Merge pull request #1015 from PMEAL/fix_nightly_builds

Moved ruff config to pyproject.toml #maint
Updated example for ibip #docs
Fixed use of skeletonize_3d #bug

pyproject.toml

@@ -185,3 +185,91 @@ exclude_lines = [
     "raise NotImplementedError",
     "if __name__ == .__main__.:",
 ]
+
+[tool.ruff]
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".git-rewrite",
+    ".hg",
+    ".ipynb_checkpoints",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pyenv",
+    ".pytest_cache",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "site-packages",
+    "venv",
+]
+
+# Same as Black.
+line-length = 92
+indent-width = 4
+
+# Assume Python 3.10
+target-version = "py310"
+
+[tool.ruff.lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+select = ["E4", "E7", "E9", "F", "W", "E2"]
+extend-select = ["I"]
+ignore = ["E731", "F841", "E226", "I001"]
+preview = true
+
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402", "F401", "F403", "I001"]
+"_gdd.py" = ["ALL"]
+"test/**" = ["F841"]
+"test_snow2.py" = ["E241"]
+
+
+[tool.ruff.format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+# Enable auto-formatting of code examples in docstrings. Markdown,
+# reStructuredText code/literal blocks and doctests are all supported.
+#
+# This is currently disabled by default, but it is planned for this
+# to be opt-out in the future.
+docstring-code-format = true
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+#
+# This only has an effect when the `docstring-code-format` setting is
+# enabled.
+docstring-code-line-length = "dynamic"

src/porespy/metrics/_regionprops.py

@@ -5,7 +5,7 @@
 from pandas import DataFrame
 from skimage.measure import mesh_surface_area, regionprops
 from skimage.measure._regionprops import RegionProperties
-from skimage.morphology import ball, skeletonize_3d
+from skimage.morphology import ball, skeletonize
 
 from porespy.tools import bbox_to_slices, extract_subsection