test.yaml

name: Test

on:
  push:
    branches: [master]
  pull_request:
    branches: [master]
  schedule:
    - cron: "0 5 1,15 * *"

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  test:
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0} # -e to fail on error

    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-13]
        python: ["3.7", "3.8", "3.9", "3.10", "3.11"]

    name: ${{ matrix.name }} Python ${{ matrix.python }}

    env:
      OS: ${{ matrix.os }}
      PYTHON: ${{ matrix.python }}

    steps:
      - uses: actions/checkout@v3

      # - name: Set up Python ${{ matrix.python }}
      #   uses: actions/setup-python@v4
      #   with:
      #     python-version: ${{ matrix.python }}
      #     cache: "pip"
      #     cache-dependency-path: "**/pyproject.toml"

      - uses: conda-incubator/setup-miniconda@v3
        with:
          mamba-version: "*"
          auto-update-conda: true
          auto-activate-base: false
          python-version: ${{ matrix.python }}
          channels: conda-forge, bioconda, defaults
          activate-environment: test_dbcan
          environment-file: envs/test.yml

      - name: export test_dbcan environment
        run: mamba env export

      # - name: Install test dependencies
      #   run: |
      #     python -m pip install --upgrade pip wheel
      # - name: create run_dbcan environment
      #   run: conda create -n run_dbcan python=${{ matrix.python }}
      # - name: activate run_dbcan environment
      #   run: conda activate run_dbcan

      - name: Install dependencies
        run: |
          pip install ${{ matrix.pip-flags }} ".[dev,test]"

      # - name: Add conda to PATH
      #   run: |
      #     echo ::add-path::$CONDA/bin

      - name: Build dbCAN Database
        run: |
          dbcan_build --cpus 1 --db-dir db --clean
          # conda install -y -c bioconda -c conda-forge hmmer diamond blast prodigal

      - name: Test
        env:
          MPLBACKEND: agg
          PLATFORM: ${{ matrix.os }}
          DISPLAY: :42
        run: |
          coverage run -m pytest -v --color=yes