Replace flake8/isort/black with ruff (#115)

* Minor formatting changes

* Replace flake8/isort/black with ruff

* Remove old config entries

* Forgot f in f-string

* Add missing colon

* Add missing space

* Ignore docs directory

* Clean up Makefile

* Do not exclude docs

* Do not globally exclude A002

.github/CONTRIBUTING.md

@@ -39,7 +39,7 @@ you can run tests by making use of the `Makefile` and
 From the project root, call:
 
 - `make test` to run tests and coverage
-- `make pep` to run style checks
+- `pre-commit run` to run style checks (Ruff and some additional hooks)
 
 ## Building the documentation
 

.github/workflows/python_tests.yml

@@ -60,7 +60,7 @@ jobs:
     - name: Check formatting
       if: ${{ matrix.platform == 'ubuntu-22.04' && matrix.python-version == '3.11' }}
       run: |
-        make pep
+        make check-manifest
         pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
 
     - name: Test with pytest

.pre-commit-config.yaml

@@ -1,27 +1,20 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
-    hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-json
-    -   id: check-ast
-    -   id: check-added-large-files
-    -   id: check-case-conflict
-    -   id: check-docstring-first
--   repo: https://github.com/pycqa/isort
-    rev: "5.12.0"
-    hooks:
-    -   id: isort
--   repo: https://github.com/psf/black
-    rev: "23.9.1"
-    hooks:
-    -   id: black
--   repo: https://github.com/pycqa/flake8
-    rev: "6.1.0"
-    hooks:
-    -   id: flake8
-        additional_dependencies: [flake8-docstrings]
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-json
+    - id: check-ast
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-docstring-first
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.2.1
+  hooks:
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format

Makefile

@@ -1,6 +1,6 @@
-.PHONY: all inplace test flake pydocstyle check-manifest isort black pep build-doc dist-build
+.PHONY: all inplace test check-manifest build-doc dist-build
 
-all: inplace pep test build-doc dist-build
+all: inplace check-manifest test build-doc dist-build
 
 inplace:
 	@echo "Installing pybv"
@@ -12,28 +12,10 @@ test:
 	@echo "Running pytest: test modules"
 	@pytest --cov=./pybv --cov-report=xml --verbose
 
-flake:
-	@echo "Running flake8"
-	@flake8 --docstring-convention numpy --count pybv
-
-pydocstyle:
-	@echo "Running pydocstyle"
-	@pydocstyle
-
 check-manifest:
 	@echo "Running check-manifest"
 	@check-manifest
 
-isort:
-	@echo "Running check-manifest"
-	@isort .
-
-black:
-	@echo "Running black"
-	@black .
-
-pep: flake pydocstyle check-manifest isort black
-
 build-doc:
 	@echo "Building documentation"
 	make -C docs/ clean

docs/conf.py

@@ -45,7 +45,7 @@
 
 # General information about the project.
 project = "pybv"
-copyright = "2018-{}, pybv developers".format(date.today().year)
+copyright = f"2018-{date.today().year}, pybv developers"  # noqa:A001
 author = "pybv developers"
 version = pybv.__version__
 release = version

docs/sphinxext/gh_substitutions.py

@@ -10,8 +10,12 @@
 from docutils.parsers.rst.roles import set_classes
 
 
-def gh_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
+def gh_role(name, rawtext, text, lineno, inliner, options=None, content=None):
     """Link to a GitHub issue."""
+    if content is None:
+        content = []
+    if options is None:
+        options = {}
     try:
         # issue/PR mode (issues/PR-num will redirect to pull/PR-num)
         int(text)

pybv/__init__.py

@@ -1,7 +1,7 @@
 """A lightweight I/O utility for the BrainVision data format."""
 
-
 __version__ = "0.8.0.dev5"
+
 from .io import write_brainvision
 
 __all__ = ["write_brainvision"]

pybv/_export.py

@@ -19,31 +19,31 @@ def _export_mne_raw(*, raw, fname, events=None, overwrite=False):
         The raw data to export.
     fname : str | pathlib.Path
         The name of the file where raw data will be exported to. Must end with
-        ``".vhdr"``, and accompanying *.vmrk* and *.eeg* files will be written
-        inside the same directory.
+        ``".vhdr"``, and accompanying *.vmrk* and *.eeg* files will be written inside
+        the same directory.
     events : np.ndarray | None
-        Events to be written to the marker file (*.vmrk*). When array, must be in
-        `MNE-Python format <https://mne.tools/stable/glossary.html#term-events>`_.
-        When ``None`` (default), events will be written based on ``raw.annotations``.
+        Events to be written to the marker file (*.vmrk*). If array, must be in
+        `MNE-Python format <https://mne.tools/stable/glossary.html#term-events>`_. If
+        ``None`` (default), events will be written based on ``raw.annotations``.
     overwrite : bool
         Whether or not to overwrite existing data. Defaults to ``False``.
+
     """
-    # Prepare file location
+    # prepare file location
     if not str(fname).endswith(".vhdr"):
         raise ValueError("`fname` must have the '.vhdr' extension for BrainVision.")
     fname = Path(fname)
     folder_out = fname.parents[0]
     fname_base = fname.stem
 
-    # Prepare data from raw
+    # prepare data from raw
     data = raw.get_data()  # gets data starting from raw.first_samp
     sfreq = raw.info["sfreq"]  # in Hz
     meas_date = raw.info["meas_date"]  # datetime.datetime
     ch_names = raw.ch_names
 
-    # write voltage units as micro-volts and all other units without
-    # scaling
-    # We write units that we don't know as n/a
+    # write voltage units as micro-volts and all other units without scaling
+    # write units that we don't know as n/a
     unit = []
     for ch in raw.info["chs"]:
         if ch["unit"] == FIFF.FIFF_UNIT_V:
@@ -54,9 +54,9 @@ def _export_mne_raw(*, raw, fname, events=None, overwrite=False):
             unit.append(_unit2human.get(ch["unit"], "n/a"))
     unit = [u if u != "NA" else "n/a" for u in unit]
 
-    # We enforce conversion to float32 format
-    # XXX: Could add a feature that checks data and optimizes `unit`, `resolution`,
-    #      and `format` so that raw.orig_format could be retained if reasonable.
+    # enforce conversion to float32 format
+    # XXX: Could add a feature that checks data and optimizes `unit`, `resolution`, and
+    #      `format` so that raw.orig_format could be retained if reasonable.
     if raw.orig_format != "single":
         warn(
             f"Encountered data in '{raw.orig_format}' format. "
@@ -67,12 +67,12 @@ def _export_mne_raw(*, raw, fname, events=None, overwrite=False):
     fmt = "binary_float32"
     resolution = 0.1
 
-    # Handle events
+    # handle events
     # if we got an ndarray, this is in MNE-Python format
     msg = "`events` must be None or array in MNE-Python format."
     if events is not None:
-        # Subtract raw.first_samp because brainvision marks events starting from
-        # the first available data point and ignores the raw.first_samp
+        # Subtract raw.first_samp because brainvision marks events starting from the
+        # first available data point and ignores the raw.first_samp
         assert isinstance(events, np.ndarray), msg
         assert events.ndim == 2, msg
         assert events.shape[-1] == 3, msg
@@ -107,14 +107,14 @@ def _mne_annots2pybv_events(raw):
     """Convert mne Annotations to pybv events."""
     events = []
     for annot in raw.annotations:
-        # Handle onset and duration: seconds to sample,
-        # relative to raw.first_samp / raw.first_time
+        # handle onset and duration: seconds to sample, relative to
+        # raw.first_samp / raw.first_time
         onset = annot["onset"] - raw.first_time
         onset = raw.time_as_index(onset).astype(int)[0]
         duration = int(annot["duration"] * raw.info["sfreq"])
 
-        # Triage type and description
-        # Defaults to type="Comment", and the full description
+        # triage type and description
+        # defaults to type="Comment" and the full description
         etype = "Comment"
         description = annot["description"]
         for start in ["Stimulus/S", "Response/R", "Comment/"]:
@@ -137,11 +137,11 @@ def _mne_annots2pybv_events(raw):
         )
 
         if "ch_names" in annot:
-            # Handle channels
+            # handle channels
             channels = list(annot["ch_names"])
             event_dict["channels"] = channels
 
-        # Add a "pybv" event
+        # add a "pybv" event
         events += [event_dict]
 
     return events