Merge pull request #558 from larrybradley/add-linters

Misc fixes caught by linters

.github/dependabot.yml

@@ -0,0 +1,14 @@
+# Keep dependencies updated with Dependabot version updates
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: ".github/workflows/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/codeql.yml

@@ -47,7 +47,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -61,7 +61,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -74,6 +74,6 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
       with:
         category: "/language:${{matrix.language}}"

.pre-commit-config.yaml

@@ -53,13 +53,25 @@ 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"]
+        args: ["--show-fixes"]
+
   - repo: https://github.com/asottile/pyupgrade
     rev: v3.17.0
     hooks:
       - id: pyupgrade
-        args: ["--py39-plus"]
+        args: ["--py310-plus"]
         exclude: ".*(extern.*)$"
 
+  - repo: https://github.com/scientific-python/cookie
+    rev: 2024.04.23
+    hooks:
+      - id: sp-repo-review
+
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:
@@ -90,6 +102,13 @@ repos:
         additional_dependencies:
           - tomli
 
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.5
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]
+
   # - repo: https://github.com/MarcoGorelli/absolufy-imports
   #   rev: v0.3.1
   #   hooks:

dev/regions_parse.py

@@ -15,7 +15,9 @@
 
 @click.group()
 def cli():
-    """astropy.regions parser debugging tool."""
+    """
+    astropy.regions parser debugging tool.
+    """
     pass
 
 

dev/regions_pyregion_comparison.py

@@ -1,6 +1,6 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 """
-Compare DS9 parsing of the astropy regions package to pyregion
+Compare DS9 parsing of the astropy regions package to pyregion.
 
 This scripts compares the DS9 parsing of the astropy regions package to
 pyregion in two regards.

docs/conf.py

@@ -181,12 +181,13 @@
 # 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

pyproject.toml

@@ -105,7 +105,14 @@ norecursedirs = [
 astropy_header = true
 doctest_plus = 'enabled'
 text_file_format = 'rst'
-addopts = '--color=yes --doctest-rst --arraydiff'
+addopts = [
+    '-ra',
+    '--color=yes',
+    '--doctest-rst',
+    '--strict-config',
+    '--strict-markers',
+]
+log_cli_level = 'INFO'
 xfail_strict = true
 remote_data_strict = true
 filterwarnings = [
@@ -151,6 +158,17 @@ exclude_lines = [
     'def _ipython_key_completions_',
 ]
 
+[tool.repo-review]
+ignore = [
+    'MY',  # ignore MyPy
+    '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
+    'PC901',  # ignore using custom pre-commit update message
+    'PY005',  # ignore having a tests/ folder
+]
+
 [tool.isort]
 skip_glob = [
     'regions/*__init__.py*',
@@ -173,3 +191,43 @@ exclude_dirs = ['*/tests/test_casa_mask.py']
 
 [tool.bandit.assert_used]
 skips = ['*_test.py', '*/test_*.py', '*/tests/helpers.py']
+
+[tool.docformatter]
+    wrap-summaries = 72
+    pre-summary-newline = true
+    make-summary-multi-line = true
+
+[tool.ruff.lint]
+select = ['E', 'F', 'UP', 'B', 'SIM', 'PL', 'FLY', 'NPY', 'PERF', 'INT',
+          'RSE', 'Q', 'N', 'W', 'D', 'I']
+ignore = [
+    'E501',
+    'B028',
+    'B905',  # revisit
+    'D100',
+    'D101',
+    'D102',
+    'D103',
+    'D105',
+    'D107',
+    'D200',
+    'D205',
+    'D212',
+    'D404',
+    'I001',
+    'PLR0912',
+    'PLR0913',
+    'PLR0915',
+    'PLR2004',
+    'PLW2901',
+    'Q000',
+    'SIM910',
+    'UP038',
+]
+
+[tool.ruff.lint.per-file-ignores]
+'__init__.py' = ['D104', 'I']
+'docs/conf.py' = ['ERA001', 'INP001', 'TRY400']
+
+[tool.ruff.lint.pydocstyle]
+convention = 'numpy'

regions/_geometry/tests/test_circular_overlap_grid.py

@@ -25,7 +25,6 @@ def test_circular_overlap_grid(grid_size, circ_size, use_exact, subsample):
     Test normalization of the overlap grid to make sure that a fully
     enclosed pixel has a value of 1.0.
     """
-
     g = circular_overlap_grid(-1.0, 1.0, -1.0, 1.0, grid_size, grid_size,
                               circ_size, use_exact, subsample)
     assert_allclose(g.max(), 1.0)

regions/_geometry/tests/test_elliptical_overlap_grid.py

@@ -31,7 +31,6 @@ def test_elliptical_overlap_grid(grid_size, maj_size, min_size, angle,
     Test normalization of the overlap grid to make sure that a fully
     enclosed pixel has a value of 1.0.
     """
-
     g = elliptical_overlap_grid(-1.0, 1.0, -1.0, 1.0, grid_size, grid_size,
                                 maj_size, min_size, angle, use_exact,
                                 subsample)

regions/_geometry/tests/test_rectangular_overlap_grid.py

@@ -25,7 +25,6 @@ def test_rectangular_overlap_grid(grid_size, rect_size, angle, subsample):
     Test normalization of the overlap grid to make sure that a fully
     enclosed pixel has a value of 1.0.
     """
-
     g = rectangular_overlap_grid(-1.0, 1.0, -1.0, 1.0, grid_size, grid_size,
                                  rect_size, rect_size, angle, 0, subsample)
     assert_allclose(g.max(), 1.0)

regions/_utils/examples.py

@@ -88,7 +88,9 @@ def __init__(self, config=None):
 
     @lazyproperty
     def wcs(self):
-        """World coordinate system (`~astropy.wcs.WCS`)."""
+        """
+        World coordinate system (`~astropy.wcs.WCS`).
+        """
         wcs = WCS(naxis=2)
         wcs.wcs.crval = self.config['crval']
         wcs.wcs.crpix = self.config['crpix']
@@ -99,7 +101,9 @@ def wcs(self):
 
     @lazyproperty
     def image(self):
-        """Counts image (`~astropy.io.fits.ImageHDU`)."""
+        """
+        Return a "counts" image (`~astropy.io.fits.ImageHDU`).
+        """
         events = self.event_table
         skycoord = SkyCoord(events['GLON'], events['GLAT'], unit='deg',
                             frame='galactic')

regions/core/attributes.py

@@ -56,7 +56,8 @@ def _validate(self, value):
 
 class ScalarPixCoord(RegionAttribute):
     """
-    Descriptor class to check that value is a scalar `~regions.PixCoord`.
+    Descriptor class to check that value is a scalar
+    `~regions.PixCoord`.
     """
 
     def _validate(self, value):
@@ -133,8 +134,8 @@ def _validate(self, value):
 
 class PositiveScalarAngle(RegionAttribute):
     """
-    Descriptor class to check that value is a strictly positive
-    scalar angle, either an `~astropy.coordinates.Angle` or
+    Descriptor class to check that value is a strictly positive scalar
+    angle, either an `~astropy.coordinates.Angle` or
     `~astropy.units.Quantity` with angular units.
     """
 

regions/core/bounding_box.py

@@ -209,9 +209,8 @@ def get_overlap_slices(self, shape):
     def extent(self):
         """
         The extent of the mask, defined as the ``(xmin, xmax, ymin,
-        ymax)`` bounding box from the bottom-left corner of the
-        lower-left pixel to the upper-right corner of the upper-right
-        pixel.
+        ymax)`` bounding box from the bottom-left corner of the lower-
+        left pixel to the upper-right corner of the upper-right pixel.
 
         The upper edges here are the actual pixel positions of the
         edges, i.e., they are not "exclusive" indices used for python
@@ -261,8 +260,8 @@ def as_artist(self, **kwargs):
 
     def to_region(self):
         """
-        Return a `~regions.RectanglePixelRegion` that
-        represents the bounding box.
+        Return a `~regions.RectanglePixelRegion` that represents the
+        bounding box.
         """
         from regions.core.pixcoord import PixCoord
         from regions.shapes import RectanglePixelRegion

regions/core/core.py

@@ -345,10 +345,10 @@ def _validate_mode(mode, subpixels):
             raise ValueError(f'Invalid mask mode: {mode} (should be one '
                              f'of {valid_modes}')
 
-        if mode == 'subpixels':
-            if not isinstance(subpixels, int) or subpixels <= 0:
-                raise ValueError(f'Invalid subpixels value: {subpixels} '
-                                 '(should be a strictly positive integer)')
+        if (mode == 'subpixels'
+                and (not isinstance(subpixels, int) or subpixels <= 0)):
+            raise ValueError(f'Invalid subpixels value: {subpixels} '
+                             '(should be a strictly positive integer)')
 
     @abc.abstractmethod
     def as_artist(self, origin=(0, 0), **kwargs):

regions/core/mask.py

@@ -59,8 +59,8 @@ def shape(self):
 
     def get_overlap_slices(self, shape):
         """
-        Get slices for the overlapping part of the region mask and a
-        2D array.
+        Get slices for the overlapping part of the region mask and a 2D
+        array.
 
         Parameters
         ----------
@@ -175,10 +175,7 @@ def cutout(self, data, fill_value=0.0, copy=False):
             return cutout
 
         # cutout is always a copy for partial overlap
-        if ~np.isfinite(fill_value):
-            dtype = float
-        else:
-            dtype = data.dtype
+        dtype = float if ~np.isfinite(fill_value) else data.dtype
         cutout = np.zeros(self.shape, dtype=dtype)
         cutout[:] = fill_value
         cutout[slices_small] = data[slices_large]
@@ -267,9 +264,8 @@ def _get_overlap_cutouts(self, shape, mask=None):
         multiple associated arrays (e.g., data and error arrays). It is
         used in this way by the `PixelAperture.do_photometry` method.
         """
-        if mask is not None:
-            if mask.shape != shape:
-                raise ValueError('mask and data must have the same shape')
+        if mask is not None and mask.shape != shape:
+            raise ValueError('mask and data must have the same shape')
 
         slc_large, slc_small = self.get_overlap_slices(shape)
         if slc_large is None:  # no overlap

regions/core/pixcoord.py

@@ -104,7 +104,7 @@ def __len__(self):
         return len(self.x)
 
     def __iter__(self):
-        for (x, y) in zip(self.x, self.y):
+        for (x, y) in zip(self.x, self.y, strict=True):
             yield PixCoord(x=x, y=y)
 
     def __getitem__(self, key):
@@ -129,8 +129,8 @@ def __sub__(self, other):
 
     def __eq__(self, other):
         """
-        Checks whether ``other`` is `PixCoord` object and whether
-        their abscissa and ordinate values are equal using
+        Check whether ``other`` is `PixCoord` object and whether their
+        abscissa and ordinate values are equal using
         `np.testing.assert_allclose` with its default tolerance values.
         """
         if isinstance(other, self.__class__):

regions/core/regions.py

@@ -67,8 +67,8 @@ def append(self, region):
 
     def extend(self, regions):
         """
-        Extend the list of regions by appending elements from the
-        input regions.
+        Extend the list of regions by appending elements from the input
+        regions.
 
         Parameters
         ----------

regions/core/registry.py

@@ -9,13 +9,15 @@
 
 
 class IORegistryError(Exception):
-    """Exception class for various registry errors."""
+    """
+    Exception class for various registry errors.
+    """
 
 
 class RegionsRegistry:
     """
-    Class to hold a registry to read, write, parse, and serialize regions
-    in various formats.
+    Class to hold a registry to read, write, parse, and serialize
+    regions in various formats.
     """
 
     registry = {}
@@ -157,7 +159,7 @@ def get_formats(cls, classobj):
         if len(rows) == 1:
             return Table()
 
-        cols = list(zip(*rows))
+        cols = list(zip(*rows, strict=True))
         tbl = Table()
         for col in cols:
             tbl[col[0]] = col[1:]