Merge pull request #7 from FOI-Bioinformatics/v0.2.0

Release v0.2.0 - Production Ready

Author: druvus

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug Report
+about: Report a bug or unexpected behavior
+title: "[BUG] "
+labels: bug
+assignees: ''
+---
+
+## Bug Description
+
+A clear and concise description of what the bug is.
+
+## To Reproduce
+
+Steps to reproduce the behavior:
+
+1. Command or code used:
+```bash
+preprimer convert --input ... --output-dir ...
+```
+
+2. Input file format:
+   - [ ] VarVAMP (.tsv)
+   - [ ] ARTIC (.bed)
+   - [ ] Olivar (.csv)
+   - [ ] STS (.sts.tsv)
+
+3. Expected behavior:
+
+
+4. Actual behavior:
+
+
+## Error Message
+
+If applicable, paste the full error message:
+
+```
+Error message here
+```
+
+## Environment
+
+- PrePrimer version: [run `preprimer --version`]
+- Python version: [run `python --version`]
+- Operating System: [e.g., Ubuntu 22.04, macOS 13]
+- Installation method: [pip, source]
+
+## Input File Sample
+
+If possible, provide a minimal example input file that reproduces the issue:
+
+```
+# Paste first few lines of input file here
+# (Remove any sensitive information)
+```
+
+## Additional Context
+
+Add any other context about the problem here (e.g., file size, number of amplicons, special characters).
+
+## Checklist
+
+- [ ] I have checked existing issues for duplicates
+- [ ] I have provided the PrePrimer version
+- [ ] I have included the error message (if applicable)
+- [ ] I have provided steps to reproduce
+- [ ] I have included a minimal example (if possible)

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature Request
+about: Suggest a new feature or enhancement
+title: "[FEATURE] "
+labels: enhancement
+assignees: ''
+---
+
+## Feature Description
+
+A clear and concise description of the feature you'd like to see.
+
+## Use Case
+
+Describe the problem this feature would solve or the workflow it would improve:
+
+**Example:**
+"I need to convert primers from X format to Y format, but currently PrePrimer doesn't support X format..."
+
+## Proposed Solution
+
+Describe how you envision this feature working:
+
+1. User action:
+2. Expected behavior:
+3. Output:
+
+## Alternatives Considered
+
+Have you considered any alternative solutions or workarounds?
+
+## Additional Context
+
+Add any other context, screenshots, or examples about the feature request here.
+
+### Related Formats
+
+If this is a format-related request:
+
+- Format name:
+- File extension:
+- Specification/documentation:
+- Example file (if available):
+
+### Impact
+
+How would this feature benefit PrePrimer users?
+
+- [ ] Enables new use cases
+- [ ] Improves existing workflow
+- [ ] Addresses common user request
+- [ ] Increases compatibility with other tools
+
+## Checklist
+
+- [ ] I have searched existing issues for similar requests
+- [ ] I have provided a clear use case
+- [ ] I have described the proposed solution
+- [ ] I have considered alternatives

.github/PULL_REQUEST_TEMPLATE.md

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+# Pull Request
+
+## Description
+
+Brief description of what this PR does and why.
+
+Fixes #(issue number)
+
+## Type of Change
+
+- [ ] Bug fix (non-breaking change that fixes an issue)
+- [ ] New feature (non-breaking change that adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentation update
+- [ ] Code refactoring
+- [ ] Performance improvement
+- [ ] Test coverage improvement
+
+## Changes Made
+
+Detailed list of changes:
+
+- Added X
+- Modified Y
+- Fixed Z
+
+## Testing
+
+### Test Coverage
+
+- [ ] New tests added for new functionality
+- [ ] All existing tests pass
+- [ ] Test coverage maintained or improved
+
+```bash
+# Commands run for testing
+python -m pytest tests/ -v
+python -m pytest --cov=preprimer
+```
+
+### Manual Testing
+
+Describe manual testing performed:
+
+1. Tested with dataset:
+2. Verified output:
+3. Checked edge cases:
+
+## Documentation
+
+- [ ] Code is commented where needed
+- [ ] Documentation updated (if applicable)
+- [ ] CHANGELOG.md updated
+- [ ] README.md updated (if applicable)
+
+## Code Quality
+
+- [ ] Code follows project style guide
+- [ ] Linting passes (`flake8 preprimer/`)
+- [ ] Formatting passes (`black --check preprimer/`)
+- [ ] Type checking passes (`mypy preprimer/`)
+- [ ] No security issues (`bandit -r preprimer/`)
+
+## Performance
+
+For features that may impact performance:
+
+- [ ] Benchmarked before and after changes
+- [ ] No significant performance regression
+- [ ] Performance improvements documented
+
+## Screenshots (if applicable)
+
+Add screenshots or output examples if relevant.
+
+## Breaking Changes
+
+If this is a breaking change, describe:
+
+1. What breaks:
+2. Migration path:
+3. Deprecation warnings (if applicable):
+
+## Checklist
+
+- [ ] My code follows the project's contribution guidelines
+- [ ] I have performed a self-review of my code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have updated the documentation accordingly
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes
+- [ ] Any dependent changes have been merged and published
+
+## Additional Notes
+
+Any additional information reviewers should know:

.github/workflows/README.md

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+# GitHub Actions Workflows
+
+Simplified CI/CD for PrePrimer.
+
+## Active Workflows
+
+### `ci.yml` - Continuous Integration
+
+**Triggers:** Push to main/develop/v0.2.0, Pull requests
+
+**What it does:**
+- **Test**: Runs full test suite on Ubuntu and macOS with Python 3.11, 3.12, 3.13
+- **Lint**: Checks code formatting, imports, linting, type checking, security
+
+**Matrix:**
+- 2 operating systems × 3 Python versions = 6 test combinations
+- Parallel execution for speed
+
+**Typical run time:** ~3-5 minutes
+
+### `release.yml` - Release Build
+
+**Triggers:** Version tags (v*.*.*)
+
+**What it does:**
+1. Run full test suite
+2. Build wheel and source distribution
+3. Validate package with twine
+4. Calculate SHA256 checksums
+5. Create GitHub release with build artifacts
+
+**Output:**
+- `preprimer-X.Y.Z.tar.gz` (source distribution)
+- `preprimer-X.Y.Z-py3-none-any.whl` (wheel)
+- `SHA256SUMS` (checksums)
+
+**Typical run time:** ~2-3 minutes
+
+## Usage
+
+### Running CI
+
+CI runs automatically on push/PR. Nothing to do!
+
+### Creating a Release
+
+```bash
+# 1. Tag the release
+git tag -a v1.0.0 -m "Release v1.0.0"
+git push origin v1.0.0
+
+# 2. Workflow runs automatically
+# 3. Check Actions tab for progress
+# 4. Release appears in GitHub Releases
+```
+
+### Manual Test Run
+
+```bash
+# Trigger CI manually from Actions tab
+# Click "CI" → "Run workflow" → Select branch
+```
+
+## What Was Removed
+
+Previous workflows had 10+ separate jobs:
+- ❌ Separate smoke tests (now: single test job)
+- ❌ Property-based testing job (now: included in tests)
+- ❌ Security testing job (now: included in lint)
+- ❌ Performance benchmarks (now: run manually with pytest-benchmark)
+- ❌ Integration testing job (now: included in tests)
+- ❌ Mutation testing (now: run manually, too slow for CI)
+- ❌ Deployment checks (now: simplified)
+- ❌ Test summary job (redundant)
+
+**Result:** 2 simple workflows instead of 3 complex ones
+
+## Archived Workflows
+
+Old workflows are kept as `.old` files for reference:
+- `test.yml.old` - Legacy quick tests
+- `comprehensive-testing.yml.old` - Over-engineered testing (13 jobs!)
+- `publish.yml.old` - Complex PyPI publishing with 6 stages
+
+## Local Testing
+
+Run the same checks locally before pushing:
+
+```bash
+# Run tests
+python -m pytest tests/ --cov=preprimer -v
+
+# Check formatting
+black --check preprimer/ tests/
+
+# Check imports
+isort --check-only preprimer/ tests/
+
+# Lint
+flake8 preprimer/ tests/ --max-line-length=88 --extend-ignore=E203,W503
+
+# Type check
+mypy preprimer/ --ignore-missing-imports
+
+# Security
+bandit -r preprimer/ -ll
+```
+
+## Troubleshooting
+
+### CI fails on "Check formatting"
+
+```bash
+# Fix locally
+black preprimer/ tests/
+git add .
+git commit -m "style: Format code"
+```
+
+### CI fails on "Check imports"
+
+```bash
+# Fix locally
+isort preprimer/ tests/
+git add .
+git commit -m "style: Sort imports"
+```
+
+### Release workflow doesn't trigger
+
+- Ensure tag follows pattern: `v*.*.*` (e.g., `v1.0.0`)
+- Tag must be pushed: `git push origin v1.0.0`
+- Check Actions tab for workflow run
+
+### Tests pass locally but fail in CI
+
+- Check Python version (CI tests 3.11, 3.12, 3.13)
+- Check OS differences (CI tests Ubuntu + macOS)
+- Review CI logs in Actions tab
+
+## Performance
+
+**Before simplification:**
+- 10 jobs, many running sequentially
+- ~15-20 minutes for full run
+- Redundant test execution
+
+**After simplification:**
+- 2 jobs, running in parallel
+- ~3-5 minutes for full run
+- Single test execution per configuration
+
+**60-75% faster! 🚀**
+
+---
+
+**Last Updated:** 2024-10-14