Dependency maintenance (drop Py3.8, add Py3.11/3.12/3.13, update numpy/pandas to 2.0) #4949
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Run tests on all platforms | |
| on: | |
| # Trigger the workflow on push but only for the master branch | |
| push: | |
| branches: | |
| - master | |
| paths-ignore: | |
| - '**.md' | |
| - '**.rst' | |
| - '**.bib' | |
| - '.github/**' | |
| - '!.github/workflows/run_tests.yml' | |
| - 'dev/**' | |
| - 'docs/**' | |
| - 'images/**' | |
| - '.gitignore' | |
| - '.pre-commit-config.yaml' | |
| - '.readthedocs.yml' | |
| # Trigger the workflow on pull requests, but reveal no secrets, do not use pull_request_target, see: | |
| # https://docs.github.com/en/actions/reference/events-that-trigger-workflows#pull_request_target | |
| pull_request: | |
| paths-ignore: | |
| - '**.md' | |
| - '**.rst' | |
| - '**.bib' | |
| - '.github/**' | |
| - '!.github/workflows/run_tests.yml' | |
| - 'dev/**' | |
| - 'docs/**' | |
| - 'images/**' | |
| - '.gitignore' | |
| - '.pre-commit-config.yaml' | |
| - '.readthedocs.yml' | |
| env: | |
| # Even when given -y, apt will still sometimes hang at a prompt if a package | |
| # has clarifications to ask; DEBIAN_FRONTEND=noninteractive prevents that, | |
| # This will be defined for non-debian platforms below too, but there's no harm in that. | |
| # (TravisCI quietly defined this on all their platforms, but we have to give it manually on GithubCI.) | |
| DEBIAN_FRONTEND: 'noninteractive' | |
| HDF5_USE_FILE_LOCKING: 'FALSE' | |
| # Skip to the headless matplotlib renderer, which is less | |
| # bug-prone in the constrained environment of CI | |
| # Tip from a matplotlib dev: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3388#issuecomment-846091012 | |
| # Ref: https://matplotlib.org/stable/users/explain/backends.html | |
| MPLBACKEND: 'Agg' | |
| jobs: | |
| ultra_matrix_test: | |
| name: Matrix Test of Python ${{ matrix.python-version }} on ${{ matrix.os }} | |
| # Default shell for ALL subsequent steps. | |
| defaults: | |
| run: | |
| shell: bash | |
| # Defining matrix for OS and Python | |
| strategy: | |
| # Ensure exhaustive testing of all scenarios to gather maximum amount of information | |
| fail-fast: false | |
| matrix: | |
| os: [ "macos-latest", "windows-latest", "ubuntu-20.04" ] | |
| python-version: [ '3.8', '3.9', '3.10', '3.11', '3.12' ] | |
| test-name: | |
| - integration-test | |
| # Matrix driven OS | |
| runs-on: ${{ matrix.os }} | |
| # Main steps for the test to be reproduced across OS x Python | |
| steps: | |
| # Step 0: Checkout code. | |
| - uses: actions/checkout@v3 | |
| # Step 1: Setup python version | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| # Step 2: Install dependencies | |
| - name: Install ivadomed | |
| run: | | |
| pip install -e .[dev] | |
| # Step 3: List installed packages | |
| - name: List installed packages | |
| run: | | |
| pip list | |
| # Step 4: Lint. | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| #flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| # Step 5: Full Pytest | |
| - name: Test with pytest | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_FLAG_NAME: ${{ matrix.test-name }} | |
| COVERALLS_PARALLEL: true | |
| run: | | |
| pytest . -v --cov ivadomed/ --cov-report term-missing | |
| coveralls --service=github | |
| # This step is MANDATORY and used to indicate matrix completion to coveralls.io | |
| # See here: https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support | |
| coveralls: | |
| needs: ultra_matrix_test | |
| runs-on: ubuntu-latest | |
| container: python:3-slim | |
| steps: | |
| - name: Finished | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| pip3 install --upgrade coveralls | |
| coveralls --finish | |