add python 3.13 pip incompatibility note #233
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| name: Unit tests | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| - main | |
| jobs: | |
| # Inspired by https://github.com/hynek/build-and-inspect-python-package/ | |
| # but revised for our needs. In particular, we have some auxiliary | |
| # files, needed for later steps of this process, that don't belong | |
| # in the sdist or wheel, that we copy into a (separate) job artifact | |
| # so those later steps don't need to check out the source tree. | |
| # In the future, we might want to build a conda package as well | |
| # as a wheel. | |
| build-package: | |
| name: Build PDR packages | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out source tree | |
| uses: actions/checkout@v4 | |
| with: | |
| path: src | |
| # Future: Any sort of validation of the source code itself, | |
| # that only needs to run once, could go here. | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| id: py | |
| with: | |
| python-version: "3.x" # latest stable | |
| update-environment: false | |
| - name: Prepare build environment | |
| run: | | |
| '${{ steps.py.outputs.python-path }}' -m venv venv | |
| . venv/bin/activate | |
| pip install --only-binary :all: --upgrade pip | |
| pip install --only-binary :all: \ | |
| build check-wheel-contents twine wheel | |
| - name: Build and verify sdist and wheel | |
| working-directory: src | |
| run: | | |
| . ../venv/bin/activate | |
| export SOURCE_DATE_EPOCH=$(git log -1 --pretty=%ct) | |
| python -BIm build --outdir=../dist | |
| check-wheel-contents ../dist/*.whl | |
| python -Im twine check --strict ../dist/* | |
| - name: Collect auxiliary files for later stages | |
| working-directory: src/.github | |
| run: | | |
| ZIPFILE=../../dist/scripts-for-jobs.zip | |
| zip -r $ZIPFILE scripts | |
| zip -j -r $ZIPFILE ../.coveragerc | |
| printf '@ .coveragerc\n@=scripts/coveragerc.raw\n' | | |
| zipnote -w $ZIPFILE | |
| - name: Upload packages | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: packages | |
| path: dist/pdr* | |
| - name: Upload build helpers | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: scripts-for-jobs | |
| path: dist/scripts-for-jobs.zip | |
| # this artifact exists only to be input to later jobs, | |
| # it does not need to be retained for long | |
| retention-days: 1 | |
| - name: Report results | |
| run: | | |
| ( cd dist | |
| printf '\n### Contents of the `packages` artifact\n\n```none\n' | |
| shasum -a 256 pdr* | |
| ) >> $GITHUB_STEP_SUMMARY | |
| conda-unit: | |
| name: | | |
| Test: ${{matrix.python}}, conda, ${{matrix.os}}, ${{matrix.deps}} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # Conda-based installations are our recommendation, so we test | |
| # comprehensively. | |
| os: [ubuntu, macos, windows] | |
| deps: [minimal, full] | |
| python: ["3.9", "3.10", "3.11", "3.12", "3.13"] | |
| needs: build-package | |
| runs-on: "${{ matrix.os }}-latest" | |
| defaults: | |
| run: | |
| # bash --login is required for conda environments to work correctly; | |
| # see https://github.com/marketplace/actions/setup-miniconda#important | |
| # something in conda's shell scripts is incompatible with -u | |
| shell: bash -l -e -o pipefail {0} | |
| steps: | |
| - name: Get build helpers | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: scripts-for-jobs | |
| - name: Extract build helpers | |
| run: unzip scripts-for-jobs.zip | |
| - name: Get just-built PDR package | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: packages | |
| path: dist | |
| - name: Extract environment file | |
| run: | | |
| tar=$(scripts/find-gnu-tar) | |
| if [[ "${{ matrix.deps }}" = minimal ]]; then | |
| conda_env=minimal_environment.yml | |
| else | |
| conda_env=environment.yml | |
| fi | |
| "$tar" --extract --to-stdout -f dist/pdr-*.tar.gz \ | |
| --wildcards \*/$conda_env > environment.yml | |
| - name: Install Python and dependencies using miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| channels: conda-forge | |
| environment-file: environment.yml | |
| - name: Install test tools | |
| run: | | |
| conda install pytest pytest-cov | |
| - name: Install PDR wheel | |
| run: | | |
| pip install --no-deps --only-binary :all: dist/pdr-*-py3-*.whl | |
| - name: Prepare for testing | |
| run: | | |
| host_os=$(python3 -c 'import os; print(os.name)') | |
| scripts/adjust-coverage-config < scripts/coveragerc.raw > coveragerc | |
| # Make the directory tree containing the actual PDR .py | |
| # files read-only. This is because we used to have a lot | |
| # of code that wrote scratch files into the PDR source tree | |
| # and we don't want it coming back. | |
| # | |
| # We only do this on Unixy platforms, because doing the same | |
| # on Windows makes setup-miniconda's cleanup pass hang. | |
| # I don't understand why actions even *have* a cleanup pass | |
| # given that they run right before the entire VM is nuked | |
| # from orbit, but so it goes. We *probably* don't have any | |
| # code that is both conda- and Windows-specific that writes | |
| # to the PDR package directory. | |
| if [ $host_os != nt ]; then | |
| chmod -R a-w dist $CONDA_PREFIX | |
| fi | |
| - name: Run unit tests | |
| run: | | |
| export PYTHONDONTWRITEBYTECODE=1 | |
| pytest -p no:cacheprovider --basetemp=$PWD/tmp --cov \ | |
| --cov-config=$PWD/coveragerc --cov-branch --cov-report=term \ | |
| --import-mode=importlib -r fEsX --pyargs pdr.tests | |
| - name: Store coverage data | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: unit-test-coverage-conda-${{ matrix.os }}-${{ matrix.python }}-${{ matrix.deps }} | |
| path: coverage.dat | |
| if-no-files-found: ignore | |
| # unmerged coverage analysis data can be ephemeral | |
| retention-days: 1 | |
| pip-unit: | |
| name: | | |
| Test: ${{matrix.python}}, pip, ${{matrix.os}}, ${{matrix.deps}} | |
| needs: build-package | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # This test exists to verify that the dependencies declared | |
| # for pip-based installs are accurate, and this should not be | |
| # drastically affected by which python we have, so we don't | |
| # test all the python versions in the support range, just the | |
| # ends. | |
| os: [ubuntu, macos, windows] | |
| python: ["3.9", "3.12"] | |
| deps: [minimal, full] | |
| runs-on: "${{ matrix.os }}-latest" | |
| defaults: | |
| run: | |
| # so I don't have to write nontrivial script fragments twice | |
| shell: bash -e -u -o pipefail {0} | |
| steps: | |
| - name: Install Python ${{ matrix.python }} | |
| uses: actions/setup-python@v5 | |
| id: py | |
| with: | |
| python-version: ${{ matrix.python }} | |
| update-environment: false | |
| - name: Get build helpers | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: scripts-for-jobs | |
| - name: Extract build helpers | |
| run: unzip scripts-for-jobs.zip | |
| - name: Get just-built PDR package | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: packages | |
| path: dist | |
| - name: Install pdr from wheel using pip | |
| id: deps | |
| run: | | |
| if [[ "${{ matrix.deps }}" = minimal ]]; then | |
| features= | |
| else | |
| features="[fits,pvl,pillow,fuzzy]" | |
| fi | |
| # Need to expand the glob naming the wheel file _before_ | |
| # it is combined with $features. | |
| wheel="$(echo dist/pdr-*-py3-*.whl)" | |
| '${{ steps.py.outputs.python-path }}' -m venv venv | |
| # I do not understand why the activation script is in a | |
| # different location on Windows. | |
| if [ ! -d venv/bin ]; then mv venv/Scripts venv/bin; fi | |
| source venv/bin/activate | |
| pip install --only-binary :all: pytest pytest-cov | |
| # If this pip command fails *and* Python is a development | |
| # version, the issue is probably that some of our | |
| # dependencies aren't available; skip the rest of the steps | |
| # but don't fail the job. continue-on-error is | |
| # insufficiently nuanced for this rule. | |
| set +e +o pipefail | |
| pip install --only-binary :all: "$wheel$features" 2>&1 | | |
| tee pip-deps.log | |
| pip_status=${PIPESTATUS[0]} | |
| python_is_experimental=$(python3 -c 'import sys; print( | |
| 1 if sys.version_info.releaselevel != "final" else 0 | |
| )') | |
| if [[ $pip_status -eq 0 ]]; then | |
| echo "available=true" >> "$GITHUB_OUTPUT" | |
| exit 0 | |
| else | |
| echo "available=false" >> "$GITHUB_OUTPUT" | |
| if [[ $python_is_experimental -eq 1 ]]; then | |
| annote=warning | |
| exitcode=0 | |
| else | |
| annote=error | |
| exitcode=1 | |
| fi | |
| sed -ne 's/^ERROR: /::'"${annote}"'::/p' < pip-deps.log | |
| exit $exitcode | |
| fi | |
| - name: Prepare for testing | |
| if: ${{ fromJSON(steps.deps.outputs.available) }} | |
| run: | | |
| host_os=$(python3 -c 'import os; print(os.name)') | |
| scripts/adjust-coverage-config < scripts/coveragerc.raw > coveragerc | |
| # Make the directory tree containing the actual PDR .py | |
| # files read-only. This is because we used to have a lot | |
| # of code that wrote scratch files into the PDR source tree | |
| # and we don't want it coming back. | |
| # We can do this on all platforms for pip-based testing. | |
| # Note: on Windows attrib +r has no effect on directories. | |
| readonly_dirs="dist venv" | |
| host_os=$(python3 -c 'import os; print(os.name)') | |
| if [ $host_os = nt ]; then | |
| export MSYS2_ARG_CONV_EXCL='*' | |
| for f in $readonly_dirs; do | |
| icacls "$f" /inheritance:r \ | |
| /grant 'CREATOR OWNER:(OI)(CI)(RX,D,DC,WDAC)' \ | |
| /grant 'BUILTIN\Users:(OI)(CI)RX' | |
| icacls "$f"'\*.*' /reset /t /l /q | |
| done | |
| else | |
| chmod -R a-w $readonly_dirs | |
| fi | |
| - name: Run unit tests | |
| if: ${{ fromJSON(steps.deps.outputs.available) }} | |
| # See comments on the matching step of the conda-unit job for | |
| # explanation. This step should be the same as that step | |
| # *except* that when using pip we have to explicitly activate | |
| # the virtualenv. | |
| run: | | |
| source venv/bin/activate | |
| export PYTHONDONTWRITEBYTECODE=1 | |
| pytest -p no:cacheprovider --basetemp=$PWD/tmp --cov \ | |
| --cov-config=$PWD/coveragerc --cov-branch --cov-report=term \ | |
| --import-mode=importlib -r fEsX --pyargs pdr.tests | |
| - name: Store coverage data | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: unit-test-coverage-pip-${{ matrix.os }}-${{ matrix.python }}-${{ matrix.deps }} | |
| path: coverage.dat | |
| if-no-files-found: ignore | |
| # unmerged coverage analysis data can be ephemeral | |
| retention-days: 1 | |
| coverage: | |
| name: Combine coverage | |
| needs: [conda-unit, pip-unit] | |
| if: always() | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| id: py | |
| with: | |
| python-version: "3.x" # latest stable | |
| update-environment: false | |
| - name: Get build helpers | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: scripts-for-jobs | |
| - name: Get just-built PDR package | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: packages | |
| path: dist | |
| - name: Get coverage data | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: unit-test-coverage-* | |
| path: cov | |
| # this does the exact opposite of what it sounds like: | |
| # if true, all the artifacts that match the pattern are | |
| # unpacked in the *same location* and clobber each other | |
| # if false they all get renamed to not collide | |
| merge-multiple: false | |
| - name: Extract build helpers | |
| run: unzip scripts-for-jobs.zip | |
| - name: Extract sources | |
| # this is guaranteed to run on Linux so we can assume "tar" is GNU tar | |
| run: | | |
| tar -xz --strip-components=1 -f dist/pdr-*.tar.gz \ | |
| --wildcards \*/.coveragerc \*/pyproject.toml \*/pdr | |
| - name: Prepare analysis environment | |
| run: | | |
| '${{ steps.py.outputs.python-path }}' -m venv venv | |
| . venv/bin/activate | |
| pip install --only-binary :all: --upgrade pip | |
| pip install --only-binary :all: coverage | |
| - name: Crunch coverage data | |
| run: | | |
| . venv/bin/activate | |
| scripts/adjust-coverage-config cov/unit-test-coverage-*/coverage.dat \ | |
| < .coveragerc > coveragerc.adjusted | |
| mv coveragerc.adjusted .coveragerc | |
| printf '### Combined coverage report\n\n' >> $GITHUB_STEP_SUMMARY | |
| python3 -m coverage combine cov/unit-test-coverage-*/coverage.dat | |
| python3 -m coverage report --format=markdown --sort=cover \ | |
| >> $GITHUB_STEP_SUMMARY | |
| - name: Store coverage report | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: unit-test-coverage-all | |
| path: coverage.dat |