Applys explcit includes ruff file

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "75f84c4adf1753af67967930c3335bc73bca9bf5",
+  "commit": "51fb616094a4d7577c8898445aa50effb89afa31",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -16,7 +16,7 @@
       "enable_dynamic_dev_versions": "y",
       "include_example_code": "n",
       "include_cruft_update_github_workflow": "y",
-      "use_extended_ruff_linting": "n",
+      "use_extended_ruff_linting": "y",
       "_sphinx_theme": "sunpy",
       "_parent_project": "",
       "_install_requires": "",

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
     # This should be before any formatting hooks like isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.7.2"
+    rev: "v0.7.1"
     hooks:
       - id: ruff
         args: ["--fix"]

.ruff.toml

@@ -12,57 +12,77 @@ select = [
   "E",
   "F",
   "W",
-  #"UP",
-  #"PT"
+  "UP",
+  "BLE",
+  "A",
+  "C4",
+  "INP",
+  "PIE",
+  "T20",
+  "PT",
+  "RET",
+  "TID",
+  "PTH",
+  "PD",
+  "PLC",
+  "PLE",
+  "FLY",
+  "NPY",
+  "PERF",
+  "RUF",
 ]
 extend-ignore = [
-  "E712",
-  "E721",
-  # pycodestyle (E, W)
+  # pycodestyle
   "E501", # ignore line length will use a formatter instead
-  # pyupgrade (UP)
+  "E712", # Avoid equality comparisons to True; use if {cond}: for truth checks
+  "E721", # type comparison Use is and is not for type comparisons, or isinstance() for isinstance checks
+   # flake8-pie
+  "PIE808", # explicit is better than implicit
+  # upgrades
+  "UP038", # Use | in isinstance - not compatible with models and is slower
+  # numpy
+  "NPY002", # TODO: migrate from np.random.rand to np.random.Generator
+  # upgrades
   "UP038", # Use | in isinstance - not compatible with models and is slower
   # pytest (PT)
-  "PT001", # Always use pytest.fixture()
-  "PT004", # Fixtures which don't return anything should have leading _
-  "PT023", # Always use () on pytest decorators
-  # flake8-pie (PIE)
+  "PT001",  # Always use pytest.fixture()
+  "PT004",  # Fixtures which don't return anything should have leading _
+  "PT011",  # except(ValueRaises) is too broad
+  "PT012",  # except statement is too lengthy
+  "PT023",  # Always use () on pytest decorators
+  "PT023",  # Always use () on pytest decorators
+  # flake8-pie
   "PIE808", # Disallow passing 0 as the first argument to range
-  # flake8-use-pathlib (PTH)
+  # flake8-use-pathlib
   "PTH123", # open() should be replaced by Path.open()
-  # Ruff (RUF)
+  # Ruff
   "RUF003", # Ignore ambiguous quote marks, doesn't allow ' in comments
-  "RUF012", # Mutable class attributes should be annotated with `typing.ClassVar`
-  "RUF013", # PEP 484 prohibits implicit `Optional`
-  "RUF015", # Prefer `next(iter(...))` over single element slice
+  "RUF012",  # Mutable class attributes should be annotated with `typing.ClassVar`
+  "RUF013",  # PEP 484 prohibits implicit `Optional`
+  "RUF015",  # Prefer `next(iter(...))` over single element slice
 ]
 
 [lint.per-file-ignores]
-"setup.py" = [
-  "INP001", # File is part of an implicit namespace package.
-]
-"conftest.py" = [
-  "INP001", # File is part of an implicit namespace package.
-]
+# Part of configuration, not a package.
+"setup.py" = ["INP001"]
+"conftest.py" = ["INP001"]
 "docs/conf.py" = [
-  "E402" # Module imports not at top of file
+  "E402"  # Module imports not at top of file
 ]
 "docs/*.py" = [
-  "INP001", # File is part of an implicit namespace package.
+  "INP001",  # Implicit-namespace-package. The examples are not a package.
+]
+"examples/*.py" = [
+  "T201",  # We need print in our examples
+  "E501",  # Line too long
+  "INP001",  # implicit namespace package
 ]
-"examples/**.py" = [
+"ndcube/*.py" = [
   "T201", # allow use of print in examples
   "INP001", # File is part of an implicit namespace package.
 ]
-"__init__.py" = [
-  "E402", # Module level import not at top of cell
-  "F401", # Unused import
-  "F403", # from {name} import * used; unable to detect undefined names
-  "F405", # {name} may be undefined, or defined from star imports
-]
-"test_*.py" = [
-  "E402", # Module level import not at top of cell
-]
+"__init__.py" = ["E402", "F401", "F403"]
+"test_*.py" = ["B011", "D", "E402", "PGH001", "S101"]
 
 [lint.pydocstyle]
 convention = "numpy"

docs/conf.py

@@ -3,6 +3,7 @@
 import os
 import warnings
 import datetime
+from pathlib import Path
 
 from astropy.utils.exceptions import AstropyDeprecationWarning
 from matplotlib import MatplotlibDeprecationWarning
@@ -58,7 +59,7 @@
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-# templates_path = ["_templates"]  # NOQA: ERA001
+# templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -116,7 +117,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-# html_static_path = ["_static"]  # NOQA: ERA001
+# html_static_path = ["_static"]
 
 # By default, when rendering docstrings for classes, sphinx.ext.autodoc will
 # make docs with the class-level docstring and the class-method docstrings,
@@ -146,11 +147,11 @@
 # -- Sphinx Gallery ---------------------------------------------------------
 
 sphinx_gallery_conf = {
-    'backreferences_dir': os.path.join('generated', 'modules'),
+    'backreferences_dir': Path('generated/modules'),
     'filename_pattern': '^((?!skip_).)*$',
-    'examples_dirs': os.path.join('..', 'examples'),
+    'examples_dirs': Path('../examples'),
     'within_subsection_order': "ExampleTitleSortKey",
-    'gallery_dirs': os.path.join('generated', 'gallery'),
+    'gallery_dirs': Path('generated/gallery'),
     'matplotlib_animations': True,
     "default_thumb_file": png_icon,
     'abort_on_example_error': False,

examples/creating_even_spaced_wavelength_visualisation.py

@@ -34,7 +34,7 @@
 # `sequence=True` causes a sequence of maps to be returned, one for each image file.
 sequence_of_maps = sunpy.map.Map(aia_files, sequence=True)
 # Sort the maps in the sequence in order of wavelength.
-sequence_of_maps.maps = list(sorted(sequence_of_maps.maps, key=lambda m: m.wavelength))
+sequence_of_maps.maps = sorted(sequence_of_maps.maps, key=lambda m: m.wavelength)
 
 #############################################################################
 # Using an `astropy.units.Quantity` of the wavelengths of the images, we can construct

ndcube/__init__.py

@@ -14,4 +14,13 @@
 from .ndcube_sequence import NDCubeSequence, NDCubeSequenceBase
 from .version import version as __version__
 
-__all__ = ['NDCube', 'NDCubeSequence', "NDCollection", "ExtraCoords", "GlobalCoords", "ExtraCoordsABC", "GlobalCoordsABC", "NDCubeBase", "NDCubeSequenceBase", "__version__"]
+__all__ = ['NDCube',
+           'NDCubeSequence',
+           "NDCollection",
+           "ExtraCoords",
+           "GlobalCoords",
+           "ExtraCoordsABC",
+           "GlobalCoordsABC",
+           "NDCubeBase",
+           "NDCubeSequenceBase",
+           "__version__"]

ndcube/_dev/scm_version.py

@@ -1,5 +1,6 @@
 # Try to use setuptools_scm to get the current version; this is only used
 # in development installations from the git repository.
+
 from pathlib import Path
 
 try:

ndcube/conftest.py

@@ -479,8 +479,7 @@ def ndcube_2d_ln_lt_uncert(wcs_2d_lt_ln):
     shape = (10, 12)
     data_cube = data_nd(shape)
     uncertainty = astropy.nddata.StdDevUncertainty(data_cube * 0.1)
-    cube = NDCube(data_cube, wcs=wcs_2d_lt_ln, uncertainty=uncertainty)
-    return cube
+    return NDCube(data_cube, wcs=wcs_2d_lt_ln, uncertainty=uncertainty)
 
 
 @pytest.fixture
@@ -493,8 +492,7 @@ def ndcube_2d_ln_lt_mask_uncert(wcs_2d_lt_ln):
     mask[2, 0] = True
     mask[3, 3] = True
     mask[4:6, :4] = True
-    cube = NDCube(data_cube, wcs=wcs_2d_lt_ln, uncertainty=uncertainty, mask=mask)
-    return cube
+    return NDCube(data_cube, wcs=wcs_2d_lt_ln, uncertainty=uncertainty, mask=mask)
 
 
 @pytest.fixture

ndcube/extra_coords/extra_coords.py

@@ -149,8 +149,8 @@ def __init__(self, ndcube=None):
 
         # Lookup tables is a list of (pixel_dim, LookupTableCoord) to allow for
         # one pixel dimension having more than one lookup coord.
-        self._lookup_tables = list()
-        self._dropped_tables = list()
+        self._lookup_tables = []
+        self._dropped_tables = []
 
         # We need a reference to the parent NDCube
         self._ndcube = ndcube
@@ -230,8 +230,8 @@ def add(self, name, array_dimension, lookup_table, physical_types=None, **kwargs
         self._lookup_tables.append((array_dimension, coord))
 
         # Sort the LUTs so that the mapping and the wcs are ordered in pixel dim order
-        self._lookup_tables = list(sorted(self._lookup_tables,
-                                          key=lambda x: x[0] if isinstance(x[0], Integral) else x[0][0]))
+        self._lookup_tables = sorted(self._lookup_tables,
+                                          key=lambda x: x[0] if isinstance(x[0], Integral) else x[0][0])
 
     @property
     def _name_lut_map(self):
@@ -243,7 +243,7 @@ def _name_lut_map(self):
     def keys(self):
         # docstring in ABC
         if not self.wcs:
-            return tuple()
+            return ()
 
         return tuple(self.wcs.world_axis_names) if self.wcs.world_axis_names else None
 
@@ -256,7 +256,7 @@ def mapping(self):
         # If mapping is not set but lookup_tables is empty then the extra
         # coords is empty, so there is no mapping.
         if not self._lookup_tables:
-            return tuple()
+            return ()
 
         # The mapping is from the array index (position in the list) to the
         # pixel dimensions (numbers in the list)
@@ -292,7 +292,7 @@ def wcs(self):
         if not self._lookup_tables:
             return None
 
-        tcoords = set(lt[1] for lt in self._lookup_tables)
+        tcoords = {lt[1] for lt in self._lookup_tables}
         # created a sorted list of unique items
         _tmp = set()  # a temporary set
         tcoords = [x[1] for x in self._lookup_tables if x[1] not in _tmp and _tmp.add(x[1]) is None]
@@ -323,8 +323,7 @@ def is_empty(self):
         # docstring in ABC
         if not self._wcs and not self._lookup_tables:
             return True
-        else:
-            return False
+        return False
 
     def _getitem_string(self, item):
         """
@@ -402,7 +401,7 @@ def __getitem__(self, item):
         if self._wcs:
             return self._getitem_wcs(item)
 
-        elif self._lookup_tables:
+        if self._lookup_tables:
             return self._getitem_lookup_tables(item)
 
         # If we get here this object is empty, so just return an empty extra coords
@@ -425,7 +424,7 @@ def dropped_world_dimensions(self):
 
             return mtc.dropped_world_dimensions
 
-        return dict()
+        return {}
 
     def resample(self, factor, offset=0, ndcube=None, **kwargs):
         """