DEPLOYMENT.md

Deployment Guide

This document provides instructions for deploying Bioinfo Tools to various package managers.

Table of Contents

• PyPI Deployment
• Conda/Bioconda Deployment
• Pixi Configuration

PyPI Deployment

Prerequisites

• PyPI account (register at https://pypi.org/)
• twine installed: pip install twine build

Steps

1. Update version number in:

   • bioinfo_tools/__init__.py
   • setup.py
   • pyproject.toml

2. Build the package:

   python -m build

   This creates distribution files in dist/

3. Test the package locally:

   pip install dist/bioinfo_tools-*.whl
   bioinfo-tools --help

4. Upload to TestPyPI (optional but recommended):

   twine upload --repository testpypi dist/*

5. Upload to PyPI:

   twine upload dist/*

6. Verify installation:

   pip install bioinfo-tools
   bioinfo-tools --version

Conda/Bioconda Deployment

Prerequisites

• Fork of bioconda-recipes repository
• Conda installed
• GitHub account

Steps

1. Create a release on GitHub:

   • Go to https://github.com/Mxrcon/Bioinfo-python-scripts/releases
   • Click "Create a new release"
   • Tag version: v1.0.0
   • Title: "Release 1.0.0"
   • Add release notes
   • Publish release

2. Get the SHA256 hash of the tarball:

   wget https://github.com/Mxrcon/Bioinfo-python-scripts/archive/refs/tags/v1.0.0.tar.gz
   sha256sum v1.0.0.tar.gz

3. Update the conda recipe:

   • Edit conda_recipe/meta.yaml
   • Update the sha256 field with the hash from step 2
   • Ensure version numbers match

4. Test the conda recipe locally:

   conda build conda_recipe/

5. Fork bioconda-recipes:

   • Go to https://github.com/bioconda/bioconda-recipes
   • Click "Fork"

6. Add your recipe to bioconda:

   git clone https://github.com/YOUR_USERNAME/bioconda-recipes.git
   cd bioconda-recipes
   git checkout -b add-bioinfo-tools
   
   # Copy your recipe
   mkdir -p recipes/bioinfo-tools
   cp ../Bioinfo-python-scripts/conda_recipe/meta.yaml recipes/bioinfo-tools/
   
   # Commit and push
   git add recipes/bioinfo-tools/
   git commit -m "Add bioinfo-tools recipe"
   git push origin add-bioinfo-tools

7. Create a Pull Request:

   • Go to your fork on GitHub
   • Click "Pull Request"
   • Title: "Add bioinfo-tools recipe"
   • Description: Brief description of the tool
   • Submit the PR

8. Wait for CI checks and review:

   • Bioconda's CI will test your recipe
   • Address any feedback from reviewers
   • Once approved and merged, the package will be available via conda

9. Installation after deployment:

   conda install -c bioconda bioinfo-tools

Pixi Configuration

Pixi is already configured in pixi.toml. Users can use it as follows:

For Users

# Install pixi (if not already installed)
curl -fsSL https://pixi.sh/install.sh | bash

# Clone and use the project
git clone https://github.com/Mxrcon/Bioinfo-python-scripts.git
cd Bioinfo-python-scripts
pixi install
pixi shell

Available Pixi Commands

# Install the package
pixi run install

# Run tests
pixi run test

# Clean build artifacts
pixi run clean

# Development environment (with linters and formatters)
pixi shell -e dev

Version Management

When releasing a new version:

1. Update version in:

   • bioinfo_tools/__init__.py
   • setup.py
   • pyproject.toml
   • pixi.toml
   • conda_recipe/meta.yaml

2. Update CHANGELOG.md with release notes

3. Commit changes:

   git add .
   git commit -m "Bump version to X.Y.Z"
   git tag -a vX.Y.Z -m "Release X.Y.Z"
   git push origin main --tags

4. Follow deployment steps above for each platform

Troubleshooting

PyPI Issues

Problem: Package name already taken
Solution: Choose a different name in setup.py and pyproject.toml

Problem: Upload fails with authentication error
Solution: Use twine upload with --username and --password or configure .pypirc

Conda Issues

Problem: Build fails with missing dependencies
Solution: Ensure all dependencies are listed in meta.yaml under requirements/run

Problem: Tests fail in conda build
Solution: Add required test files to the source distribution or simplify tests in meta.yaml

Pixi Issues

Problem: Command not found
Solution: Ensure you're in a pixi shell or use pixi run <command>

Problem: Dependencies not installing
Solution: Check that all channels are properly configured in pixi.toml

Contact

For deployment help or questions:

• Open an issue: https://github.com/Mxrcon/Bioinfo-python-scripts/issues
• Email: davijosuemarcon@gmail.com