Add pre-commit (#11541)

Co-authored-by: Eric Larson <[email protected]>
Co-authored-by: Daniel McCloy <[email protected]>

.github/workflows/precommit.yml

@@ -0,0 +1,14 @@
+name: Pre-commit
+
+on: [push, pull_request]
+
+jobs:
+  style:
+    name: Pre-commit
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - uses: pre-commit/[email protected]

.gitignore

@@ -92,5 +92,5 @@ cover
 venv/
 *.json
 .hypothesis/
-
+.ruff_cache/
 .ipynb_checkpoints/

.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+default_language_version:
+    python: python3.11
+
+repos:
+# - repo: https://github.com/psf/black
+#   rev: 23.1.0
+#   hooks:
+#     - id: black
+#       args: [--quiet]
+
+# Ruff mne
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.262
+  hooks:
+    - id: ruff
+      name: ruff mne
+      files: ^mne/
+
+# Ruff tutorials and examples
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.262
+  hooks:
+    - id: ruff
+      name: ruff tutorials and examples
+      # D103: missing docstring in public function
+      # D400: docstring first line must end with period
+      args: ["--ignore=D103,D400"]
+      files: ^tutorials/|^examples/
+
+# Codespell
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.3
+  hooks:
+    - id: codespell
+      files: ^mne/|^doc/|^examples/|^tutorials/
+      types_or: [python, bib, rst, inc]

MANIFEST.in

@@ -57,6 +57,7 @@ exclude tools
 exclude Makefile
 exclude .coveragerc
 exclude *.yml
+exclude *.yaml
 exclude ignore_words.txt
 exclude .mailmap
 exclude codemeta.json

Makefile

@@ -2,7 +2,6 @@
 
 PYTHON ?= python
 PYTESTS ?= py.test
-CTAGS ?= ctags
 CODESPELL_SKIPS ?= "doc/_build,doc/auto_*,*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg,references.bib,*.css,*.edf,*.bdf,*.vhdr"
 CODESPELL_DIRS ?= mne/ doc/ tutorials/ examples/
 all: clean inplace test test-doc
@@ -25,13 +24,6 @@ clean-cache:
 
 clean: clean-build clean-pyc clean-so clean-ctags clean-cache
 
-in: inplace # just a shortcut
-inplace:
-	$(PYTHON) setup.py build_ext -i
-
-wheel:
-	$(PYTHON) setup.py sdist bdist_wheel
-
 wheel_quiet:
 	$(PYTHON) setup.py -q sdist bdist_wheel
 
@@ -43,79 +35,27 @@ testing_data:
 
 pytest: test
 
-test: in
-	rm -f .coverage
-	$(PYTESTS) -m 'not ultraslowtest' mne
-
-test-verbose: in
-	rm -f .coverage
-	$(PYTESTS) -m 'not ultraslowtest' mne --verbose
-
-test-fast: in
-	rm -f .coverage
-	$(PYTESTS) -m 'not slowtest' mne
-
-test-full: in
-	rm -f .coverage
-	$(PYTESTS) mne
-
 test-no-network: in
 	sudo unshare -n -- sh -c 'MNE_SKIP_NETWORK_TESTS=1 py.test mne'
 
 test-no-testing-data: in
 	@MNE_SKIP_TESTING_DATASET_TESTS=true \
 	$(PYTESTS) mne
 
-test-no-sample-with-coverage: in testing_data
-	rm -rf coverage .coverage
-	$(PYTESTS) --cov=mne --cov-report html:coverage
-
 test-doc: sample_data testing_data
 	$(PYTESTS) --doctest-modules --doctest-ignore-import-errors --doctest-glob='*.rst' ./doc/ --ignore=./doc/auto_examples --ignore=./doc/auto_tutorials --ignore=./doc/_build --ignore=./doc/conf.py --ignore=doc/sphinxext --fulltrace
 
-test-coverage: testing_data
-	rm -rf coverage .coverage
-	$(PYTESTS) --cov=mne --cov-report html:coverage
-# what's the difference with test-no-sample-with-coverage?
-
-test-mem: in testing_data
-	ulimit -v 1097152 && $(PYTESTS) mne
-
-trailing-spaces:
-	find . -name "*.py" | xargs perl -pi -e 's/[ \t]*$$//'
+pre-commit:
+	@pre-commit run -a
 
-ctags:
-	# make tags for symbol based navigation in emacs and vim
-	# Install with: sudo apt-get install exuberant-ctags
-	$(CTAGS) -R *
-
-upload-pipy:
-	python setup.py sdist bdist_egg register upload
-
-flake:
-	@if command -v flake8 > /dev/null; then \
-		echo "Running flake8"; \
-		flake8 --count; \
-	else \
-		echo "flake8 not found, please install it!"; \
-		exit 1; \
-	fi;
-	@echo "flake8 passed"
+# Aliases for stuff we used to support or users might think of
+ruff: pre-commit
+flake: pre-commit
+pep: pre-commit
 
 codespell:  # running manually
 	@codespell --builtin clear,rare,informal,names,usage -w -i 3 -q 3 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt --uri-ignore-words-list=bu $(CODESPELL_DIRS)
 
-codespell-error:  # running on travis
-	@codespell --builtin clear,rare,informal,names,usage -i 0 -q 7 -S $(CODESPELL_SKIPS) --ignore-words=ignore_words.txt --uri-ignore-words-list=bu $(CODESPELL_DIRS)
-
-pydocstyle:
-	@echo "Running pydocstyle"
-	@pydocstyle mne
-
-docstring:
-	@echo "Running docstring tests"
-	@$(PYTESTS) --doctest-modules mne/tests/test_docstring_parameters.py
-
 check-manifest:
 	check-manifest -q --ignore .circleci/config.yml,doc,logo,mne/io/*/tests/data*,mne/io/tests/data,mne/preprocessing/tests/data,.DS_Store,mne/_version.py
 
@@ -125,26 +65,3 @@ check-readme: clean wheel_quiet
 nesting:
 	@echo "Running import nesting tests"
 	@$(PYTESTS) mne/tests/test_import_nesting.py
-
-pep:
-	@$(MAKE) -k flake pydocstyle docstring codespell-error check-manifest nesting check-readme
-
-manpages:
-	@echo "I: generating manpages"
-	set -e; mkdir -p _build/manpages && \
-	cd bin && for f in mne*; do \
-			descr=$$(grep -h -e "^ *'''" -e 'DESCRIP =' $$f -h | sed -e "s,.*' *\([^'][^']*\)'.*,\1,g" | head -n 1); \
-	PYTHONPATH=../ \
-			help2man -n "$$descr" --no-discard-stderr --no-info --version-string "$(uver)" ./$$f \
-			>| ../_build/manpages/$$f.1; \
-	done
-
-build-doc-dev:
-	cd doc; make clean
-	cd doc; DISPLAY=:1.0 xvfb-run -n 1 -s "-screen 0 1280x1024x24 -noreset -ac +extension GLX +render" make html_dev
-
-build-doc-stable:
-	cd doc; make clean
-	cd doc; DISPLAY=:1.0 xvfb-run -n 1 -s "-screen 0 1280x1024x24 -noreset -ac +extension GLX +render" make html_stable
-
-docstyle: pydocstyle

azure-pipelines.yml

@@ -39,7 +39,7 @@ stages:
     pool:
       vmImage: 'ubuntu-latest'
     variables:
-      PYTHON_VERSION: '3.9'
+      PYTHON_VERSION: '3.11'
       PYTHON_ARCH: 'x64'
     steps:
     - bash: echo $(COMMIT_MSG)
@@ -50,23 +50,14 @@ stages:
         addToPath: true
       displayName: 'Get Python'
     - bash: |
-        set -e
+        set -eo pipefail
         python -m pip install --progress-bar off --upgrade pip setuptools wheel
         python -m pip install --progress-bar off -r requirements_base.txt -r requirements_hdf5.txt -r requirements_testing.txt
+        pre-commit install --install-hooks
       displayName: Install dependencies
     - bash: |
-        make flake
-      displayName: make flake
-    - bash: |
-        make codespell-error
-      displayName: make codespell
-    - bash: |
-        make pydocstyle
-      displayName: make pydocstyle
-      condition: always()
-    - bash: |
-        make docstring
-      displayName: make docstring
+        make pre-commit
+      displayName: make ruff
       condition: always()
     - bash: |
         make nesting

doc/install/contributing.rst

@@ -694,11 +694,16 @@ Adhere to standard Python style guidelines
 All contributions to MNE-Python are checked against style guidelines described
 in `PEP 8`_. We also check for common coding errors (such as variables that are
 defined but never used). We allow very few exceptions to these guidelines, and
-use tools such as pep8_, pyflakes_, and flake8_ to check code style
+use tools such as ruff_ to check code style
 automatically. From the :file:`mne-python` root directory, you can check for
-style violations by running::
+style violations by first installing our pre-commit hook::
 
-    $ make flake
+    $ pip install pre-commit
+    $ pre-commit install --install-hooks
+
+Then running::
+
+    $ make ruff  # alias for `pre-commit run -a`
 
 in the shell. Several text editors or IDEs also have Python style checking,
 which can highlight style errors while you code (and train you to make those
@@ -748,7 +753,7 @@ but complete docstrings are appropriate when private functions/methods are
 relatively complex. To run some basic tests on documentation, you can use::
 
     $ pytest mne/tests/test_docstring_parameters.py
-    $ make docstyle
+    $ make ruff
 
 
 Cross-reference everywhere
@@ -1097,8 +1102,7 @@ it can serve as a useful example of what to expect from the PR review process.
 .. linting
 
 .. _PEP 8: https://www.python.org/dev/peps/pep-0008/
-.. _pyflakes: https://pypi.org/project/pyflakes
-.. _Flake8: http://flake8.pycqa.org/
+.. _ruff: https://beta.ruff.rs/docs
 
 .. misc
 

examples/simulation/simulate_evoked_data.py

@@ -55,7 +55,7 @@
 
 
 def data_fun(times):
-    """Function to generate random source time courses"""
+    """Generate random source time courses."""
     return (50e-9 * np.sin(30. * times) *
             np.exp(- (times - 0.15 + 0.05 * rng.randn(1)) ** 2 / 0.01))
 

examples/simulation/simulated_raw_data_using_subject_anatomy.py

@@ -124,8 +124,7 @@
 
 
 def data_fun(times, latency, duration):
-    """Function to generate source time courses for evoked responses,
-    parametrized by latency and duration."""
+    """Generate source time courses for evoked responses."""
     f = 15  # oscillating frequency, beta band [Hz]
     sigma = 0.375 * duration
     sinusoid = np.sin(2 * np.pi * f * (times - latency))

examples/visualization/topo_customized.py

@@ -47,7 +47,8 @@
 
 
 def my_callback(ax, ch_idx):
-    """
+    """Handle axes callback.
+
     This block of code is executed once you click on one of the channel axes
     in the plot. To work with the viz internals, this function should only take
     two parameters, the axis and the channel or data index.

mne/beamformer/tests/test_resolution_matrix.py

@@ -85,9 +85,9 @@ def test_resolution_matrix_lcmv():
     # Some rows are off by about 0.1 - not yet clear why
     corr = []
 
-    for (f, l) in zip(resmat_fwd, resmat_lcmv):
+    for (f, lf) in zip(resmat_fwd, resmat_lcmv):
 
-        corr.append(np.corrcoef(f, l)[0, 1])
+        corr.append(np.corrcoef(f, lf)[0, 1])
 
     # all row correlations should at least be above ~0.8
     assert_allclose(corr, 1., atol=0.2)

mne/chpi.py

@@ -1212,8 +1212,8 @@ def compute_chpi_locs(info, chpi_amplitudes, t_step_max=1., too_close='raise',
         # check if data has sufficiently changed
         if last['sin_fit'] is not None:  # first iteration
             corrs = np.array(
-                [np.corrcoef(s, l)[0, 1]
-                    for s, l in zip(sin_fit, last['sin_fit'])])
+                [np.corrcoef(s, lst)[0, 1]
+                    for s, lst in zip(sin_fit, last['sin_fit'])])
             corrs *= corrs
             # check to see if we need to continue
             if fit_time - last['coil_fit_time'] <= t_step_max - 1e-7 and \

mne/io/base.py

@@ -570,7 +570,10 @@ def time_as_index(self, times, use_rounding=False, origin=None):
 
     @property
     def _raw_lengths(self):
-        return [l - f + 1 for f, l in zip(self._first_samps, self._last_samps)]
+        return [
+            last - first + 1
+            for first, last in zip(self._first_samps, self._last_samps)
+        ]
 
     @property
     def annotations(self):  # noqa: D401

mne/utils/check.py

@@ -1122,6 +1122,7 @@ def _to_rgb(*args, name='color', alpha=False):
 
 @deprecated('has_nibabel is deprecated and will be removed in 1.5')
 def has_nibabel():
+    """Check if nibabel is installed."""
     return check_version('nibabel')  # pragma: no cover