python-publish.yml

# This workflow will upload a Python Package using Twine when a release is created
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries

# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.

name: Upload Python Package

on:
  release:
    types: [published]

permissions:
  contents: read

jobs:
  update:
    name: Update docs
    runs-on: ubuntu-latest
    permissions: 
      contents: write

    steps:
      - uses: actions/checkout@v3
        with:
            fetch-depth: 0
            token: ${{ secrets.PAT }}
            ref: main
      - name: Install dependencies
        run: |
          conda create --name proteinflow -y python=3.9
          conda run -n proteinflow python -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
          conda run -n proteinflow python -m pip install numpy
          conda run -n proteinflow python -m pip install -e .
      - name: Install pdoc3 and black
        run: |
          conda run -n proteinflow python -m pip install pdoc3 black
      - name: Reformat the code
        run: |
          conda run -n proteinflow black .
      - name: Update the docs
        run: |
          git pull origin main
          conda run -n proteinflow . dev/make_docs.sh
          echo ${{ needs.test.outputs.update }}
      - uses: stefanzweifel/git-auto-commit-action@v4
        with:
          commit_message: auto update
          skip_checkout: true

  conda:
    name: Push to Anaconda
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}

    steps:
    - uses: actions/checkout@v3
    - name: Setup miniconda
      uses: conda-incubator/setup-miniconda@v2
      with:
        auto-update-conda: true
        miniforge-variant: Mambaforge
        channels: conda-forge
        python-version: 3.9
        use-mamba: true
    - name: Install dependencies
      run: |
        mamba install -y boa -c conda-forge
        mamba install -y anaconda-client
        anaconda login --username ${{ secrets.CONDA_USERNAME }} --password ${{ secrets.CONDA_PASSWORD }}
    - name: Build and upload the conda packages for linux-64 and osx-64
      run: |
        conda mambabuild --no-anaconda-upload .conda/default -c conda-forge -c bioconda --output-folder .
        anaconda upload --force ./linux-64/*.tar.bz2
        conda convert --platform osx-64 ./linux-64/*.tar.bz2
        anaconda upload --force ./osx-64/*.tar.bz2
    - name: Build and upload the conda packages for osx-arm64
      run: |
        conda mambabuild --no-anaconda-upload .conda/arm64 -c conda-forge -c bioconda --output-folder .
        conda convert --platform osx-arm64 ./linux-64/*.tar.bz2
        anaconda upload --force ./osx-arm64/*.tar.bz2
    
  pypi_and_dockerhub:
    runs-on: ubuntu-latest
    name: Push to PyPI and DockerHub

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python
      uses: actions/setup-python@v3
      with:
        python-version: '3.9'
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install build
    - name: Build package
      run: python -m build
    - name: Publish package
      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
      with:
        user: __token__
        password: ${{ secrets.PYPI_API_TOKEN }}
    - name: Login to Docker Hub
      uses: docker/login-action@v2
      with:
        username: adaptyvbio
        password: ${{ secrets.DOCKER_PASS }}
    - name: Build and push Docker image
      run: |
        docker build -t adaptyvbio/proteinflow:${{ github.event.release.tag_name }} .
        docker image push adaptyvbio/proteinflow:${{ github.event.release.tag_name }}
        docker tag adaptyvbio/proteinflow:${{ github.event.release.tag_name }} adaptyvbio/proteinflow:latest
        docker image push adaptyvbio/proteinflow:latest
    - name: Push README to Dockerhub
      uses: christian-korneck/update-container-description-action@v1
      env:
        DOCKER_USER: adaptyvbio
        DOCKER_PASS: ${{ secrets.DOCKER_PASS }}
      with:
        destination_container_repo: adaptyvbio/proteinflow
        provider: dockerhub
        short_description: 'Versatile pipeline for processing protein structure data for deep learning applications.'
        readme_file: 'README.md'