python-app.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: CI

on:
  push:
  pull_request:
  schedule:
    - cron: '0 12 * * 1'

permissions:
  contents: read
  
defaults:
  run:
    shell: bash -el {0}  # Lets conda work

jobs:
  build:

    strategy:
        matrix:
          os: [ubuntu-latest, macos-latest]
        max-parallel: 5
    runs-on: ${{ matrix.os }}
    timeout-minutes: 30

    steps:
    - uses: actions/checkout@v3
    - uses: conda-incubator/setup-miniconda@v2
      with:
        environment-file: ${{ matrix.os == 'ubuntu-latest' && 'envs/environment-cpu.yml' || 'envs/environment-macos.yml' }}
        activate-environment: test
        auto-activate-base: true
        auto-update-conda: false
        remove-profiles: true
        architecture: x64
        clean-patched-environment-file: true
        run-post: true
        use-mamba: true
        miniforge-version: latest
    - name: Display Environment
      run: conda list
    - name: Install test dependencies
      run: |
        pip install -e .[test]
    - name: Lint with flake8
      run: |
        pip install flake8
        flake8 examol tests
    - name: Add quantum chemistry tools (Linux)
      if: ${{ matrix.os == 'ubuntu-latest' }}
      run: |
         # CP2K package has disappeared as of 21Jan25
         # sudo apt update
         # sudo apt install -y cp2k lammps

         # Link the cp2k.ssmp executable to the cp2k_shell needed for ASE
         mkdir -p bin
         cp2k_path=`which cp2k.ssmp`
         export CP2K_DATA_DIR=`which cp2k.ssmp | xargs dirname`/../share/cp2k/data/
         echo -e "#!/bin/bash\nCP2K_DATA_DIR=$CP2K_DATA_DIR `which cp2k.ssmp` --shell \$@" > bin/cp2k_shell
         chmod u+x bin/cp2k_shell
         cat `which cp2k_shell`
         echo -n | ./bin/cp2k_shell --version
    - name: Run example
      run: examol run examples/redoxmers/spec.py:spec
    - name: Test with pytest
      if: ${{ matrix.os == 'ubuntu-latest' }}
      run: pytest --cov=examol --timeout=300 tests
    - name: Coveralls
      if: ${{ matrix.os == 'ubuntu-latest' }}
      run: |
        pip install coveralls
        coveralls --service=github
      env:
        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}