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: ["3.9", "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 }}
  #         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
  #       run: |
  #         conda install -y -q --file extra_requirements.txt python=${{ matrix.python-version }} -c acellera -c conda-forge
  #         # scikit-learn, joblib, biopython are only used for rarely-used functions in smallmol
  #         conda 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>=1.23.5" "Cython>=0.29.21"
  #         pip install .
  #         pip install "versioneer==0.28"
  #         python setup.py build_ext --inplace

  #     - name: List conda environment
  #       run: conda 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: ["3.10"]

  #   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>=1.23.5 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: ["3.10"]
  #       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: Install build deps
  #       shell: bash -l {0}
  #       run: |
  #         git config --global --add safe.directory '*'
  #         conda install anaconda-client rattler-build python=${{ matrix.python-version }} -c conda-forge
  #         pip install versioneer==0.28 toml pyyaml

  #     - name: Build conda package
  #       shell: bash -l {0}
  #       run: |
  #         python package/moleculekit/insert_placeholder_values.py
  #         rattler-build build --recipe ./package/moleculekit/recipe.yaml --output-dir ../pkg/ --no-include-recipe -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-*.conda

  # 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: ["3.10"]

  #   steps:
  #     - uses: actions/checkout@v4

  #     - uses: ilammy/msvc-dev-cmd@v1

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

  #     - name: Install build deps
  #       shell: bash -l {0}
  #       run: |
  #         git config --global --add safe.directory '*'
  #         conda install anaconda-client rattler-build python=${{ matrix.python-version }} -c conda-forge
  #         pip install versioneer==0.28 toml pyyaml

  #     - name: Build conda package
  #       shell: bash -l {0}
  #       run: |
  #         python package/moleculekit/insert_placeholder_values.py
  #         rattler-build build --recipe ./package/moleculekit/recipe.yaml --output-dir ../pkg/ --no-include-recipe -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-*.conda

  windows_build:
    runs-on: ${{ matrix.os }}

    strategy:
      fail-fast: false
      matrix:
        os: ["windows-2019"]
        python-version: ["3.10"]

    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: Add compiler to PATH
        run: |
          echo "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Tools\MSVC\14.16.27023\bin\HostX64\x64\" | Out-File -Append -FilePath $env:GITHUB_PATH -Encoding utf8

      - name: Install build deps
        shell: bash -l {0}
        run: |
          git config --global --add safe.directory '*'
          conda install anaconda-client rattler-build python=${{ matrix.python-version }} -c conda-forge
          pip install versioneer==0.28 toml pyyaml

      - name: Build conda package
        shell: bash -l {0}
        run: |
          python package/moleculekit/insert_placeholder_values.py
          rattler-build build --recipe ./package/moleculekit/recipe.yaml --output-dir ../pkg/ --no-include-recipe -c acellera -c conda-forge