run ruff format . and ruff --check . --fix

- also fix things that couldn't be fixed automatically

docs/source/conf.py

@@ -12,51 +12,47 @@
 
 import os
 import sys
-
-import sphinx_rtd_theme
 from unittest import mock
 
-sys.path.insert(0, os.path.abspath('../../python'))
+sys.path.insert(0, os.path.abspath("../../python"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'stempy'
-copyright = '2020, Kitware, INC'
-author = 'Kitware, INC'
+project = "stempy"
+copyright = "2020, Kitware, INC"
+author = "Kitware, INC"
 
 # The full version, including alpha/beta/rc tags
-release = '1.0'
+release = "1.0"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx_rtd_theme',
-    'recommonmark'
-]
+extensions = ["sphinx.ext.autodoc", "sphinx_rtd_theme", "recommonmark"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
+
 # Unfortunately, if we have a class that inherits sphinx's mock
 # object, and we use that class in a default argument, we run into
 # attribute errors. Fix it by defining an explicit mock of the class.
 class MockReader:
     class H5Format:
         Frame = 1
 
-sys.modules['stempy._io'] = mock.Mock()
-_io_mock = sys.modules['stempy._io']
+
+sys.modules["stempy._io"] = mock.Mock()
+_io_mock = sys.modules["stempy._io"]
 
 # We have to override these so we get don't get conflicting metaclasses
 _io_mock._sector_reader = MockReader
@@ -70,36 +66,33 @@ class H5Format:
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # 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']
+html_static_path = ["_static"]
 
 # Get autodoc to mock these imports, because we don't actually need them
 # for generating the docs
-autodoc_mock_imports = [
-    'stempy._image',
-    'numpy',
-    'h5py'
-]
+autodoc_mock_imports = ["stempy._image", "numpy", "h5py"]
+
 
 # Modify this function to customize which classes/functions are skipped
 def autodoc_skip_member_handler(app, what, name, obj, skip, options):
     # Exclude any names that start with a string in this list
-    exclude_startswith_list = ['_']
+    exclude_startswith_list = ["_"]
 
-    if any([name.startswith(x) for x in exclude_startswith_list]):
+    if any(name.startswith(x) for x in exclude_startswith_list):
         return True
 
     # Exclude any names that match a string in this list
     exclude_names = [
-        'ReaderMixin',
-        'PyReader',
-        'SectorReader',
-        'get_hdf5_reader',
-        'SectorThreadedMultiPassReader',
+        "ReaderMixin",
+        "PyReader",
+        "SectorReader",
+        "get_hdf5_reader",
+        "SectorThreadedMultiPassReader",
     ]
 
     return name in exclude_names
@@ -109,4 +102,4 @@ def autodoc_skip_member_handler(app, what, name, obj, skip, options):
 def setup(app):
     # Connect the autodoc-skip-member event from apidoc to the callback
     # This allows us to customize which classes/functions are skipped
-    app.connect('autodoc-skip-member', autodoc_skip_member_handler)
+    app.connect("autodoc-skip-member", autodoc_skip_member_handler)

python/stempy/__init__.py

@@ -3,5 +3,5 @@
 __version__ = get_version()
 
 __all__ = [
-    '__version__',
+    "__version__",
 ]

python/stempy/contrib/__init__.py

@@ -18,9 +18,7 @@ class FileSuffix(Enum):
 
 def check_only_one_filepath(file_path):
     if len(file_path) > 1:
-        raise ValueError(
-            "Multiple files match that input. Add scan_id to be more specific."
-        )
+        raise ValueError("Multiple files match that input. Add scan_id to be more specific.")
     elif len(file_path) == 0:
         raise FileNotFoundError("No file with those parameters can be found.")
 
@@ -125,13 +123,9 @@ def get_scan_path_version_1(
         if file_suffix == FileSuffix.STANDARD:
             file_pattern = f"FOURD_*_{str(scan_id).zfill(5)}_?????.{filetype}"
         else:
-            file_pattern = (
-                f"FOURD_*_{str(scan_id).zfill(5)}_?????{file_suffix.value}.{filetype}"
-            )
+            file_pattern = f"FOURD_*_{str(scan_id).zfill(5)}_?????{file_suffix.value}.{filetype}"
     elif scan_num is not None:
-        file_pattern = (
-            f"FOURD_*_*_{str(scan_num).zfill(5)}{file_suffix.value}.{filetype}"
-        )
+        file_pattern = f"FOURD_*_*_{str(scan_num).zfill(5)}{file_suffix.value}.{filetype}"
 
     file_path = list(directory.glob(file_pattern))
     check_only_one_filepath(file_path)
@@ -188,9 +182,7 @@ def get_scan_path(
             th=th,
             file_suffix=file_suffix,
         ),
-        1: lambda: get_scan_path_version_1(
-            directory, scan_num=scan_num, scan_id=scan_id, file_suffix=file_suffix
-        ),
+        1: lambda: get_scan_path_version_1(directory, scan_num=scan_num, scan_id=scan_id, file_suffix=file_suffix),
     }
 
     for ver in versions_to_try:
@@ -202,6 +194,4 @@ def get_scan_path(
         except FileNotFoundError:
             continue
 
-    raise FileNotFoundError(
-        "No file with those parameters can be found for any version."
-    )
+    raise FileNotFoundError("No file with those parameters can be found for any version.")