ci-testing.yaml

# This is the main workflow for testing the code, notebooks and package.
# It is divided into three jobs:
# 1. Code-quality:
#    - Check the validity of pyproject.toml
#    - Check code linting
#    - Check code formatting
#    - Check Jupyter notebooks formatting
#    - Check formatting of Markdown, YAML, TOML, etc. files
# 2. Test-code:
#    - Test the code base and upload coverage to Codecov
#    - Create the Python package
#    - Upload the Python package for the next job
# 3. Test-package:
#    - Download the Python package from the previous job
#    - Install the downloaded Python package
#    - Test the code base
#    - Check if Jupyter Notebooks run without errors

name: Test code, notebooks and package

on:
  # Trigger the workflow on push
  push:
    # Every branch
    branches:
      - '**'
    # But do not run this workflow on creating a new tag starting with 'v', e.g. 'v1.0.3' (see pypi-publish.yml)
    tags-ignore:
      - 'v*'
  # Trigger the workflow on pull request
  pull_request:
    branches:
      - '**'
  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

# Allow only one concurrent workflow, skipping runs queued between the run in-progress and latest queued.
# And cancel in-progress runs.
concurrency:
  group:
    ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  # Job 1: Check code quality and consistency
  code-quality:
    strategy:
      matrix:
        os: [ubuntu-latest]
        python-version: ['3.12']

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

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: '0' # full history with tags to get the version number by versioningit

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

      - name: Install Python dependencies
        # Install 'validate-pyproject' for checking pyproject.toml
        # Install 'ruff' for code linting and formatting
        # Install 'nbqa' for quality assurance of Jupyter notebooks
        run: pip install 'validate-pyproject[all]' ruff nbqa

      - name: Install npm dependencies
        # Install 'prettier' for code formatting of Markdown, YAML, etc. files
        # Install 'prettier-plugin-toml' plugin for code formatting of TOML files
        run: npm install prettier prettier-plugin-toml --save-dev --save-exact

      # Check the validity of pyproject.toml
      - name: Check validity of pyproject.toml
        id: check_pyproject
        continue-on-error: true
        run: validate-pyproject pyproject.toml

      # Check code linting with Ruff in the project root
      - name: Check code linting
        id: check_code_linting
        continue-on-error: true
        run: ruff check .

      - name: Suggestion to fix code linting issues (for *.py files)
        if: steps.check_code_linting.outcome == 'failure'
        run:
          echo "In project root run 'ruff check . --fix' and commit changes to
          fix issues."

      # Check code formatting with Ruff in the project root
      - name: Check code formatting
        id: check_code_formatting
        continue-on-error: true
        run: ruff format . --check

      - name: Suggestion to fix code formatting issues (for *.py files)
        if: steps.check_code_formatting.outcome == 'failure'
        run:
          echo "In project root run 'ruff format .' and commit changes to fix
          issues."

      # Check Jupyter notebooks with nbQA in the sample directory
      - name: Check Jupyter notebooks formatting
        id: check_notebooks
        continue-on-error: true
        run: nbqa ruff examples/

      - name: Suggestion to fix notebook formatting issues (for *.ipynb files)
        if: steps.check_notebooks.outcome == 'failure'
        run:
          echo "In project root run 'nbqa ruff examples/ --fix' and commit
          changes to fix issues."

      # Check formatting of Markdown, YAML, TOML, etc. files with Prettier in the project root
      - name: Check formatting of Markdown, YAML, TOML, etc. files
        id: check_others_formatting
        continue-on-error: true
        run: npx prettier . --check --config=prettierrc.toml

      - name: Suggestion to fix non-code formatting issues (for *.md, etc.)
        if: steps.check_others_formatting.outcome == 'failure'
        run:
          echo "In project root run 'npx prettier . --write
          --config=prettierrc.toml' and commit changes to fix issues."

      - name: Force fail if any of the previous steps failed
        if: |
          steps.check_pyproject.outcome == 'failure' ||
          steps.check_code_linting.outcome == 'failure' ||
          steps.check_code_formatting.outcome == 'failure' || 
          steps.check_notebooks.outcome == 'failure' || 
          steps.check_others_formatting.outcome == 'failure'
        run: exit 1

  # Job 2: Test code and upload coverage to Codecov.
  test-code:
    needs: code-quality # previous job 'code-quality' need to be finished first

    # current job matrix. if modified, remember to UPDATE the strategy in the next job
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-24.04, windows-2022, macos-13, macos-14]
        python-version: ['3.10', '3.11', '3.12']

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

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
        with:
          fetch-depth: '0' # full history with tags to get the version number by versioningit

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

      - name: Upgrade package installer for Python
        run: python -m pip install --upgrade pip

      - name: Install Python dependencies
        run: pip install '.[dev,charts]'

      - name: Run Python tests and create coverage report
        run: >
          pytest tests/ --cov=./ --cov-report=xml:coverage/coverage.xml
          --junitxml=./coverage/junit.xml --color=yes -n auto

      #- name: Upload test results to Codecov
      #  if: ${{ !cancelled() }}
      #  uses: codecov/test-results-action@v1
      #  with:
      #    files: ./coverage/junit.xml
      #    fail_ci_if_error: true  # optional (default = false)
      #    name: Pytest results
      #    token: ${{ secrets.CODECOV_TOKEN }}

      #- name: Upload coverage report to Codecov
      #  uses: codecov/codecov-action@v4
      #  with:
      #    files: ./coverage/coverage.xml
      #    env_vars: OS,PYTHON
      #    fail_ci_if_error: true  # optional (default = false)
      #    name: Pytest coverage
      #    token: ${{ secrets.CODECOV_TOKEN }}
      #  env:
      #    OS: ${{ matrix.os }}
      #    PYTHON: ${{ matrix.python-version }}

      - name: Create Python package
        run: python -m build --wheel --outdir dist

      - name:
          Upload zipped Python package (with tests and examples) for next job
        uses: actions/upload-artifact@v4
        with:
          name:
            EasyDiffractionLib_py${{ matrix.python-version }}_${{ matrix.os
            }}_${{ runner.arch }}
          path: |
            dist/*.whl
            tests/
            examples/
          if-no-files-found: 'error'
          compression-level: 0

  # Job 3: Test the package
  test-package:
    needs: test-code # the previous job needs to be finished first

    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-24.04, windows-2022, macos-13, macos-14]
        python-version: ['3.10', '3.11', '3.12']

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

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

      - name: Upgrade package installer for Python
        run: python -m pip install --upgrade pip

      - name:
          Download zipped Python package (with tests and examples) from previous
          job
        uses: actions/download-artifact@v4
        with: # name or path are taken from the upload step of the previous job
          name:
            EasyDiffractionLib_py${{ matrix.python-version }}_${{ matrix.os
            }}_${{ runner.arch }}
          path: . # directory to extract downloaded zipped artifacts

      # The local version must be higher than the PyPI version for pip to
      # prefer the local version. So, after a new release and a new tag,
      # remember to merge the master branch with the develop branch,
      # and then create a new feature branch from the develop branch.
      - name: Install Python package from previous job with 'dev' extras
        run: pip install 'easydiffraction[dev]' --find-links=dist

      - name: Run Python tests
        run: >
          pytest tests/ --color=yes -n auto

      - name: Check if Jupyter Notebooks run without errors
        shell: bash
        run: >
          pytest --nbmake examples/ --ignore-glob='examples/*emcee*'
          --nbmake-timeout=300 --color=yes -n=auto