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Release v2.2.1: All modules debugged, dashboard verified, 413 tests passing
- Version bump to 2.2.1 - Dashboard: 9 pages verified, 16 bugs fixed - Quality page: 7 visualization tabs (PCA 2D/3D, RLE, dendrogram, BCV) - Optimization: 4 scientific methods - Visualization: complete rewrite with 12 plot types - Professional styling across all pages - Added .gitignore, .github templates, .streamlit config
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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug Report
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about: Report a bug in RAPTOR
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title: '\[BUG] '
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labels: bug
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assignees: ''
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---
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\## Bug Description
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A clear and concise description of the bug.
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\## To Reproduce
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Steps to reproduce the behavior:
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1\. Import/run '...'
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2\. Use parameters '...'
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3\. Execute command '...'
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4\. See error
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\## Expected Behavior
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What you expected to happen.
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\## Actual Behavior
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What actually happened.
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\## Error Message
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```
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Paste full error message/traceback here
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```
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\## Environment
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\- \*\*RAPTOR version:\*\* (e.g., 2.2.0)
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\- \*\*Python version:\*\* (e.g., 3.10.5)
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\- \*\*Operating System:\*\* (e.g., Ubuntu 22.04, Windows 11, macOS 13)
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\- \*\*Installation method:\*\* (pip, conda, source)
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```bash
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\# Run this and paste output:
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python -c "import raptor; print(raptor.\_\_version\_\_)"
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python --version
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```
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\## Data Information (if applicable)
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\- \*\*Number of samples:\*\*
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\- \*\*Number of genes:\*\*
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\- \*\*File size:\*\*
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\- \*\*Data type:\*\* (counts, FASTQ, etc.)
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\## Additional Context
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Add any other context about the problem here (screenshots, related issues, etc.).
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\## Checklist
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\- \[ ] I have searched existing issues to avoid duplicates
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\- \[ ] I have included the full error traceback
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\- \[ ] I have provided my environment information
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\- \[ ] I can reproduce this bug consistently
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‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: false
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contact_links:
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- name: 📚 Documentation
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url: https://github.com/AyehBlk/RAPTOR/blob/main/README.md
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about: Check the documentation for answers to common questions
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- name: 💬 Discussions
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url: https://github.com/AyehBlk/RAPTOR/discussions
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about: Ask questions and discuss ideas with the community
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- name: 📧 Direct Contact
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url: mailto:ayehbolouki1988@gmail.com
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about: For private inquiries, reach out via email

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature Request
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about: Suggest a new feature or enhancement for RAPTOR
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title: '[FEATURE] '
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labels: enhancement
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assignees: ''
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---
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## Feature Description
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A clear and concise description of the feature you'd like to see in RAPTOR.
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## Problem or Use Case
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**Is your feature request related to a problem? Please describe.**
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Example: I'm always frustrated when [...] or I need to [...] but currently can't.
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## Proposed Solution
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**Describe the solution you'd like**
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A clear description of what you want to happen. Include:
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- How it would work
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- What commands/functions would be involved
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- Expected behavior
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## Alternative Solutions
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**Describe alternatives you've considered**
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Are there workarounds or alternative approaches you've thought about?
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## Example Usage
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**How would you use this feature?**
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```python
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# Example code showing how you'd use the new feature
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from raptor import new_feature
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result = new_feature(
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data='counts.csv',
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parameter='value'
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)
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```
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Or CLI example:
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```bash
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raptor new-command --option value
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```
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## Benefits
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**Who would benefit from this feature?**
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- [ ] Researchers analyzing RNA-seq data
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- [ ] Bioinformaticians
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- [ ] Pipeline developers
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- [ ] Students/educators
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- [ ] Other: _____________
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## Module/Component
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**Which RAPTOR module would this affect?**
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- [ ] Module 2: Quality Assessment
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- [ ] Module 3: Data Profiler
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- [ ] Module 4: Pipeline Recommender
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- [ ] Module 5: Pipelines (alignment/quantification)
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- [ ] Module 6: Differential Expression
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- [ ] Module 7: DE Import
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- [ ] Module 8: Parameter Optimization
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- [ ] Module 9: Ensemble Analysis
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- [ ] Dashboard
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- [ ] CLI
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- [ ] Other: _____________
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## Priority
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**How important is this feature to your workflow?**
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- [ ] Critical - Blocking my work
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- [ ] High - Would significantly improve my workflow
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- [ ] Medium - Nice to have
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- [ ] Low - Minor improvement
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## Additional Context
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Add any other context, screenshots, mockups, or examples about the feature request here.
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**Related issues or discussions:**
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- Issue #XXX
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- Discussion #XXX
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## Willingness to Contribute
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**Would you be willing to help implement this feature?**
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- [ ] Yes, I can implement this feature
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- [ ] Yes, I can help test this feature
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- [ ] Yes, I can help document this feature
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- [ ] No, but I'd love to see it implemented
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- [ ] Unsure
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## Environment (Optional)
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If relevant, what environment are you working in?
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- **RAPTOR version:** (e.g., 2.2.0)
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- **Python version:** (e.g., 3.10.5)
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- **Operating System:** (e.g., Ubuntu 22.04, Windows 11, macOS 13)

‎.github/ISSUE_TEMPLATE/pull_request_template.md‎

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## Description
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Please include a summary of the changes and the related issue. Include relevant motivation and context.
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Fixes # (issue number)
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## Type of Change
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Please delete options that are not relevant.
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- [ ] Bug fix (non-breaking change which fixes an issue)
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- [ ] New feature (non-breaking change which adds functionality)
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- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
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- [ ] Documentation update
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- [ ] Performance improvement
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- [ ] Code refactoring
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- [ ] Tests
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## Changes Made
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Please provide a bulleted list of the changes:
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-
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-
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-
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## How Has This Been Tested?
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Please describe the tests that you ran to verify your changes:
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- [ ] Existing test suite passes (`pytest tests/`)
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- [ ] Added new tests for new functionality
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- [ ] Tested manually with example data
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- [ ] Tested on multiple Python versions
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- [ ] Tested on multiple operating systems
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**Test Configuration:**
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- Python version:
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- Operating System:
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- RAPTOR version:
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## Checklist
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Please confirm the following:
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- [ ] My code follows the style guidelines of this project (PEP 8)
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- [ ] I have performed a self-review of my own code
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- [ ] I have commented my code, particularly in hard-to-understand areas
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- [ ] I have made corresponding changes to the documentation
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- [ ] My changes generate no new warnings
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- [ ] I have added tests that prove my fix is effective or that my feature works
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- [ ] New and existing unit tests pass locally with my changes
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- [ ] Any dependent changes have been merged and published
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- [ ] I have updated the CHANGELOG.md with my changes
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- [ ] I have run `black` and `isort` to format my code
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- [ ] I have run `flake8` to check for linting issues
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## Module/Component Affected
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Which RAPTOR modules are affected by this change?
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- [ ] Module 2: Quality Assessment
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- [ ] Module 3: Data Profiler
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- [ ] Module 4: Pipeline Recommender
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- [ ] Module 5: Pipelines
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- [ ] Module 6: DE Analysis
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- [ ] Module 7: DE Import
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- [ ] Module 8: Parameter Optimization
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- [ ] Module 9: Ensemble Analysis
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- [ ] Dashboard
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- [ ] CLI
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- [ ] Tests
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- [ ] Documentation
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- [ ] Build/CI/CD
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## Breaking Changes
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Does this PR introduce any breaking changes? If yes, please describe:
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-
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## Additional Notes
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Add any additional notes, screenshots, or context about the pull request here.
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## Related Issues/PRs
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- Related to #XXX
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- Depends on #XXX
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- Fixes #XXX

‎.gitignore‎

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# Python
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__pycache__/
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*.py[cod]
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*.egg-info/
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*.egg
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# Build
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dist/
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build/
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sdist/
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# Virtual environment
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.venv/
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venv/
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env/
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# IDE
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.idea/
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.vscode/
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*.swp
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*.swo
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*~
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# Testing
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.pytest_cache/
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.coverage
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htmlcov/
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test_results/
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# OS
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.DS_Store
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Thumbs.db
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# Logs
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*.log
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# MyPy
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.mypy_cache/
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dmypy.json

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