test_and_publish.yml

name: Test and deploy code

on: [push]

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

    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest"]
        python-version: ["3.8", "3.9", "3.10"]

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

    steps:
      - uses: actions/checkout@v3
        with:
          lfs: true
          submodules: true

      - uses: conda-incubator/setup-miniconda@v2
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}
          use-mamba: true
          miniforge-variant: Mambaforge
          channels: acellera,conda-forge,defaults

      - name: Install HTMD conda deps # psfgen should not be included by default in HTMD due to licensing
        run: |
          mamba install --file package/htmd-deps/DEPENDENCIES python=${{ matrix.python-version }} -y

      - name: Install pip dependencies
        run: |
          pip install flake8 pytest
          pip install .

      - name: Lint with flake8
        run: |
          # 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: Test
        run: |
          export HTMD_NONINTERACTIVE=1
          pytest --verbose --durations=10 ./htmd/

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

    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-latest"]
        python-version: ["3.8", "3.9", "3.10"]

    steps:
      - uses: actions/checkout@v3

      - uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: writedeps
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}
          uses-mamba: true
          miniforge-variant: Mambaforge
          channels: acellera,conda-forge,defaults

      - name: Dump exact dependencies yaml file
        shell: bash -l {0}
        run: |
          mamba install --file package/htmd-deps/DEPENDENCIES python=${{ matrix.python-version }} -y
          python package/htmd-deps/write_meta_yaml.py package/htmd-deps

      - uses: conda-incubator/setup-miniconda@v2
        with:
          auto-activate-base: true
          activate-environment: build
          python-version: ${{ matrix.python-version }}
          uses-mamba: true
          miniforge-variant: Mambaforge

      - name: Build htmd-deps conda package
        shell: bash -l {0}
        run: |
          export TAG_DESCRIBE=$(git describe)
          export BUILD_VERSION=$(echo $TAG_DESCRIBE | sed 's/-/ /g'  | awk '{print $1}')
          mamba install anaconda-client conda-build python=${{ matrix.python-version }} boa
          conda mambabuild --python ${{ matrix.python-version }} package/htmd-deps --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c acellera -c conda-forge

      - name: Build htmd conda package
        shell: bash -l {0}
        run: |
          export TAG_DESCRIBE=$(git describe)
          export BUILD_VERSION=$(echo $TAG_DESCRIBE | sed 's/-/ /g'  | awk '{print $1}')
          conda mambabuild --python ${{ matrix.python-version }} package/htmd --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/*/htmd-*.tar.bz2