docs: update describe tool configuration table with missing options

Use `pip install` with `--no-cache-dir` in `Dockerfile.github_action`

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,38 @@
+name: "\U0001FAB2 Bug Report"
+description: Submit a bug report
+labels: ["bug"]
+body:
+
+  - type: dropdown
+    id: information-git-provider
+    attributes:
+      label: Git provider
+      description: 'The problem arises when using:'
+      options:
+        - "Github Cloud"
+        - "Github Enterprise"
+        - "Gitlab"
+        - "Bitbucket Cloud"
+        - "Bitbucket Server"
+        - "Azure"
+        - "Other"
+    validations:
+      required: true
+
+  - type: textarea
+    id: system-info
+    attributes:
+      label: System Info
+      description: Please share your system info with us.
+      placeholder: model used, deployment type (action/app/cli/...), etc...
+    validations:
+      required: true
+
+  - type: textarea
+    id: bug-details
+    attributes:
+      label: Bug details
+      description: Please describe the problem.
+      placeholder: Describe the problem
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,10 @@
+blank_issues_enabled: false
+version: 0.1
+contact_links:
+  - name: Discussions
+    url: https://github.com/qodo-ai/pr-agent/discussions
+    about: GitHub Discussions
+
+  - name: Discord community
+    url: https://discord.com/channels/1057273017547378788/1126104260430528613
+    about: Join our discord community

.github/ISSUE_TEMPLATE/feature-request.yml

@@ -0,0 +1,21 @@
+name: "\U0001F4A1 Feature request"
+description: Submit a proposal/request for a new PR-Agent feature
+labels: ["feature"]
+body:
+  - type: textarea
+    id: feature-request
+    validations:
+      required: true
+    attributes:
+      label: Feature request
+      description: |
+        Description of the feature proposal.
+
+  - type: textarea
+    id: motivation
+    validations:
+      required: true
+    attributes:
+      label: Motivation
+      description: |
+        Outline the motivation for the proposal.

.github/ISSUE_TEMPLATE/miscellaneous.yml

@@ -0,0 +1,36 @@
+name: "❔ General Issue"
+description: Submit a general issue
+labels: ["general"]
+body:
+
+  - type: dropdown
+    id: information-git-provider
+    attributes:
+      label: Git provider (optional)
+      description: 'Git Provider:'
+      options:
+        - "Github Cloud"
+        - "Github Enterprise"
+        - "Gitlab"
+        - "Bitbucket Cloud"
+        - "Bitbucket Server"
+        - "Azure"
+        - "Other"
+
+  - type: textarea
+    id: system-info
+    attributes:
+      label: System Info (optional)
+      description: Please share your system info with us.
+      placeholder: model used, deployment type (action/app/cli/...), etc...
+    validations:
+      required: false
+
+  - type: textarea
+    id: issues-details
+    attributes:
+      label: Issues details
+      description: Please share the issues details.
+      placeholder: Describe the issue
+    validations:
+      required: true

CODE_OF_CONDUCT.md

@@ -0,0 +1,45 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, and in the interest of fostering an open
+and welcoming community, we pledge to respect all people who contribute through reporting
+issues, posting feature requests, updating documentation, submitting pull requests or
+patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age,
+religion, or nationality.
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery
+* Personal attacks
+* Trolling or insulting/derogatory comments
+* Public or private harassment
+* Publishing other's private information, such as physical or electronic addresses,
+  without explicit permission
+* Other unethical or unprofessional conduct
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this
+Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors
+that they deem inappropriate, threatening, offensive, or harmful.
+
+By adopting this Code of Conduct, project maintainers commit themselves to fairly and
+consistently applying these principles to every aspect of managing this project. Project
+maintainers who do not follow or enforce the Code of Conduct may be permanently removed
+from the project team.
+
+This Code of Conduct applies both within project spaces and in public spaces when an
+individual is representing the project or its community.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by
+contacting a project maintainer at tal.r@qodo.ai . All complaints will
+be reviewed and investigated and will result in a response that is deemed necessary and
+appropriate to the circumstances. Maintainers are obligated to maintain confidentiality
+with regard to the reporter of an incident.
+
+This Code of Conduct is adapted from the
+[Contributor Covenant](https://contributor-covenant.org), version 1.3.0, available at
+[contributor-covenant.org/version/1/3/0/](https://contributor-covenant.org/version/1/3/0/)
+

CONTRIBUTING.md

@@ -0,0 +1,38 @@
+# Contributing to PR-Agent
+
+Thank you for your interest in contributing to the PR-Agent project! 
+
+## Getting Started
+
+1. Fork the repository and clone your fork
+2. Install Python 3.10 or higher
+3. Install dependencies (`requirements.txt` and `requirements-dev.txt`)
+4. Create a new branch for your contribution:
+   - For new features: `git checkout -b feature/your-feature-name`
+   - For bug fixes: `git checkout -b fix/issue-description`
+5. Make your changes
+6. Write or update tests as needed
+7. Run tests locally to ensure everything passes
+8. Commit your changes using conventional commit messages
+9. Push to your fork and submit a pull request
+
+## Development Guidelines
+
+- Keep pull requests focused on a single feature or fix
+- Follow the existing code style and formatting conventions
+- Add unit tests for any new functionality using pytest
+- Ensure test coverage for your changes
+- Update documentation as needed
+
+## Pull Request Process
+
+1. Ensure your PR includes a clear description of the changes
+2. Link any related issues
+3. Update the README.md if needed
+4. Wait for review from maintainers
+
+## Questions or Need Help?
+
+- Join our [Discord community](https://discord.com/channels/1057273017547378788/1126104260430528613) for questions and discussions
+- Check the [documentation](https://qodo-merge-docs.qodo.ai/) for detailed information
+- Report bugs or request features through [GitHub Issues](https://github.com/qodo-ai/pr-agent/issues)

Dockerfile.github_action

@@ -3,7 +3,7 @@ FROM python:3.12 as base
 WORKDIR /app
 ADD pyproject.toml .
 ADD requirements.txt .
-RUN pip install . && rm pyproject.toml requirements.txt
+RUN pip install --no-cache-dir . && rm pyproject.toml requirements.txt
 ENV PYTHONPATH=/app
 ADD docs docs
 ADD pr_agent pr_agent

README.md

@@ -10,6 +10,12 @@
 
 </picture>
 <br/>
+
+ [Installation Guide](https://qodo-merge-docs.qodo.ai/installation/) | 
+[Usage Guide](https://qodo-merge-docs.qodo.ai/usage-guide/) | 
+[Tools Guide](https://qodo-merge-docs.qodo.ai/tools/) | 
+[Qodo Merge](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) 💎
+
 PR-Agent aims to help efficiently review and handle pull requests, by providing AI feedback and suggestions
 </div>
 
@@ -22,13 +28,16 @@ PR-Agent aims to help efficiently review and handle pull requests, by providing
 </a>
 </div>
 
-### [Documentation](https://qodo-merge-docs.qodo.ai/)
+[//]: # (### [Documentation]&#40;https://qodo-merge-docs.qodo.ai/&#41;)
 
-- See the [Installation Guide](https://qodo-merge-docs.qodo.ai/installation/) for instructions on installing PR-Agent on different platforms.
+[//]: # ()
+[//]: # (- See the [Installation Guide]&#40;https://qodo-merge-docs.qodo.ai/installation/&#41; for instructions on installing PR-Agent on different platforms.)
 
-- See the [Usage Guide](https://qodo-merge-docs.qodo.ai/usage-guide/) for instructions on running PR-Agent tools via different interfaces, such as CLI, PR Comments, or by automatically triggering them when a new PR is opened.
+[//]: # ()
+[//]: # (- See the [Usage Guide]&#40;https://qodo-merge-docs.qodo.ai/usage-guide/&#41; for instructions on running PR-Agent tools via different interfaces, such as CLI, PR Comments, or by automatically triggering them when a new PR is opened.)
 
-- See the [Tools Guide](https://qodo-merge-docs.qodo.ai/tools/) for a detailed description of the different tools, and the available configurations for each tool.
+[//]: # ()
+[//]: # (- See the [Tools Guide]&#40;https://qodo-merge-docs.qodo.ai/tools/&#41; for a detailed description of the different tools, and the available configurations for each tool.)
 
 
 ## Table of Contents
@@ -37,12 +46,17 @@ PR-Agent aims to help efficiently review and handle pull requests, by providing
 - [Overview](#overview)
 - [Example results](#example-results)
 - [Try it now](#try-it-now)
-- [Qodo Merge 💎](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/)
+- [Qodo Merge](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/)
 - [How it works](#how-it-works)
 - [Why use PR-Agent?](#why-use-pr-agent)
 
 ## News and Updates
 
+### Feb 6, 2025
+New design for the `/improve` tool:
+
+<kbd><img src="https://github.com/user-attachments/assets/26506430-550e-469a-adaa-af0a09b70c6d" width="512"></kbd>
+
 ### Jan 25, 2025
 
 The open-source GitHub organization was updated:
@@ -69,40 +83,7 @@ Update logic and [documentation](https://qodo-merge-docs.qodo.ai/usage-guide/cha
 
 ### December 30, 2024
 
-Following [feedback](https://research.kudelskisecurity.com/2024/08/29/careful-where-you-code-multiple-vulnerabilities-in-ai-powered-pr-agent/) from the community, we have addressed two vulnerabilities identified in the open-source PR-Agent project. The fixes are now included in the newly released version (v0.26), available as of today.
-
-### December 25, 2024
-
-The `review` tool previously included a legacy feature for providing code suggestions (controlled by '--pr_reviewer.num_code_suggestion'). This functionality has been deprecated. Use instead the [`improve`](https://qodo-merge-docs.qodo.ai/tools/improve/) tool, which offers higher quality and more actionable code suggestions.
-
-### December 2, 2024
-
-Open-source repositories can now freely use Qodo Merge, and enjoy easy one-click installation using a marketplace [app](https://github.com/apps/qodo-merge-pro-for-open-source).
-
-<kbd><img src="https://github.com/user-attachments/assets/b0838724-87b9-43b0-ab62-73739a3a855c" width="512"></kbd>
-
-See [here](https://qodo-merge-docs.qodo.ai/installation/pr_agent_pro/) for more details about installing Qodo Merge for private repositories.
-
-
-### November 18, 2024
-
-A new mode was enabled by default for code suggestions - `--pr_code_suggestions.focus_only_on_problems=true`:
-
-- This option reduces the number of code suggestions received
-- 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".
-
-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>
+Following feedback from the community, we have addressed two vulnerabilities identified in the open-source PR-Agent project. The [fixes](https://github.com/qodo-ai/pr-agent/pull/1425) are now included in the newly released version (v0.26), available as of today.
 
 
 ## Overview

SECURITY.md

@@ -0,0 +1,62 @@
+# Security Policy
+
+PR-Agent is an open-source tool to help efficiently review and handle pull requests. Qodo Merge is a paid version of PR-Agent, designed for companies and teams that require additional features and capabilities. 
+
+This document describes the security policy of PR-Agent. For Qodo Merge's security policy, see [here](https://qodo-merge-docs.qodo.ai/overview/data_privacy/#qodo-merge).
+
+## PR-Agent Self-Hosted Solutions
+
+When using PR-Agent with your OpenAI (or other LLM provider) API key, the security relationship is directly between you and the provider. We do not send your code to Qodo servers.
+
+Types of [self-hosted solutions](https://qodo-merge-docs.qodo.ai/installation):
+- Locally
+- GitHub integration
+- GitLab integration
+- BitBucket integration
+- Azure DevOps integration
+
+
+## PR-Agent Supported Versions
+
+This section outlines which versions of PR-Agent are currently supported with security updates.
+
+### Docker Deployment Options
+
+#### Latest Version
+
+For the most recent updates, use our latest Docker image which is automatically built nightly:
+```yaml
+uses: qodo-ai/pr-agent@main
+```
+
+#### Specific Release Version
+
+For a fixed version, you can pin your action to a specific release version. Browse available releases at:
+[PR-Agent Releases](https://github.com/qodo-ai/pr-agent/releases)
+
+For example, to github action:
+
+```yaml
+steps:
+  - name: PR Agent action step
+    id: pragent
+    uses: docker://codiumai/pr-agent:0.26-github_action
+```
+
+#### Enhanced Security with Docker Digest
+
+For maximum security, you can specify the Docker image using its digest:
+```yaml
+steps:
+  - name: PR Agent action step
+    id: pragent
+    uses: docker://codiumai/pr-agent@sha256:14165e525678ace7d9b51cda8652c2d74abb4e1d76b57c4a6ccaeba84663cc64
+```
+
+## Reporting a Vulnerability
+
+We take the security of PR-Agent seriously. If you discover a security vulnerability, please report it immediately to:
+
+Email: tal.r@qodo.ai
+
+Please include a description of the vulnerability, steps to reproduce, and the affected PR-Agent version.

docker/Dockerfile

@@ -4,7 +4,7 @@ WORKDIR /app
 ADD pyproject.toml .
 ADD requirements.txt .
 ADD docs docs
-RUN pip install . && rm pyproject.toml requirements.txt
+RUN pip install --no-cache-dir . && rm pyproject.toml requirements.txt
 ENV PYTHONPATH=/app
 
 FROM base AS github_app
@@ -33,7 +33,7 @@ CMD ["python", "pr_agent/servers/azuredevops_server_webhook.py"]
 
 FROM base AS test
 ADD requirements-dev.txt .
-RUN pip install -r requirements-dev.txt && rm requirements-dev.txt
+RUN pip install --no-cache-dir -r requirements-dev.txt && rm requirements-dev.txt
 ADD pr_agent pr_agent
 ADD tests tests
 

docker/Dockerfile.lambda

@@ -5,8 +5,8 @@ RUN yum update -y && \
     yum clean all
 
 ADD pyproject.toml requirements.txt .
-RUN pip install . && rm pyproject.toml
-RUN pip install mangum==0.17.0
+RUN pip install --no-cache-dir . && rm pyproject.toml
+RUN pip install --no-cache-dir mangum==0.17.0
 COPY pr_agent/ ${LAMBDA_TASK_ROOT}/pr_agent/
 
 CMD ["pr_agent.servers.serverless.serverless"]

docs/docs/core-abilities/index.md

@@ -19,6 +19,7 @@ Here are some additional technical blogs from Qodo, that delve deeper into the c
 These resources provide more comprehensive insights into leveraging LLMs for software development.
 
 ### Code Generation and LLMs
+- [Effective AI code suggestions: less is more](https://www.qodo.ai/blog/effective-code-suggestions-llms-less-is-more/)
 - [State-of-the-art Code Generation with AlphaCodium – From Prompt Engineering to Flow Engineering](https://www.qodo.ai/blog/qodoflow-state-of-the-art-code-generation-for-code-contests/)
 - [RAG for a Codebase with 10k Repos](https://www.qodo.ai/blog/rag-for-large-scale-code-repos/)
 

docs/docs/installation/qodo_merge.md

@@ -15,7 +15,7 @@ Qodo Merge for GitHub cloud is available for installation through the [GitHub Ma
 
 ### GitHub Enterprise Server
 
-To use Qodo Merge application on your private GitHub Enterprise Server, you will need to contact us for starting an [Enterprise](https://www.codium.ai/pricing/) trial.
+To use Qodo Merge application on your private GitHub Enterprise Server, you will need to [contact](https://www.qodo.ai/contact/#pricing) Qodo for starting an Enterprise trial.
 
 ### GitHub Open Source Projects
 
@@ -34,7 +34,9 @@ Qodo Merge for Bitbucket Cloud is available for installation through the followi
 To use Qodo Merge application on your private Bitbucket Server, you will need to contact us for starting an [Enterprise](https://www.qodo.ai/pricing/) trial.
 
 
-## Install Qodo Merge for GitLab (Teams & Enterprise)
+## Install Qodo Merge for GitLab 
+
+### GitLab Cloud
 
 Since GitLab platform does not support apps, installing Qodo Merge for GitLab is a bit more involved, and requires the following steps:
 
@@ -79,3 +81,7 @@ Enable SSL verification: Check the box.
 You’re all set!
 
 Open a new merge request or add a MR comment with one of Qodo Merge’s commands such as /review, /describe or /improve.
+
+### GitLab Server
+
+For a trial period of two weeks on your private GitLab Server, the same [installation steps](#gitlab-cloud) as for GitLab Cloud apply. After the trial period, you will need to [contact](https://www.qodo.ai/contact/#pricing) Qodo for moving to an Enterprise account.

docs/docs/overview/pr_agent_pro.md

@@ -1,6 +1,6 @@
 ### Overview
 
-[Qodo Merge](https://www.codium.ai/pricing/){:target="_blank"} is a hosted version of open-source [PR-Agent](https://github.com/Codium-ai/pr-agent){:target="_blank"}. A complimentary two-week trial is offered, followed by a monthly subscription fee.
+[Qodo Merge](https://www.codium.ai/pricing/){:target="_blank"} is a paid, hosted version of open-source [PR-Agent](https://github.com/Codium-ai/pr-agent){:target="_blank"}. A complimentary two-week trial is offered, followed by a monthly subscription fee.
 Qodo Merge is designed for companies and teams that require additional features and capabilities. It provides the following benefits:
 
 1. **Fully managed** - We take care of everything for you - hosting, models, regular updates, and more. Installation is as simple as signing up and adding the Qodo Merge app to your GitHub\GitLab\BitBucket repo.

docs/docs/tools/describe.md

@@ -85,7 +85,19 @@ publish_labels = true
   </tr>
   <tr>
     <td><b>collapsible_file_list</b></td>
-    <td>If set to true, the file list in the "Changes walkthrough" section will be collapsible. If set to "adaptive", the file list will be collapsible only if there are more than 8 files. Default is "adaptive".</td>
+    <td>If set to true, the file list in the "Changes walkthrough" section will be collapsible. If set to "adaptive", the file list will be collapsible only if the number of files exceeds the threshold defined by `collapsible_file_list_threshold`. Default is "adaptive".</td>
+  </tr>
+  <tr>
+    <td><b>collapsible_file_list_threshold</b></td>
+    <td>The number of files threshold for when to make the file list collapsible when using 'adaptive' mode. Default is 8.</td>
+  </tr>
+  <tr>
+    <td><b>inline_file_summary</b></td>
+    <td>Controls where and how file summaries are displayed:
+    <br>- 'table': Displays file changes walkthrough table on both "Files changed" and "Conversation" tabs
+    <br>- true: Adds a collapsible file comment with changes title and summary for each file
+    <br>- false: Shows file changes walkthrough only in the "Conversation" tab
+    <br>Default is false.</td>
   </tr>
   <tr>
     <td><b>enable_large_pr_handling</b></td>
@@ -95,6 +107,14 @@ publish_labels = true
     <td><b>enable_help_text</b></td>
     <td>If set to true, the tool will display a help text in the comment. Default is false.</td>
   </tr>
+  <tr>
+    <td><b>enable_help_comment</b></td>
+    <td>If set to true, the help guidance text is displayed in the comment. Default is true.</td>
+  </tr>
+  <tr>
+    <td><b>enable_override_title_with_parent_tag</b></td>
+    <td>If set to true, the tool will set the PR title to the next patch version from the latest tag in the target branch, with an RC suffix (e.g., v1.0.1-rc.1). Default is false.</td>
+  </tr>
 </table>
 
 

docs/docs/tools/implement.md

@@ -1,3 +1,5 @@
+`Platforms supported: GitHub, GitLab, Bitbucket`
+
 ## Overview
 
 The `implement` tool converts human code review discussions and feedback into ready-to-commit code changes.

docs/docs/usage-guide/PR_agent_pro_models.md

@@ -1,18 +0,0 @@
-## Qodo Merge Models
-
-The default models used by Qodo Merge are a combination of Claude-3.5-sonnet and  OpenAI's GPT-4 models.
-
-Users can configure Qodo Merge to use solely a specific model by editing the [configuration](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/) file.
-
-For example, to restrict Qodo Merge to using only `Claude-3.5-sonnet`, add this setting:
-
-```
-[config]
-model="claude-3-5-sonnet"
-```
-
-Or to restrict Qodo Merge to using only `GPT-4o`, add this setting:
-```
-[config]
-model="gpt-4o"
-```

docs/docs/usage-guide/changing_a_model.md

@@ -51,7 +51,7 @@ api_base = "http://localhost:11434" # or whatever port you're running Ollama on
     
     Commercial models such as GPT-4, Claude Sonnet, and Gemini have demonstrated robust capabilities in generating structured output for code analysis tasks with large input. In contrast, most open-source models currently available (as of January 2025) face challenges with these complex tasks.
 
-    Based on our testing, local open-source models are suitable for experimentation and learning purposes, but they are not suitable for production-level code analysis tasks.
+    Based on our testing, local open-source models are suitable for experimentation and learning purposes (mainly for the `ask` command), but they are not suitable for production-level code analysis tasks.
     
     Hence, for production workflows and real-world usage, we recommend using commercial models.
 

docs/docs/usage-guide/index.md

@@ -24,4 +24,4 @@ It includes information on how to adjust Qodo Merge configurations, define which
     - [Changing a model](./additional_configurations.md#changing-a-model)
     - [Patch Extra Lines](./additional_configurations.md#patch-extra-lines)
     - [Editing the prompts](./additional_configurations.md#editing-the-prompts)
-- [Qodo Merge Models](./PR_agent_pro_models.md)
+- [Qodo Merge Models](./qodo_merge_models)

docs/docs/usage-guide/qodo_merge_models.md

@@ -0,0 +1,37 @@
+
+The default models used by Qodo Merge are a combination of Claude-3.5-sonnet and  OpenAI's GPT-4 models.
+
+### Selecting a Specific Model
+
+Users can configure Qodo Merge to use a specific model by editing the [configuration](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/) file.
+The models supported by Qodo Merge are:
+
+- `claude-3-5-sonnet`
+- `gpt-4o`
+- `deepseek-r1`
+- `o3-mini`
+
+To restrict Qodo Merge to using only `Claude-3.5-sonnet`, add this setting:
+
+```
+[config]
+model="claude-3-5-sonnet"
+```
+
+To restrict Qodo Merge to using only `GPT-4o`, add this setting:
+```
+[config]
+model="gpt-4o"
+```
+
+To restrict Qodo Merge to using only `deepseek-r1`, add this setting:
+```
+[config]
+model="deepseek/r1"
+```
+
+To restrict Qodo Merge to using only `o3-mini`, add this setting:
+```
+[config]
+model="o3-mini"
+```

docs/mkdocs.yml

@@ -20,7 +20,7 @@ nav:
     - Managing Mail Notifications: 'usage-guide/mail_notifications.md'
     - Changing a Model: 'usage-guide/changing_a_model.md'
     - Additional Configurations: 'usage-guide/additional_configurations.md'
-    - 💎 Qodo Merge Models: 'usage-guide/PR_agent_pro_models'
+    - 💎 Qodo Merge Models: 'usage-guide/qodo_merge_models.md'
   - Tools:
     - 'tools/index.md'
     - Describe: 'tools/describe.md'

pr_agent/algo/__init__.py

@@ -26,6 +26,8 @@ MAX_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
+    'o3-mini': 204800,  # 200K, but may be limited by config.max_model_tokens
+    'o3-mini-2025-01-31': 204800,  # 200K, but may be limited by config.max_model_tokens
     'claude-instant-1': 100000,
     'claude-2': 100000,
     'command-nightly': 4096,
@@ -81,3 +83,13 @@ MAX_TOKENS = {
     "watsonx/ibm/granite-34b-code-instruct": 8191,
     "watsonx/mistralai/mistral-large": 32768,
 }
+
+USER_MESSAGE_ONLY_MODELS = [
+    "deepseek/deepseek-reasoner",
+    "o1-mini",
+    "o1-mini-2024-09-12",
+    "o1",
+    "o1-2024-12-17",
+    "o3-mini",
+    "o3-mini-2025-01-31"
+]

pr_agent/algo/ai_handlers/litellm_ai_handler.py

@@ -6,6 +6,7 @@ import requests
 from litellm import acompletion
 from tenacity import retry, retry_if_exception_type, stop_after_attempt
 
+from pr_agent.algo import USER_MESSAGE_ONLY_MODELS
 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
@@ -94,6 +95,9 @@ class LiteLLMAIHandler(BaseAiHandler):
         if get_settings().get("DEEPSEEK.KEY", None):
             os.environ['DEEPSEEK_API_KEY'] = get_settings().get("DEEPSEEK.KEY")
 
+        # Models that only use user meessage
+        self.user_message_only_models = USER_MESSAGE_ONLY_MODELS
+
     def prepare_logs(self, response, system, user, resp, finish_reason):
         response_log = response.dict().copy()
         response_log['system'] = system
@@ -197,10 +201,8 @@ class LiteLLMAIHandler(BaseAiHandler):
                 messages[1]["content"] = [{"type": "text", "text": messages[1]["content"]},
                                           {"type": "image_url", "image_url": {"url": img_path}}]
 
-            # Currently, model OpenAI o1 series does not support a separate system and user prompts
-            O1_MODEL_PREFIX = 'o1'
-            model_type = model.split('/')[-1] if '/' in model else model
-            if (model_type.startswith(O1_MODEL_PREFIX)) or ("deepseek-reasoner" in model):
+            # Currently, some models do not support a separate system and user prompts
+            if self.user_message_only_models and any(entry.lower() in model.lower() for entry in self.user_message_only_models):
                 user = f"{system}\n\n\n{user}"
                 system = ""
                 get_logger().info(f"Using model {model}, combining system and user prompts")

pr_agent/algo/utils.py

@@ -735,7 +735,7 @@ def try_fix_yaml(response_text: str,
         get_logger().info(f"Successfully parsed AI prediction after adding |-\n")
         return data
     except:
-        get_logger().info(f"Failed to parse AI prediction after adding |-\n")
+        pass
 
     # second fallback - try to extract only range from first ```yaml to ````
     snippet_pattern = r'```(yaml)?[\s\S]*?```'
@@ -779,9 +779,18 @@ def try_fix_yaml(response_text: str,
         except:
             pass
 
+    # fifth fallback - try to remove leading '+' (sometimes added by AI for 'existing code' and 'improved code')
+    response_text_lines_copy = response_text_lines.copy()
+    for i in range(0, len(response_text_lines_copy)):
+        response_text_lines_copy[i] = ' ' + response_text_lines_copy[i][1:]
+    try:
+        data = yaml.safe_load('\n'.join(response_text_lines_copy))
+        get_logger().info(f"Successfully parsed AI prediction after removing leading '+'")
+        return data
+    except:
+        pass
 
-    # fifth fallback - try to remove last lines
-    data = {}
+    # sixth fallback - try to remove last lines
     for i in range(1, len(response_text_lines)):
         response_text_lines_tmp = '\n'.join(response_text_lines[:-i])
         try:

pr_agent/git_providers/github_provider.py

@@ -9,7 +9,7 @@ from datetime import datetime
 from typing import Optional, Tuple
 from urllib.parse import urlparse
 
-from github import AppAuthentication, Auth, Github
+from github import AppAuthentication, Auth, Github, GithubException
 from retry import retry
 from starlette_context import context
 
@@ -475,8 +475,17 @@ class GithubProvider(GitProvider):
             return False
 
     def edit_comment(self, comment, body: str):
-        body = self.limit_output_characters(body, self.max_comment_chars)
-        comment.edit(body=body)
+        try:
+            body = self.limit_output_characters(body, self.max_comment_chars)
+            comment.edit(body=body)
+        except GithubException as e:
+            if hasattr(e, "status") and e.status == 403:
+                # Log as warning for permission-related issues (usually due to polling)
+                get_logger().warning(
+                    "Failed to edit github comment due to permission restrictions",
+                    artifact={"error": e})
+            else:
+                get_logger().exception(f"Failed to edit github comment", artifact={"error": e})
 
     def edit_comment_from_comment_id(self, comment_id: int, body: str):
         try:

pr_agent/servers/github_action_runner.py

@@ -81,7 +81,7 @@ async def run_action():
         get_logger().info(f"github action: failed to apply repo settings: {e}")
 
     # Handle pull request opened event
-    if GITHUB_EVENT_NAME == "pull_request":
+    if GITHUB_EVENT_NAME == "pull_request" or GITHUB_EVENT_NAME == "pull_request_target":
         action = event_payload.get("action")
 
         # Retrieve the list of actions from the configuration

pr_agent/servers/github_polling.py

@@ -130,12 +130,14 @@ async def is_valid_notification(notification, headers, handled_ids, session, use
                                                       artifact={"comment": comment_body})
                                     return True, handled_ids, comment, comment_body, pr_url, user_tag
 
-                            get_logger().error(f"Failed to fetch comments for PR: {pr_url}")
+                            get_logger().warning(f"Failed to fetch comments for PR: {pr_url}",
+                                                    artifact={"comments": comments})
                             return False, handled_ids
 
         return False, handled_ids
     except Exception as e:
-        get_logger().error(f"Error processing notification: {e}", artifact={"traceback": traceback.format_exc()})
+        get_logger().exception(f"Error processing polling notification",
+                               artifact={"notification": notification, "error": e})
         return False, handled_ids
 
 

pr_agent/settings/configuration.toml

@@ -121,6 +121,9 @@ max_history_len=4
 apply_suggestions_checkbox=true
 # suggestions scoring
 suggestions_score_threshold=0 # [0-10]| recommend not to set this value above 8, since above it may clip highly relevant suggestions
+new_score_mechanism=true
+new_score_mechanism_th_high=9
+new_score_mechanism_th_medium=7
 # params for '/improve --extended' mode
 auto_extended_mode=true
 num_code_suggestions_per_chunk=4

pr_agent/settings/pr_code_suggestions_prompts.toml

@@ -90,7 +90,7 @@ class CodeSuggestion(BaseModel):
 {%- 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.")
+    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 not necessarily on a critical level.")
 {%- endif %}
 
 

pr_agent/settings/pr_help_prompts.toml

@@ -13,7 +13,7 @@ The output must be a YAML object equivalent to type $DocHelper, according to the
 =====
 class relevant_section(BaseModel):
     file_name: str = Field(description="The name of the relevant file")
-    relevant_section_header_string: str = Field(description="From the relevant file, exact text of the relevant section heading. If no markdown heading is relevant, return empty string")
+    relevant_section_header_string: str = Field(description="The exact text of the relevant markdown section heading from the relevant file  (starting with '#', '##', etc.). Return empty string if the entire file is the relevant section, or if the relevant section has no heading")
 
 class DocHelper(BaseModel):
     user_question: str = Field(description="The user's question")

pr_agent/tools/pr_code_suggestions.py

@@ -720,7 +720,7 @@ class PRCodeSuggestions:
             header = f"Suggestion"
             delta = 66
             header += "  " * delta
-            pr_body += f"""<thead><tr><td>Category</td><td align=left>{header}</td><td align=center>Score</td></tr>"""
+            pr_body += f"""<thead><tr><td><strong>Category</strong></td><td align=left><strong>{header}</strong></td><td align=center><strong>Impact</strong></td></tr>"""
             pr_body += """<tbody>"""
             suggestions_labels = dict()
             # add all suggestions related to each label
@@ -740,7 +740,7 @@ class PRCodeSuggestions:
             counter_suggestions = 0
             for label, suggestions in suggestions_labels.items():
                 num_suggestions = len(suggestions)
-                pr_body += f"""<tr><td rowspan={num_suggestions}><strong>{label.capitalize()}</strong></td>\n"""
+                pr_body += f"""<tr><td rowspan={num_suggestions}>{label.capitalize()}</td>\n"""
                 for i, suggestion in enumerate(suggestions):
 
                     relevant_file = suggestion['relevant_file'].strip()
@@ -794,14 +794,19 @@ class PRCodeSuggestions:
 
 {example_code.rstrip()}
 """
-                    pr_body += f"<details><summary>Suggestion importance[1-10]: {suggestion['score']}</summary>\n\n"
-                    pr_body += f"Why: {suggestion['score_why']}\n\n"
-                    pr_body += f"</details>"
+                    if suggestion.get('score_why'):
+                        pr_body += f"<details><summary>Suggestion importance[1-10]: {suggestion['score']}</summary>\n\n"
+                        pr_body += f"__\n\nWhy: {suggestion['score_why']}\n\n"
+                        pr_body += f"</details>"
 
                     pr_body += f"</details>"
 
                     # # add another column for 'score'
-                    pr_body += f"</td><td align=center>{suggestion['score']}\n\n"
+                    score_int = int(suggestion.get('score', 0))
+                    score_str = f"{score_int}"
+                    if get_settings().pr_code_suggestions.new_score_mechanism:
+                        score_str = self.get_score_str(score_int)
+                    pr_body += f"</td><td align=center>{score_str}\n\n"
 
                     pr_body += f"</td></tr>"
                     counter_suggestions += 1
@@ -814,6 +819,16 @@ class PRCodeSuggestions:
             get_logger().info(f"Failed to publish summarized code suggestions, error: {e}")
             return ""
 
+    def get_score_str(self, score: int) -> str:
+        th_high = get_settings().pr_code_suggestions.get('new_score_mechanism_th_high', 9)
+        th_medium = get_settings().pr_code_suggestions.get('new_score_mechanism_th_medium', 7)
+        if score >= th_high:
+            return "High"
+        elif score >= th_medium:
+            return "Medium"
+        else:  # score < 7
+            return "Low"
+
     async def self_reflect_on_suggestions(self,
                                           suggestion_list: List,
                                           patches_diff: str,

pr_agent/tools/pr_help_message.py

@@ -1,4 +1,5 @@
 import copy
+import re
 from functools import partial
 from pathlib import Path
 
@@ -9,10 +10,9 @@ 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, clip_tokens, load_yaml
+from pr_agent.algo.utils import ModelType, clip_tokens, load_yaml, get_max_tokens
 from pr_agent.config_loader import get_settings
-from pr_agent.git_providers import (BitbucketServerProvider, GithubProvider,
-                                    get_git_provider_with_context)
+from pr_agent.git_providers import BitbucketServerProvider, GithubProvider, get_git_provider_with_context
 from pr_agent.log import get_logger
 
 
@@ -30,10 +30,11 @@ def extract_header(snippet):
     return res
 
 class PRHelpMessage:
-    def __init__(self, pr_url: str, args=None, ai_handler: partial[BaseAiHandler,] = LiteLLMAIHandler):
+    def __init__(self, pr_url: str, args=None, ai_handler: partial[BaseAiHandler,] = LiteLLMAIHandler, return_as_string=False):
         self.git_provider = get_git_provider_with_context(pr_url)
         self.ai_handler = ai_handler()
         self.question_str = self.parse_args(args)
+        self.return_as_string = return_as_string
         self.num_retrieved_snippets = get_settings().get('pr_help.num_retrieved_snippets', 5)
         if self.question_str:
             self.vars = {
@@ -65,6 +66,34 @@ class PRHelpMessage:
             question_str = ""
         return question_str
 
+    def format_markdown_header(self, header: str) -> str:
+        try:
+            # First, strip common characters from both ends
+            cleaned = header.strip('# 💎\n')
+
+            # Define all characters to be removed/replaced in a single pass
+            replacements = {
+                "'": '',
+                "`": '',
+                '(': '',
+                ')': '',
+                ',': '',
+                '.': '',
+                '?': '',
+                '!': '',
+                ' ': '-'
+            }
+
+            # Compile regex pattern for characters to remove
+            pattern = re.compile('|'.join(map(re.escape, replacements.keys())))
+
+            # Perform replacements in a single pass and convert to lowercase
+            return pattern.sub(lambda m: replacements[m.group()], cleaned).lower()
+        except Exception:
+            get_logger().exception(f"Error while formatting markdown header", artifacts={'header': header})
+            return ""
+
+
     async def run(self):
         try:
             if self.question_str:
@@ -106,7 +135,10 @@ class PRHelpMessage:
                 get_logger().debug(f"Token count of full documentation website: {token_count}")
 
                 model = get_settings().config.model
-                max_tokens_full = MAX_TOKENS[model] # note - here we take the actual max tokens, without any reductions. we do aim to get the full documentation website in the prompt
+                if model in MAX_TOKENS:
+                    max_tokens_full = MAX_TOKENS[model] # note - here we take the actual max tokens, without any reductions. we do aim to get the full documentation website in the prompt
+                else:
+                    max_tokens_full = get_max_tokens(model)
                 delta_output = 2000
                 if token_count > max_tokens_full - delta_output:
                     get_logger().info(f"Token count {token_count} exceeds the limit {max_tokens_full - delta_output}. Skipping the PR Help message.")
@@ -114,8 +146,16 @@ class PRHelpMessage:
                 self.vars['snippets'] = docs_prompt.strip()
 
                 # run the AI model
-                response = await retry_with_fallback_models(self._prepare_prediction, model_type=ModelType.WEAK)
+                response = await retry_with_fallback_models(self._prepare_prediction, model_type=ModelType.REGULAR)
                 response_yaml = load_yaml(response)
+                if isinstance(response_yaml, str):
+                    get_logger().warning(f"failing to parse response: {response_yaml}, publishing the response as is")
+                    if get_settings().config.publish_output:
+                        answer_str = f"### Question: \n{self.question_str}\n\n"
+                        answer_str += f"### Answer:\n\n"
+                        answer_str += response_yaml
+                        self.git_provider.publish_comment(answer_str)
+                    return ""
                 response_str = response_yaml.get('response')
                 relevant_sections = response_yaml.get('relevant_sections')
 
@@ -138,7 +178,7 @@ class PRHelpMessage:
                     for section in relevant_sections:
                         file = section.get('file_name').strip().removesuffix('.md')
                         if str(section['relevant_section_header_string']).strip():
-                            markdown_header = section['relevant_section_header_string'].strip().strip('#').strip().lower().replace(' ', '-').replace("'", '').replace('(', '').replace(')', '').replace(',', '').replace('.', '').replace('?', '').replace('!', '')
+                            markdown_header = self.format_markdown_header(section['relevant_section_header_string'])
                             answer_str += f"> - {base_path}{file}#{markdown_header}\n"
                         else:
                             answer_str += f"> - {base_path}{file}\n"

pr_agent/tools/pr_reviewer.py

@@ -371,7 +371,7 @@ class PRReviewer:
                     else:
                         get_logger().warning(f"Unexpected type for estimated_effort: {type(estimated_effort)}")
                     if 1 <= estimated_effort_number <= 5:  # 1, because ...
-                        review_labels.append(f'Review effort [1-5]: {estimated_effort_number}')
+                        review_labels.append(f'Review effort {estimated_effort_number}/5')
                 if get_settings().pr_reviewer.enable_review_labels_security and get_settings().pr_reviewer.require_security_review:
                     security_concerns = data['review']['security_concerns']  # yes, because ...
                     security_concerns_bool = 'yes' in security_concerns.lower() or 'true' in security_concerns.lower()

setup.py

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