Merge pull request #3 from moldyn/improve_defaults

Improve default values

CHANGELOG.md

@@ -14,6 +14,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 
 ## [Unreleased]
+#### API changes warning ⚠️:
+- Changed default for invariant measure to `volume`
+- Changed default for normalization method to `geometric`
+
+#### Added Features and Improvements 🙌:
+- Added an icon, thx to @gegabo
 
 
 ## [0.1.1] - 2023-11-07

src/normi/_estimators.py

@@ -42,15 +42,15 @@ class NormalizedMI(BaseEstimator):
     ----------
     n_dims : int, default=1
         Dimensionality of input vectors.
-    normalize_method : str, default='joint'
+    normalize_method : str, default='geometric'
         Determines the normalization factor for the mutual information:<br/>
         - `'joint'` is the joint entropy<br/>
         - `'max'` is the maximum of the individual entropies<br/>
         - `'arithmetic'` is the mean of the individual entropies<br/>
         - `'geometric'` is the square root of the product of the individual
           entropies<br/>
         - `'min'` is the minimum of the individual entropies
-    invariant_measure : str, default='radius'
+    invariant_measure : str, default='volume'
         - `'radius'` normalizing by mean k-nn radius<br/>
         - `'volume'` normalizing by mean k-nn volume<br/>
         - `'kraskov'` no normalization
@@ -95,8 +95,8 @@ def __init__(
         self,
         *,
         n_dims: PositiveInt = 1,
-        normalize_method: NormString = 'joint',
-        invariant_measure: InvMeasureString = 'radius',
+        normalize_method: NormString = 'geometric',
+        invariant_measure: InvMeasureString = 'volume',
         k: PositiveInt = 5,
         n_jobs: Int = -1,
         verbose: bool = True,

tests/test__estimators.py

@@ -101,25 +101,25 @@ def test__reset(normalize_method, X, kwargs):
 
 
 @pytest.mark.parametrize('X, kwargs, result, error', [
-    (X1(), {}, X1_result('joint', 'radius'), None),
+    (X1(), {}, X1_result('geometric', 'volume'), None),
     (
         X1(),
         {'normalize_method': 'joint', 'invariant_measure': 'radius'},
         X1_result('joint', 'radius'),
         None,
     ),
-    (X1(), {'normalize_method': 'max'}, X1_result('max', 'radius'), None),
-    (X1(), {'normalize_method': 'min'}, X1_result('min', 'radius'), None),
+    (X1(), {'normalize_method': 'max'}, X1_result('max', 'volume'), None),
+    (X1(), {'normalize_method': 'min'}, X1_result('min', 'volume'), None),
     (
         X1(),
         {'normalize_method': 'arithmetic'},
-        X1_result('arithmetic', 'radius'),
+        X1_result('arithmetic', 'volume'),
         None,
     ),
     (
         X1(),
         {'normalize_method': 'geometric'},
-        X1_result('geometric', 'radius'),
+        X1_result('geometric', 'volume'),
         None,
     ),
     (