Enable ruff UP rules (#146)

* enable ruff up rules

* fix

* exclude pyi globally

pycrostates/cluster/_base.py

@@ -1086,7 +1086,7 @@ def _reject_edge_segments(segmentation: NDArray[int]) -> NDArray[int]:
         segmentation[:n] = -1
 
         # set last segment to unlabeled
-        n = np.flip((segmentation != segmentation[-1])).argmax()
+        n = np.flip(segmentation != segmentation[-1]).argmax()
         segmentation[-n:] = -1
 
         return segmentation

pycrostates/conftest.py

@@ -66,7 +66,7 @@ def matplotlib_config():
 
     class CallbackRegistryReraise(orig):
         def __init__(self, exception_handler=None, signals=None):
-            super(CallbackRegistryReraise, self).__init__(exception_handler)
+            super().__init__(exception_handler)
 
     cbook.CallbackRegistry = CallbackRegistryReraise
 

pycrostates/preprocessing/tests/test_spatial_filter.py

@@ -129,7 +129,7 @@ def test_spatial_filter_custom_adjacency():
     adjacency_matrix, ch_names = find_ch_adjacency(raw_all.info, "eeg")
     apply_spatial_filter(raw_all.copy(), "eeg", adjacency=adjacency_matrix)
     with pytest.raises(ValueError, match="Adjacency must have exactly 2 dimensions"):
-        apply_spatial_filter(raw_all.copy(), "eeg", adjacency=np.ones((len(ch_names))))
+        apply_spatial_filter(raw_all.copy(), "eeg", adjacency=np.ones(len(ch_names)))
     with pytest.raises(ValueError, match="Adjacency must be of shape"):
         apply_spatial_filter(
             raw_all.copy(), "eeg", adjacency=adjacency_matrix[:-2, :-2]

pycrostates/segmentation/tests/test_segmentation.py

@@ -205,7 +205,7 @@ def test_plot_segmentation(ModK, inst):
 )
 def test_invalid_segmentation(Segmentation, inst, bad_inst, caplog):
     """Test that we can not create an invalid segmentation."""
-    labels = np.zeros((inst.times.size))
+    labels = np.zeros(inst.times.size)
     cluster_centers = np.zeros((4, len(inst.ch_names) - len(inst.info["bads"])))
     cluster_names = ["a", "b", "c", "d"]
 

pycrostates/utils/_checks.py

@@ -42,7 +42,7 @@ def _ensure_int(item, item_name=None):
         item = int(operator.index(item))
     except TypeError:
         item_name = "Item" if item_name is None else "'%s'" % item_name
-        raise TypeError("%s must be an int, got %s instead." % (item_name, type(item)))
+        raise TypeError(f"{item_name} must be an int, got {type(item)} instead.")
 
     return item
 
@@ -161,9 +161,9 @@ def _check_value(item, allowed_values, item_name=None, extra=None):
         if len(allowed_values) == 1:
             options = "The only allowed value is %s" % repr(allowed_values[0])
         elif len(allowed_values) == 2:
-            options = "Allowed values are %s and %s" % (
-                repr(allowed_values[0]),
-                repr(allowed_values[1]),
+            options = (
+                f"Allowed values are {repr(allowed_values[0])} "
+                f"and {repr(allowed_values[1])}"
             )
         else:
             options = "Allowed values are "
@@ -286,7 +286,8 @@ def _check_picks_uniqueness(info, picks):
         ch_types = info.get_channel_types(unique=False)
         ch_types, counts = np.unique(ch_types, return_counts=True)
         channels_msg = ", ".join(
-            "%s '%s' channel(s)" % t for t in zip(counts, ch_types)
+            "%s '%s' channel(s)" % t  # noqa: UP031
+            for t in zip(counts, ch_types)
         )
         raise ValueError(
             f"Only one datatype can be selected, but 'picks' results in {channels_msg}."

pycrostates/utils/_config.py

@@ -61,7 +61,7 @@ def get_config():
     if not os.path.isfile(config_path):
         # create default config
         _save_config(default_config)
-    with open(config_path, "r", encoding="utf-8") as f:
+    with open(config_path, encoding="utf-8") as f:
         config = json.load(f)
     return config
 

pycrostates/utils/_fixes.py

@@ -4,7 +4,7 @@
 
 
 # https://github.com/sphinx-gallery/sphinx-gallery/issues/1112
-class _WrapStdOut(object):
+class _WrapStdOut:
     """Dynamically wrap to sys.stdout.
 
     This makes packages that monkey-patch sys.stdout (e.g.doctest, sphinx-gallery) work

pycrostates/utils/tests/test_docs.py

@@ -220,7 +220,7 @@ def test_docdict_order():
         del docdict_[key]
     docs_path = Path(__file__).parents[1] / "_docs.py"
     assert docs_path.is_file()
-    with open(docs_path, "r", encoding="UTF-8") as fid:
+    with open(docs_path, encoding="UTF-8") as fid:
         docs = fid.read()
     entries = re.findall(r'docdict\[(?:\n    )?["\'](.+)["\']\n?\] = ', docs)
     # test length, uniqueness and order

pycrostates/utils/tests/test_logs.py

@@ -133,7 +133,7 @@ def test_file_handler(tmp_path):
 
     logger.handlers[-1].close()
 
-    with open(fname, mode="r") as file:
+    with open(fname) as file:
         lines = file.readlines()
 
     assert len(lines) == 2

pyproject.toml

@@ -156,18 +156,21 @@ minversion = '6.0'
 
 [tool.ruff]
 extend-exclude = [
+  '*.pyi',
   'doc',
   'setup.py',
 ]
+ignore = [
+  "UP007", # 'Use `X | Y` for type annotations', requires python 3.10
+]
 line-length = 88
-select = ["E", "F", "W"]
+select = ["E", "F", "UP", "W"]
 target-version = 'py39'
 
 [tool.ruff.format]
 docstring-code-format = true
 
 [tool.ruff.per-file-ignores]
-'*.pyi' = ['E501']
 '__init__.py' = ['F401']
 
 [tool.setuptools]