Fix ruff/style configuration and add missing tests (#9)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.codespellignore

@@ -0,0 +1 @@
+fro

.pre-commit-config.yaml

@@ -1,20 +1,12 @@
 repos:
-    - repo: https://github.com/pycqa/isort
-      rev: 5.13.2
-      hooks:
-          - id: isort
-            files: (src/antio|tests|setup.py)
-
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.5.6
+      rev: v0.6.0
       hooks:
           - id: ruff
             name: ruff linter
             args: [--fix, --show-fixes]
-            files: (src/antio|tests|setup.py)
           - id: ruff-format
             name: ruff formatter
-            files: (src/antio|tests|setup.py)
 
     - repo: https://github.com/codespell-project/codespell
       rev: v2.3.0
@@ -24,13 +16,6 @@ repos:
             additional_dependencies: [tomli]
             files: (src/antio|tests)
 
-    - repo: https://github.com/pycqa/pydocstyle
-      rev: 6.3.0
-      hooks:
-          - id: pydocstyle
-            files: (src/antio|tests)
-            additional_dependencies: [tomli]
-
     - repo: https://github.com/pappasam/toml-sort
       rev: v0.23.1
       hooks:

pyproject.toml

@@ -27,16 +27,16 @@ dependencies = [
 ]
 description = 'Python package to handle I/O with the CNT format from ANT Neuro. '
 keywords = [
-  'python',
-  'eeg',
   'ant neuro',
-  'eego',
   'cnt',
+  'eeg',
+  'eego',
+  'python',
 ]
 license = {file = 'LICENSE'}
 maintainers = [
   {email = '[email protected]', name = 'Mathieu Scheltienne'},
-  {name= 'Eric Larson'},
+  {name = 'Eric Larson'},
 ]
 name = 'antio'
 readme = 'README.md'
@@ -53,9 +53,7 @@ full = [
 ]
 style = [
   'codespell[toml]>=2.2.4',
-  'isort',
-  'pydocstyle[toml]',
-  'ruff>=0.1.8',
+  'ruff>=0.6.0',
   'toml-sort',
   'yamllint',
 ]
@@ -75,9 +73,9 @@ source = 'https://github.com/mscheltienne/antio'
 tracker = 'https://github.com/mscheltienne/antio/issues'
 
 [tool.cibuildwheel]
+archs = "native"
 build = "cp312-*"
 skip = "*musllinux*"
-archs = "native"
 test-command = "pytest {project}/tests"
 test-extras = ["test"]
 
@@ -86,6 +84,7 @@ repair-wheel-command = [
   "auditwheel repair -w {dest_dir} {wheel}",
   "pipx run abi3audit --strict --report {wheel}",
 ]
+
 [tool.cibuildwheel.macos]
 repair-wheel-command = [
   "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
@@ -121,20 +120,6 @@ omit = [
   '**/antio/_version.py',
 ]
 
-[tool.isort]
-extend_skip_glob = []
-line_length = 88
-multi_line_output = 3
-profile = 'black'
-py_version = 39
-
-[tool.pydocstyle]
-add_ignore = 'D100,D104,D107'
-convention = 'numpy'
-ignore-decorators = '(copy_doc|property|.*setter|.*getter|pyqtSlot|Slot)'
-match = '^(?!__init__|test_).*\.py'
-match-dir = '^.*antio.*'
-
 [tool.pytest.ini_options]
 addopts = ['--color=yes', '--cov-report=', '--durations=20', '--junit-xml=junit-results.xml', '--strict-config', '--tb=short', '-ra', '-v']
 filterwarnings = [
@@ -154,16 +139,23 @@ line-ending = "lf"
 
 [tool.ruff.lint]
 ignore = []
-select = ['A', 'B', 'E', 'F', 'G', 'LOG', 'NPY', 'PIE', 'PT', 'T20', 'UP', 'W']
+select = ['A', 'B', 'D', 'E', 'F', 'G', 'I', 'LOG', 'NPY', 'PIE', 'PT', 'T20', 'UP', 'W']
+
+[tool.ruff.lint.isort]
+known-first-party = ["antio"]
 
 [tool.ruff.lint.per-file-ignores]
 '*' = [
   'B904', # 'Within an except clause, raise exceptions with raise ... from ...'
+  'D100', # 'Missing docstring in public module'
+  'D104', # 'Missing docstring in public package'
   'UP007', # 'Use `X | Y` for type annotations', requires python 3.10
 ]
-'*.pyi' = ['E501']
 '__init__.py' = ['F401']
 
+[tool.ruff.lint.pydocstyle]
+convention = 'numpy'
+
 [tool.setuptools]
 include-package-data = false
 

setup.py

@@ -23,12 +23,12 @@
     lib_files = []
 
 
-class BinaryDistribution(Distribution):
-    def has_ext_modules(self):
+class BinaryDistribution(Distribution):  # noqa: D101
+    def has_ext_modules(self):  # noqa: D102
         return True
 
 
-class build_ext(_build_ext):
+class build_ext(_build_ext):  # noqa: D101
     def run(self):
         """Build libeep with cmake as part of the extension build process."""
         src_dir = Path(__file__).parent / "src" / "libeep"
@@ -81,8 +81,8 @@ def run(self):
 
 # Adapted from
 # https://github.com/joerick/python-abi3-package-sample/blob/main/setup.py
-class bdist_wheel_abi3(bdist_wheel):
-    def get_tag(self):
+class bdist_wheel_abi3(bdist_wheel):  # noqa: D101
+    def get_tag(self):  # noqa: D102
         python, abi, plat = super().get_tag()
 
         if python.startswith("cp"):

src/antio/commands/main.py

@@ -6,8 +6,8 @@
 
 
 @click.group()
-def run() -> None:  # noqa: D401
-    """Main package entry-point."""
+def run() -> None:
+    """Main package entry-point."""  # noqa: D401
 
 
 run.add_command(sys_info)

src/antio/datasets/ca_208.py

@@ -33,7 +33,7 @@ def _make_registry(
     pooch.make_registry(folder, output=output, recursive=True)
 
 
-def data_path(path: str | Path | None) -> Path:  # pragma: no cover
+def data_path(path: str | Path | None = None) -> Path:  # pragma: no cover
     """Return the path to the dataset, downloaded if needed.
 
     Parameters

src/antio/io.py

@@ -31,14 +31,6 @@ def read_raw_ant(
         )
 
     from mne.io import read_raw_ant
-    from mne.utils import warn
-
-    warn(
-        "This function is deprecated in favor of mne.io.read_raw_ant() and will be "
-        "removed in the future.",
-        DeprecationWarning,
-        module="antio",
-    )
 
     return read_raw_ant(
         fname=fname,