julearn 0.3.6.dev15__tar.gz → 0.3.6.dev33__tar.gz

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/.github/workflows/ci-docs.yml

@@ -22,11 +22,9 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - '3.9'
-          - '3.10'
-          - '3.11'
           - '3.12'
           - '3.13'
+          - '3.14'
     steps:
       - run: 'echo "No build required"'
       - name: Create mock coverage.xml file
@@ -53,7 +51,7 @@ jobs:
           echo '</coverage>' >> coverage.xml
         if: matrix.python-version == 3.12
       - name: Upload mock coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: true

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/.github/workflows/ci.yml

@@ -21,11 +21,9 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - '3.9'
-          - '3.10'
-          - '3.11'
           - '3.12'
           - '3.13'
+          - '3.14'
 
     steps:
     - uses: actions/checkout@v6
@@ -39,9 +37,9 @@ jobs:
     - name: Test with tox
       run: |
         tox
-    - uses: codecov/codecov-action@v5
+    - uses: codecov/codecov-action@v6
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true
         flags: julearn
-      if: success() && matrix.python-version == 3.12
+      if: success() && matrix.python-version == 3.13

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/.github/workflows/docs.yml

@@ -25,7 +25,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools wheel
         python -m pip install -e .[docs,viz]
-        python -m pip install git+https://github.com/dls-controls/sphinx-multiversion@only-arg
     - name: Checkout gh-pages
       # As we already did a deploy of gh-pages above, it is guaranteed to be there
       # so check it out so we can selectively build docs below

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/.github/workflows/publish.yml

@@ -32,7 +32,7 @@ jobs:
       run:
         python -m build
     - uses: pypa/gh-action-pypi-publish@release/v1
-    - uses: softprops/action-gh-release@v2
+    - uses: softprops/action-gh-release@v3
       with:
         files: |
           dist/*.tar.gz

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: julearn
-Version: 0.3.6.dev15
+Version: 0.3.6.dev33
 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>
@@ -18,17 +18,16 @@ Classifier: Natural Language :: English
 Classifier: Topic :: Software Development
 Classifier: Topic :: Scientific/Engineering
 Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.9
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.rst
-Requires-Dist: numpy<3.0.0,>=1.26.0
-Requires-Dist: pandas<4.0.0,>=2.1.0
+Requires-Dist: numpy<3.0.0,>=2.3.0
+Requires-Dist: pandas<4.0.0,>=2.2.0
 Requires-Dist: statsmodels<0.15,>=0.13
 Requires-Dist: scikit-learn<1.9.0,>=1.5.0
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
@@ -38,18 +37,20 @@ Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: towncrier; extra == "dev"
 Provides-Extra: docs
+Requires-Dist: furo>=2025.7.19; extra == "docs"
+Requires-Dist: numpydoc>=1.9.0; extra == "docs"
+Requires-Dist: optuna<5.0.0,>=4.0.0; extra == "docs"
+Requires-Dist: optuna-integration<5.0.0,>=4.0.0; extra == "docs"
+Requires-Dist: scikit-optimize<0.11.0,>=0.10.2; extra == "docs"
 Requires-Dist: seaborn<0.14.0,>=0.13.0; extra == "docs"
-Requires-Dist: sphinx<8.1.0,>=7.3.0; extra == "docs"
-Requires-Dist: sphinx-gallery<=0.19.0,>=0.17.0; extra == "docs"
-Requires-Dist: furo<=2025.7.19,>=2024.4.27; extra == "docs"
-Requires-Dist: numpydoc<=1.9.0,>=1.6.0; extra == "docs"
-Requires-Dist: sphinx-copybutton<0.5.3,>=0.5.1; extra == "docs"
-Requires-Dist: towncrier<24.7.0,>=23.10.0; extra == "docs"
-Requires-Dist: sphinxcontrib-towncrier==0.4.0a0; 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: setuptools-scm>=8; extra == "docs"
+Requires-Dist: setuptools-scm<11.0.0,>=10.0.0; extra == "docs"
+Requires-Dist: sphinx<10.0.0,>=8.2.3; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5.2; extra == "docs"
+Requires-Dist: sphinx-gallery>=0.21.0; extra == "docs"
+Requires-Dist: sphinx-multiversion>=0.2.4; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=3.6.1; extra == "docs"
+Requires-Dist: sphinxcontrib-towncrier>=0.5.0a0; extra == "docs"
+Requires-Dist: towncrier>=25.8.0; extra == "docs"
 Provides-Extra: deslib
 Requires-Dist: deslib<0.4.0,>=0.3.5; extra == "deslib"
 Provides-Extra: viz
@@ -57,10 +58,10 @@ Requires-Dist: panel>=1.3.0; extra == "viz"
 Requires-Dist: bokeh>=3.0.0; extra == "viz"
 Requires-Dist: param>=2.0.0; extra == "viz"
 Provides-Extra: skopt
-Requires-Dist: scikit-optimize<0.11,>=0.10.0; extra == "skopt"
+Requires-Dist: scikit-optimize<0.11.0,>=0.10.2; 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<5.0.0,>=4.0.0; extra == "optuna"
+Requires-Dist: optuna_integration<5.0.0,>=4.0.0; extra == "optuna"
 Provides-Extra: all
 Requires-Dist: julearn[optuna,skopt,viz]; extra == "all"
 Dynamic: license-file

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/docs/Makefile

@@ -23,14 +23,28 @@ clean:
 local:
 	make _build_local; STATUS=$$?; exit $$STATUS
 
+## First build will create warnings for auto_examples. Second one will work correctly.
 _build_local:
+	sphinx-build "$(SOURCEDIR)" "$(BUILDDIR)" "-E" $(O)
 	sphinx-build "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 html:
 	make _html; STATUS=$$?; exit $$STATUS
 
+
+## Build only tags that are not already built, and ignore dev tags. This is useful for CI to avoid building all tags on every push, but still build new tags when they are created.
 _html:
-	$(SPHINXBUILD) "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS)
+	@regex=$$( \
+		for tag in $$(git tag -l); do \
+			if [ ! -d "$(BUILDDIR)/$$tag" ]; then \
+				echo "$$tag"; \
+			fi; \
+		done | \
+		grep -v dev | \
+		paste -sd'|' - \
+	); \
+	echo "$$regex"; \
+	$(SPHINXBUILD) "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) -D "smv_tag_whitelist='^($$regex)$$'"  $(O)
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).

julearn-0.3.6.dev33/docs/_templates/protocol.rst

@@ -0,0 +1,17 @@
+.. note::
+
+   This page is a reference documentation. It only explains the function signature, and not how to use it.
+   Please refer to the :ref:`What you really need to know <need_to_know>` section for the big picture.
+
+
+{{ fullname | underline(line="-") }}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+
+
+.. raw:: html
+
+    <div style='clear:both'></div>

julearn-0.3.6.dev33/docs/_templates/type.rst

@@ -0,0 +1,15 @@
+.. note::
+
+   This page is a reference documentation. It only explains the function signature, and not how to use it.
+   Please refer to the :ref:`What you really need to know <need_to_know>` section for the big picture.
+
+
+{{ fullname | underline(line="-") }}
+
+.. currentmodule:: {{ module }}
+
+.. autotype:: {{ objname }}
+
+.. raw:: html
+
+    <div style='clear:both'></div>

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/docs/api/base.rst

@@ -19,7 +19,6 @@ Classes
     JuTransformer
     WrapModel
     ColumnTypes
-    ColumnTypesLike
 
 Functions
 ---------

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/docs/api/model_selection.rst

@@ -22,6 +22,7 @@ Classes
     ContinuousStratifiedGroupKFold
     RepeatedContinuousStratifiedGroupKFold
     StratifiedBootstrap
+    final_model_cv._JulearnFinalModelCV
 
 Functions
 ---------

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/docs/api/utils.rst

@@ -5,16 +5,15 @@ Utils
    :no-members:
    :no-inherited-members:
 
-Classes
+Members
 -------
 
 .. currentmodule:: julearn.utils
 
 .. autosummary::
    :toctree: generated/
-   :template: class.rst
 
-    logger
+   logger
 
 Functions
 ---------
@@ -36,17 +35,36 @@ Typing
    :no-members:
    :no-inherited-members:
 
-Classes
--------
+
+Types
+-----
 
 .. currentmodule:: julearn.utils.typing
 
 .. autosummary::
    :toctree: generated/
-   :template: class.rst
+   :template: type.rst
 
-    JuEstimatorLike
+    DataLike
+    ScorerLike
     EstimatorLike
+    CVLike
+    ColumnTypesLike
+
+
+Protocols
+---------
+
+.. currentmodule:: julearn.utils.typing
+
+.. autosummary::
+   :toctree: generated/
+   :template: protocol.rst
+
     EstimatorLikeFit1
     EstimatorLikeFit2
     EstimatorLikeFity
+    TransformerLike
+    ModelLike
+    JuEstimatorLike
+    JuModelLike

julearn-0.3.6.dev33/docs/changes/newsfragments/307.bugfix

@@ -0,0 +1 @@
+Fix a bug in which RandomizedSearchCV using uniform distributions specifications used an extended search space `Fede Raimondo`_

julearn-0.3.6.dev33/docs/changes/newsfragments/307.misc

@@ -0,0 +1 @@
+Configure the project to support uv as a package manager and bump minimum Python version to 3.12 `Fede Raimondo`_

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/docs/conf.py

@@ -9,9 +9,13 @@
 import datetime
 from functools import partial
 from pathlib import Path
+import sys
 
 from setuptools_scm import get_version
 
+import types
+from typing import TypeAliasType
+from sphinx_autodoc_typehints import format_annotation
 
 # Check if sphinx-multiversion is installed
 use_multiversion = False
@@ -65,10 +69,14 @@ extensions = [
     "sphinx_copybutton",  # copy button for code blocks
     "sphinxcontrib.towncrier.ext",  # towncrier fragment support
     "bokeh.sphinxext.bokeh_plot",  # bokeh plot support
+    "sphinx_autodoc_typehints",  # automatically document type hints
 ]
 
 if use_multiversion:
+    print("using sphinx-multiversion for documentation")
     extensions.append("sphinx_multiversion")
+else:
+    print("sphinx-multiversion not found, building documentation without it")
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = [
@@ -99,8 +107,19 @@ nitpick_ignore_regex = [
     ("py:class", "pipeline.Pipeline"),
     ("py:class", "sklearn.utils.metadata_routing.MetadataRequest"),
     ("py:class", "julearn.inspect._pipeline.PipelineInspector"),
+    ("py:class", "sklearn.model_selection._split.*"),
+    ("py:class", "sklearn.metrics._scorer.*"),
 ]
 
+to_ignore = ["array-like", "shape", "optional", "or", "the", "options",
+             "n_samples", "default=.*", "n_features", "n_outputs", "True",
+             "False"]
+
+for i in to_ignore:
+    nitpick_ignore_regex.append(("py:class", i))
+
+suppress_warnings = ["sphinx_autodoc_typehints", "config.cache"]
+
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -143,8 +162,23 @@ html_sidebars = {
 # -- sphinx.ext.autodoc configuration ----------------------------------------
 
 autoclass_content = "both"
-autodoc_typehints = "description"
-autodoc_typehints_description_target = "documented"
+# autodoc_typehints = "description"
+# autodoc_typehints_description_target = "documented"
+autodoc_type_aliases = {
+    "ColumnTypes": "julearn.base.column_types.ColumnTypes",
+    "Pipeline": "sklearn.pipeline.Pipeline",
+    "RandomState": "numpy.random.RandomState",
+#     "ColumnTypesLike": "julearn.utils.typing.ColumnTypesLike",
+#     "DataLike": "julearn.utils.typing.DataLike",
+#     "ScorerLike": "julearn.utils.typing.ScorerLike",
+#     "EstimatorLike": "julearn.utils.typing.EstimatorLike",
+#     "ModelLike": "julearn.utils.typing.ModelLike",
+#     "TransformerLike": "julearn.utils.typing.TransformerLike",
+#     "JuModelLike": "julearn.utils.typing.JuModelLike",
+#     "JuTransformerLike": "julearn.utils.typing.JuTransformerLike",
+#     "CVLike": "julearn.utils.typing.CVLike",
+}
+
 
 # -- sphinx.ext.autosummary configuration ------------------------------------
 
@@ -178,6 +212,7 @@ intersphinx_mapping = {
         "https://optuna-integration.readthedocs.io/en/stable",
         None,
     ),
+    "panel": ("https://panel.holoviz.org/", None),
 }
 
 # -- sphinx.ext.extlinks configuration ---------------------------------------
@@ -265,3 +300,67 @@ smv_released_pattern = r"^tags/v.*$"
 towncrier_draft_autoversion_mode = "draft"
 towncrier_draft_include_empty = True
 towncrier_draft_working_directory = PROJECT_ROOT_DIR
+
+# -- sphinx_autodoc_typehints configuration ---------------------------------------
+always_use_bars_union = True
+simplify_optional_unions = True
+typehints_defaults = "comma"
+# Don't show return types at all
+typehints_document_rtype = False
+
+# Don't show "None" return types, but show all others
+typehints_document_rtype_none = False
+
+# Show the return type inline with the return description
+# instead of as a separate block
+typehints_use_rtype = False
+
+def _get_canonical_type_alias_name(annotation: TypeAliasType) -> str:
+    """
+    Get canonical public qualified name for a TypeAliasType.
+
+    For types defined in private modules (e.g. ``numpy._typing.ArrayLike``),
+    search ``sys.modules`` for a public re-export
+    (e.g. ``numpy.typing.ArrayLike``).
+    """
+    module = getattr(annotation, "__module__", "") or ""
+    name = getattr(annotation, "__name__", "") or ""
+    if not module or not name:
+        return ""
+    if not any(part.startswith("_") for part in module.split(".")):
+        return f"{module}.{name}"
+    top_pkg = module.split(".")[0]
+    for mod_name in sorted(sys.modules):
+        if not mod_name.startswith(top_pkg):
+            continue
+        mod = sys.modules[mod_name]
+        if not isinstance(mod, types.ModuleType):
+            continue
+        if any(part.startswith("_") for part in mod_name.split(".")):
+            continue
+        if getattr(mod, name, None) is annotation:
+            return f"{mod_name}.{name}"
+    return f"{module}.{name}"
+
+
+def _typehints_formatter(annotation, config):
+    """Handle formatting of PEP695 type aliases in sphinx-autodoc-typehints."""
+    if isinstance(annotation, TypeAliasType):
+        module = getattr(annotation, "__module__", "") or ""
+        name = getattr(annotation, "__name__", "") or ""
+        intersphinx_mapping = getattr(config, "intersphinx_mapping", {})
+        is_external = module and any(
+            module == pkg or module.startswith(f"{pkg}.")
+            for pkg in intersphinx_mapping
+        )
+        # Handle external PEP695 type aliases
+        if is_external and name:
+            canonical = _get_canonical_type_alias_name(annotation)
+            if canonical:
+                return f":py:obj:`~{canonical}`"
+        # Unwrap internal PEP695 type aliases to their underlying types
+        return format_annotation(annotation.__value__, config)
+    return None
+
+
+typehints_formatter = _typehints_formatter

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/julearn/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.3.6.dev15'
-__version_tuple__ = version_tuple = (0, 3, 6, 'dev15')
+__version__ = version = '0.3.6.dev33'
+__version_tuple__ = version_tuple = (0, 3, 6, 'dev33')
 
-__commit_id__ = commit_id = 'g4baf848be'
+__commit_id__ = commit_id = 'gd95c8f6d1'

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/julearn/api.py

@@ -5,7 +5,6 @@
 # License: AGPL
 
 import inspect
-from typing import Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -36,24 +35,24 @@ sklearn.set_config(enable_metadata_routing=True)
 def _validate_api_params(  # noqa: C901
     X: list[str],  # noqa: N803
     y: str,
-    model: Union[str, PipelineCreator, BaseEstimator, list[PipelineCreator]],
+    model: str | PipelineCreator | BaseEstimator | list[PipelineCreator],
     data: pd.DataFrame,
-    X_types: Optional[dict] = None,  # noqa: N803
-    problem_type: Optional[str] = None,
-    preprocess: Union[None, str, list[str]] = None,
-    return_estimator: Optional[str] = None,
+    X_types: dict | None = None,  # noqa: N803
+    problem_type: str | None = None,
+    preprocess: None | str | list[str] = None,
+    return_estimator: str | None = None,
     return_inspector: bool = False,
-    groups: Optional[str] = None,
-    pos_labels: Union[str, list[str], None] = None,
-    model_params: Optional[dict] = None,
-    search_params: Optional[dict] = None,
-    seed: Optional[int] = None,
+    groups: str | None = None,
+    pos_labels: str | list[str] | None = None,
+    model_params: dict | None = None,
+    search_params: dict | None = None,
+    seed: int | None = None,
 ) -> tuple[
     pd.DataFrame,
     pd.Series,
-    Optional[pd.Series],
-    Union[Pipeline, BaseSearchCV],
-    Optional[str],
+    pd.Series | None,
+    Pipeline | BaseSearchCV,
+    str | None,
     bool,
     bool,
     str,
@@ -215,7 +214,7 @@ def _validate_api_params(  # noqa: C901
         )
 
     wrap_score = False
-    if isinstance(model, (PipelineCreator, list)):
+    if isinstance(model, PipelineCreator | list):
         logger.debug(
             "Generating pipeline from PipelineCreator or list of them"
         )
@@ -278,7 +277,7 @@ def _validate_api_params(  # noqa: C901
             wrap_score = True
         problem_type = model[0].problem_type
 
-    elif not isinstance(model, (str, BaseEstimator)):
+    elif not isinstance(model, str | BaseEstimator):
         raise_error(
             "Model has to be a PipelineCreator, a string or a "
             "scikit-learn compatible model."
@@ -409,23 +408,23 @@ def _check_configure_joblib_backend() -> None:
 def run_cross_validation(
     X: list[str],  # noqa: N803
     y: str,
-    model: Union[str, PipelineCreator, BaseEstimator, list[PipelineCreator]],
+    model: str | PipelineCreator | BaseEstimator | list[PipelineCreator],
     data: pd.DataFrame,
-    X_types: Optional[dict] = None,  # noqa: N803
-    problem_type: Optional[str] = None,
-    preprocess: Union[None, str, list[str]] = None,
-    return_estimator: Optional[str] = None,
+    X_types: dict | None = None,  # noqa: N803
+    problem_type: str | None = None,
+    preprocess: None | str | list[str] = None,
+    return_estimator: str | None = None,
     return_inspector: bool = False,
     return_train_score: bool = False,
-    cv: Optional[CVLike] = None,
-    groups: Optional[str] = None,
-    scoring: Union[str, list[str], None] = None,
-    pos_labels: Union[str, list[str], None] = None,
-    model_params: Optional[dict] = None,
-    search_params: Optional[dict] = None,
-    seed: Optional[int] = None,
-    n_jobs: Optional[int] = None,
-    verbose: Optional[int] = 0,
+    cv: CVLike | None = None,
+    groups: str | None = None,
+    scoring: str | list[str] | None = None,
+    pos_labels: str | list[str] | None = None,
+    model_params: dict | None = None,
+    search_params: dict | None = None,
+    seed: int | None = None,
+    n_jobs: int | None = None,
+    verbose: int | None = 0,
 ):
     """Run cross validation and score.
 
@@ -706,17 +705,17 @@ def run_cross_validation(
 def run_fit(
     X: list[str],  # noqa: N803
     y: str,
-    model: Union[str, PipelineCreator, BaseEstimator, list[PipelineCreator]],
+    model: str | PipelineCreator | BaseEstimator | list[PipelineCreator],
     data: pd.DataFrame,
-    X_types: Optional[dict] = None,  # noqa: N803
-    problem_type: Optional[str] = None,
-    preprocess: Union[None, str, list[str]] = None,
-    groups: Optional[str] = None,
-    pos_labels: Union[str, list[str], None] = None,
-    model_params: Optional[dict] = None,
-    search_params: Optional[dict] = None,
-    seed: Optional[int] = None,
-    verbose: Optional[int] = 0,
+    X_types: dict | None = None,  # noqa: N803
+    problem_type: str | None = None,
+    preprocess: None | str | list[str] = None,
+    groups: str | None = None,
+    pos_labels: str | list[str] | None = None,
+    model_params: dict | None = None,
+    search_params: dict | None = None,
+    seed: int | None = None,
+    verbose: int | None = 0,
 ):
     """Fit the model on all the data.
 

{julearn-0.3.6.dev15 → julearn-0.3.6.dev33}/julearn/base/__init__.py

@@ -9,7 +9,6 @@ from .column_types import (
     get_column_type,
     make_type_selector,
     ColumnTypes,
-    ColumnTypesLike,
     ensure_column_types,
 )