ci_workflow.yml

name: CI Tests

on:
  pull_request:
  push:
    branches:
      - master
      - 'push-action/**'

jobs:
  tests:
    name: External
    uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.3
    with:
      # General
      install_extras: "[dev,docs]"

      # pre-commit
      run_pre-commit: true
      python_version_pre-commit: "3.9"
      skip_pre-commit_hooks: pylint

      # pylint
      run_pylint: true
      python_version_pylint_safety: "3.9"
      pylint_options: "--rcfile=pyproject.toml"
      pylint_targets: "*.py tools emmopy ontopy"


      # safety-specific settings
      run_safety: true
      # 48547: RDFLib vulnerability: https://pyup.io/vulnerabilities/PVE-2022-48547/48547/
      # 44715-44717: NumPy vulnerabilities:
      #  https://pyup.io/vulnerabilities/CVE-2021-41495/44715/
      #  https://pyup.io/vulnerabilities/CVE-2021-41496/44716/
      #  https://pyup.io/vulnerabilities/CVE-2021-34141/44717/
      # 70612: Jinja2 vulnerability. Only used as subdependency for mkdocs++ in tripper.
      #  https://data.safetycli.com/v/70612/97c/
      safety_options: |
        --ignore=48547
        --ignore=44715
        --ignore=44716
        --ignore=44717
        --ignore=70612

      # Build distribution
      run_build_package: true
      python_version_package: "3.9"
      build_cmd: "python -m build"

      # Build documentation
      # Exclude base classes in emmopy.emmocheck
      run_build_docs: true
      python_version_docs: "3.9"
      update_python_api_ref: true
      update_docs_landing_page: true
      package_dirs: |
        emmopy
        ontopy
      special_file_api_ref_options: "emmopy/emmocheck.py,show_bases: false"
      landing_page_replacements: |
        (LICENSE.txt),(LICENSE.md)
        (tools),(../tools)


  pytest:
    name: pytest
    runs-on: ubuntu-latest

    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]

    steps:
    - name: Checkout repository
      uses: actions/checkout@v4

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

    - name: Install system dependencies
      run: sudo apt-get update && sudo apt-get install -y graphviz openjdk-11-jre-headless

    - name: Install Python dependencies (and EMMOntoPy)
      run: |
        python -m pip install --upgrade pip
        pip install -U setuptools wheel
        pip install -U -e .[dev]

    - name: Test
      run: pytest -vvv --cov=ontopy --cov=emmopy --cov-report=xml --cov-report=term --doctest-modules

    - name: Upload coverage to Codecov
      if: matrix.python-version == '3.9' && github.repository == 'emmo-repo/EMMOntoPy'
      uses: codecov/codecov-action@v3
      with:
        token: ${{ secrets.CODECOV_TOKEN }}

    # - name: Run vertical demo
    #   run: |
    #     cd demo/vertical
    #     python define_ontology.py
    #     python plot_ontology.py
    #     cd -

    # - name: Run horizontal demo
    #   run: |
    #     cd demo/horizontal
    #     python step1_generate_metadata.py
    #     python step2_define_metadata.py
    #     python step3_instantiate.py
    #     python step4_map_instance.py
    #     cd -


  ontodoc:
    name: EMMO documentation (test using ontodoc)
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4

    - name: Set up Python 3.9
      uses: actions/setup-python@v5
      with:
        python-version: "3.9"

    - name: Check Ubuntu version we are running under
      run: |
        uname -a
        sudo apt-get update

    - name: Current environment
      run: env

    - name: Install pandoc 2.1.2
      run: |
        #sudo apt-get install -y pandoc
        wget https://github.com/jgm/pandoc/releases/download/2.1.2/pandoc-2.1.2-1-amd64.deb
        sudo apt-get install -y ./pandoc-2.1.2-1-amd64.deb

    - name: Install tzdata non-interactively
      run: |
        sudo ln -fs /usr/share/zoneinfo/Europe/Oslo /etc/localtime
        DEBIAN_FRONTEND=noninteractive sudo apt-get install -y --no-install-recommends tzdata
        sudo dpkg-reconfigure --frontend noninteractive tzdata

    - name: Install other dependencies
      run: |
        python -m pip install --upgrade pip
        pip install -r requirements.txt
        sudo apt-get update
        sudo apt-get install -y graphviz
        sudo apt-get install -y texlive-xetex
        sudo apt-get install -y texlive-latex-extra

    - name: Install EMMOntoPy
      run: |
        python setup.py install

    - name: Create EMMO documentation
      run: |
        cd examples/emmodoc
        python ../../tools/ontodoc -f simple-html emmo-inferred emmo-simple.html
        python ../../tools/ontodoc -t emmo.md -p no-self-contained emmo-inferred emmo.html
        # pdf generation is commented out as there is a xetex error which
        # needs to be resolved if we decide to keep ontodoc as a tool.
        # python ../../tools/ontodoc -t emmo.md emmo-inferred emmo.pdf
        cd -