Merge pull request #26 from KarelZe/linting-formatter

Add basic support for linting / format🐍

.pre-commit-config.yaml

@@ -11,3 +11,10 @@ repos:
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.1
+    hooks:
+    - id: ruff
+      args:
+      - --fix
+    - id: ruff-format

pyproject.toml

@@ -31,6 +31,7 @@ dependencies = [
 dev=[
     "build",
     "pre-commit",
+    "ruff"
 ]
 
 notebook=[
@@ -54,3 +55,34 @@ build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
 packages = ["sage"]
+
+[tool.ruff]
+
+
+include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"]
+
+
+[tool.ruff.lint]
+
+# See rules: https://beta.ruff.rs/docs/rules/
+select = [
+    "I",    # isort
+    "N",    # pep8-naming
+    "NPY",  # numpy
+    "RUF",  # ruff-specific rules
+]
+
+ignore = [
+    "N803",  # argument name should be lowercase; fine for matrices
+    "N806",  # variable name should be lowercase; fine for matrices
+    "NPY002", # allow calls to np.random; could cause slightly different results
+]
+
+preview = true
+
+[tool.ruff.format]
+preview = true
+
+[tool.ruff.lint.isort]
+known-first-party = ["sage"]
+section-order = ["future", "standard-library", "third-party", "first-party", "local-folder"]

sage/__init__.py

@@ -1,9 +1,10 @@
-from sage import utils, core, imputers, grouped_imputers, plotting, datasets
+from sage import core, datasets, grouped_imputers, imputers, plotting, utils
+
 from .core import Explanation, load
-from .plotting import plot, comparison_plot
-from .imputers import DefaultImputer, MarginalImputer
 from .grouped_imputers import GroupedDefaultImputer, GroupedMarginalImputer
-from .permutation_estimator import PermutationEstimator
+from .imputers import DefaultImputer, MarginalImputer
 from .iterated_estimator import IteratedEstimator
 from .kernel_estimator import KernelEstimator
+from .permutation_estimator import PermutationEstimator
+from .plotting import comparison_plot, plot
 from .sign_estimator import SignEstimator

sage/core.py

@@ -1,40 +1,44 @@
 import pickle
+
 import numpy as np
+
 from sage import plotting
 
 
 class Explanation:
-    '''
+    """
     For storing and plotting Explanations.
-    
+
     Args:
       values: explanation values.
       std: standard deviation confidence intervals for explanation values.
       explanation_type: 'SAGE' or 'Shapley Effects' (used only for plotting).
-    '''
+    """
 
-    def __init__(self, values, std, explanation_type='SAGE'):
+    def __init__(self, values, std, explanation_type="SAGE"):
         self.values = values
         self.std = std
         self.explanation_type = explanation_type
 
-    def plot(self,
-             feature_names=None,
-             sort_features=True,
-             max_features=np.inf,
-             orientation='horizontal',
-             error_bars=True,
-             confidence_level=0.95,
-             capsize=5,
-             color='tab:green',
-             title='Feature Importance',
-             title_size=20,
-             tick_size=16,
-             tick_rotation=None,
-             label_size=16,
-             figsize=(10, 7),
-             return_fig=False):
-        '''
+    def plot(
+        self,
+        feature_names=None,
+        sort_features=True,
+        max_features=np.inf,
+        orientation="horizontal",
+        error_bars=True,
+        confidence_level=0.95,
+        capsize=5,
+        color="tab:green",
+        title="Feature Importance",
+        title_size=20,
+        tick_size=16,
+        tick_rotation=None,
+        label_size=16,
+        figsize=(10, 7),
+        return_fig=False,
+    ):
+        """
         Plot SAGE values.
 
         Args:
@@ -53,32 +57,48 @@ def plot(self,
           label_size: font size for label.
           figsize: figure size (if fig is None).
           return_fig: whether to return matplotlib figure object.
-        '''
+        """
         return plotting.plot(
-            self, feature_names, sort_features, max_features, orientation,
-            error_bars, confidence_level, capsize, color, title, title_size,
-            tick_size, tick_rotation, label_size, figsize, return_fig)
-
-    def comparison(self,
-                   other_values,
-                   comparison_names=None,
-                   feature_names=None,
-                   sort_features=True,
-                   max_features=np.inf,
-                   orientation='vertical',
-                   error_bars=True,
-                   confidence_level=0.95,
-                   capsize=5,
-                   colors=None,
-                   title='Feature Importance Comparison',
-                   title_size=20,
-                   tick_size=16,
-                   tick_rotation=None,
-                   label_size=16,
-                   legend_loc=None,
-                   figsize=(10, 7),
-                   return_fig=False):
-        '''
+            self,
+            feature_names,
+            sort_features,
+            max_features,
+            orientation,
+            error_bars,
+            confidence_level,
+            capsize,
+            color,
+            title,
+            title_size,
+            tick_size,
+            tick_rotation,
+            label_size,
+            figsize,
+            return_fig,
+        )
+
+    def comparison(
+        self,
+        other_values,
+        comparison_names=None,
+        feature_names=None,
+        sort_features=True,
+        max_features=np.inf,
+        orientation="vertical",
+        error_bars=True,
+        confidence_level=0.95,
+        capsize=5,
+        colors=None,
+        title="Feature Importance Comparison",
+        title_size=20,
+        tick_size=16,
+        tick_rotation=None,
+        label_size=16,
+        legend_loc=None,
+        figsize=(10, 7),
+        return_fig=False,
+    ):
+        """
         Plot comparison with another set of SAGE values.
 
         Args:
@@ -100,28 +120,45 @@ def comparison(self,
           legend_loc: legend location.
           figsize: figure size (if fig is None).
           return_fig: whether to return matplotlib figure object.
-        '''
+        """
         return plotting.comparison_plot(
-            (self, other_values), comparison_names, feature_names,
-            sort_features, max_features, orientation, error_bars,
-            confidence_level, capsize, colors, title, title_size, tick_size,
-            tick_rotation, label_size, legend_loc, figsize, return_fig)
-
-    def plot_sign(self,
-                  feature_names,
-                  sort_features=True,
-                  max_features=np.inf,
-                  orientation='horizontal',
-                  confidence_level=0.95,
-                  capsize=5,
-                  title='Feature Importance Sign',
-                  title_size=20,
-                  tick_size=16,
-                  tick_rotation=None,
-                  label_size=16,
-                  figsize=(10, 7),
-                  return_fig=False):
-        '''
+            (self, other_values),
+            comparison_names,
+            feature_names,
+            sort_features,
+            max_features,
+            orientation,
+            error_bars,
+            confidence_level,
+            capsize,
+            colors,
+            title,
+            title_size,
+            tick_size,
+            tick_rotation,
+            label_size,
+            legend_loc,
+            figsize,
+            return_fig,
+        )
+
+    def plot_sign(
+        self,
+        feature_names,
+        sort_features=True,
+        max_features=np.inf,
+        orientation="horizontal",
+        confidence_level=0.95,
+        capsize=5,
+        title="Feature Importance Sign",
+        title_size=20,
+        tick_size=16,
+        tick_rotation=None,
+        label_size=16,
+        figsize=(10, 7),
+        return_fig=False,
+    ):
+        """
         Plot SAGE values, focusing on their sign.
 
         Args:
@@ -138,31 +175,44 @@ def plot_sign(self,
           label_size: font size for label.
           figsize: figure size (if fig is None).
           return_fig: whether to return matplotlib figure object.
-        '''
+        """
         return plotting.plot_sign(
-            self, feature_names, sort_features, max_features, orientation,
-            confidence_level, capsize, title, title_size, tick_size,
-            tick_rotation, label_size, figsize, return_fig)
+            self,
+            feature_names,
+            sort_features,
+            max_features,
+            orientation,
+            confidence_level,
+            capsize,
+            title,
+            title_size,
+            tick_size,
+            tick_rotation,
+            label_size,
+            figsize,
+            return_fig,
+        )
 
     def save(self, filename):
-        '''Save Explanation object.'''
+        """Save Explanation object."""
         if isinstance(filename, str):
-            with open(filename, 'wb') as f:
+            with open(filename, "wb") as f:
                 pickle.dump(self, f)
         else:
-            raise TypeError('filename must be str')
+            raise TypeError("filename must be str")
 
     def __repr__(self):
-        with np.printoptions(precision=2, threshold=12, floatmode='fixed'):
-            return '{} Explanation(\n  (Mean): {}\n  (Std):  {}\n)'.format(
-                self.explanation_type, self.values, self.std)
+        with np.printoptions(precision=2, threshold=12, floatmode="fixed"):
+            return "{} Explanation(\n  (Mean): {}\n  (Std):  {}\n)".format(
+                self.explanation_type, self.values, self.std
+            )
 
 
 def load(filename):
-    '''Load Explanation object.'''
-    with open(filename, 'rb') as f:
+    """Load Explanation object."""
+    with open(filename, "rb") as f:
         sage_values = pickle.load(f)
         if isinstance(sage_values, Explanation):
             return sage_values
         else:
-            raise ValueError('object is not instance of Explanation class')
+            raise ValueError("object is not instance of Explanation class")