Merge pull request #28 from larrybradley/add-ruff

Add Ruff to pre-commit checks

.pre-commit-config.yaml

@@ -53,6 +53,12 @@ repos:
       - id: python-check-blanket-noqa
         # Enforce that all noqa annotations always occur with specific codes.
 
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.4.7"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+
   - repo: https://github.com/asottile/pyupgrade
     rev: v3.17.0
     hooks:

docs/conf.py

@@ -19,16 +19,21 @@
 from importlib import metadata
 from pathlib import Path
 
+from sphinx.util import logging
+
 if sys.version_info < (3, 11):
     import tomli as tomllib
 else:
     import tomllib
 
+logger = logging.getLogger(__name__)
+
 try:
     from sphinx_astropy.conf.v1 import *  # noqa: F403
 except ImportError:
-    print('ERROR: the documentation requires the sphinx-astropy package to '
-          'be installed')
+    msg = ('The documentation requires the sphinx-astropy package to be '
+           'installed. Please install the "docs" requirements.')
+    logger.error(msg)
     sys.exit(1)
 
 # Get configuration information from pyproject.toml
@@ -44,7 +49,8 @@
 # needs_sphinx = '3.0'
 
 # Extend astropy intersphinx_mapping with packages we use here
-# intersphinx_mapping['skimage'] = ('https://scikit-image.org/docs/stable/', None) noqa: F405
+# intersphinx_mapping.update(  # nosq: F405
+#     {'skimage': = ('https://scikit-image.org/docs/stable/', None)})
 
 # Exclude astropy intersphinx_mapping for unused packages
 del intersphinx_mapping['h5py']  # noqa: F405
@@ -159,12 +165,13 @@
 # Uncomment the following lines to enable the exceptions:
 nitpick_filename = 'nitpick-exceptions.txt'
 if os.path.isfile(nitpick_filename):
-    for line in open(nitpick_filename):
-        if line.strip() == '' or line.startswith('#'):
-            continue
-        dtype, target = line.split(None, 1)
-        target = target.strip()
-        nitpick_ignore.append((dtype, target))
+    with open(nitpick_filename) as fh:
+        for line in fh:
+            if line.strip() == '' or line.startswith('#'):
+                continue
+            dtype, target = line.split(None, 1)
+            target = target.strip()
+            nitpick_ignore.append((dtype, target))
 
 # -- Options for linkcheck output ---------------------------------------------
 linkcheck_retry = 5

lacosmic/conftest.py

@@ -1,7 +1,7 @@
-# This file is used to configure the behavior of pytest when using the Astropy
-# test infrastructure. It needs to live inside the package in order for it to
-# get picked up when running the tests inside an interpreter using
-# packagename.test
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+"""
+Configuration file for the pytest test suite.
+"""
 
 import numpy as np
 from astropy.utils import minversion

lacosmic/core.py

@@ -96,7 +96,8 @@ def lacosmic(data, contrast, cr_threshold, neighbor_threshold,
         that case, try inputing a ``mask`` or increasing the value of
         ``cr_threshold``.
 
-    border_mode : {'reflect', 'constant', 'nearest', 'mirror', 'wrap'}, optional
+    border_mode : {'reflect', 'constant', 'nearest', 'mirror', 'wrap'}, \
+            optional
         The mode in which the array borders are handled during
         convolution and median filtering.  For 'constant', the fill
         value is 0.  The default is 'mirror', which matches the original
@@ -119,9 +120,8 @@ def lacosmic(data, contrast, cr_threshold, neighbor_threshold,
         clean_data += background
     final_crmask = np.zeros(data.shape, dtype=bool)
 
-    if error is not None:
-        if data.shape != error.shape:
-            raise ValueError('error and data must have the same shape')
+    if error is not None and data.shape != error.shape:
+        raise ValueError('error and data must have the same shape')
     clean_error_image = error
 
     ncosmics, ncosmics_tot = 0, 0

lacosmic/tests/test_core.py

@@ -7,7 +7,7 @@
 import pytest
 from numpy.testing import assert_allclose, assert_array_equal
 
-from ..core import lacosmic
+from lacosmic.core import lacosmic
 
 size = 25
 npts = 20
@@ -93,13 +93,15 @@ def test_error_image_size(self):
         image.
         """
         error = np.zeros((7, 7))
-        with pytest.raises(ValueError):
+        match = 'error and data must have the same shape'
+        with pytest.raises(ValueError, match=match):
             lacosmic(CR_IMG, 3, 2, 2, effective_gain=1, readnoise=0,
                      error=error)
 
     def test_error_inputs(self):
-        with pytest.raises(ValueError):
+        match = 'effective_gain and readnoise must be input if error is not'
+        with pytest.raises(ValueError, match=match):
             lacosmic(CR_IMG, 3, 2, 2, effective_gain=1, error=None)
 
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match=match):
             lacosmic(CR_IMG, 3, 2, 2, readnoise=0, error=None)

pyproject.toml

@@ -133,13 +133,10 @@ exclude_lines = [
 [tool.repo-review]
 ignore = [
     'MY',  # ignore MyPy
-    'RF',  # ignore Ruff
     'PC110',  # ignore using black or ruff-format in pre-commit
     'PC111',  # ignore using blacken-docs in pre-commit
     'PC140',  # ignore using mypy in pre-commit
     'PC180',  # ignore using prettier in pre-commit
-    'PC190',  # ignore using Ruff in pre-commit
-    'PC191',  # ignore showing Ruff fixes in pre-commit
     'PC901',  # ignore using custom pre-commit update message
     'PY005',  # ignore having a tests/ folder
 ]
@@ -189,3 +186,35 @@ exclude = [
     wrap-summaries = 72
     pre-summary-newline = true
     make-summary-multi-line = true
+
+[tool.ruff]
+line-length = 79
+
+[tool.ruff.lint.pylint]
+max-statements = 130
+
+[tool.ruff.lint]
+select = ['ALL']
+ignore = [
+    'ANN',
+    'COM812',
+    'D102',
+    'D200',
+    'D203',
+    'D205',
+    'D212',
+    'D413',
+    'EM101',
+    'FBT002',
+    'FIX002',
+    'I001',
+    'PLR0913',
+    'PTH',
+    'Q000',
+    'TRY003',
+]
+
+[tool.ruff.lint.per-file-ignores]
+'__init__.py' = ['D104', 'I']
+'conftest.py' = ['D103']
+'docs/conf.py' = ['ERA001', 'INP001', 'TRY400']