CI_build.yml

name: CI Build

on:
  push:
  pull_request:
    types: [opened, reopened]
  workflow_dispatch:
    inputs:
      tag:
        description: Tag for manually running CI Build workflow
        required: False
        default: ''

jobs:

  first_check:
    name: first code check / python-3.10 / ubuntu-latest
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python 3.10
        uses: actions/setup-python@v5
        with:
          python-version: '3.10'
      - name: Python info
        run: |
          which python
          python --version
      - name: Build package and create dev environment
        run: |
          python -m pip install --upgrade pip poetry
          poetry install
      - name: Show pip list
        run: |
          pip list
      - name: Test with coverage
        run: |
          poetry run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
      - name: Correct coverage paths
        run: sed -i "s+$PWD/++g" coverage.xml
      - name: Check style against standards using prospector
        shell: bash -l {0}
        run: prospector -o grouped -o pylint:pylint-report.txt
      - name: Check whether import statements are used consistently
        run: isort . --check-only --diff

  build_pypi:
    name: Test pypi build
    runs-on: ubuntu-latest
    needs: first_check
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python 3.10
        uses: actions/setup-python@v5
        with:
          python-version: '3.10'
      - name: Python info
        run: |
          which python
          python --version
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip poetry
      - name: Build package
        run: |
          poetry build
      - name: Test package
        run: |
          poetry install --only dev
          python -m twine check dist/*
      - name: Show pip list
        run: |
          pip list
      - name: Install development dependencies
        run: |
          poetry install
      - name: Show pip list again
        run: |
          pip list
      - name: Run tests
        run: |
          poetry run pytest
      - name: Show environment variables
        shell: bash -l {0}
        run: |
          env | sort

  test_dev:
    name: test dev environment / python-${{ matrix.python-version }} / ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    needs: first_check
    strategy:
      fail-fast: false
      matrix:
        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
        python-version: ['3.10', '3.11', '3.12', '3.13']
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Python info
        run: |
          which python
          python --version
      - name: Install dependencies (includinv dev + chemistry)
        run: |
          python -m pip install --upgrade pip poetry
          poetry install
      - name: Show pip list
        run: |
          pip list
      - name: Run tests
        run: |
          poetry run pytest

  test_with_conda:
    name: Anaconda build and test documentation
    runs-on: ubuntu-latest
    needs: first_check
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: "0"
      - name: Create conda environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          python-version: '3.10'
      - name: Show conda config
        shell: bash -l {0}
        run: |
          conda info
          conda list
          conda config --show-sources
          conda config --show
          conda env list
      - name: Python info
        shell: bash -l {0}
        run: |
          which python
          python --version
      - name: Show environment variables
        shell: bash -l {0}
        run: |
          env | sort
      - name: Install conda dependencies
        shell: bash -l {0}
        run: |
          conda install -c conda-forge poetry
      - name: Install with development dependencies
        shell: bash -l {0}
        run: |
          python -m pip install --upgrade pip
          poetry install --with dev,docs
      - name: Build documentation
        shell: bash -l {0}
        run: |
          make coverage doctest html
        working-directory: readthedocs/
        env:
          SPHINXOPTS: "-n"  # enable nit-picky mode
      - name: Check documentation coverage threshold
        run: |
          cat readthedocs/_build/coverage/python.txt
          UNCOVERED_MEMBERS=$(grep '*' readthedocs/_build/coverage/python.txt | wc -l)
          UNCOVERED_MEMBERS_ALLOWED=10
          if (( $UNCOVERED_MEMBERS > $UNCOVERED_MEMBERS_ALLOWED )) ; then echo "There are currently ${UNCOVERED_MEMBERS} uncovered members in the documentation, which is more than the ${UNCOVERED_MEMBERS_ALLOWED} allowed." && exit 1;fi
          echo "The code is sufficiently documented with ${UNCOVERED_MEMBERS} uncovered members out of ${UNCOVERED_MEMBERS_ALLOWED} allowed.";
      - name: Test with coverage
        shell: bash -l {0}
        run: |
          poetry run pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml
      - name: Correct coverage paths
        run: sed -i "s+$PWD/++g" coverage.xml
      - name: Store PR metadata in json file
        env:
          PR_NUMBER: ${{ github.event.pull_request.number }}
          HEAD_REF: ${{ github.event.pull_request.head.ref }}
          BASE_REF: ${{ github.event.pull_request.base.ref }}
        run: |
          jq -n --arg pr_number "$PR_NUMBER"\
                --arg head_ref "$HEAD_REF"\
                --arg base_ref "$BASE_REF"\
            '{"pr_number": $pr_number, "head_ref": $head_ref, "base_ref": $base_ref}' > pr_metadata.json
      - uses: actions/upload-artifact@v4
        with:
          name: sonarcloud-data-conda
          path: |
            coverage.xml
            xunit-result.xml
            pr_metadata.json