pytest.yaml

name: Pytest

on:
  push:
    branches:
      - "main"
  pull_request:
    branches:
      - "main"

jobs:
  pytest_conda:
    name: Pytest (conda) on ${{ matrix.os }}, Python ${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: ["ubuntu-latest"]
        python-version: ["3.8", "3.10"]
    defaults:
      run:
        shell: bash -l {0}
    steps:
    - uses: actions/checkout@v4

    - name: Additional info about the build
      run: |
        uname -a
        df -h
        ulimit -a
    # Get date for the cache key
    - name: Get current time
      uses: josStorer/get-current-time@v2.0.2
      id: current-time
    - name: Cache conda env
      uses: actions/cache@v4
      id: cache
      env:
        # Increase this value to reset cache if mols.yml has not changed
        CACHE_NUMBER: 0
      with:
        path: ~/conda_pkgs_dir
        key:
          # Key contains current year and month to ensure it is updated once a month
          ${{ runner.os }}-py${{ matrix.python-version }}-conda-${{ steps.current-time.outputs.year }}-${{
          steps.current-time.outputs.month }}-${{ hashFiles('devtools/conda-envs/mols.yml') }}-${{
          env.CACHE_NUMBER }}

    # More info on the whole conda setup: https://github.com/conda-incubator/setup-miniconda
    - name: Setup Conda
      uses: conda-incubator/setup-miniconda@v3
      id: conda-setup
      with:
        # mamba-version: "*" # uncomment to activate mamba
        python-version: ${{ matrix.python-version }}
        miniforge-variant: Mambaforge
        channels: conda-forge,defaults
        environment-file: devtools/conda-envs/mols.yml

        activate-environment: molsimp
        use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!

    - name: Install package
      run: |
        pip install -e . --no-deps
        pip install pytest-cov
        conda list

    - name: Run tests
      run: |
        pytest -v --cov=molSimplify --cov-report=xml

    - name: Run doctest
      # For now still excluding several subfolders and files
      run: |
        pytest --doctest-modules --ignore=molSimplify/Informatics/MOF --ignore=molSimplify/Informatics/protein --ignore=molSimplify/Scripts/in_b3lyp_usetc.py --ignore=molSimplify/Informatics/jupyter_vis.py --ignore=molSimplify/Informatics/macrocycle_synthesis.py --ignore=molSimplify/Informatics/organic_fingerprints.py molSimplify

    - name: Upload coverage report to codecov
      uses: codecov/codecov-action@v4
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        directory: ./coverage/reports/
        env_vars: OS,PYTHON
        files: ./coverage.xml
        flags: unittests
        name: codecov-umbrella
        verbose: true

    - name: Report Status
      # Slack notifications only on the main repo
      if: ${{job.status == 'failure' && github.event_name != 'pull_request' && github.repository == 'hjkgrp/molSimplify' }}
      #uses: ravsamhq/notify-slack-action@v1
      uses: 8398a7/action-slack@v3
      with:
        job_name: Pytest (conda) on ${{ matrix.os }}, Python ${{ matrix.python-version }}
        fields: message,commit,author,workflow,job,took
        status: ${{ job.status }}
      env:
        SLACK_WEBHOOK_URL: ${{secrets.SLACK_WEBHOOK}}
        #MATRIX_CONTEXT: ${{ toJson(matrix) }} # required

  pytest_pip:
    name: Pytest (pip) on ${{ matrix.os }}, Python ${{ matrix.python-version }}
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: ["ubuntu-latest"]
        python-version: ["3.8"]
    steps:
    - uses: actions/checkout@v4

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install package
      run: |
        pip install -e .[dev]

    - name: Run pytest
      run: |
        pytest -v