🐛 Fix ruff errors

Author: shaneahmed

docs/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# flake8: noqa
 #
 # tiatoolbox documentation build configuration file, created by
 # sphinx-quickstart on Fri Jun  9 13:47:02 2017.
@@ -19,9 +18,9 @@
 # absolute, like shown here.
 #
 import os
-from pathlib import Path
 import shutil
 import sys
+from pathlib import Path
 
 sys.path.insert(0, os.path.abspath(".."))
 
@@ -84,7 +83,7 @@
 
 # General information about the project.
 project = "TIA Toolbox"
-copyright = "2025, TIA Lab"
+copyright = "2025, TIA Lab"  # noqa: A001
 author = "TIA Lab"
 
 # The version info for the project you're documenting, acts as replacement
@@ -140,9 +139,11 @@
             "name": "TIA",
             "url": "https://warwick.ac.uk/fac/cross_fac/tia/",
             "html": """
-                <svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+                <svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg"
+                xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
                      viewBox="0 0 173 175" style="enable-background:new 0 0 173 175;" xml:space="preserve">
-                <image style="overflow:visible;" width="519" height="525" xlink:href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAgcAAAINCAYAAACqOtxdAAABemlDQ1BJQ0MgUHJvZmlsZQAAKJF9
+                <image style="overflow:visible;" width="519" height="525"
+                xlink:href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAgcAAAINCAYAAACqOtxdAAABemlDQ1BJQ0MgUHJvZmlsZQAAKJF9
                 kE0rRFEYx38GjbxEsbCwuHlbDTFKbJSZNKYsNChvmzvXnRllrtudK2RjoWwVJTbeFnwCNhbKWilF
                 Sna+ALGRrufMjMZLeeo5z+885zn/zvmDL6Db9lxJB6Qt14lFQtr4xKTmf8KHnxqqqNeNjN0/PDyE
                 xFf9GW+3FKl606a0/p7/GxUzZsaAojLhPsN2XOFB4aZF11as9OoceZTwquJkjrcUx3N8kp0ZjYWF
@@ -1874,7 +1875,13 @@
             "url": "https://github.com/TissueImageAnalytics/tiatoolbox",
             "html": """
                 <svg height="32" aria-hidden="true" viewBox="0 0 16 16" version="1.1" width="32" data-view-component="true" class="octicon octicon-mark-github v-align-middle">
-                    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0016 8c0-4.42-3.58-8-8-8z"></path>
+                    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29
+                    6.53 5.47 7.59.4.07.55-.17.55-.38
+                    0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94
+                    -.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21
+                    1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95
+                    0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21
+                    2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0016 8c0-4.42-3.58-8-8-8z"></path>
                 </svg>
             """,
             "class": "only-light",
@@ -1901,8 +1908,7 @@
 html_static_path = []
 
 # These paths are either relative to html_static_path
-# or fully qualified paths (eg. https://...)
-# html_css_files = []
+# or fully qualified paths (e.g., https://...)
 
 # -- Options for HTMLHelp output ---------------------------------------
 
@@ -1963,15 +1969,6 @@
     "Sphinx": ("https://www.sphinx-doc.org/en/stable/", None),
 }
 
-# create latex preamble so that we can build arbitrary nested depth
-fh = open("latex_preamble.tex", "r+")
-PREAMBLE = fh.read()
-fh.close()
-latex_elements = {
-    # Additional stuff for the LaTeX preamble.
-    "preamble": PREAMBLE,
-}
-
 # -- Options for autodoc -----------------------------------------------
 
 autodoc_typehints = "description"
@@ -1980,9 +1977,9 @@
     "ArrayLike": "ArrayLike",
 }
 
-print("=" * 43)
+print("=" * 43)  # noqa: T201
 print("Copy example notebooks into docs/_notebooks")
-print("=" * 43)
+print("=" * 43)  # noqa: T201
 
 
 def all_but_ipynb(dir_path, contents):
@@ -2004,13 +2001,8 @@ def all_but_ipynb(dir_path, contents):
     ignore=all_but_ipynb,
 )
 
-# shutil.copy(
-#     os.path.join(PROJ_ROOT, "docs/usage_examples.rst"),
-#     os.path.join(PROJ_ROOT, "docs/_notebooks/usage_examples.rst"),
-# )
-
 # Read in the file
-with open("../examples/README.md", "r") as file:
+with open("../examples/README.md") as file:
     file_data = file.read()
 
 # Replace the target string