julearn 0.3.2.dev80__tar.gz → 0.3.3__tar.gz

{julearn-0.3.2.dev80 → julearn-0.3.3}/.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-ast
       - id: check-docstring-first
@@ -17,27 +17,27 @@ repos:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.12.2
+    rev: v0.17
     hooks:
       - id: validate-pyproject
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.4.2
     hooks:
       - id: black
         exclude: ^(docs/|examples/)
         args: [--check]
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.267
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
     hooks:
       - id: ruff
         exclude: ^(__init__.py)
-        args: [--format, grouped, --show-fixes]
+        args: [--output-format, grouped, --show-fixes]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.2.6
     hooks:
       - id: codespell
         exclude: ^(.github/|docs/)
-        args: [--config, tox.ini]
+        args: [--toml, pyproject.toml]
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:

{julearn-0.3.2.dev80 → julearn-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: julearn
-Version: 0.3.2.dev80
+Version: 0.3.3
 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>
@@ -62,6 +62,7 @@ Requires-Dist: julearn[optuna,skopt,viz]; extra == "all"
 ![PyPI](https://img.shields.io/pypi/v/julearn?style=flat-square)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/julearn?style=flat-square)
 ![PyPI - Wheel](https://img.shields.io/pypi/wheel/julearn?style=flat-square)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/julearn/badges/version.svg)](https://anaconda.org/conda-forge/julearn)
 ![GitHub](https://img.shields.io/github/license/juaml/julearn?style=flat-square)
 ![Codecov](https://img.shields.io/codecov/c/github/juaml/julearn?style=flat-square)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
@@ -83,6 +84,12 @@ Use `pip` to install from PyPI like so:
 pip install julearn
 ```
 
+You can also install via `conda`, like so:
+
+```
+conda install -c conda-forge julearn
+```
+
 ## Licensing
 
 julearn is released under the AGPL v3 license:

{julearn-0.3.2.dev80 → julearn-0.3.3}/README.md

@@ -3,6 +3,7 @@
 ![PyPI](https://img.shields.io/pypi/v/julearn?style=flat-square)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/julearn?style=flat-square)
 ![PyPI - Wheel](https://img.shields.io/pypi/wheel/julearn?style=flat-square)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/julearn/badges/version.svg)](https://anaconda.org/conda-forge/julearn)
 ![GitHub](https://img.shields.io/github/license/juaml/julearn?style=flat-square)
 ![Codecov](https://img.shields.io/codecov/c/github/juaml/julearn?style=flat-square)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
@@ -24,6 +25,12 @@ Use `pip` to install from PyPI like so:
 pip install julearn
 ```
 
+You can also install via `conda`, like so:
+
+```
+conda install -c conda-forge julearn
+```
+
 ## Licensing
 
 julearn is released under the AGPL v3 license:

{julearn-0.3.2.dev80 → julearn-0.3.3}/docs/changes/contributors.inc

@@ -4,3 +4,4 @@
 .. _Shammi More: https://www.fz-juelich.de/SharedDocs/Personen/INM/INM-7/EN/More_s.html?nn=654218
 .. _Leonard Sasse: https://github.com/LeSasse
 .. _Synchon Mandal: https://github.com/synchon
+.. _Dante Culaciati: https://github.com/Dante-010

{julearn-0.3.2.dev80 → julearn-0.3.3}/docs/getting_started.rst

@@ -12,17 +12,17 @@ packages:
 
 * ``numpy>=1.24,<1.27``
 * ``pandas>=1.5.0,<2.2``
-* ``scikit-learn>=1.2,<1.4``
+* ``scikit-learn>=1.2.0,<1.5.0``
 * ``statsmodels>=0.13,<0.15``
 
 Running the examples require:
 
 * ``seaborn>=0.12.2,<0.13``
 * ``bokeh>=3.0.0``
-* ``panel>=1.0.0b1``
-* ``param>=1.11.0``
+* ``panel>=1.3.0``
+* ``param>=2.0.0``
 
-Depending on the installation method (e.g. the `pip install` option below),
+Depending on the installation method (e.g. the ``pip install`` option below),
 these packages might be installed automatically. It is nevertheless good to be
 aware of these dependencies as installing ``julearn`` might lead to changes in
 these packages.
@@ -47,17 +47,23 @@ Installing
     developer version until we release the next stable ``julearn`` version.
 
 
-Depending on your aimed usage of ``julearn`` you have two different options
+Depending on your aimed usage of ``julearn`` you have different options
 how to install ``julearn``:
 
 #. Install the *latest release*: Likely most suitable for most
    **end users**. This is done by installing the latest stable release from
-   PyPI.
+   PyPI:
 
    .. code-block:: bash
 
        pip install -U julearn
 
+   or via ``conda`` like so:
+
+   .. code-block:: bash
+
+     conda install -c conda-forge julearn
+
 #. Install the *latest pre-relase*: This version will have the
    **latest updates**. However, it is still under development and not yet
    officially released. Some features might still change before the next stable
@@ -90,4 +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.
 * ``all``: Install all optional functional dependencies (except ``deslib``).

{julearn-0.3.2.dev80 → julearn-0.3.3}/docs/index.rst

@@ -86,14 +86,14 @@ Indices and tables
 Indices and tables
 ==================
 
-If you use julearn in a scientific publication, please use the following 
+If you use julearn in a scientific publication, please use the following
 reference
 
-    Hamdan, Sami, Shammi More, Leonard Sasse, Vera Komeyer, 
-    Kaustubh R. Patil, and Federico Raimondo. ‘Julearn: 
-    An Easy-to-Use Library for Leakage-Free Evaluation and Inspection of 
-    ML Models’. arXiv, 19 October 2023. 
+    Hamdan, Sami, Shammi More, Leonard Sasse, Vera Komeyer,
+    Kaustubh R. Patil, and Federico Raimondo. ‘Julearn:
+    An Easy-to-Use Library for Leakage-Free Evaluation and Inspection of
+    ML Models’. arXiv, 19 October 2023.
     https://doi.org/10.48550/arXiv.2310.12568.
 
-Since julearn is also heavily reliant on scikit-learn, please also cite 
+Since julearn is also heavily reliant on scikit-learn, please also cite
 them: https://scikit-learn.org/stable/about.html#citing-scikit-learn

{julearn-0.3.2.dev80 → julearn-0.3.3}/docs/links.inc

@@ -41,4 +41,5 @@
 
 .. _`DESlib`: https://github.com/scikit-learn-contrib/DESlib
 .. _`scikit-optimize`: https://scikit-optimize.readthedocs.io/en/stable/
-.. _`Optuna`: https://optuna.org
+.. _`Optuna`: https://optuna.org
+.. _`optuna_integration`: https://github.com/optuna/optuna-integration

{julearn-0.3.2.dev80 → julearn-0.3.3}/docs/what_really_need_know/cross_validation.rst

@@ -16,7 +16,7 @@ Cross-validation - The fundamentals
 This means that in order to evaluate if a model is *successful* in learning,
 we need to evaluate if it is able to predict new data. Thus, we need to have
 separate data for learning and testing. At the same time, data is a valuable
-resource in machine learning and one wants to use it as efficeint as possible.
+resource in machine learning and one wants to use it as efficiently as possible.
 
 To solve this, we use *cross validation*. The core idea is that we want to
 train (also named *fit*) a model on a subset of our data and evaluate it on a

{julearn-0.3.2.dev80 → julearn-0.3.3}/docs/whats_new.rst

@@ -8,6 +8,24 @@ What's new
 
 .. towncrier release notes start
 
+Julearn 0.3.3 (2024-05-16)
+--------------------------
+
+Bugfixes
+^^^^^^^^
+
+- Fix ``OptunaSearchCV`` issue
+  (https://github.com/optuna/optuna-integration/issues/118) with an internal
+  implementation until the issue is fixed in ``optuna-integration`` by `Fede
+  Raimondo`_ (:gh:`265`)
+
+
+Improved Documentation
+^^^^^^^^^^^^^^^^^^^^^^
+
+- Fixed a typo in cross validation by `Dante Culaciati`_ (:gh:`258`)
+
+
 Julearn 0.3.2 (2024-05-03)
 --------------------------
 

{julearn-0.3.2.dev80 → julearn-0.3.3}/examples/99_docs/run_hyperparameters_docs.py

@@ -253,7 +253,7 @@ pprint(model_tuned.best_params_)
 # hyperparameters values.
 #
 # Other searchers that ``julearn`` provides are the
-# :class:`~sklearn.model_selection.RandomizedSearchCV`, 
+# :class:`~sklearn.model_selection.RandomizedSearchCV`,
 # :class:`~skopt.BayesSearchCV` and
 # :class:`~optuna_integration.sklearn.OptunaSearchCV`.
 #
@@ -383,14 +383,14 @@ pprint(model_tuned.best_params_)
 # searcher. However, the optuna searcher behaviour is controlled by a
 # :class:`~optuna.study.Study` object. This object can be passed to the
 # searcher using the ``study`` parameter in the ``search_params`` dictionary.
-# 
+#
 # .. important::
 #    The optuna searcher requires that all the hyperparameters are specified
-#    as distributions, even the categorical ones. 
+#    as distributions, even the categorical ones.
 #
 # We first modify the pipeline creator so the ``select_k`` parameter is
 # specified as a distribution. We exemplarily use a categorical distribution
-# for the ``class_weight`` hyperparameter, trying the ``"balanced"`` and 
+# for the ``class_weight`` hyperparameter, trying the ``"balanced"`` and
 # ``None`` values.
 
 creator = PipelineCreator(problem_type="classification")
@@ -445,12 +445,12 @@ pprint(model_tuned.best_params_)
 # searcher, bayesian searcher and optuna searcher. The distributions are
 # either specified toolbox-specific method or  a tuple convention with the
 # following format: ``(low, high, distribution)`` where the distribution can
-# be either ``"log-uniform"`` or ``"uniform"`` or 
+# be either ``"log-uniform"`` or ``"uniform"`` or
 # ``(a, b, c, d, ..., "categorical")`` where ``a``, ``b``, ``c``, ``d``, etc.
 # are the possible categorical values for the hyperparameter.
 #
-# For example, we can specify the ``C`` and ``gamma`` hyperparameters of the 
-# :class:`~sklearn.svm.SVC` as  log-uniform distributions, while keeping 
+# For example, we can specify the ``C`` and ``gamma`` hyperparameters of the
+# :class:`~sklearn.svm.SVC` as  log-uniform distributions, while keeping
 # the ``with_mean`` parameter of the
 # :class:`~sklearn.preprocessing.StandardScaler` as a categorical parameter
 # with two options.
@@ -469,7 +469,7 @@ print(creator)
 # While this will work for any of the ``random``, ``bayes`` or ``optuna``
 # searcher options, it is important to note that both ``bayes`` and ``optuna``
 # searchers accept further parameters to specify distributions. For example,
-# the ``bayes`` searcher distributions are defined using the 
+# the ``bayes`` searcher distributions are defined using the
 # :class:`~skopt.space.space.Categorical`, :class:`~skopt.space.space.Integer`
 # and :class:`~skopt.space.space.Real`.
 #
@@ -493,7 +493,7 @@ print(creator)
 #
 #
 # For example, we can define a uniform distribution from 0.5 to 0.9 with a 0.05
-# step for the ``n_components`` of a :class:`~sklearn.decomposition.PCA` 
+# step for the ``n_components`` of a :class:`~sklearn.decomposition.PCA`
 # transformer, while keeping a log-uniform distribution for the ``C`` and
 # ``gamma`` hyperparameters of the :class:`~sklearn.svm.SVC` model.
 from optuna.distributions import FloatDistribution

{julearn-0.3.2.dev80 → julearn-0.3.3}/ignore_words.txt

@@ -5,4 +5,4 @@ fpr
 master
 whis
 jupyter
-arange
+arange

{julearn-0.3.2.dev80 → julearn-0.3.3}/julearn/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.3.2.dev80'
-__version_tuple__ = version_tuple = (0, 3, 2, 'dev80')
+__version__ = version = '0.3.3'
+__version_tuple__ = version_tuple = (0, 3, 3)

{julearn-0.3.2.dev80 → julearn-0.3.3}/julearn/conftest.py

@@ -286,6 +286,7 @@ def bayes_search_params(request: FixtureRequest) -> Optional[Dict]:
 
     return request.param
 
+
 @fixture(
     params=[
         {"kind": "optuna", "n_trials": 10, "cv": 3},
@@ -310,6 +311,7 @@ def optuna_search_params(request: FixtureRequest) -> Optional[Dict]:
 
     return request.param
 
+
 _tuning_params = {
     "zscore": {"with_mean": [True, False]},
     "pca": {"n_components": [0.2, 0.7]},