[Auto-generated] Update dependencies #2248
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| name: CI Tests | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - master | |
| - 'push-action/**' | |
| jobs: | |
| tests: | |
| name: External | |
| uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.2 | |
| 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 - |