MDDB-workflow/.github/workflows/CI.yml at master · mmb-irb/MDDB-workflow · GitHub

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name: CI

on:
  workflow_dispatch: ~
  push:
    # Only run on pushes to the master branch
    branches: [ master ]
    # Only run on changes to the mddb_workflow directory
    paths:
      - 'mddb_workflow/**'
      - 'envs/environment.yml'
      - 'test/**'
  pull_request:
    branches: [ master ]
    paths:
      - 'mddb_workflow/**'
      - 'envs/environment.yml'
  # everyday Monday to Saturday at 7am UTC
  schedule:
    - cron: "0 7 * * 1-6"

jobs:
  # Name of the Job
  install_and_test:
    strategy:
      matrix:
        os: [ubuntu-latest]
        python-version: ["3.11"]
    runs-on: ${{ matrix.os }}
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4

      - run: echo "Repository -> ${{ github.repository }}"
      - run: echo "Branch -> ${{ github.ref }}"
      - run: echo "Trigger event -> ${{ github.event_name }}"
      - run: echo "Runner OS -> ${{ runner.os }}"

      - name: List files in the repository
        run: |
          ls ${{ github.workspace }}

      # - name: Remove all micromamba installations
      #   run: |
      #     rm -rf $HOME/.bash_profile $HOME/.conda $HOME/micromamba $HOME/micromamba-bin 2>/dev/null
      #     touch $HOME/.bash_profile

      - name: Setup-micromamba
        uses: mamba-org/setup-micromamba@v2.0.4
        with:
          generate-run-shell: true
          micromamba-version: '2.0.2-2'
          post-cleanup: 'all'
          init-shell: bash
          environment-file: envs/environment.yml
          create-args: >-
            python=${{ matrix.python-version }}
            pytest
            pytest-cov
            pip
          cache-environment: true
          cache-downloads: true

      - name: List installed package versions
        shell: bash -l {0}
        run: micromamba list

      - name: Install mddb_workflow
        shell: bash -l {0}
        run: python -m pip install -e .

      - name: Run CI tests
        if: github.event_name == 'push' || github.event_name == 'pull_request'
        shell: bash -l {0}
        run: pytest -m CI
        timeout-minutes: 20

      - name: Run all tests
        if: github.event_name == 'schedule'
        shell: bash -l {0}
        run: pytest --all
        timeout-minutes: 60