Development & Release Guide

Development Workflow¶

1. Normal Development

   # Always work in devel branch
   git add .
   git commit -m "your changes"
   git push origin devel

2. Creating a Release

   # 1. Create a Pull Request on GitHub
   # - Go to GitHub repository
   # - Create PR from devel to main
   # - Add description of changes
   # - Wait for review and approval
   # - Merge PR to main
   
   # 2. Update local main branch
   git checkout main
   git pull origin main
   
   # 3. Prepare environment (optional if already set up)
   uv venv .venv
   source .venv/bin/activate
   uv pip install ".[dev]"
   
   # 4. Set the release version in pyproject.toml
   # - Edit [project] version = "X.Y.Z"
   # - Commit the change on main
   uv run python -c "import tomllib, pathlib; print(tomllib.loads(pathlib.Path('pyproject.toml').read_bytes().decode())['project']['version'])"  # verify
   
   # 5. Create the release
   make release
   # This will:
   # - Verify you are on main and working tree is clean
   # - Pull with --ff-only
   # - Read version from pyproject.toml and tag vX.Y.Z
   # - Run tests (uv run pytest)
   # - Build sdist+wheel (uv run python -m build)
   # - Upload to PyPI (uvx twine upload)
   
   # 6. Verify installation (optional)
   uv pip install --no-cache-dir seqspec==<version>
   seqspec --help
   
   # 7. Return to development
   git checkout devel

Version Numbering¶

Follow semantic versioning:

• 0.3.1 → 0.3.2 for bug fixes (patch)

• 0.3.1 → 0.4.0 for new features (minor)

• 0.3.1 → 1.0.0 for breaking changes (major)

Important Notes¶

1. Never manually edit __init__.py

   • Version is managed through git tags

   • __init__.py is updated automatically

2. Always release from main branch

   • Makefile enforces releasing from main with a clean tree

   • Version is stored in pyproject.toml and tags are derived from it

   • Git tags point to correct code

   • Tests are run automatically during release

3. Version management

   • Bump [project].version in pyproject.toml before releases

   • Example: 0.3.1 → 0.4.0 for new features

Using uv for Development¶

Setting up a Development Environment¶

1. Create a new environment

   # Create a new environment
   uv venv .venv
   
   # Activate the environment
   source .venv/bin/activate  # On Unix/macOS
   # or
   .venv/Scripts/activate  # On Windows

2. Install Dependencies

   # Install runtime dependencies
   uv pip install .
   
   # Install development dependencies
   uv pip install ".[dev]"

Using uv for Package Management¶

1. Installing seqspec

   # Install latest release
   uv pip install seqspec
   
   # Install specific version
   uv pip install seqspec==0.3.1
   
   # Install from git
   uv pip install git+https://github.com/sbooeshaghi/seqspec.git
   
   # Install from git branch
   uv pip install git+https://github.com/sbooeshaghi/seqspec.git@devel

2. Development Workflow with uv

   # Create new environment for testing
   uv venv test-env
   source test-env/bin/activate
   
   # Install all dependencies
   uv pip install ".[dev]"
   
   # Run tests
   uv run pytest

Best Practices with uv¶

1. Environment Management

   • Use separate environments for different projects

   • Keep development environment separate from system Python

   • Use uv venv to create isolated environments

2. Dependency Management

   • Runtime dependencies are in pyproject.toml under [project]

   • Development dependencies are under [project.optional-dependencies]

   • Install with uv pip install ".[dev]" for development

   • Install with uv pip install . for runtime only

3. Testing with uv

   # Create test environment
   uv venv test-env
   source test-env/bin/activate
   
   # Install all dependencies
   uv pip install ".[dev]"
   
   # Run tests
   pytest

4. Building with uv

   # Install build dependencies
   uv pip install ".[dev]"
   
   # Build package
   make build

Troubleshooting¶

Release Issues¶

If make release fails:

1. Ensure you’re on main and the working tree is clean (git status)

2. Ensure main is up to date (git pull --ff-only)

3. Check that tests pass locally (uv run pytest)

4. Check PyPI credentials are correct

5. Confirm git tags are being pushed (git push origin --tags)

uv Issues¶

1. Common Issues

   • If uv pip install fails, try --no-deps flag

   • If environment activation fails, check path

   • If package not found, check PyPI index

2. Updating uv

   # Update uv itself
   uv pip install --upgrade uv

3. Cleaning up

   # Remove old environments
   rm -rf .venv test-env
   
   # Clear uv cache
   uv cache clean

Common Commands¶

# Check current version
make version

# Build package without releasing
make build

# Clean build artifacts
make clean

Dependencies¶

All dependencies are managed in pyproject.toml:

• Runtime dependencies under [project]

• Development dependencies under [project.optional-dependencies] (includes twine for uploads)

Versioning is manual (single source of truth):

• Set [project].version in pyproject.toml (e.g., 0.4.0)

• seqspec/__init__.py reads the installed distribution version via importlib.metadata

No separate requirements.txt or dev-requirements.txt files are needed.