test.yaml

---
name: Coverage test

defaults:
  run:
    shell: bash

env:
  CFLAGS: -Og


on:
  push:
    branches: [main]
    paths:
      - '**.py'
      - '**.ipynb'
  pull_request:
    paths:
      - '**.py'
      - '**.ipynb'
  schedule:
    # only once every 4 days
    # We can always force run this.
    - cron: '37 10 */4 * *'
  workflow_dispatch:
    inputs:
      branch:
        description: 'Which branch to test'
        required: false
        default: 'main'
      marks:
        description: 'Which marks to test'
        required: false
        default: ''
      verbose:
        description: 'Run pytest with -vvv'
        required: false
        type: boolean

jobs:

  # Define a few jobs that can be runned
  lint:
    uses: ./.github/workflows/linter.yml

  runnable:
    if: |
      github.event_name == 'schedule'
      && github.actor != 'dependabot[bot]'
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          ref: '${{ github.event.inputs.branch }}'
      - run: test -n $(git rev-list --after="1 week" --max-count=1 ${{ github.sha }})

  test:
    needs: [lint, runnable]
    if: |
      always() &&
      contains(needs.lint.result, 'success') &&
      (contains(needs.runnable.result, 'success') || contains(needs.runnable.result, 'skipped'))
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        python-version: ['3.9', '3.13']
        full-test: [true, false]
        minimal-dep: [true, false]
        os: [ubuntu-latest, macos-13, macos-latest]
        exclude:
          # only full test suite on 3.13
          - python-version: '3.13'
            full-test: false
          # no minimal dependency on 3.13
          - python-version: '3.13'
            minimal-dep: true
          # minimal dependency on ARM does not make sense (wheels not present)
          - os: macos-latest
            minimal-dep: true
          # only run full test suite for minimal-dependency checks
          - full-test: false
            minimal-dep: true

    steps:
    - name: Checkout sisl
      uses: actions/checkout@v4
      with:
        ref: '${{ github.event.inputs.branch }}'
        # The files submodule is required for tests purposes
        submodules: ${{ matrix.full-test }}
        # the 'files' submodule uses lfs
        lfs: ${{ matrix.full-test }}

    - name: Ensure fortran
      uses: fortran-lang/setup-fortran@v1
      with:
        compiler: gcc
        version: 11

    - name: Print-out commit information
      id: info
      run: |
        echo "branch: ${{ github.event.inputs.branch }}"
        echo "hash: ${{ github.sha }}"
        echo "python-version: ${{ matrix.python-version }}"

        # Put stuff in the environment
        #
        # Test everything including LSF files submodule?
        if [[ "${{ matrix.full-test }}" == "true" ]]; then
          echo "sisl_extras=test,viz" >> $GITHUB_OUTPUT
        else
          echo "sisl_extras=test" >> $GITHUB_OUTPUT
        fi
        # Test minimal versioning?
        if [[ "${{ matrix.minimal-dep }}" == "true" ]]; then
          echo "sisl_install_packages='numpy==1.21.*' 'scipy==1.6.*' 'xarray==0.21.*'" >> $GITHUB_OUTPUT
        else
          echo "sisl_install_packages=" >> $GITHUB_OUTPUT
        fi

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

    - name: Upgrade pip
      run: |
        python -m pip install --progress-bar=off --upgrade pip

    - name: Python minimal versions
      if: ${{ matrix.minimal-dep }}
      run: |
        python -m pip install --progress-bar=off -v ${{ steps.info.outputs.sisl_install_packages }}

    - name: Install sisl + dependencies
      env:
        SKBUILD_CMAKE_ARGS: -DWITH_COVERAGE:bool=true;-DWITH_LINE_DIRECTIVES:bool=true
        CC: gcc
        FC: gfortran
      run: |
        python -m pip install --progress-bar=off -v .[${{ steps.info.outputs.sisl_extras }}] \
          ${{ steps.info.outputs.sisl_install_packages }}

    - name: sisl debug info
      run: |
        python -c 'from sisl._debug_info import * ; print_debug_info()'

    - name: sisl import test
      run: |
        sgeom --help
        stoolbox atom-plot --help

    - name: sisl tests
      env:
        SISL_NUM_PROCS: 1
        OMP_NUM_THREADS: 1
        SISL_FILES_TESTS: ${{ github.workspace }}/files/tests
      run: |
        ls -al
        if [[ "${{ github.event.inputs.marks }}" == "" ]]; then
         ADD_FLAGS=""
        else
         ADD_FLAGS="-m ${{ github.event.inputs.marks }}"
        fi
        if [[ "${{ github.event.inputs.verbose }}" == "true" ]]; then
         ADD_FLAGS="$ADD_FLAGS -vvv"
        fi
        ADD_TOOLS=""
        for tool in btd models ; do
          ADD_TOOLS="$ADD_TOOLS sisl_toolbox.$tool"
        done
        for tool in atom minimizer ; do
          ADD_TOOLS="$ADD_TOOLS sisl_toolbox.siesta.$tool"
        done
        for tool in poisson ; do
          ADD_TOOLS="$ADD_TOOLS sisl_toolbox.transiesta.$tool"
        done
        # Try to enable code-coverage in the tests
        coverage run -m pytest --pyargs sisl $ADD_FLAGS $ADD_TOOLS
        ls -al

    - name: Upload code-coverage
      if: ${{ github.event.inputs.marks == '' }}
      uses: codecov/codecov-action@v4
      with:
        verbose: true
        token: ${{ secrets.CODECOV_TOKEN }}