julearn 0.3.4.dev4__tar.gz → 0.3.4.dev13__tar.gz

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/.github/workflows/ci-docs.yml

@@ -42,7 +42,7 @@ jobs:
           echo '</coverage>' >> coverage.xml
         if: matrix.python-version == 3.10
       - name: Upload mock coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/.github/workflows/ci.yml

@@ -33,7 +33,7 @@ jobs:
       run: |
         tox
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: julearn
-Version: 0.3.4.dev4
+Version: 0.3.4.dev13
 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>
@@ -42,7 +42,7 @@ Requires-Dist: numpydoc<1.6,>=1.5.0; extra == "docs"
 Requires-Dist: towncrier<24; extra == "docs"
 Requires-Dist: scikit-optimize<0.11,>=0.10.0; extra == "docs"
 Requires-Dist: optuna<3.7,>=3.6.0; extra == "docs"
-Requires-Dist: optuna_integration<3.7,>=3.6.0; extra == "docs"
+Requires-Dist: optuna_integration<4.1,>=3.6.0; extra == "docs"
 Provides-Extra: deslib
 Requires-Dist: deslib<0.4,>=0.3.5; extra == "deslib"
 Provides-Extra: viz
@@ -53,7 +53,7 @@ Provides-Extra: skopt
 Requires-Dist: scikit-optimize<0.11,>=0.10.0; extra == "skopt"
 Provides-Extra: optuna
 Requires-Dist: optuna<3.7,>=3.6.0; extra == "optuna"
-Requires-Dist: optuna_integration<3.7,>=3.6.0; extra == "optuna"
+Requires-Dist: optuna_integration<4.1,>=3.6.0; extra == "optuna"
 Provides-Extra: all
 Requires-Dist: julearn[optuna,skopt,viz]; extra == "all"
 

julearn-0.3.4.dev13/docs/changes/newsfragments/270.enh

@@ -0,0 +1 @@
+Remove final model fit requirement for inspector to be returned by :func:`.run_cross_validation` by `Fede Raimondo`_.

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/docs/getting_started.rst

@@ -96,5 +96,5 @@ The following optional dependencies are available:
   module is not compatible with newer Python versions and it is unmaintained.
 * ``skopt``: Using the ``"bayes"`` searcher (:class:`~skopt.BayesSearchCV`)
   requires the `scikit-optimize`_ package.
-* ``optuna``: Using the ``"optuna"`` searcher (:class:`~optuna_integration.sklearn.OptunaSearchCV`) requires the `Optuna`_ and `optuna_integration`_ packages.
+* ``optuna``: Using the ``"optuna"`` searcher (:class:`~optuna_integration.OptunaSearchCV`) requires the `Optuna`_ and `optuna_integration`_ packages.
 * ``all``: Install all optional functional dependencies (except ``deslib``).

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/docs/whats_new.rst

@@ -56,7 +56,7 @@ Enhancements
 Features
 ^^^^^^^^
 
-- Add :class:`~optuna_integration.sklearn.OptunaSearchCV` to the list of
+- Add :class:`~optuna_integration.OptunaSearchCV` to the list of
   available searchers as ``optuna`` by `Fede Raimondo`_ (:gh:`262`)
 
 

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/examples/99_docs/run_hyperparameters_docs.py

@@ -255,7 +255,7 @@ pprint(model_tuned.best_params_)
 # Other searchers that ``julearn`` provides are the
 # :class:`~sklearn.model_selection.RandomizedSearchCV`,
 # :class:`~skopt.BayesSearchCV` and
-# :class:`~optuna_integration.sklearn.OptunaSearchCV`.
+# :class:`~optuna_integration.OptunaSearchCV`.
 #
 # The randomized searcher
 # (:class:`~sklearn.model_selection.RandomizedSearchCV`) is similar to the
@@ -275,7 +275,7 @@ pprint(model_tuned.best_params_)
 # :class:`~skopt.BayesSearchCV` documentation, including how to specify
 # the prior distributions of the hyperparameters.
 #
-# The Optuna searcher (:class:`~optuna_integration.sklearn.OptunaSearchCV`)
+# The Optuna searcher (:class:`~optuna_integration.OptunaSearchCV`)
 # uses the Optuna library to find the best hyperparameter set. Optuna is a
 # hyperparameter optimization framework that has several algorithms to find
 # the best hyperparameter set. For more information, see the

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/julearn/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.3.4.dev4'
-__version_tuple__ = version_tuple = (0, 3, 4, 'dev4')
+__version__ = version = '0.3.4.dev13'
+__version_tuple__ = version_tuple = (0, 3, 4, 'dev13')

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/julearn/api.py

@@ -142,7 +142,7 @@ def run_cross_validation(  # noqa: C901
             :class:`~sklearn.model_selection.RandomizedSearchCV`
           * ``"bayes"`` : :class:`~skopt.BayesSearchCV`
           * ``"optuna"`` :
-            :class:`~optuna_integration.sklearn.OptunaSearchCV`
+            :class:`~optuna_integration.OptunaSearchCV`
           * user-registered searcher name : see
             :func:`~julearn.model_selection.register_searcher`
           * ``scikit-learn``-compatible searcher
@@ -194,11 +194,11 @@ def run_cross_validation(  # noqa: C901
         )
     if return_inspector:
         if return_estimator is None:
-            logger.info("Inspector requested: setting return_estimator='all'")
             return_estimator = "all"
-        if return_estimator != "all":
+        if return_estimator not in ["all", "cv"]:
             raise_error(
-                "return_inspector=True requires return_estimator to be `all`."
+                "return_inspector=True requires return_estimator to be `all` "
+                "or `cv`"
             )
 
     X_types = {} if X_types is None else X_types
@@ -441,6 +441,9 @@ def run_cross_validation(  # noqa: C901
             groups=df_groups,
             cv=cv_outer,
         )
-        out = scores_df, pipeline, inspector
+        if isinstance(out, tuple):
+            out = (*out, inspector)
+        else:
+            out = out, inspector
 
     return out

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/julearn/inspect/tests/test_inspector.py

@@ -54,7 +54,9 @@ def test_normal_usage(df_iris: "pd.DataFrame") -> None:
 
     """
     X = list(df_iris.iloc[:, :-1].columns)
-    scores, pipe, inspect = run_cross_validation(
+
+    # All estimators
+    out = run_cross_validation(
         X=X,
         y="species",
         data=df_iris,
@@ -63,6 +65,7 @@ def test_normal_usage(df_iris: "pd.DataFrame") -> None:
         return_inspector=True,
         problem_type="classification",
     )
+    scores, pipe, inspect = out
     assert pipe == inspect.model._model  # type: ignore
     for (_, score), inspect_fold in zip(
         scores.iterrows(),  # type: ignore
@@ -70,6 +73,24 @@ def test_normal_usage(df_iris: "pd.DataFrame") -> None:
     ):
         assert score["estimator"] == inspect_fold.model._model
 
+    del pipe
+    # only CV estimators
+    out = run_cross_validation(
+        X=X,
+        y="species",
+        data=df_iris,
+        model="svm",
+        return_estimator="cv",
+        return_inspector=True,
+        problem_type="classification",
+    )
+    scores, inspect = out
+    for (_, score), inspect_fold in zip(
+        scores.iterrows(),  # type: ignore
+        inspect.folds,  # type: ignore
+    ):
+        assert score["estimator"] == inspect_fold.model._model
+
 
 def test_normal_usage_with_search(df_iris: "pd.DataFrame") -> None:
     """Test inspector with search.

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/julearn/pipeline/pipeline_creator.py

@@ -944,7 +944,7 @@ def _prepare_hyperparameter_tuning(
             :class:`~sklearn.model_selection.RandomizedSearchCV`
           * ``"bayes"`` : :class:`~skopt.BayesSearchCV`
           * ``"optuna"`` :
-            :class:`~optuna_integration.sklearn.OptunaSearchCV`
+            :class:`~optuna_integration.OptunaSearchCV`
           * user-registered searcher name : see
             :func:`~julearn.model_selection.register_searcher`
           * ``scikit-learn``-compatible searcher

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/julearn.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: julearn
-Version: 0.3.4.dev4
+Version: 0.3.4.dev13
 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>
@@ -42,7 +42,7 @@ Requires-Dist: numpydoc<1.6,>=1.5.0; extra == "docs"
 Requires-Dist: towncrier<24; extra == "docs"
 Requires-Dist: scikit-optimize<0.11,>=0.10.0; extra == "docs"
 Requires-Dist: optuna<3.7,>=3.6.0; extra == "docs"
-Requires-Dist: optuna_integration<3.7,>=3.6.0; extra == "docs"
+Requires-Dist: optuna_integration<4.1,>=3.6.0; extra == "docs"
 Provides-Extra: deslib
 Requires-Dist: deslib<0.4,>=0.3.5; extra == "deslib"
 Provides-Extra: viz
@@ -53,7 +53,7 @@ Provides-Extra: skopt
 Requires-Dist: scikit-optimize<0.11,>=0.10.0; extra == "skopt"
 Provides-Extra: optuna
 Requires-Dist: optuna<3.7,>=3.6.0; extra == "optuna"
-Requires-Dist: optuna_integration<3.7,>=3.6.0; extra == "optuna"
+Requires-Dist: optuna_integration<4.1,>=3.6.0; extra == "optuna"
 Provides-Extra: all
 Requires-Dist: julearn[optuna,skopt,viz]; extra == "all"
 

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/julearn.egg-info/SOURCES.txt

@@ -54,6 +54,7 @@ docs/api/viz.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
 docs/changes/newsfragments/268.bugfix
+docs/changes/newsfragments/270.enh
 docs/images/corrected_ttest.png
 docs/images/final_estimator.png
 docs/images/iris_X.png

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/julearn.egg-info/requires.txt

@@ -23,11 +23,11 @@ numpydoc<1.6,>=1.5.0
 towncrier<24
 scikit-optimize<0.11,>=0.10.0
 optuna<3.7,>=3.6.0
-optuna_integration<3.7,>=3.6.0
+optuna_integration<4.1,>=3.6.0
 
 [optuna]
 optuna<3.7,>=3.6.0
-optuna_integration<3.7,>=3.6.0
+optuna_integration<4.1,>=3.6.0
 
 [skopt]
 scikit-optimize<0.11,>=0.10.0

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/pyproject.toml

@@ -61,7 +61,7 @@ docs = [
     "towncrier<24",
     "scikit-optimize>=0.10.0,<0.11",
     "optuna>=3.6.0,<3.7",
-    "optuna_integration>=3.6.0,<3.7",
+    "optuna_integration>=3.6.0,<4.1",
 ]
 deslib = ["deslib>=0.3.5,<0.4"]
 viz = [
@@ -72,7 +72,7 @@ viz = [
 skopt = ["scikit-optimize>=0.10.0,<0.11"]
 optuna = [
     "optuna>=3.6.0,<3.7",
-    "optuna_integration>=3.6.0,<3.7",
+    "optuna_integration>=3.6.0,<4.1",
 ]
 # Add all optional functional dependencies (skip deslib until its fixed)
 # This does not include dev/docs building dependencies

{julearn-0.3.4.dev4 → julearn-0.3.4.dev13}/tox.ini

@@ -16,7 +16,7 @@ deps =
     seaborn
     scikit-optimize>=0.10.0,<0.11
     optuna>=3.6.0,<3.7
-    optuna_integration>=3.6.0,<3.7
+    optuna_integration>=3.6.0,<4.1
 commands =
     pytest {toxinidir}/julearn
 
@@ -45,7 +45,7 @@ deps =
     param
     scikit-optimize>=0.10.0,<0.11
     optuna>=3.6.0,<3.7
-    optuna_integration>=3.6.0,<3.7
+    optuna_integration>=3.6.0,<4.1
 commands =
     pytest -vv {toxinidir}/julearn
 
@@ -69,7 +69,7 @@ deps =
     param
     scikit-optimize>=0.10.0,<0.11
     optuna>=3.6.0,<3.7
-    optuna_integration>=3.6.0,<3.7
+    optuna_integration>=3.6.0,<4.1
 commands =
     pytest --cov={envsitepackagesdir}/julearn --cov=./julearn --cov-report=xml --cov-report=term -vv