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[MNT] Add pre-commit, drop python 3.8, add python 3.12, add yamllint,…
… add toml-sort (#124) * use yaml format everywhere * use single quote in pyproject.toml * add codecov configuration * sort pyproject.toml * drop python 3.8, add 3.12 and sort pyproject.toml * add pre-commit and yamllint configuration * fix yaml style * fix more * better azp workflow * try different method * try again * fix doc * fix order * fix spelling * more fixes * rm check_version("mne", 1.2) * try patch for MNE 1.6 * fix type-hint * try again * fix style * fix doc build * turn warnings into errors * skip conftest in coverage and ignore pytest warn * add comment * try again * add ignore * improve test config * try github-actions for comparison * don't hard pin pytest version..... * sort pypyproject.toml * add cache to gh-action * remove plt.close("all") duplicate calls and set show to plt.isinteractive() * add cache for pip-pre * fix test * fix F401 * use constrained-layout in matplotlib * drop azp (temp, revert if needed!!) * Update pycrostates/conftest.py * Update pycrostates/conftest.py * Update pycrostates/conftest.py * fix import * Add pre-commit badge * ignore deprecation * fix joblib deprecation warning * one more --------- Co-authored-by: vferat <[email protected]>
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,25 @@ | ||
| comment: false | ||
| github_checks: # too noisy, even though "a" interactively disables them | ||
| annotations: false | ||
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| codecov: | ||
| notify: | ||
| require_ci_to_pass: false | ||
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| coverage: | ||
| status: | ||
| patch: | ||
| default: | ||
| informational: true | ||
| target: 95% | ||
| if_no_uploads: error | ||
| if_not_found: success | ||
| if_ci_failed: failure | ||
| project: | ||
| default: false | ||
| library: | ||
| informational: true | ||
| target: 90% | ||
| if_no_uploads: error | ||
| if_not_found: success | ||
| if_ci_failed: failure |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,109 @@ | ||
| name: pytest | ||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }} | ||
| cancel-in-progress: true | ||
| on: # yamllint disable-line rule:truthy | ||
| pull_request: | ||
| push: | ||
| branches: [main] | ||
| workflow_dispatch: | ||
| schedule: | ||
| - cron: '0 8 * * 1' | ||
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| jobs: | ||
| pytest: | ||
| timeout-minutes: 30 | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: [ubuntu, macos, windows] | ||
| python-version: [3.9, "3.10", "3.11", "3.12"] | ||
| name: ${{ matrix.os }} - py${{ matrix.python-version }} | ||
| runs-on: ${{ matrix.os }}-latest | ||
| defaults: | ||
| run: | ||
| shell: bash | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
| - name: Setup Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| architecture: 'x64' | ||
| - name: Install package | ||
| run: | | ||
| python -m pip install --progress-bar off --upgrade pip setuptools | ||
| python -m pip install --progress-bar off .[test] | ||
| - name: Display system information | ||
| run: pycrostates-sys_info --developer | ||
| - name: Display MNE info | ||
| run: mne sys_info -pd | ||
| - name: Get testing dataset version | ||
| run: | | ||
| curl https://raw.githubusercontent.com/mne-tools/mne-testing-data/master/version.txt -o mne_testing_data_version.txt | ||
| - name: Cache testing dataset | ||
| uses: actions/cache@v3 | ||
| with: | ||
| key: mne-testing-${{ hashFiles('mne_testing_data_version.txt') }} | ||
| path: ~/mne_data | ||
| - name: Download testing dataset | ||
| run: python -c "import mne; mne.datasets.testing.data_path(verbose=True)" | ||
| - name: Run pytest | ||
| run: pytest pycrostates --cov=pycrostates --cov-report=xml --cov-config=pyproject.toml | ||
| - name: Upload to codecov | ||
| uses: codecov/codecov-action@v3 | ||
| with: | ||
| files: ./coverage.xml | ||
| flags: unittests # optional | ||
| name: codecov-umbrella # optional | ||
| verbose: true # optional (default = false) | ||
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| pytest-pip-pre: | ||
| timeout-minutes: 30 | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| python-version: ["3.11"] | ||
| name: pip pre-release - py${{ matrix.python-version }} | ||
| runs-on: ubuntu-latest | ||
| defaults: | ||
| run: | ||
| shell: bash | ||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
| - name: Setup Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| architecture: 'x64' | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --progress-bar off --upgrade pip setuptools | ||
| python -m pip install --progress-bar off .[test] | ||
| python -m pip install --progress-bar off --upgrade git+https://github.com/mne-tools/mne-python | ||
| python -m pip install --progress-bar off --upgrade --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 numpy scipy scikit-learn matplotlib | ||
| - name: Display system information | ||
| run: pycrostates-sys_info --developer | ||
| - name: Display MNE info | ||
| run: mne sys_info -pd | ||
| - name: Get testing dataset version | ||
| run: | | ||
| curl https://raw.githubusercontent.com/mne-tools/mne-testing-data/master/version.txt -o mne_testing_data_version.txt | ||
| - name: Cache testing dataset | ||
| uses: actions/cache@v3 | ||
| with: | ||
| key: mne-testing-${{ hashFiles('mne_testing_data_version.txt') }} | ||
| path: ~/mne_data | ||
| - name: Download testing dataset | ||
| run: python -c "import mne; mne.datasets.testing.data_path(verbose=True)" | ||
| - name: Run pytest | ||
| run: pytest pycrostates --cov=pycrostates --cov-report=xml --cov-config=pyproject.toml | ||
| - name: Upload to codecov | ||
| uses: codecov/codecov-action@v3 | ||
| with: | ||
| files: ./coverage.xml | ||
| flags: unittests # optional | ||
| name: codecov-umbrella # optional | ||
| verbose: true # optional (default = false) |
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| ci: | ||
| skip: [codespell, pydocstyle, yamllint] | ||
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| repos: | ||
| - repo: https://github.com/pycqa/isort | ||
| rev: 5.12.0 | ||
| hooks: | ||
| - id: isort | ||
| files: pycrostates | ||
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| - repo: https://github.com/psf/black-pre-commit-mirror | ||
| rev: 23.10.1 | ||
| hooks: | ||
| - id: black | ||
| args: [--quiet] | ||
| files: pycrostates | ||
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| - repo: https://github.com/astral-sh/ruff-pre-commit | ||
| rev: v0.1.0 | ||
| hooks: | ||
| - id: ruff | ||
| args: [--fix, --exit-non-zero-on-fix] | ||
| files: pycrostates | ||
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| - repo: https://github.com/codespell-project/codespell | ||
| rev: v2.2.6 | ||
| hooks: | ||
| - id: codespell | ||
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| - repo: https://github.com/pycqa/pydocstyle | ||
| rev: 6.3.0 | ||
| hooks: | ||
| - id: pydocstyle | ||
| files: pycrostates | ||
| additional_dependencies: [tomli] | ||
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| - repo: https://github.com/mscheltienne/bibclean | ||
| rev: 0.7.1 | ||
| hooks: | ||
| - id: bibclean-fix | ||
| files: docs/references.bib | ||
| args: [--exit-non-zero-on-fix] | ||
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| - repo: https://github.com/pappasam/toml-sort | ||
| rev: v0.23.1 | ||
| hooks: | ||
| - id: toml-sort-fix | ||
| files: pyproject.toml | ||
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| - repo: https://github.com/adrienverge/yamllint | ||
| rev: v1.32.0 | ||
| hooks: | ||
| - id: yamllint | ||
| args: [--strict, -c, .yamllint.yaml] | ||
| files: (.github/|.codecov.yaml|.pre-commit-config.yaml|.prospector.yaml|.readthedocs.yaml) |
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@@ -28,4 +28,4 @@ pep257: | |
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| pylint: | ||
| disable: | ||
| - too-many-arguments | ||
| - too-many-arguments | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,5 @@ | ||
| extends: default | ||
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| rules: | ||
| line-length: disable | ||
| document-start: disable |
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