test.yml

# Runs the complete test suite incl. many external command line dependencies (like Openbabel)
# as well as the pymatgen.ext package. Coverage used to be computed based on this workflow.
name: Tests

on:
  push:
    branches: [master]
  pull_request:
    branches: [master]

permissions:
  contents: read

jobs:
  test:
    defaults:
      run:
        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
    strategy:
      fail-fast: false
      matrix:
        # pytest-split automatically distributes work load so parallel jobs finish in similar time
        os: [ubuntu-latest]
        python-version: ["3.11"]

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

    env:
      PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
      PMG_VASP_PSP_DIR: /home/runner/work/matgenb/matgenb/psp

    steps:
      - name: Check out repo
        uses: actions/checkout@v4

      - name: Set up micromamba
        uses: mamba-org/setup-micromamba@main

      - name: Create mamba environment
        run: |
          micromamba create -n venv python=${{ matrix.python-version }} --yes
          micromamba install -n venv -c conda-forge enumlib packmol bader openbabel openff-toolkit --yes

      - name: Install uv
        run: micromamba run -n venv pip install uv

      - name: Install dependencies
        run: |
          micromamba activate venv
          uv pip install numpy cython
          uv pip install --upgrade -r requirements-ci.txt

      - name: pytest
        run: |
          micromamba activate venv
          cd notebooks
          pwd
          pytest --ignore-glob=*notest.ipynb --nbmake .