julearn 0.3.4__tar.gz → 0.3.4.dev4__tar.gz

{julearn-0.3.4 → julearn-0.3.4.dev4}/.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@v4
+        uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true

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

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

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: julearn
-Version: 0.3.4
+Version: 0.3.4.dev4
 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>
@@ -26,9 +26,9 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: numpy<1.27,>=1.24
-Requires-Dist: pandas<2.3,>=1.5.0
+Requires-Dist: pandas<2.2,>=1.5.0
 Requires-Dist: statsmodels<0.15,>=0.13
-Requires-Dist: scikit-learn<1.6.0,>=1.2.0
+Requires-Dist: scikit-learn<1.5.0,>=1.2.0
 Provides-Extra: dev
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
@@ -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<4.1,>=3.6.0; extra == "docs"
+Requires-Dist: optuna_integration<3.7,>=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<4.1,>=3.6.0; extra == "optuna"
+Requires-Dist: optuna_integration<3.7,>=3.6.0; extra == "optuna"
 Provides-Extra: all
 Requires-Dist: julearn[optuna,skopt,viz]; extra == "all"
 

{julearn-0.3.4 → julearn-0.3.4.dev4}/docs/api/main.rst

@@ -15,4 +15,3 @@ Functions
    :template: function.rst
 
     run_cross_validation
-    run_fit

julearn-0.3.4.dev4/docs/changes/newsfragments/268.bugfix

@@ -0,0 +1 @@
+Fix usage of optuna distributions as hyperparameters in older versions of scikit-learn by `Fede Raimondo`_.

{julearn-0.3.4 → julearn-0.3.4.dev4}/docs/configuration.rst

@@ -47,10 +47,3 @@ Here you can find the comprehensive list of flags that can be set:
      - | Disable printing the list of expanded column names in ``X_types``.
        | If set to ``True``, the list of types of X will not be printed.
      - The user will not see the expanded ``X_types`` column names.
-   * - ``enable_parallel_column_transformers``
-     - | This flag enables parallel execution of column transformers by
-       | reverting to the default behaviour of scikit-learn
-       | (instead of using ``n_jobs=1``)
-       | If set to ``True``, the parameter will be set back to None.
-     - | Column transformers will be applied in parallel, using more resources.
-       | than expected.

{julearn-0.3.4 → julearn-0.3.4.dev4}/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.OptunaSearchCV`) requires the `Optuna`_ and `optuna_integration`_ packages.
+* ``optuna``: Using the ``"optuna"`` searcher (:class:`~optuna_integration.sklearn.OptunaSearchCV`) requires the `Optuna`_ and `optuna_integration`_ packages.
 * ``all``: Install all optional functional dependencies (except ``deslib``).

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

@@ -8,31 +8,6 @@ What's new
 
 .. towncrier release notes start
 
-Julearn 0.3.4 (2024-10-17)
---------------------------
-
-Bugfixes
-^^^^^^^^
-
-- Fix usage of optuna distributions as hyperparameters in older versions of
-  scikit-learn by `Fede Raimondo`_. (:gh:`268`)
-
-
-Enhancements
-^^^^^^^^^^^^
-
-- Remove final model fit requirement for inspector to be returned by
-  :func:`.run_cross_validation` by `Fede Raimondo`_. (:gh:`270`)
-- Add :func:`.run_fit` that implements a model fitting procedure with the same
-  API as :func:`.run_cross_validation` by `Fede Raimondo`_. (:gh:`271`)
-- Optimise wrapping of steps and models in the pipeline only when a subset of
-  features is being used, by `Fede Raimondo`_ (:gh:`274`)
-- Place the final model CV split at the beginning instead of the end of the CV
-  iterator wrapper by `Fede Raimondo`_ (:gh:`275`)
-- Change the internal logic of :func:`.run_cross_validation` to optimise joblib
-  calls by `Fede Raimondo`_ (:gh:`293`)
-
-
 Julearn 0.3.3 (2024-05-16)
 --------------------------
 
@@ -81,7 +56,7 @@ Enhancements
 Features
 ^^^^^^^^
 
-- Add :class:`~optuna_integration.OptunaSearchCV` to the list of
+- Add :class:`~optuna_integration.sklearn.OptunaSearchCV` to the list of
   available searchers as ``optuna`` by `Fede Raimondo`_ (:gh:`262`)
 
 

{julearn-0.3.4 → julearn-0.3.4.dev4}/examples/02_inspection/plot_preprocess.py

@@ -121,7 +121,7 @@ X_after_zscore = preprocess(model, X=X, data=df, until="zscore")
 fig, axes = plt.subplots(1, 2, figsize=(12, 6))
 sns.scatterplot(x=X[0], y=X[1], data=df, ax=axes[0])
 axes[0].set_title("Raw features")
-sns.scatterplot(x="pca0", y="pca1", data=X_after_pca, ax=axes[1])
+sns.scatterplot(x="pca__pca0", y="pca__pca1", data=X_after_pca, ax=axes[1])
 axes[1].set_title("PCA components")
 
 ###############################################################################

{julearn-0.3.4 → julearn-0.3.4.dev4}/examples/02_inspection/run_binary_inspect_folds.py

@@ -44,6 +44,7 @@ creator = PipelineCreator(problem_type="classification")
 creator.add("zscore")
 creator.add("svm")
 
+cv = ShuffleSplit(n_splits=5, train_size=0.7, random_state=200)
 cv = RepeatedStratifiedKFold(n_splits=5, n_repeats=4, random_state=200)
 
 scores, model, inspector = run_cross_validation(

{julearn-0.3.4 → julearn-0.3.4.dev4}/examples/04_confounds/run_return_confounds.py

@@ -172,4 +172,4 @@ scores
 # (including confounds and categorical variables).
 # Here we can see that the model is using 10 features (9 deconfounded features
 # and the confound).
-print(len(model.steps[-1][1].coef_))
+print(len(model.steps[-1][1].model.coef_))

{julearn-0.3.4 → julearn-0.3.4.dev4}/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.OptunaSearchCV`.
+# :class:`~optuna_integration.sklearn.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.OptunaSearchCV`)
+# The Optuna searcher (:class:`~optuna_integration.sklearn.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 → julearn-0.3.4.dev4}/examples/99_docs/run_model_inspection_docs.py

@@ -140,7 +140,7 @@ c_values = []
 for fold_inspector in inspector.folds:
     fold_model = fold_inspector.model
     c_values.append(
-        fold_model.get_fitted_params()["svm__C"]
+        fold_model.get_fitted_params()["svm__model_"].get_params()["C"]
     )
 
 ##############################################################################

{julearn-0.3.4 → julearn-0.3.4.dev4}/julearn/__init__.py

@@ -14,5 +14,5 @@ from . import utils
 from . import prepare
 from . import api
 from . import stats
-from .api import run_cross_validation, run_fit
+from .api import run_cross_validation
 from .pipeline import PipelineCreator, TargetPipelineCreator

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

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