Speed up quantiles with sorting #7100
Workflow file for this run
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| name: xclim Testing Suite | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - CHANGELOG.rst | |
| - README.rst | |
| - pyproject.toml | |
| - xclim/__init__.py | |
| pull_request: | |
| types: | |
| - opened | |
| - reopened | |
| - synchronize | |
| pull_request_review: | |
| types: | |
| - submitted | |
| env: | |
| XCLIM_TESTDATA_BRANCH: v2023.12.14 | |
| concurrency: | |
| # For a given workflow, if we push to the same branch, cancel all previous builds on that branch except on main. | |
| group: "${{ github.workflow }}-${{ github.ref }}" | |
| cancel-in-progress: ${{ github.ref != 'refs/heads/main' }} | |
| permissions: | |
| contents: read | |
| pull-requests: read | |
| jobs: | |
| lint: | |
| name: Lint (Python${{ matrix.python-version }}) | |
| runs-on: ubuntu-latest | |
| if: | | |
| (github.event.action != 'labeled') || | |
| (github.event.review.state == 'approved') || | |
| (github.event_name == 'push') | |
| strategy: | |
| matrix: | |
| python-version: | |
| - "3.9" | |
| steps: | |
| - name: Harden Runner | |
| uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0 | |
| with: | |
| disable-sudo: true | |
| egress-policy: block | |
| allowed-endpoints: > | |
| files.pythonhosted.org:443 | |
| github.com:443 | |
| pypi.org:443 | |
| - name: Checkout Repository | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7 | |
| - name: Set up Python${{ matrix.python-version }} | |
| uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install CI libraries | |
| run: | | |
| python -m pip install --require-hashes -r CI/requirements_ci.txt | |
| - name: Run pylint | |
| run: | | |
| python -m pylint --rcfile=.pylintrc.toml --disable=import-error --exit-zero xclim | |
| - name: Run linting suite | |
| run: | | |
| python -m tox -e lint | |
| test-py39: | |
| name: Python${{ matrix.python-version }} (${{ matrix.tox-env }}, ${{ matrix.os }}) | |
| needs: lint | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| include: | |
| - tox-env: "py39" | |
| python-version: "3.9" | |
| os: ubuntu-latest | |
| steps: | |
| - name: Harden Runner | |
| uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0 | |
| with: | |
| disable-sudo: true | |
| egress-policy: block | |
| allowed-endpoints: > | |
| api.github.com:443 | |
| dap.service.does.not.exist:443 | |
| files.pythonhosted.org:443 | |
| github.com:443 | |
| pypi.org:443 | |
| raw.githubusercontent.com:443 | |
| - name: Checkout Repository | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7 | |
| - name: Set up Python${{ matrix.python-version }} | |
| uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install CI libraries | |
| run: | | |
| python -m pip install --require-hashes -r CI/requirements_ci.txt | |
| - name: Test with tox | |
| run: | | |
| python -m tox -e ${{ matrix.tox-env }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| test-pypi: | |
| needs: lint | |
| name: Python${{ matrix.python-version }} (${{ matrix.tox-env }}, ${{ matrix.os }}) | |
| if: | | |
| contains(github.event.pull_request.labels.*.name, 'approved') || | |
| (github.event.review.state == 'approved') || | |
| (github.event_name == 'push') | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| include: | |
| # Windows builds | |
| - tox-env: py39-coverage-prefetch | |
| python-version: "3.9" | |
| markers: -m 'not slow' | |
| os: windows-latest | |
| # macOS builds | |
| - tox-env: py310-coverage-lmoments-doctest | |
| python-version: "3.10" | |
| markers: -m 'not slow' | |
| os: macos-latest | |
| # Linux builds | |
| - tox-env: py39-coverage-sbck-doctest | |
| python-version: "3.9" | |
| markers: -m 'not slow' | |
| os: ubuntu-latest | |
| - tox-env: py310-coverage-lmoments # No markers -- includes slow tests | |
| python-version: "3.10" | |
| os: ubuntu-latest | |
| - tox-env: py311-coverage-sbck-extras | |
| python-version: "3.11" | |
| markers: -m 'not slow' | |
| os: ubuntu-latest | |
| - tox-env: py312-coverage-lmoments-doctest | |
| python-version: "3.12" | |
| markers: -m 'not slow' | |
| os: ubuntu-latest | |
| - tox-env: notebooks | |
| python-version: "3.10" | |
| os: ubuntu-latest | |
| - tox-env: offline-prefetch | |
| python-version: "3.11" | |
| markers: -m 'not slow and not requires_internet' | |
| os: ubuntu-latest | |
| steps: | |
| - name: Harden Runner | |
| uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0 | |
| with: | |
| egress-policy: block | |
| allowed-endpoints: > | |
| api.github.com:443 | |
| azure.archive.ubuntu.com:80 | |
| coveralls.io:443 | |
| dap.service.does.not.exist:443 | |
| esm.ubuntu.com:443 | |
| files.pythonhosted.org:443 | |
| github.com:443 | |
| motd.ubuntu.com:443 | |
| packages.microsoft.com:443 | |
| ppa.launchpadcontent.net:443 | |
| pypi.org:443 | |
| raw.githubusercontent.com:443 | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7 | |
| - name: Install Eigen3 | |
| if: contains(matrix.tox-env, 'sbck') | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libeigen3-dev | |
| - name: Set up Python${{ matrix.python-version }} | |
| uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install CI libraries | |
| run: | | |
| python -m pip install --require-hashes -r CI/requirements_ci.txt | |
| - name: Test with tox | |
| run: | | |
| python -m tox -e ${{ matrix.tox-env }} -- ${{ matrix.markers }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_FLAG_NAME: run-{{ matrix.tox-env }}-{{ matrix.os }} | |
| COVERALLS_PARALLEL: true | |
| COVERALLS_SERVICE_NAME: github | |
| test-conda: | |
| needs: lint | |
| name: Python${{ matrix.python-version }} (Conda, ${{ matrix.os }}) | |
| if: | | |
| contains(github.event.pull_request.labels.*.name, 'approved') || | |
| (github.event.review.state == 'approved') || | |
| (github.event_name == 'push') | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.9", "3.12"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Harden Runner | |
| uses: step-security/harden-runner@0d381219ddf674d61a7572ddd19d7941e271515c # v2.9.0 | |
| with: | |
| disable-sudo: true | |
| egress-policy: block | |
| allowed-endpoints: > | |
| api.github.com:443 | |
| conda.anaconda.org:443 | |
| coveralls.io:443 | |
| dap.service.does.not.exist:443 | |
| files.pythonhosted.org:443 | |
| github.com:443 | |
| objects.githubusercontent.com:443 | |
| pypi.org:443 | |
| raw.githubusercontent.com:443 | |
| repo.anaconda.com:443 | |
| - name: Checkout Repository | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7 | |
| - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }} | |
| uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822 # v1.9.0 | |
| with: | |
| cache-downloads: true | |
| cache-environment: true | |
| environment-file: environment.yml | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| - name: Conda and Mamba versions | |
| run: | | |
| echo "micromamba: $(micromamba --version)" | |
| - name: Install xclim | |
| run: | | |
| python -m pip install --no-user --editable . | |
| - name: Check versions | |
| run: | | |
| conda list | |
| xclim show_version_info | |
| python -m pip check || true | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest --numprocesses=logical --durations=10 --cov=xclim --cov-report=term-missing | |
| # - name: Install tox | |
| # shell: bash -l {0} | |
| # run: | | |
| # mamba install -n xclim39 tox tox-conda | |
| # - name: Test | |
| # shell: bash -l {0} | |
| # run: | | |
| # conda activate xclim39 | |
| # tox -e opt-slow | |
| # env: | |
| # CONDA_EXE: mamba | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Report coverage | |
| run: | | |
| coveralls | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_FLAG_NAME: run-{{ matrix.tox-env }}-opt-slow | |
| COVERALLS_PARALLEL: true | |
| COVERALLS_SERVICE_NAME: github | |
| finish: | |
| needs: | |
| - test-pypi | |
| - test-conda | |
| runs-on: ubuntu-latest | |
| container: python:3-slim | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7 | |
| with: | |
| sparse-checkout: | | |
| CI/requirements_ci.txt | |
| - name: Install CI libraries | |
| run: | | |
| python -m pip install --require-hashes -r CI/requirements_ci.txt | |
| - name: Coveralls finished | |
| run: | | |
| python -m coveralls --finish | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_SERVICE_NAME: github |