rules for ruff and formatting.

Author: quentinhaenn

pyproject.toml

@@ -71,5 +71,61 @@ doc = [
 [tool.setuptools]
 packages = ["radius_clustering"]
 
+[tool.ruff]
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".git",
+    ".git-rewrite",
+    ".pytest_cache",
+    ".ruff_cache",
+    ".venv",
+    ".vscode",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "site-packages",
+    "venv",
+    "**.egg-info",
+    "tests",
+    "examples",
+]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
 [tool.ruff.lint]
-select = ["NPY201"]
+# 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 = ["E", "F"]
+ignore = []
+
+# 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.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.
+docstring-code-format = true
+
+# Set the line length limit used when formatting code snippets in
+# docstrings.
+docstring-code-line-length = "dynamic"

radius_clustering/radius_clustering.py

@@ -2,7 +2,8 @@
 Radius Clustering
 
 This module provides functionality for Minimum Dominating Set (MDS) based clustering.
-It includes methods for solving MDS problems and applying the solutions to clustering tasks.
+It includes methods for solving MDS problems and applying the solutions to
+clustering tasks.
 
 This module serves as the main interface for the Radius clustering library.
 """
@@ -71,14 +72,17 @@ def fit(self, X, y=None):
         >>> from radius_clustering import RadiusClustering
         >>> from sklearn import datasets
         >>> # Load the Iris dataset
-        >>> iris = datasets.fetch_openml(name='iris', version=1, parser='auto')
-        >>> X = iris['data']  # Use dictionary-style access instead of attribute access
-        >>> rad = RadiusClustering(manner="exact", threshold=1.43).fit(X) #Threshold set to 1.43 because it is the optimal
-        ...                                                            #threshold for the Iris dataset
+        >>> iris = datasets.fetch_openml(name="iris", version=1, parser="auto")
+        >>> X = iris["data"]  # Use dictionary-style access instead of attribute access
+        >>> rad = RadiusClustering(manner="exact", threshold=1.43).fit(
+        ...     X
+        ... )  # Threshold set to 1.43 because it is the optimal
+        ... # threshold for the Iris dataset
         >>> rad.centers_
         [96, 49, 102]
 
-        For examples on common datasets and differences with kmeans, see :ref:`sphx_glr_auto_examples_plot_iris_example.py`
+        For examples on common datasets and differences with kmeans,
+        see :ref:`sphx_glr_auto_examples_plot_iris_example.py`
         """
         self.X = check_array(X)
 
@@ -164,7 +168,8 @@ def _compute_effective_radius(self):
         """
         Compute the effective radius of the clustering.
 
-        The effective radius is the maximum radius among all clusters. That means EffRad = max(R(C_i)) for all i.
+        The effective radius is the maximum radius among all clusters.
+        That means EffRad = max(R(C_i)) for all i.
         """
         self.effective_radius = np.min(self.dist_mat[:, self.centers_], axis=1).max()
 

setup.py

@@ -13,7 +13,7 @@
 if not CPU:
     CPU = platform.machine()
 
-if (SYSTEM != "Darwin") and (CPU not in 'arm64'):
+if (SYSTEM != "Darwin") and (CPU not in "arm64"):
     C_COMPILE_ARGS.append("-march=native")
     CXX_COMPILE_ARGS.append("-march=native")
     CXX_LINK_ARGS.append("-fopenmp")