main.yml

name: Python Test and Package

on:
  push:
    branches:
      - main
    tags:
      - 'v*'
  pull_request:
    branches:
      - main

jobs:
  linting:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
    - name: Set up Python 3.11
      uses: actions/setup-python@v5
      with:
        python-version: 3.11
        cache: 'pip'
    - name: Linting with pre-commit
      run: |
        python -m pip install pre-commit
        pre-commit run --all-files

  test:
    needs: linting
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.8, 3.9, 3.12]

    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
    - name: Create LFS file list
      run: |
        git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id

    - name: Restore LFS cache
      uses: actions/cache@v3
      id: lfs-cache
      with:
        path: .git/lfs
        key: lfs-v1-${{ hashFiles('.lfs-assets-id') }}
        restore-keys:
          lfs-v1-
    - name: Git LFS Pull
      run: |
        git lfs pull
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install -e .[dev]
    - name: Test with pytest
      run: |
        python -m pytest

  package:
    needs: test
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      - name: Create LFS file list
        run: |
          git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id

      - name: Restore LFS cache
        uses: actions/cache@v3
        id: lfs-cache
        with:
          path: .git/lfs
          key: lfs-v1-${{ hashFiles('.lfs-assets-id') }}
          restore-keys: |
            lfs-v1-
      - name: Git LFS Pull
        run: |
          git lfs pull
      - name: Set up Python 3.9
        uses: actions/setup-python@v5
        with:
          python-version: 3.9
      - name: Build package
        run: |
          python -m pip install twine build
          python -m build --wheel --sdist
          python -m twine check dist/*
          ls -la dist
      - name: Upload package
        if: github.event_name == 'push'
        uses: actions/upload-artifact@v4
        with:
          name: python-packages
          path: dist

  publish_release:
    if: startsWith(github.ref, 'refs/tags/v')
    needs: package
    runs-on: ubuntu-latest
    steps:
      - uses: actions/download-artifact@v4
        id: download
        with:
          name: python-packages
      - name: Extract Python Packages
        id: files
        run: |
          cd ${{steps.download.outputs.download-path}}
      - name: Create Release and Upload
        id: create_release
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          gh release create ${{ github.ref_name }} --repo ${{ github.repository }} --verify-tag --generate-notes --title "Release ${{ github.ref_name }}"
          gh release upload ${{ github.ref_name }} --repo ${{ github.repository }} ${{steps.download.outputs.download-path}}/*

      - name: bcbb-pypi upload
        run: |
          python -m pip install twine
          python -m twine check ${{steps.download.outputs.download-path}}/*
          python -m twine upload ${{steps.download.outputs.download-path}}/*
        env:
          TWINE_REPOSITORY_URL: https://artifactory.niaid.nih.gov/artifactory/api/pypi/bcbb-pypi
          TWINE_PASSWORD: ${{secrets.BCBB_PYPI_PASSWORD}}
          TWINE_USERNAME: ${{secrets.BCBB_PYPI_USERNAME}}