julearn 0.3.5.dev112__tar.gz → 0.3.5.dev124__tar.gz

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: julearn
-Version: 0.3.5.dev112
+Version: 0.3.5.dev124
 Summary: Juelich Machine Learning Library
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Sami Hamdan <s.hamdan@fz-juelich.de>
 Maintainer-email: Sami Hamdan <s.hamdan@fz-juelich.de>
@@ -27,10 +27,10 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
-Requires-Dist: numpy<2.0.0,>=1.26.0
-Requires-Dist: pandas<2.4.0,>=2.0.0
+Requires-Dist: numpy<3.0.0,>=1.26.0
+Requires-Dist: pandas<4.0.0,>=2.1.0
 Requires-Dist: statsmodels<0.15,>=0.13
-Requires-Dist: scikit-learn<1.8.0,>=1.5.0
+Requires-Dist: scikit-learn<1.9.0,>=1.5.0
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
 Provides-Extra: dev
 Requires-Dist: tox; extra == "dev"

julearn-0.3.5.dev124/docs/changes/newsfragments/297.bugfix

@@ -0,0 +1 @@
+Fix a bug in which ``OptunaSearchCV`` would fail when expecting the ``group`` parameter in the ``fit`` method by `Fede Raimondo`_.

julearn-0.3.5.dev124/docs/changes/newsfragments/297.misc

@@ -0,0 +1 @@
+Update julearn.viz module to support param version 2.3.0 by `Fede Raimondo`_

julearn-0.3.5.dev124/docs/changes/newsfragments/299.misc

@@ -0,0 +1 @@
+Update versions of dependencies in pyproject.toml to support pandas 3.X.X, numpy 2.X.X and scikit-learn 1.8.X by `Fede Raimondo`_

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/examples/00_starting/plot_cm_acc_multiclass.py

@@ -89,7 +89,7 @@ print(cm)
 ###############################################################################
 # Now that we have our confusion matrix, let's build another matrix with
 # annotations.
-cm_sum = np.sum(cm, axis=1, keepdims=True)
+cm_sum = np.sum(cm, axis=1)
 cm_perc = cm / cm_sum.astype(float) * 100
 annot = np.empty_like(cm).astype(str)
 nrows, ncols = cm.shape

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/examples/99_docs/run_model_inspection_docs.py

@@ -57,6 +57,7 @@ penguins_df = penguins_df.query("species != 'Chinstrap'").dropna()
 penguins_df["species"] = penguins_df["species"].replace(
     {"Adelie": 0, "Gentoo": 1}
 )
+penguins_df["species"] = penguins_df["species"].astype(int)
 features = [x for x in penguins_df.columns if x != "species"]
 
 ##############################################################################

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/julearn/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.3.5.dev112'
-__version_tuple__ = version_tuple = (0, 3, 5, 'dev112')
+__version__ = version = '0.3.5.dev124'
+__version_tuple__ = version_tuple = (0, 3, 5, 'dev124')
 
-__commit_id__ = commit_id = 'g5776e7ecc'
+__commit_id__ = commit_id = 'g90c95d23b'

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/julearn/external/optuna_searchcv.py

@@ -58,6 +58,7 @@ with try_import() as _imports:
 
     import sklearn
     from sklearn.base import BaseEstimator
+    from sklearn.model_selection._search import BaseSearchCV
     from sklearn.base import clone
     from sklearn.base import is_classifier
     from sklearn.metrics import check_scoring
@@ -402,7 +403,7 @@ class _Objective:
 
 
 @experimental_class("0.17.0")
-class OptunaSearchCV(BaseEstimator):
+class OptunaSearchCV(BaseSearchCV, BaseEstimator):
     """Hyperparameter search with cross-validation.
 
     Args:
@@ -629,7 +630,6 @@ class OptunaSearchCV(BaseEstimator):
 
         return self.study_.user_attrs
 
-    @property
     def decision_function(self) -> Callable[..., OneDimArrayLikeType | TwoDimArrayLikeType]:
         """Call ``decision_function`` on the best estimator.
 
@@ -641,7 +641,6 @@ class OptunaSearchCV(BaseEstimator):
 
         return self.best_estimator_.decision_function
 
-    @property
     def inverse_transform(self) -> Callable[..., TwoDimArrayLikeType]:
         """Call ``inverse_transform`` on the best estimator.
 
@@ -653,7 +652,7 @@ class OptunaSearchCV(BaseEstimator):
 
         return self.best_estimator_.inverse_transform
 
-    @property
+
     def predict(self) -> Callable[..., OneDimArrayLikeType | TwoDimArrayLikeType]:
         """Call ``predict`` on the best estimator.
 
@@ -665,7 +664,6 @@ class OptunaSearchCV(BaseEstimator):
 
         return self.best_estimator_.predict
 
-    @property
     def predict_log_proba(self) -> Callable[..., TwoDimArrayLikeType]:
         """Call ``predict_log_proba`` on the best estimator.
 
@@ -677,7 +675,6 @@ class OptunaSearchCV(BaseEstimator):
 
         return self.best_estimator_.predict_log_proba
 
-    @property
     def predict_proba(self) -> Callable[..., TwoDimArrayLikeType]:
         """Call ``predict_proba`` on the best estimator.
 
@@ -709,7 +706,7 @@ class OptunaSearchCV(BaseEstimator):
 
         return self.study_.set_user_attr
 
-    @property
+    
     def transform(self) -> Callable[..., TwoDimArrayLikeType]:
         """Call ``transform`` on the best estimator.
 

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/julearn/prepare.py

@@ -395,6 +395,15 @@ def check_consistency(
     # Check problem type and the target.
     n_classes = np.unique(y.values).shape[0]  # type: ignore
     if problem_type == "classification":
+        is_numeric = isinstance(y.values.dtype, np.dtype) and np.issubdtype(
+            y.values.dtype, np.number
+        )  # type: ignore
+        if not is_numeric:
+            warn_with_log(
+                f"The kind of values in y ({y.values.dtype}) is not "
+                "suitable for a classification. Values should be numeric."
+            )
+
         # If not exactly two classes:
         if n_classes == 1:
             raise_error(
@@ -417,7 +426,9 @@ def check_consistency(
             logger.info("Binary classification problem detected.")
     elif problem_type == "regression":
         # Regression
-        is_numeric = np.issubdtype(y.values.dtype, np.number)  # type: ignore
+        is_numeric = isinstance(y.values.dtype, np.dtype) and np.issubdtype(
+            y.values.dtype, np.number
+        )  # type: ignore
         if not is_numeric:
             warn_with_log(
                 f"The kind of values in y ({y.values.dtype}) is not "

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/julearn/tests/test_prepare.py

@@ -701,7 +701,16 @@ def test_check_consistency() -> None:
     with pytest.warns(RuntimeWarning, match="larger than the number"):
         check_consistency(y=y, cv=cv, groups=groups, problem_type=problem_type)
 
-    # Test with wrong problem type
+    # Test with wrong dtype in series
+    y = pd.Series(np.random.randint(0, 2, size=10)).astype(object)
+    problem_type = "classification"
+    groups = None
+    cv = 5
+    with pytest.warns(RuntimeWarning, match="should be numeric"):
+        check_consistency(y=y, cv=cv, groups=groups, problem_type=problem_type)
+
+
+    # Test with wrong dtype in series
     y = pd.Series(["A"] * 10)
     problem_type = "regression"
     groups = None

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/julearn/transformers/confound_remover.py

@@ -259,7 +259,7 @@ class ConfoundRemover(JuTransformer):
         if self.threshold is not None:
             # Accounting for correlated rounding errors for very small
             # residuals
-            residuals = residuals.applymap(  # type: ignore
+            residuals = residuals.map(  # type: ignore
                 lambda x: 0 if abs(x) <= self.threshold else x
             )
         return residuals

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/julearn/viz/_scores.py

@@ -44,7 +44,7 @@ class _JulearnScoresViewer(param.Parameterized):
 
     """
 
-    metric = param.Selector([], default=None)  # type: ignore
+    metric = param.Selector(objects=[], default=None)  # type: ignore
     models: Sequence = param.ListSelector(default=None, objects=[])
     sets: Sequence = param.ListSelector(default=None, objects=[])
     show_stats: bool = param.Boolean(False)

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/julearn.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: julearn
-Version: 0.3.5.dev112
+Version: 0.3.5.dev124
 Summary: Juelich Machine Learning Library
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Sami Hamdan <s.hamdan@fz-juelich.de>
 Maintainer-email: Sami Hamdan <s.hamdan@fz-juelich.de>
@@ -27,10 +27,10 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
-Requires-Dist: numpy<2.0.0,>=1.26.0
-Requires-Dist: pandas<2.4.0,>=2.0.0
+Requires-Dist: numpy<3.0.0,>=1.26.0
+Requires-Dist: pandas<4.0.0,>=2.1.0
 Requires-Dist: statsmodels<0.15,>=0.13
-Requires-Dist: scikit-learn<1.8.0,>=1.5.0
+Requires-Dist: scikit-learn<1.9.0,>=1.5.0
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
 Provides-Extra: dev
 Requires-Dist: tox; extra == "dev"

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/julearn.egg-info/SOURCES.txt

@@ -8,6 +8,7 @@ ignore_words.txt
 pyproject.toml
 setup.py
 tox.ini
+uv.lock
 .github/dependabot.yml
 .github/ISSUE_TEMPLATE/bug_report.yaml
 .github/ISSUE_TEMPLATE/config.yml
@@ -69,6 +70,9 @@ docs/changes/newsfragments/285.bugfix
 docs/changes/newsfragments/286.bugfix
 docs/changes/newsfragments/288.bugfix
 docs/changes/newsfragments/291.bugfix
+docs/changes/newsfragments/297.bugfix
+docs/changes/newsfragments/297.misc
+docs/changes/newsfragments/299.misc
 docs/images/corrected_ttest.png
 docs/images/final_estimator.png
 docs/images/iris_X.png

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/julearn.egg-info/requires.txt

@@ -1,7 +1,7 @@
-numpy<2.0.0,>=1.26.0
-pandas<2.4.0,>=2.0.0
+numpy<3.0.0,>=1.26.0
+pandas<4.0.0,>=2.1.0
 statsmodels<0.15,>=0.13
-scikit-learn<1.8.0,>=1.5.0
+scikit-learn<1.9.0,>=1.5.0
 
 [:python_version >= "3.12"]
 looseversion==1.3.0

{julearn-0.3.5.dev112 → julearn-0.3.5.dev124}/pyproject.toml

@@ -34,10 +34,10 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "numpy>=1.26.0,<2.0.0",
-    "pandas>=2.0.0,<2.4.0",
+    "numpy>=1.26.0,<3.0.0",
+    "pandas>=2.1.0,<4.0.0",
     "statsmodels>=0.13,<0.15",
-    "scikit-learn>=1.5.0,<1.8.0",
+    "scikit-learn>=1.5.0,<1.9.0",
     "looseversion==1.3.0; python_version>='3.12'",
 ]
 dynamic = ["version"]