test_and_publish.yml

name: Test code and publish package

on: [push]

jobs:
  test:
    runs-on: ${{ matrix.os }}

    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest", "macos-latest", "macos-13", "windows-2019"]
        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]

    defaults: # Needed for conda
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v4
        with:
          lfs: true
          submodules: true

      - uses: conda-incubator/setup-miniconda@v3
        with:
          python-version: ${{ matrix.python-version }}
          mamba-version: "*"
          miniforge-variant: Mambaforge
          channels: acellera,conda-forge,defaults

      - name: Lint with flake8
        run: |
          pip install flake8 coverage pytest-cov pytest pytest-subtests
          # stop the build if there are Python syntax errors or undefined names
          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

      - name: Install moleculekit conda deps. Force rdkit version for tests
        run: |
          mamba install -y -q --file extra_requirements.txt python=${{ matrix.python-version }} -c acellera -c conda-forge
          mamba install -y rdkit=2024.03.4
          # scikit-learn, joblib, biopython are only used for rarely-used functions in smallmol
          mamba install -y -q scikit-learn joblib biopython -c conda-forge

      # - name: Install cdpkit
      #   if: ${{ matrix.os == 'ubuntu-latest' }}
      #   run: |
      #     # for testing CDPKit SmallMol
      #     pip install cdpkit

      - name: Install moleculekit
        run: |
          pip install "numpy>=1.18.5" "Cython>=0.29.21"
          pip install .
          pip install "versioneer==0.28"
          python setup.py build_ext --inplace

      - name: List conda environment
        run: mamba list

      - name: Test
        run: |
          pytest ./moleculekit
        env:
          GITHUB_ACTIONS: 1

      # - name: Upload coverage to Codecov
      #   uses: codecov/codecov-action@v3

  deploypypi:
    if: startsWith(github.event.ref, 'refs/tags/')
    needs: test
    runs-on: ${{ matrix.os }}

    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest"]
        python-version: ["3.9"]

    steps:
      - uses: actions/checkout@v4

      - uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: deploy
          python-version: ${{ matrix.python-version }}

      - name: Build PyPI 📦
        run: |
          pip install numpy>=1.18.5 Cython>=0.29.21 build
          python -m build --sdist --outdir dist/ .

      - name: Publish distribution 📦 to PyPI
        uses: pypa/gh-action-pypi-publish@release/v1
        with:
          password: ${{ secrets.PUBLIC_PYPI_API_TOKEN }}
          skip_existing: true

  deploy_linux:
    if: startsWith(github.event.ref, 'refs/tags/')
    needs: test
    runs-on: ${{ matrix.os }}
    container: ${{ matrix.container }}

    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest"]
        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
        container: ["quay.io/pypa/manylinux_2_28_x86_64"]

    steps:
      - uses: actions/checkout@v4

      - uses: conda-incubator/setup-miniconda@v2
        with:
          miniconda-version: "latest"
          activate-environment: ../deploy-env
          python-version: ${{ matrix.python-version }}

      - name: Build moleculekit package
        shell: bash -l {0}
        run: |
          git config --global --add safe.directory '*'
          conda install anaconda-client conda-build python=${{ matrix.python-version }} toml
          pip install versioneer==0.28
          python package/moleculekit/insert_placeholder_values.py
          conda build --python ${{ matrix.python-version }} package/moleculekit/ --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge

      - name: Upload to conda
        shell: bash -l {0}
        run: |
          anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera ./pkg/*/moleculekit-*.tar.bz2

  deploy_osx_win:
    if: startsWith(github.event.ref, 'refs/tags/')
    needs: test
    runs-on: ${{ matrix.os }}

    strategy:
      fail-fast: false
      matrix:
        os: ["macos-latest", "macos-13", "windows-2019"]
        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4

      - uses: conda-incubator/setup-miniconda@v3
        with:
          miniconda-version: "latest"
          activate-environment: ../deploy-env
          python-version: ${{ matrix.python-version }}

      - name: Build moleculekit package
        shell: bash -l {0}
        run: |
          git config --global --add safe.directory '*'
          conda install anaconda-client conda-build python=${{ matrix.python-version }} toml
          pip install versioneer==0.28
          python package/moleculekit/insert_placeholder_values.py
          conda build --python ${{ matrix.python-version }} package/moleculekit/ --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge

      - name: Upload to conda
        shell: bash -l {0}
        run: |
          anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera ./pkg/*/moleculekit-*.tar.bz2