Remove flake8, pydocstyle, black, etc. in favor of ruff (#1203)

* remove flake8, pydocstyle

* ruff: use 'UP' and 'I' configs

* remove black

* run: ruff --format .

* run ruff check --fix mne_bids

* run: ruff check --fix examples/ --ignore=D103,D400,D205

* add ruff format as precommit hook

* run: pre-commit run -a

* fix botched autofixe

* remove 'UP' config for ruff again, it's done its job

* add and run new pre-commit hooks (yaml, EOL, ...)

* run some pre-commit hooks in CI

* fix python AST

* do not need to run pre-commit checks in ci, we have pre-commit.ci CI

* fix pyproj section name for pytest

Author: sappelhoff

.github/workflows/cffconvert.yml

@@ -6,7 +6,7 @@ on:
       - CITATION.cff
   pull_request:
     paths:
-      - CITATION.cff        
+      - CITATION.cff
 
 jobs:
   validate:

.github/workflows/unit_tests.yml

@@ -21,7 +21,6 @@ jobs:
         python-version: ["3.12"]
     steps:
     - uses: actions/checkout@v4
-    - uses: psf/black@stable
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -33,7 +32,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pydocstyle flake8 check-manifest black
+        python -m pip install ruff check-manifest
     - name: Display versions and environment information
       run: |
         python --version

.pre-commit-config.yaml

@@ -1,10 +1,4 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.11.0
-    hooks:
-      - id: black
-        args: [--quiet]
-
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.1.6
     hooks:
@@ -18,3 +12,21 @@ repos:
         # D205: 1 blank line required between summary line and description
         args: ["--ignore=D103,D400,D205"]
         files: ^examples/
+      - id: ruff-format
+        name: ruff format mne_bids/
+        files: ^mne_bids/
+      - id: ruff-format
+        name: ruff format examples/
+        files: ^examples/
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    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

CONTRIBUTING.md

@@ -116,8 +116,8 @@ you can simply use the following command from the root of the `mne-bids` reposit
 make pep
 ```
 
-We use [Black](https://github.com/psf/black) to format our code.
-You can simply call `black .` from the root of the `mne-bids` repository
+We use [ruff](https://docs.astral.sh/ruff/) to format our code.
+You can simply call `make ruff-format` from the root of the `mne-bids` repository
 to automatically convert your code to follow the appropriate style.
 
 ### git pre-commit hooks

LICENSE

@@ -27,4 +27,3 @@ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-

Makefile

@@ -1,4 +1,4 @@
-.PHONY: all clean-pyc clean-so clean-build clean-ctags clean-cache clean-e clean inplace test check-manifest flake black pydocstyle pep build-doc dist-build
+.PHONY: all clean-pyc clean-so clean-build clean-ctags clean-cache clean-e clean inplace test check-manifest ruff-check ruff-format pep build-doc dist-build
 
 all: clean inplace pep test build-doc dist-build
 
@@ -24,7 +24,7 @@ clean-e:
 clean: clean-build clean-pyc clean-so clean-ctags clean-cache clean-e
 
 inplace:
-	@python -m pip install -e .[full]
+	@python -m pip install -e .[dev]
 
 test:
 	@echo "Running tests"
@@ -41,19 +41,17 @@ check-manifest:
 	@echo "Checking MANIFEST.in"
 	@check-manifest .
 
-flake:
-	@echo "Running flake8"
-	@flake8 --count mne_bids examples
+ruff-format:
+	@echo "Running ruff format"
+	@ruff format mne_bids/
+	@ruff format examples/
 
-black:
-	@echo "Running black"
-	@black --check .
+ruff-check:
+	@echo "Running ruff check"
+	@ruff check mne_bids/
+	@ruff check examples/ --ignore=D103,D400,D205
 
-pydocstyle:
-	@echo "Running pydocstyle"
-	@pydocstyle .
-
-pep: flake pydocstyle check-manifest black
+pep: ruff-check check-manifest ruff-format
 
 build-doc:
 	@echo "Building documentation"
@@ -64,4 +62,6 @@ build-doc:
 dist-build:
 	@echo "Building dist"
 	rm -rf dist
+	@python -m pip install wheel setuptools build twine
 	@python -m build
+	@python -m twine check --strict dist/*

examples/anonymize_dataset.py

@@ -24,15 +24,17 @@
 # %%
 import shutil
 from pathlib import Path
+
 import mne
+
 from mne_bids import (
     BIDSPath,
-    write_raw_bids,
+    anonymize_dataset,
+    print_dir_tree,
     write_anat,
     write_meg_calibration,
     write_meg_crosstalk,
-    anonymize_dataset,
-    print_dir_tree,
+    write_raw_bids,
 )
 
 data_path = Path(mne.datasets.sample.data_path())

examples/convert_eeg_to_bids.py

@@ -34,7 +34,7 @@
 import mne
 from mne.datasets import eegbci
 
-from mne_bids import write_raw_bids, BIDSPath, print_dir_tree
+from mne_bids import BIDSPath, print_dir_tree, write_raw_bids
 from mne_bids.stats import count_events
 
 # %%
@@ -221,7 +221,7 @@
 # If you are preparing a manuscript, please make sure to also cite MNE-BIDS
 # there.
 readme = op.join(bids_root, "README")
-with open(readme, "r", encoding="utf-8-sig") as fid:
+with open(readme, encoding="utf-8-sig") as fid:
     text = fid.read()
 print(text)
 

examples/convert_empty_room.py

@@ -31,13 +31,12 @@
 
 import os.path as op
 import shutil
-
 from datetime import datetime, timezone
 
 import mne
 from mne.datasets import sample
 
-from mne_bids import write_raw_bids, read_raw_bids, BIDSPath, print_dir_tree
+from mne_bids import BIDSPath, print_dir_tree, read_raw_bids, write_raw_bids
 
 # %%
 # And define the paths and event_id dictionary.

examples/convert_group_studies.py

@@ -26,11 +26,11 @@
 from mne.datasets import eegbci
 
 from mne_bids import (
-    write_raw_bids,
     BIDSPath,
     get_anonymization_daysback,
     make_report,
     print_dir_tree,
+    write_raw_bids,
 )
 from mne_bids.stats import count_events