julearn 0.3.6.dev17__tar.gz → 0.3.6.dev42__tar.gz

{julearn-0.3.6.dev17 → julearn-0.3.6.dev42}/.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

{julearn-0.3.6.dev17 → julearn-0.3.6.dev42}/.github/workflows/ci.yml

@@ -21,27 +21,32 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - '3.9'
-          - '3.10'
-          - '3.11'
           - '3.12'
           - '3.13'
+          - '3.14'
 
     steps:
     - uses: actions/checkout@v6
+
     - uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
     - name: Install Python dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install tox tox-gh-actions
+        uv sync --locked --extra dev
+        uv pip install tox-gh-actions
+
     - name: Test with tox
       run: |
-        tox
+        uv run tox
+
     - 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.dev17 → julearn-0.3.6.dev42}/.github/workflows/docs-preview.yml

@@ -24,15 +24,20 @@ jobs:
         fetch-depth: 0
     - uses: actions/setup-python@v6
       with:
-          python-version: "3.x"
+        python-version-file: "pyproject.toml"
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
     - name: Install Python dependencies
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install -e .[docs,viz]
+        uv sync --locked --extra docs
+
     - name: Test build docs
       run: |
-        BUILDDIR=_build/main make -C docs/ local
+        uv run make -C docs/ local
+
     - uses: rossjrw/pr-preview-action@v1
       with:
-        source-dir: docs/_build/main
+        source-dir: docs/_build/dev
       if: github.event_name == 'pull_request'

{julearn-0.3.6.dev17 → julearn-0.3.6.dev42}/.github/workflows/docs.yml

@@ -18,14 +18,19 @@ jobs:
       with:
         # require all of history to see all tagged versions' docs
         fetch-depth: 0
-    - uses: actions/setup-python@v6
+
+    - name: Set up Python
+      uses: actions/setup-python@v6
       with:
-        python-version: "3.x"
+        python-version-file: "pyproject.toml"
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
     - name: Install Python dependencies
       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
+        uv sync --locked --extra docs
+
     - 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
@@ -33,10 +38,11 @@ jobs:
       with:
           ref: gh-pages
           path: docs/_build
+
     - name: Build docs
-      # Use the args we normally pass to sphinx-build, but run sphinx-multiversion
+      # Use the args we normally pass to sphinx-build, but run sphinx-polyversion
       run: |
-        make -C docs/ html
+        uv run make -C docs/ html
         touch docs/_build/.nojekyll
         cp docs/redirect.html docs/_build/index.html
     - uses: peaceiris/actions-gh-pages@v4

{julearn-0.3.6.dev17 → julearn-0.3.6.dev42}/.github/workflows/lint.yml

@@ -11,12 +11,14 @@ jobs:
       - uses: actions/checkout@v6
       - uses: actions/setup-python@v6
         with:
-          python-version: "3.x"
+          python-version-file: "pyproject.toml"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
       - name: Install Python dependencies
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox "ruff>=0.1.0"
+          uv sync --locked --extra dev
       - name: Run ruff
-        run: ruff check --output-format=github .
+        run: uv run ruff check --output-format=github .
       - name: Run codespell
-        run: tox -e codespell
+        run: uv run tox -e codespell

{julearn-0.3.6.dev17 → julearn-0.3.6.dev42}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: julearn
-Version: 0.3.6.dev17
+Version: 0.3.6.dev42
 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>
@@ -18,38 +18,36 @@ 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"
 Provides-Extra: dev
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: towncrier; extra == "dev"
-Provides-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: ruff<0.16.0,>=0.15.14; extra == "dev"
+Requires-Dist: towncrier>=25.8.0; extra == "dev"
+Provides-Extra: sphinx
+Requires-Dist: furo>=2025.7.19; extra == "sphinx"
+Requires-Dist: numpydoc>=1.9.0; extra == "sphinx"
+Requires-Dist: seaborn<0.14.0,>=0.13.0; extra == "sphinx"
+Requires-Dist: setuptools-scm<11.0.0,>=10.0.0; extra == "sphinx"
+Requires-Dist: sphinx<10.0.0,>=8.2.3; extra == "sphinx"
+Requires-Dist: sphinx-copybutton>=0.5.2; extra == "sphinx"
+Requires-Dist: sphinx-gallery>=0.21.0; extra == "sphinx"
+Requires-Dist: sphinx-autodoc-typehints>=3.6.1; extra == "sphinx"
+Requires-Dist: sphinx-polyversion>=2.0.0; extra == "sphinx"
+Requires-Dist: sphinxcontrib-towncrier>=0.5.0a0; extra == "sphinx"
+Requires-Dist: towncrier>=25.8.0; extra == "sphinx"
 Provides-Extra: deslib
 Requires-Dist: deslib<0.4.0,>=0.3.5; extra == "deslib"
 Provides-Extra: viz
@@ -57,10 +55,12 @@ 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: docs
+Requires-Dist: julearn[optuna,skopt,sphinx,viz]; extra == "docs"
 Provides-Extra: all
 Requires-Dist: julearn[optuna,skopt,viz]; extra == "all"
 Dynamic: license-file

{julearn-0.3.6.dev17 → julearn-0.3.6.dev42}/docs/Makefile

@@ -3,34 +3,40 @@
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?="-W" "-E"
-SPHINXBUILD   ?= sphinx-multiversion
+SPHINXBUILD   = sphinx-build
+POLYBUILD     = sphinx-polyversion
 SOURCEDIR     = .
-BUILDDIR      ?= _build
+BUILDDIR      ?= docs/_build
+SPHINXOPTS    ?= -E -v
+
 
 # Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) --help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) --help "$(SOURCEDIR)" "$(BUILDDIR)" $(O)
 
-.PHONY: help Makefile clean local news _build_local _html
+.PHONY: help Makefile clean cleanall local _build_local _html
 
 clean:
-	rm -rf $(BUILDDIR)/*
+	rm -rf $(BUILDDIR)/main
 	rm -rf auto_examples/
 	rm -rf api/generated/
 
+cleanall: clean
+	rm -rf $(BUILDDIR)/*
+
 # For local build
 local:
 	make _build_local; STATUS=$$?; exit $$STATUS
 
 _build_local:
-	sphinx-build "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+# 	$(POLYBUILD) ./poly.py -vv -l -o NO_PATCH=True -o OUTPUT_DIR="$(BUILDDIR)" -o SOURCE_DIR="$(SOURCEDIR)" -o TAG_REGEX="^$$"
+	$(SPHINXBUILD) "$(SOURCEDIR)" _build/dev $(SPHINXOPTS) $(O)
 
 html:
 	make _html; STATUS=$$?; exit $$STATUS
 
 _html:
-	$(SPHINXBUILD) "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS)
+	$(POLYBUILD) ./poly.py -vv -o OUTPUT_DIR="$(BUILDDIR)" -o SOURCE_DIR="$(SOURCEDIR)"
 
 # 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.dev42/docs/_static/css/version_selector.css

@@ -0,0 +1,126 @@
+/* Furo-native version selector styles.
+   Uses furo CSS variables for full light/dark mode compatibility. */
+
+/* ── Sidebar version selector ────────────────────────────────────────────── */
+
+#version-selector {
+    border-top: 1px solid var(--color-sidebar-search-border);
+    padding-top: calc(var(--sidebar-item-spacing-vertical) / 2);
+}
+
+/* Remove default browser <details> marker */
+.version-details > summary {
+    list-style: none;
+}
+.version-details > summary::-webkit-details-marker {
+    display: none;
+}
+
+/* Summary row: looks like a furo sidebar caption */
+.version-summary {
+    cursor: pointer;
+    display: flex;
+    align-items: center;
+    gap: 0.4em;
+    padding: var(--sidebar-item-spacing-vertical)
+        var(--sidebar-item-spacing-horizontal);
+    font-size: var(--font-size--small--2);
+    font-weight: bold;
+    text-transform: uppercase;
+    letter-spacing: 1px;
+    color: var(--color-sidebar-caption-text);
+    user-select: none;
+}
+
+.version-summary:hover {
+    background-color: var(--color-sidebar-item-background--hover);
+}
+
+/* Chevron: points right when closed, down when open */
+.version-summary::after {
+    content: "▶";
+    font-size: 0.6em;
+    margin-left: auto;
+    transition: transform 0.15s ease;
+    color: var(--color-sidebar-caption-text);
+}
+
+.version-details[open] > .version-summary::after {
+    transform: rotate(90deg);
+}
+
+/* Colored status dot */
+.version-status-dot {
+    width: 8px;
+    height: 8px;
+    border-radius: 50%;
+    display: inline-block;
+    flex-shrink: 0;
+}
+
+.version-status-dot--latest { background-color: #28a745; }
+.version-status-dot--old    { background-color: #dc3545; }
+.version-status-dot--dev    { background-color: #e67e00; }
+
+/* Version list */
+.version-details ul {
+    margin: 0;
+    padding: 0;
+    list-style: none;
+}
+
+.version-details .toctree-l1 > a {
+    display: block;
+    padding: var(--sidebar-item-spacing-vertical)
+        var(--sidebar-item-spacing-horizontal);
+    color: var(--color-sidebar-link-text);
+    font-size: var(--sidebar-item-font-size);
+    text-decoration: none;
+}
+
+.version-details .toctree-l1 > a:hover {
+    background-color: var(--color-sidebar-item-background--hover);
+    color: var(--color-sidebar-link-text--top-level);
+}
+
+.version-details .toctree-l1.current > a {
+    background-color: var(--color-sidebar-item-background--current, transparent);
+    color: var(--color-sidebar-link-text--top-level);
+    font-weight: bold;
+}
+
+.version-details .toctree-l1 > a em {
+    font-size: 0.85em;
+    opacity: 0.75;
+}
+
+/* ── Version banner (toc-drawer / right sidebar) ─────────────────────────── */
+
+.version-banner {
+    padding: 0.6rem 0.75rem;
+    margin: 0.75rem 0.5rem 0;
+    border-radius: 0.2rem;
+    border-left: 3px solid;
+    font-size: var(--font-size--small--2);
+    line-height: 1.4;
+}
+
+.version-banner a {
+    font-weight: bold;
+    color: inherit;
+}
+
+.version-banner--latest {
+    background-color: rgba(40, 167, 69, 0.12);
+    border-left-color: #28a745;
+}
+
+.version-banner--old {
+    background-color: rgba(220, 53, 69, 0.12);
+    border-left-color: #dc3545;
+}
+
+.version-banner--dev {
+    background-color: rgba(230, 126, 0, 0.12);
+    border-left-color: #e67e00;
+}

julearn-0.3.6.dev42/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.dev42/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.dev42/docs/_templates/versions.html

@@ -0,0 +1,11 @@
+{# Furo-native version selector.
+   This placeholder is rendered by Sphinx at build time.
+   poly.py replaces it with the full multi-version list when patching. #}
+<div id="version-selector" class="sidebar-tree version-selector">
+  <details class="version-details" open>
+    <summary class="version-summary">
+      <span class="version-status-dot version-status-dot--latest"></span>
+      <span class="caption-text">Version</span>
+    </summary>
+  </details>
+</div>

{julearn-0.3.6.dev17 → julearn-0.3.6.dev42}/docs/api/base.rst

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

{julearn-0.3.6.dev17 → julearn-0.3.6.dev42}/docs/api/model_selection.rst

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

{julearn-0.3.6.dev17 → julearn-0.3.6.dev42}/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.dev42/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.dev42/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`_