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: ''


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_runs:
    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:
        os: [ubuntu-latest]
        python-version: ['3.8', '3.11']

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

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

    # This should generally not be required, but in the end it is just easier
    - name: Ensure system dependencies
      run: |
        sudo apt-get update
        sudo apt-get install gcc gfortran

    - name: Python installation
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install sisl + dependencies
      run: |
        python -m pip install --progress-bar=off --upgrade pip
        python -m pip install --progress-bar=off Cython "scikit-build-core[pyproject]"
        python -m pip install --progress-bar=off -r ci/requirements.txt -r ci/requirements-viz.txt -r requirements.txt
        CC=gcc FC=gfortran python -m pip install -vvv .

    - name: Running sisl tests
      env:
        SISL_FILES_TESTS: ${{ github.workspace }}/files/tests
      run: |
        # This needs to be done in a separate folder
        # Otherwise the import will try to use the one in the current folder
        mkdir sisl-test-dir ; cd sisl-test-dir
        if [[ "${{ github.event.inputs.marks }}" == "" ]]; then
         ADD_FLAGS=""
        else
         ADD_FLAGS="-m ${{ github.event.inputs.marks }}"
        fi
        # --cov forces the reading of .coveragerc
        ADD_TOOLS=""
        for tool in btd models ; do
          ADD_TOOLS="$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
        py.test -vv -rX --cov --cov-report term-missing --cov-report xml --cov-config=../.coveragerc $ADD_FLAGS --pyargs sisl $ADD_TOOLS
        #cp coverage.xml ../

    - name: Upload code-coverage
      if: ${{ github.event.inputs.marks == '' }}
      uses: codecov/codecov-action@v3
      with:
        directory: ./sisl-test-dir/
        verbose: true