"\n\n```diff\n{patch.rstrip()}\n```"
+                    body_fallback += diff_code
 
                     # Create a general note on the file in the MR
                     self.mr.notes.create({
@@ -301,6 +311,7 @@ class GitLabProvider(GitProvider):
                             'file_path': f'{target_file.filename}',
                         }
                     })
+                    get_logger().debug(f"Created fallback comment in MR {self.id_mr} with position {pos_obj}")
 
                     # get_logger().debug(
                     #     f"Failed to create comment in MR {self.id_mr} with position {pos_obj} (probably not a '+' line)")

pr_agent/git_providers/local_git_provider.py

@@ -4,9 +4,9 @@ from typing import List
 
 from git import Repo
 
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.config_loader import _find_repository_root, get_settings
 from pr_agent.git_providers.git_provider import GitProvider
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.log import get_logger
 
 

pr_agent/git_providers/utils.py

@@ -3,11 +3,12 @@ import os
 import tempfile
 
 from dynaconf import Dynaconf
+from starlette_context import context
 
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider, get_git_provider_with_context
+from pr_agent.git_providers import (get_git_provider,
+                                    get_git_provider_with_context)
 from pr_agent.log import get_logger
-from starlette_context import context
 
 
 def apply_repo_settings(pr_url):
@@ -98,5 +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/identity_providers/__init__.py

@@ -1,5 +1,6 @@
 from pr_agent.config_loader import get_settings
-from pr_agent.identity_providers.default_identity_provider import DefaultIdentityProvider
+from pr_agent.identity_providers.default_identity_provider import \
+    DefaultIdentityProvider
 
 _IDENTITY_PROVIDERS = {
     'default': DefaultIdentityProvider

pr_agent/identity_providers/default_identity_provider.py

@@ -1,4 +1,5 @@
-from pr_agent.identity_providers.identity_provider import Eligibility, IdentityProvider
+from pr_agent.identity_providers.identity_provider import (Eligibility,
+                                                           IdentityProvider)
 
 
 class DefaultIdentityProvider(IdentityProvider):

pr_agent/secret_providers/__init__.py

@@ -8,12 +8,10 @@ def get_secret_provider():
     provider_id = get_settings().config.secret_provider
     if provider_id == 'google_cloud_storage':
         try:
-            from pr_agent.secret_providers.google_cloud_storage_secret_provider import GoogleCloudStorageSecretProvider
+            from pr_agent.secret_providers.google_cloud_storage_secret_provider import \
+                GoogleCloudStorageSecretProvider
             return GoogleCloudStorageSecretProvider()
         except Exception as e:
             raise ValueError(f"Failed to initialize google_cloud_storage secret provider {provider_id}") from e
     else:
         raise ValueError("Unknown SECRET_PROVIDER")
-
-
-

pr_agent/servers/azuredevops_server_webhook.py

@@ -9,9 +9,9 @@ import secrets
 from urllib.parse import unquote
 
 import uvicorn
-from fastapi import APIRouter, Depends, FastAPI, HTTPException
+from fastapi import APIRouter, Depends, FastAPI, HTTPException, Request
-from fastapi.security import HTTPBasic, HTTPBasicCredentials
 from fastapi.encoders import jsonable_encoder
+from fastapi.security import HTTPBasic, HTTPBasicCredentials
 from starlette import status
 from starlette.background import BackgroundTasks
 from starlette.middleware import Middleware
@@ -23,9 +23,6 @@ from pr_agent.agent.pr_agent import PRAgent, command2class
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.utils import apply_repo_settings
-from pr_agent.log import get_logger
-from fastapi import Request, Depends
-from fastapi.security import HTTPBasic, HTTPBasicCredentials
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 
 setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
@@ -67,6 +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

@@ -77,6 +77,9 @@ async def handle_manifest(request: Request, response: Response):
 
 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
@@ -98,11 +101,14 @@ async def _perform_commands_bitbucket(commands_conf: str, agent: PRAgent, api_ur
 
 def is_bot_user(data) -> bool:
     try:
-        if data["data"]["actor"]["type"] != "user":
+        actor = data.get("data", {}).get("actor", {})
-            get_logger().info(f"BitBucket actor type is not 'user': {data['data']['actor']['type']}")
+        # allow actor type: user . if it's "AppUser" or "team" then it is a bot user
+        allowed_actor_types = {"user"}
+        if actor and actor["type"].lower() not in allowed_actor_types:
+            get_logger().info(f"BitBucket actor type is not 'user', skipping: {actor}")
             return True
     except Exception as e:
-        get_logger().error("Failed 'is_bot_user' logic: {e}")
+        get_logger().error(f"Failed 'is_bot_user' logic: {e}")
     return False
 
 
@@ -161,16 +167,18 @@ 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 = data["data"]["actor"]["username"]
+                    username = actor["username"]
                 except KeyError:
                     try:
-                    username = data["data"]["actor"]["display_name"]
+                        username = actor["display_name"]
                     except KeyError:
-                    username = data["data"]["actor"]["nickname"]
+                        username = actor["nickname"]
                 log_context["sender"] = username
 
-            sender_id = data["data"]["actor"]["account_id"]
+            sender_id = data.get("data", {}).get("actor", {}).get("account_id", "")
             log_context["sender_id"] = sender_id
             jwt_parts = input_jwt.split(".")
             claim_part = jwt_parts[1]

pr_agent/servers/bitbucket_server_webhook.py

@@ -6,20 +6,20 @@ from typing import List
 import uvicorn
 from fastapi import APIRouter, FastAPI
 from fastapi.encoders import jsonable_encoder
+from fastapi.responses import RedirectResponse
 from starlette import status
 from starlette.background import BackgroundTasks
 from starlette.middleware import Middleware
 from starlette.requests import Request
 from starlette.responses import JSONResponse
 from starlette_context.middleware import RawContextMiddleware
+
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.servers.utils import verify_signature
-from fastapi.responses import RedirectResponse
-
 
 setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
 router = APIRouter()
@@ -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

@@ -15,7 +15,8 @@ from starlette_context.middleware import RawContextMiddleware
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings, global_settings
-from pr_agent.git_providers import get_git_provider, get_git_provider_with_context
+from pr_agent.git_providers import (get_git_provider,
+                                    get_git_provider_with_context)
 from pr_agent.git_providers.git_provider import IncrementalPR
 from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.identity_providers import get_identity_provider
@@ -373,6 +374,9 @@ 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

@@ -1,11 +1,12 @@
 import asyncio
 import multiprocessing
-from collections import deque
-import traceback
-from datetime import datetime, timezone
 import time
-import requests
+import traceback
+from collections import deque
+from datetime import datetime, timezone
+
 import aiohttp
+import requests
 
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.config_loader import get_settings
@@ -83,6 +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:
@@ -100,7 +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

@@ -1,6 +1,6 @@
 import copy
-import re
 import json
+import re
 from datetime import datetime
 
 import uvicorn
@@ -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}", {})

pr_agent/servers/serverless.py

@@ -5,7 +5,6 @@ from starlette_context.middleware import RawContextMiddleware
 
 from pr_agent.servers.github_app import router
 
-
 middleware = [Middleware(RawContextMiddleware)]
 app = FastAPI(middleware=middleware)
 app.include_router(router)

pr_agent/servers/utils.py

@@ -2,7 +2,7 @@ import hashlib
 import hmac
 import time
 from collections import defaultdict
-from typing import Callable, Any
+from typing import Any, Callable
 
 from fastapi import HTTPException
 

pr_agent/settings/configuration.toml

@@ -1,18 +1,20 @@
 [config]
 # models
-model="gpt-4-turbo-2024-04-09"
+model="gpt-4o-2024-11-20"
-model_turbo="gpt-4o-2024-08-06"
+fallback_models=["gpt-4o-2024-08-06"]
-fallback_models=["gpt-4o-2024-05-13"]
+#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
 publish_output_progress=true
+publish_output_no_suggestions=true
 verbosity_level=0 # 0,1,2
 use_extra_bad_extensions=false
 # Configurations
 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
@@ -53,10 +55,6 @@ 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
@@ -90,6 +88,7 @@ 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
@@ -98,7 +97,6 @@ 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 #
@@ -106,13 +104,13 @@ enable_help_text=false
 
 
 [pr_code_suggestions] # /improve #
-max_context_tokens=14000
+max_context_tokens=16000
 #
 commitable_code_suggestions = false
 dual_publishing_score_threshold=-1 # -1 to disable, [0-10] to set the threshold (>=) for publishing a code suggestion both in a table and as commitable
+focus_only_on_problems=true
 #
 extra_instructions = ""
-rank_suggestions = false
 enable_help_text=false
 enable_chat_text=false
 enable_intro_text=true
@@ -127,7 +125,7 @@ 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
@@ -137,6 +135,7 @@ 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 = """\
@@ -160,6 +159,7 @@ 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
@@ -216,7 +216,7 @@ 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
@@ -228,27 +228,27 @@ 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",
+    "/review",
-    "/improve --pr_code_suggestions.commitable_code_suggestions=true --pr_code_suggestions.suggestions_score_threshold=7",
+    "/improve --pr_code_suggestions.commitable_code_suggestions=true",
 ]
 avoid_full_files = false
 
@@ -273,8 +273,8 @@ avoid_full_files = false
 url = ""
 pr_commands = [
     "/describe --pr_description.final_update_message=false",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
-    "/improve --pr_code_suggestions.commitable_code_suggestions=true --pr_code_suggestions.suggestions_score_threshold=7",
+    "/improve --pr_code_suggestions.commitable_code_suggestions=true",
 ]
 
 [litellm]

pr_agent/settings/pr_code_suggestions_prompts.toml

@@ -1,7 +1,10 @@
 [pr_code_suggestions_prompt]
 system="""You are PR-Reviewer, an AI specializing in Pull Request (PR) code analysis and suggestions.
-Your task is to examine the provided code diff, focusing on new code (lines prefixed with '+'), and offer concise, actionable suggestions to fix possible bugs and problems, and enhance code quality, readability, and performance.
+{%- if not focus_only_on_problems %}
-
+Your task is to examine the provided code diff, focusing on new code (lines prefixed with '+'), and offer concise, actionable suggestions to fix possible bugs and problems, and enhance code quality and performance.
+{%- else %}
+Your task is to examine the provided code diff, focusing on new code (lines prefixed with '+'), and offer concise, actionable suggestions to fix critical bugs and problems.
+{%- endif %}
 
 The PR code diff will be in the following structured format:
 ======
@@ -42,9 +45,17 @@ __new hunk__
 
 
 Specific guidelines for generating code suggestions:
+{%- if not focus_only_on_problems %}
 - Provide up to {{ num_code_suggestions }} distinct and insightful 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.
+{%- 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.
+{%- else %}
+- Only give suggestions that address critical problems and bugs in the PR code. If no relevant suggestions are applicable, return an empty list.
+{%- 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.
@@ -69,7 +80,11 @@ class CodeSuggestion(BaseModel):
     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.")
     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.")
+{%- 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 %}
+    label: str = Field(description="A single, descriptive label that best characterizes the suggestion type. Possible labels include 'security', 'critical bug', 'general'. The 'general' section should be used for suggestions that address a major issue, but are necessarily on a critical level.")
+{%- endif %}
 
 
 class PRCodeSuggestions(BaseModel):

pr_agent/settings/pr_description_prompts.toml

@@ -9,7 +9,7 @@ Your task is to provide a full description for the PR content - files walkthroug
 - 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 (').
+- When quoting variables, names or file paths from the code, use backticks (`) instead of single quote (').
 
 {%- if extra_instructions %}
 
@@ -38,23 +38,22 @@ class PRType(str, Enum):
 {%- if enable_semantic_files_types %}
 
 class FileDescription(BaseModel):
-    filename: str = Field(description="The full file path of the relevant file.")
+    filename: str = Field(description="The full file path of the relevant file")
-    language: str = Field(description="The programming language of the relevant file.")
+    language: str = Field(description="The programming language 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')")
 {%- 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")
+    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 %}
     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.")
-{%- endif %}
 =====
 
 
@@ -70,25 +69,20 @@ pr_files:
     ...
   language: |
     ...
+{%- if include_file_summary_changes %}
   changes_summary: |
     ...
+{%- endif %}
   changes_title: |
     ...
   label: |
-    ...
+    label_key_1
 ...
 {%- endif %}
 description: |
   ...
 title: |
   ...
-{%- if enable_custom_labels %}
-labels:
-- |
-  ...
-- |
-  ...
-{%- 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 ('|')

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 '+')
 
 
@@ -49,16 +45,6 @@ __new hunk__
 {%- endif %}
 - When quoting variables or names 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_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. Don't state line numbers here")
+    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")
 
@@ -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 ('|')

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).
+Your task is to add a brief summary of this PR's changes to CHANGELOG.md file of the project:
-- 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.
+- Follow the file's existing format and style conventions like dates, section titles, etc.
-- Don't repeat previous changes. Generate only new content, that is not already in the CHANGELOG.md file.
+- 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. Ignore non-relevant subsections.
+- 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

@@ -1,26 +1,30 @@
 import asyncio
 import copy
+import difflib
+import re
 import textwrap
 import traceback
 from functools import partial
 from typing import Dict, List
+
 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, get_pr_multi_diffs, retry_with_fallback_models, \
+from pr_agent.algo.pr_processing import (add_ai_metadata_to_diff_files,
-    add_ai_metadata_to_diff_files
+                                         get_pr_diff, get_pr_multi_diffs,
+                                         retry_with_fallback_models)
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import load_yaml, replace_code_tags, ModelType, show_relevant_configurations
+from pr_agent.algo.utils import (ModelType, load_yaml, replace_code_tags,
+                                 show_relevant_configurations)
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider, get_git_provider_with_context, GithubProvider, GitLabProvider, \
+from pr_agent.git_providers import (AzureDevopsProvider, GithubProvider,
-    AzureDevopsProvider
+                                    GitLabProvider, get_git_provider,
-from pr_agent.git_providers.git_provider import get_main_pr_language
+                                    get_git_provider_with_context)
+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
-import difflib
-import re
 
 
 class PRCodeSuggestions:
@@ -76,6 +80,7 @@ class PRCodeSuggestions:
             "commit_messages_str": self.git_provider.get_commit_messages(),
             "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),
         }
         self.pr_code_suggestions_prompt_system = get_settings().pr_code_suggestions_prompt.system
 
@@ -98,6 +103,8 @@ 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"):
@@ -105,33 +112,26 @@ 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."
+                await self.publish_no_suggestions()
-                if get_settings().config.publish_output:
-                    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": ""}
                 return
 
-            if (not self.is_extended and get_settings().pr_code_suggestions.rank_suggestions) or \
+            # publish the suggestions
-                    (self.is_extended and get_settings().pr_code_suggestions.rank_extended_suggestions):
-                get_logger().info('Ranking Suggestions...')
-                data['code_suggestions'] = await self.rank_suggestions(data['code_suggestions'])
-
             if get_settings().config.publish_output:
+                # 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")):
 
@@ -141,10 +141,7 @@ 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 = await self.add_self_review_text(pr_body)
-                        pr_body += f"\n\n- [ ]  {text}"
-                        if get_settings().pr_code_suggestions.approve_pr_on_self_review:
-                            pr_body += ' <!-- approve pr self-review -->'
 
                     # add usage guide
                     if (get_settings().pr_code_suggestions.enable_chat_text and get_settings().config.is_auto_command
@@ -160,13 +157,13 @@ class PRCodeSuggestions:
                         pr_body += show_relevant_configurations(relevant_section='pr_code_suggestions')
 
                     # publish the PR comment
-                    if get_settings().pr_code_suggestions.persistent_comment:
+                    if get_settings().pr_code_suggestions.persistent_comment: # true by default
-                        final_update_message = False
+                        self.publish_persistent_comment_with_history(self.git_provider,
-                        self.publish_persistent_comment_with_history(pr_body,
+                                                                     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:
@@ -177,29 +174,15 @@ class PRCodeSuggestions:
 
                     # dual publishing mode
                     if int(get_settings().pr_code_suggestions.dual_publishing_score_threshold) > 0:
-                        data_above_threshold = {'code_suggestions': []}
+                        await self.dual_publishing(data)
-                        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}")
                 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}",
@@ -212,47 +195,108 @@ 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)
+                new_comment = git_provider.publish_comment(pr_comment)
-            return
+            return new_comment
 
         history_header = f"#### Previous suggestions\n"
-        last_commit_num = self.git_provider.get_latest_commit_url().split('/')[-1][:7]
+        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>")]
 
@@ -273,7 +317,7 @@ 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
@@ -300,11 +344,12 @@ 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)
+                            git_provider.edit_comment(progress_response, pr_comment_updated)
-                            self.git_provider.remove_comment(comment)
+                            git_provider.remove_comment(comment)
+                            comment = progress_response
                         else:
-                            self.git_provider.edit_comment(comment, pr_comment_updated)
+                            git_provider.edit_comment(comment, pr_comment_updated)
-                        return
+                        return comment
             except Exception as e:
                 get_logger().exception(f"Failed to update persistent review, error: {e}")
                 pass
@@ -313,9 +358,12 @@ 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"<!--.*?-->")
@@ -332,6 +380,8 @@ class PRCodeSuggestions:
                                         model,
                                         add_line_numbers_to_hunks=True,
                                         disable_extra_lines=False)
+        self.patches_diff_list = [self.patches_diff]
+        self.patches_diff_no_line_number = self.remove_line_numbers([self.patches_diff])[0]
 
         if self.patches_diff:
             get_logger().debug(f"PR diff", artifact=self.patches_diff)
@@ -364,9 +414,19 @@ class PRCodeSuggestions:
         response_reflect = await self.self_reflect_on_suggestions(data["code_suggestions"],
                                                                   patches_diff, model=model_reflection)
         if response_reflect:
+            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"]):
+                suggestion["score"] = 7
+                suggestion["score_why"] = ""
+
+        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["code_suggestions"]
+        code_suggestions_feedback = response_reflect_yaml.get("code_suggestions", [])
-            if len(code_suggestions_feedback) == len(data["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"]
@@ -382,8 +442,14 @@ class PRCodeSuggestions:
 
                     try:
                         if get_settings().config.publish_output:
-                                suggestion_statistics_dict = {'score': int(suggestion["score"]),
+                            if not suggestion["score"]:
-                                                              'label': suggestion["label"].lower().strip()}
+                                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:
@@ -408,13 +474,6 @@ class PRCodeSuggestions:
                             suggestion['existing_code'] = ""
                 except Exception as e:
                     get_logger().error(f"Error processing suggestion {i + 1}, error: {e}")
-        else:
-            # get_logger().error(f"Could not self-reflect on suggestions. using default score 7")
-            for i, suggestion in enumerate(data["code_suggestions"]):
-                suggestion["score"] = 7
-                suggestion["score_why"] = ""
-
-        return data
 
     @staticmethod
     def _truncate_if_needed(suggestion):
@@ -451,6 +510,11 @@ class PRCodeSuggestions:
                 if not is_valid_keys:
                     continue
 
+                if get_settings().get("pr_code_suggestions.focus_only_on_problems", False):
+                    CRITICAL_LABEL = 'critical'
+                    if CRITICAL_LABEL in suggestion['label'].lower(): # we want the published labels to be less declarative
+                        suggestion['label'] = 'possible issue'
+
                 if suggestion['one_sentence_summary'] in one_sentence_summary_list:
                     get_logger().debug(f"Skipping suggestion {i + 1}, because it is a duplicate: {suggestion}")
                     continue
@@ -474,7 +538,7 @@ 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']:
@@ -572,7 +636,9 @@ 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():
@@ -630,62 +696,6 @@ 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"
@@ -801,7 +811,12 @@ 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 ""
 
@@ -814,13 +829,21 @@ class PRCodeSuggestions:
                          'suggestion_str': suggestion_str,
                          "diff": patches_diff,
                          'num_code_suggestions': len(suggestion_list),
+                         'prev_suggestions_str': prev_suggestions_str,
                          "is_ai_metadata": get_settings().get("config.enable_ai_metadata", False)}
             environment = Environment(undefined=StrictUndefined)
+
+            if dedicated_prompt:
                 system_prompt_reflect = environment.from_string(
-                get_settings().pr_code_suggestions_reflect_prompt.system).render(
+                    get_settings().get(dedicated_prompt).system).render(variables)
-                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,
@@ -829,4 +852,3 @@ class PRCodeSuggestions:
             get_logger().info(f"Could not reflect on suggestions, error: {e}")
             return ""
         return response_reflect
-

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
 
@@ -9,19 +10,24 @@ 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, get_pr_diff_multiple_patchs, \
+from pr_agent.algo.pr_processing import (OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD,
-    OUTPUT_BUFFER_TOKENS_HARD_THRESHOLD
+                                         get_pr_diff,
+                                         get_pr_diff_multiple_patchs,
+                                         retry_with_fallback_models)
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import set_custom_labels, PRDescriptionHeader
+from pr_agent.algo.utils import (ModelType, PRDescriptionHeader, clip_tokens,
-from pr_agent.algo.utils import load_yaml, get_user_labels, ModelType, show_relevant_configurations, get_max_tokens, \
+                                 get_max_tokens, get_user_labels, load_yaml,
-    clip_tokens
+                                 set_custom_labels,
+                                 show_relevant_configurations)
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider, GithubProvider, get_git_provider_with_context
+from pr_agent.git_providers import (GithubProvider, get_git_provider,
+                                    get_git_provider_with_context)
 from pr_agent.git_providers.git_provider import get_main_pr_language
 from pr_agent.log import get_logger
 from pr_agent.servers.help import HelpMessage
-from pr_agent.tools.ticket_pr_compliance_check import extract_ticket_links_from_pr_description, extract_tickets, \
+from pr_agent.tools.ticket_pr_compliance_check import (
-    extract_and_cache_pr_tickets
+    extract_and_cache_pr_tickets, extract_ticket_links_from_pr_description,
+    extract_tickets)
 
 
 class PRDescription:
@@ -52,6 +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(),
@@ -64,6 +71,7 @@ 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
         }
 
         self.user_description = self.git_provider.get_user_description()
@@ -80,7 +88,6 @@ 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:
@@ -94,7 +101,7 @@ 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()
@@ -109,6 +116,8 @@ 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()
@@ -132,6 +141,7 @@ class PRDescription:
                 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)
@@ -159,43 +169,49 @@ 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(
+            get_logger().info("Markers were enabled, but user description does not contain markers. skipping AI prediction")
-                "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,
+        output = get_pr_diff(self.git_provider, self.token_handler, model, large_pr_handling=large_pr_handling, return_remaining_files=True)
-                             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):
+                # extend the prediction with additional files not shown
-                    get_logger().debug(f"Extending additional files, {len(remaining_files_list)} files")
+                if get_settings().pr_description.enable_semantic_files_types:
-                    self.prediction = await self.extend_additional_files(remaining_files_list)
+                    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
@@ -280,43 +296,81 @@ class PRDescription:
                                                             prompt="pr_description_only_description_prompts")
             prediction_headers = prediction_headers.strip().removeprefix('```yaml').strip('`').strip()
 
-            # manually add extra files to final prediction
+            # extend the tables with the files not shown
-            MAX_EXTRA_FILES_TO_OUTPUT = 100
+            files_walkthrough_extended = await self.extend_uncovered_files(files_walkthrough)
-            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
 
             # 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:
@@ -388,31 +442,31 @@ 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(',')
+                pr_labels = self.data['labels'].split(',')
-        elif 'type' in self.data:
+        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_labels = self.data['type'].split(',')
-        pr_types = [label.strip() for label in pr_types]
+        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}")
@@ -519,14 +573,18 @@ 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:
@@ -569,12 +627,14 @@ extra_file_yaml =
                 for filename, file_changes_title, file_change_description in list_tuples:
                     filename = filename.replace("'", "`").rstrip()
                     filename_publish = filename.split("/")[-1]
-
+                    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()
@@ -583,6 +643,8 @@ 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
 
@@ -591,8 +653,39 @@ 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 = 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>
@@ -613,17 +706,7 @@ extra_file_yaml =
 
 </tr>
 """
-                if use_collapsible_file_list:
+        return pr_body
-                    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
-
 
 def count_chars_without_html(string):
     if '<' not in string:
@@ -632,11 +715,14 @@ 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_generate_labels.py

@@ -9,7 +9,7 @@ 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.algo.utils import load_yaml, set_custom_labels, get_user_labels
+from pr_agent.algo.utils import get_user_labels, load_yaml, set_custom_labels
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language

pr_agent/tools/pr_help_message.py

@@ -9,10 +9,10 @@ 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 retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import ModelType, load_yaml, clip_tokens
+from pr_agent.algo.utils import ModelType, clip_tokens, load_yaml
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import GithubProvider, BitbucketServerProvider, \
+from pr_agent.git_providers import (BitbucketServerProvider, GithubProvider,
-    get_git_provider_with_context
+                                    get_git_provider_with_context)
 from pr_agent.log import get_logger
 
 
@@ -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')

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

@@ -6,8 +6,8 @@ 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.git_patch_processing import convert_to_hunks_with_lines_numbers, \
+from pr_agent.algo.git_patch_processing import (
-    extract_hunk_lines_from_patch
+    convert_to_hunks_with_lines_numbers, extract_hunk_lines_from_patch)
 from pr_agent.algo.pr_processing import get_pr_diff, retry_with_fallback_models
 from pr_agent.algo.token_handler import TokenHandler
 from pr_agent.algo.utils import ModelType
@@ -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

@@ -4,19 +4,27 @@ import traceback
 from collections import OrderedDict
 from functools import partial
 from typing import List, Tuple
+
 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, add_ai_metadata_to_diff_files
+from pr_agent.algo.pr_processing import (add_ai_metadata_to_diff_files,
+                                         get_pr_diff,
+                                         retry_with_fallback_models)
 from pr_agent.algo.token_handler import TokenHandler
-from pr_agent.algo.utils import github_action_output, load_yaml, ModelType, \
+from pr_agent.algo.utils import (ModelType, PRReviewHeader,
-    show_relevant_configurations, convert_to_markdown_v2, PRReviewHeader
+                                 convert_to_markdown_v2, github_action_output,
+                                 load_yaml, show_relevant_configurations)
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider, get_git_provider_with_context
+from pr_agent.git_providers import (get_git_provider,
-from pr_agent.git_providers.git_provider import IncrementalPR, get_main_pr_language
+                                    get_git_provider_with_context)
+from pr_agent.git_providers.git_provider import (IncrementalPR,
+                                                 get_main_pr_language)
 from pr_agent.log import get_logger
 from pr_agent.servers.help import HelpMessage
-from pr_agent.tools.ticket_pr_compliance_check import extract_tickets, extract_and_cache_pr_tickets
+from pr_agent.tools.ticket_pr_compliance_check import (
+    extract_and_cache_pr_tickets, extract_tickets)
 
 
 class PRReviewer:
@@ -78,7 +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,
@@ -140,7 +147,7 @@ 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
@@ -160,8 +167,10 @@ class PRReviewer:
                     self.git_provider.publish_comment(pr_review)
 
                 self.git_provider.remove_initial_comment()
-                if get_settings().pr_reviewer.inline_code_comments:
+            else:
-                    self._publish_inline_code_comments()
+                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}")
 
@@ -223,33 +232,6 @@ 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:
@@ -258,7 +240,9 @@ 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:
@@ -278,38 +262,6 @@ 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.

pr_agent/tools/pr_similar_issue.py

@@ -34,9 +34,9 @@ class PRSimilarIssue:
 
         if get_settings().pr_similar_issue.vectordb == "pinecone":
             try:
+                import pandas as pd
                 import pinecone
                 from pinecone_datasets import Dataset, DatasetMetadata
-                import pandas as pd
             except:
                 raise Exception("Please install 'pinecone' and 'pinecone_datasets' to use pinecone as vectordb")
             # assuming pinecone api key and environment are set in secrets file

pr_agent/tools/pr_update_changelog.py

@@ -3,14 +3,16 @@ from datetime import date
 from functools import partial
 from time import sleep
 from typing import Tuple
+
 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.algo.utils import ModelType, show_relevant_configurations
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import get_git_provider, GithubProvider
+from pr_agent.git_providers import GithubProvider, get_git_provider
 from pr_agent.git_providers.git_provider import get_main_pr_language
 from pr_agent.log import get_logger
 
@@ -39,6 +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,
@@ -71,7 +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()
 
@@ -100,12 +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

@@ -108,7 +108,7 @@ async def extract_tickets(git_provider):
 
 
 async def extract_and_cache_pr_tickets(git_provider, vars):
-    if get_settings().get('config.require_ticket_analysis_review', False):
+    if not get_settings().get('pr_reviewer.require_ticket_analysis_review', False):
         return
     related_tickets = get_settings().get('related_tickets', [])
     if not related_tickets:

pyproject.toml

@@ -4,21 +4,21 @@ 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"}]
+authors = [{ name = "CodiumAI", email = "tal.r@codium.ai" }]
 
 maintainers = [
-  {name = "Tal Ridnik", email = "tal.r@codium.ai"},
+  { name = "Tal Ridnik", email = "tal.r@codium.ai" },
-  {name = "Ori Kotek", email = "ori.k@codium.ai"},
+  { name = "Ori Kotek", email = "ori.k@codium.ai" },
-  {name = "Hussam Lawen", email = "hussam.l@codium.ai"},
+  { name = "Hussam Lawen", email = "hussam.l@codium.ai" },
 ]
 
 description = "CodiumAI PR-Agent aims to help efficiently review and handle pull requests, by providing AI feedbacks and suggestions."
 readme = "README.md"
 requires-python = ">=3.10"
 keywords = ["AI", "Agents", "Pull Request", "Automation", "Code Review"]
-license = {name = "Apache 2.0", file = "LICENSE"}
+license = { name = "Apache 2.0", file = "LICENSE" }
 
 classifiers = [
   "Intended Audience :: Developers",
@@ -28,7 +28,7 @@ dynamic = ["dependencies"]
 
 
 [tool.setuptools.dynamic]
-dependencies = {file = ["requirements.txt"]}
+dependencies = { file = ["requirements.txt"] }
 
 [project.urls]
 "Homepage" = "https://github.com/Codium-ai/pr-agent"
@@ -40,41 +40,43 @@ license-files = ["LICENSE"]
 
 [tool.setuptools.packages.find]
 where = ["."]
-include = ["pr_agent*"] # include pr_agent and any sub-packages it finds under it.
+include = [
+  "pr_agent*",
+] # include pr_agent and any sub-packages it finds under it.
 
 [project.scripts]
 pr-agent = "pr_agent.cli:run"
 
-
 [tool.ruff]
-
 line-length = 120
 
-select = [
+lint.select = [
   "E",    # Pyflakes
   "F",    # Pyflakes
   "B",    # flake8-bugbear
   "I001", # isort basic checks
   "I002", # isort missing-required-import
-  ]
+]
 
 # First commit - only fixing isort
-fixable = [
+lint.fixable = [
   "I001", # isort basic checks
 ]
 
-unfixable = [
+lint.unfixable = [
   "B", # Avoid trying to fix flake8-bugbear (`B`) violations.
-  ]
-
-exclude = [
-  "api/code_completions",
 ]
 
-ignore = [
+lint.exclude = ["api/code_completions"]
-  "E999", "B008"
-]
 
-[tool.ruff.per-file-ignores]
+lint.ignore = ["E999", "B008"]
-"__init__.py" = ["E402"]  # Ignore `E402` (import violations) in all `__init__.py` files, and in `path/to/file.py`.
+
-# TODO: should decide if maybe not to ignore these.
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = [
+  "E402",
+] # Ignore `E402` (import violations) in all `__init__.py` files, and in `path/to/file.py`.
+
+[tool.bandit]
+exclude_dirs = ["tests"]
+skips = ["B101"]
+tests = []

requirements-dev.txt

@@ -1,3 +1,4 @@
 pytest==7.4.0
 poetry
 twine
+pre-commit>=4,<5

requirements.txt

@@ -1,5 +1,5 @@
 aiohttp==3.9.5
-anthropic[vertex]==0.37.1
+anthropic[vertex]==0.39.0
 atlassian-python-api==3.41.4
 azure-devops==7.1.0b3
 azure-identity==1.15.0
@@ -12,17 +12,17 @@ google-cloud-aiplatform==1.38.0
 google-generativeai==0.8.3
 google-cloud-storage==2.10.0
 Jinja2==3.1.2
-litellm==1.50.2
+litellm==1.52.12
 loguru==0.7.2
 msrest==0.7.1
-openai==1.52.1
+openai==1.55.3
 pytest==7.4.0
 PyGithub==1.59.*
 PyYAML==6.0.1
 python-gitlab==3.15.0
 retry==0.9.2
 starlette-context==0.3.6
-tiktoken==0.7.0
+tiktoken==0.8.0
 ujson==5.8.0
 uvicorn==0.22.0
 tenacity==8.2.3

tests/e2e_tests/e2e_utils.py

@@ -32,4 +32,3 @@ def main():
 if __name__ == '__main__':
     main()
 """
-

tests/e2e_tests/test_bitbucket_app.py

@@ -5,16 +5,16 @@ import time
 from datetime import datetime
 
 import jwt
-from atlassian.bitbucket import Cloud
-
 import requests
+from atlassian.bitbucket import Cloud
 from requests.auth import HTTPBasicAuth
 
 from pr_agent.config_loader import get_settings
-from pr_agent.log import setup_logger, get_logger
+from pr_agent.log import get_logger, setup_logger
-from tests.e2e_tests.e2e_utils import NEW_FILE_CONTENT, FILE_PATH, PR_HEADER_START_WITH, REVIEW_START_WITH, \
+from tests.e2e_tests.e2e_utils import (FILE_PATH,
-    IMPROVE_START_WITH_REGEX_PATTERN, NUM_MINUTES
+                                       IMPROVE_START_WITH_REGEX_PATTERN,
-
+                                       NEW_FILE_CONTENT, NUM_MINUTES,
+                                       PR_HEADER_START_WITH, REVIEW_START_WITH)
 
 log_level = os.environ.get("LOG_LEVEL", "INFO")
 setup_logger(log_level)

tests/e2e_tests/test_github_app.py

@@ -5,9 +5,11 @@ from datetime import datetime
 
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
-from pr_agent.log import setup_logger, get_logger
+from pr_agent.log import get_logger, setup_logger
-from tests.e2e_tests.e2e_utils import NEW_FILE_CONTENT, FILE_PATH, PR_HEADER_START_WITH, REVIEW_START_WITH, \
+from tests.e2e_tests.e2e_utils import (FILE_PATH,
-    IMPROVE_START_WITH_REGEX_PATTERN, NUM_MINUTES
+                                       IMPROVE_START_WITH_REGEX_PATTERN,
+                                       NEW_FILE_CONTENT, NUM_MINUTES,
+                                       PR_HEADER_START_WITH, REVIEW_START_WITH)
 
 log_level = os.environ.get("LOG_LEVEL", "INFO")
 setup_logger(log_level)

tests/e2e_tests/test_gitlab_webhook.py

@@ -7,9 +7,11 @@ import gitlab
 
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
-from pr_agent.log import setup_logger, get_logger
+from pr_agent.log import get_logger, setup_logger
-from tests.e2e_tests.e2e_utils import NEW_FILE_CONTENT, FILE_PATH, PR_HEADER_START_WITH, REVIEW_START_WITH, \
+from tests.e2e_tests.e2e_utils import (FILE_PATH,
-    IMPROVE_START_WITH_REGEX_PATTERN, NUM_MINUTES
+                                       IMPROVE_START_WITH_REGEX_PATTERN,
+                                       NEW_FILE_CONTENT, NUM_MINUTES,
+                                       PR_HEADER_START_WITH, REVIEW_START_WITH)
 
 log_level = os.environ.get("LOG_LEVEL", "INFO")
 setup_logger(log_level)

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

@@ -1,8 +1,10 @@
+from unittest.mock import MagicMock
+
+from atlassian.bitbucket import Bitbucket
+
+from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 from pr_agent.git_providers import BitbucketServerProvider
 from pr_agent.git_providers.bitbucket_provider import BitbucketProvider
-from unittest.mock import MagicMock
-from atlassian.bitbucket import Bitbucket
-from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
 
 
 class TestBitbucketProvider:

tests/unittest/test_codecommit_client.py

@@ -1,4 +1,5 @@
 from unittest.mock import MagicMock
+
 from pr_agent.git_providers.codecommit_client import CodeCommitClient
 
 

tests/unittest/test_codecommit_provider.py

@@ -1,9 +1,11 @@
-import pytest
 from unittest.mock import patch
-from pr_agent.git_providers.codecommit_provider import CodeCommitFile
+
-from pr_agent.git_providers.codecommit_provider import CodeCommitProvider
+import pytest
-from pr_agent.git_providers.codecommit_provider import PullRequestCCMimic
+
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
+from pr_agent.git_providers.codecommit_provider import (CodeCommitFile,
+                                                        CodeCommitProvider,
+                                                        PullRequestCCMimic)
 
 
 class TestCodeCommitFile:

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_tests': 'No\n', 'possible_issues': 'No\n', 'security_concerns': 'No\n'}}
-            {'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)'}]}
 
 
-        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

@@ -1,4 +1,5 @@
 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

tests/unittest/test_file_filter.py

@@ -1,7 +1,9 @@
 import pytest
+
 from pr_agent.algo.file_filter import filter_ignored
 from pr_agent.config_loader import global_settings
 
+
 class TestIgnoreFilter:
     def test_no_ignores(self):
         """

tests/unittest/test_find_line_number_of_relevant_line_in_file.py

@@ -1,9 +1,10 @@
 
 # Generated by CodiumAI
+import pytest
+
 from pr_agent.algo.types import FilePatchInfo
 from pr_agent.algo.utils import find_line_number_of_relevant_line_in_file
 
-import pytest
 
 class TestFindLineNumberOfRelevantLineInFile:
     # Tests that the function returns the correct line number and absolute position when the relevant line is found in the patch

tests/unittest/test_github_action_output.py

@@ -1,7 +1,9 @@
-import os
 import json
+import os
+
 from pr_agent.algo.utils import get_settings, github_action_output
 
+
 class TestGitHubOutput:
     def test_github_action_output_enabled(self, monkeypatch, tmp_path):
         get_settings().set('GITHUB_ACTION_CONFIG.ENABLE_OUTPUT', True)

tests/unittest/test_load_yaml.py

@@ -47,7 +47,3 @@ PR Feedback:
 
         expected_output = [{'relevant file': 'src/app.py:\n', 'suggestion content': 'The print statement is outside inside the if __name__ ==:'}]
         assert load_yaml(yaml_str) == expected_output
-
-
-
-

tests/unittest/test_try_fix_yaml.py

@@ -1,10 +1,10 @@
 
 # Generated by CodiumAI
+import pytest
+
 from pr_agent.algo.utils import try_fix_yaml
 
 
-import pytest
-
 class TestTryFixYaml:
 
     # The function successfully parses a valid YAML string.