julearn 0.3.1.dev50__tar.gz → 0.3.1.dev58__tar.gz

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/.gitignore

@@ -134,4 +134,4 @@ cython_debug/
 # Versioning
 julearn/_version.py
 scratch/
-docs/whats_new.rst
+docs/whats_new.rst

julearn-0.3.1.dev58/.pre-commit-config.yaml

@@ -0,0 +1,48 @@
+ci:
+  autofix_prs: false
+  autoupdate_commit_msg: "chore: bump pre-commit repositories"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-ast
+      - id: check-docstring-first
+      - id: check-executables-have-shebangs
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: check-toml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.12.2
+    hooks:
+      - id: validate-pyproject
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+        exclude: ^(docs/|examples/)
+        args: [--check]
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.267
+    hooks:
+      - id: ruff
+        exclude: ^(__init__.py)
+        args: [--format, grouped, --show-fixes]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        exclude: ^(.github/|docs/)
+        args: [--config, tox.ini]
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-no-eval
+      - id: python-no-log-warn
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/AUTHORS.rst

@@ -2,4 +2,4 @@ Original Authors
 ===============
 * Sami Hamdan `@samihamdan <https://github.com/samihamdan>`_.
 * Kaustubh Patil `@kaurao <https://github.com/kaurao>`_.
-* Federico Raimondo `@fraimondo <https://github.com/fraimondo>`_.
+* Federico Raimondo `@fraimondo <https://github.com/fraimondo>`_.

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/LICENSE.md

@@ -648,4 +648,4 @@ specific requirements.
 You should also get your employer (if you work as a programmer) or school,
 if any, to sign a “copyright disclaimer” for the program, if necessary.
 For more information on this, and how to apply and follow the GNU AGPL, see
-&lt;<http://www.gnu.org/licenses/>&gt;.
+&lt;<http://www.gnu.org/licenses/>&gt;.

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: julearn
-Version: 0.3.1.dev50
+Version: 0.3.1.dev58
 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>
@@ -32,6 +32,8 @@ License-File: AUTHORS.rst
 
 # julearn
 
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+
 The Forschungszentrum Jülich Machine Learning Library
 
 Check our full documentation here: https://juaml.github.io/julearn/index.html
@@ -64,4 +66,3 @@ We still do not have a publication that you can use to cite julearn in your
 manuscript. However, julearn realies heavily on scikit-learn.
 
 Please cite scikit-learn: https://scikit-learn.org/stable/about.html#citing-scikit-learn
-

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/README.md

@@ -1,5 +1,7 @@
 # julearn
 
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
+
 The Forschungszentrum Jülich Machine Learning Library
 
 Check our full documentation here: https://juaml.github.io/julearn/index.html
@@ -32,4 +34,3 @@ We still do not have a publication that you can use to cite julearn in your
 manuscript. However, julearn realies heavily on scikit-learn.
 
 Please cite scikit-learn: https://scikit-learn.org/stable/about.html#citing-scikit-learn
-

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/codecov.yml

@@ -36,4 +36,4 @@ flag_management:
           threshold: 1%
         - type: patch
           target: 95%
-          threshold: 1%
+          threshold: 1%

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/_static/css/custom.css

@@ -18,4 +18,4 @@
 
 .sphx-glr-download {
   visibility: hidden;
-}
+}

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/_static/js/custom.js

@@ -11,4 +11,4 @@ for (i = 0; i < coll.length; i++) {
       content.style.display = "block";
     }
   });
-}
+}

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/_templates/class.rst

@@ -23,4 +23,4 @@
 
 .. raw:: html
 
-    <div style='clear:both'></div>
+    <div style='clear:both'></div>

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/_templates/versions.html

@@ -24,4 +24,4 @@
     {%- endif %}
   </div>
 </div>
-{%- endif %}
+{%- endif %}

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/api/base.rst

@@ -33,4 +33,4 @@ Functions
     change_column_type
     get_column_type
     make_type_selector
-    ensure_column_types
+    ensure_column_types

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/api/index.rst

@@ -19,4 +19,4 @@ API Reference
    utils.rst
    prepare.rst
    stats.rst
-   viz.rst
+   viz.rst

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/api/inspect.rst

@@ -27,4 +27,4 @@ Functions
    :toctree: generated/
    :template: function.rst
 
-    preprocess
+    preprocess

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/api/main.rst

@@ -14,4 +14,4 @@ Functions
    :toctree: generated/
    :template: function.rst
 
-    run_cross_validation
+    run_cross_validation

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/api/model_selection.rst

@@ -35,4 +35,4 @@ Functions
     get_searcher
     list_searchers
     register_searcher
-    reset_searcher_register
+    reset_searcher_register

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/api/models.rst

@@ -41,4 +41,4 @@ Classes
    :toctree: generated/
    :template: class.rst
 
-    DynamicSelection
+    DynamicSelection

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/api/pipeline.rst

@@ -18,4 +18,4 @@ Classes
     PipelineCreator
     TargetPipelineCreator
     pipeline.JuTargetPipeline
-    pipeline.pipeline_creator.Step
+    pipeline.pipeline_creator.Step

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/api/prepare.rst

@@ -13,6 +13,6 @@ Functions
 .. autosummary::
    :toctree: generated/
    :template: function.rst
-  
+
     prepare_input_data
     check_consistency

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/api/scoring.rst

@@ -37,4 +37,4 @@ Functions
    :template: function.rst
 
     r_corr
-    r2_corr
+    r2_corr

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/api/transformers.rst

@@ -30,7 +30,7 @@ Functions
 .. autosummary::
    :toctree: generated/
    :template: function.rst
-  
+
     list_transformers
     get_transformer
     register_transformer
@@ -65,9 +65,8 @@ Functions
 .. autosummary::
    :toctree: generated/
    :template: function.rst
-  
+
     get_target_transformer
     list_target_transformers
     register_target_transformer
     reset_target_transformer_register
-

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/available_pipeline_steps.rst

@@ -6,21 +6,21 @@ Overview of available Pipeline Steps
 ====================================
 
 The following is a list of all available steps that can be used to create
-a pipeline by name. The overview is sorted based on the type of the step: 
+a pipeline by name. The overview is sorted based on the type of the step:
 :ref:`available_transformers` or :ref:`available_models`.
 
-The column 'Name (str)' refers to the string-name of 
+The column 'Name (str)' refers to the string-name of
 the respective step, i.e. how it should be specified when passed to e.g. the
-``PipelineCreator``. The column 'Description' gives a short 
-description of what the step is doing. The column 'Class' either indicates the 
-underlying `scikit-learn`_ class of the respective pipeline-step together with 
-a link to the class in the `scikit-learn`_ documentation (follow the link to 
-see the valid parameters) or indicates the class in 
-the Julearn code, so one can have a closer look at it in Julearn's 
+``PipelineCreator``. The column 'Description' gives a short
+description of what the step is doing. The column 'Class' either indicates the
+underlying `scikit-learn`_ class of the respective pipeline-step together with
+a link to the class in the `scikit-learn`_ documentation (follow the link to
+see the valid parameters) or indicates the class in
+the Julearn code, so one can have a closer look at it in Julearn's
 :ref:`api`.
 
-For feature transformations the :ref:`available_transformers` have to be used 
-with the ``PipelineCreator`` and for target transformation with the 
+For feature transformations the :ref:`available_transformers` have to be used
+with the ``PipelineCreator`` and for target transformation with the
 ``TargetPipelineCreator``.
 
 .. _available_transformers:
@@ -109,8 +109,8 @@ DataFrame operations
    * - ``confound_removal``
      - Removing confounds from features,
        by subtracting the prediction of each feature given all confounds.
-       By default this is equal to "independently regressing out 
-       the confounds from the features" 
+       By default this is equal to "independently regressing out
+       the confounds from the features"
      - :class:`.ConfoundRemover`
    * - ``drop_columns``
      - Drop columns from the dataframe
@@ -137,7 +137,7 @@ Decomposition
    * - ``pca``
      - Principal Component Analysis
      - :class:`~sklearn.decomposition.PCA`
-  
+
 Custom
 ~~~~~~
 
@@ -149,7 +149,7 @@ Custom
      - Description
      - Class
    * - ``cbpm``
-     - Connectome-based Predictive Modeling (CBPM) 
+     - Connectome-based Predictive Modeling (CBPM)
      - :class:`.CBPM`
 
 .. _available_models:
@@ -215,7 +215,7 @@ Ensemble
      - Y
      - Y
    * - ``gradientboost``
-     - Gradient Boosting 
+     - Gradient Boosting
      - :class:`~sklearn.ensemble.GradientBoostingClassifier` and :class:`~sklearn.ensemble.GradientBoostingRegressor`
      - Y
      - Y
@@ -329,7 +329,7 @@ Naive Bayes
      - Y
      - N
    * - ``nb_gaussian``
-     - Gaussian Naive Bayes 
+     - Gaussian Naive Bayes
      - :class:`~sklearn.naive_bayes.GaussianNB`
      - Y
      - Y

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/changes/latest.inc

@@ -1,5 +1,5 @@
 .. NOTE: we are now using links to highlight new functions and classes.
-   Please follow the examples below like 
+   Please follow the examples below like
    :func:`julearn.api.run_cross_validation`, so the
    whats_new page will have a link to the function/class documentation.
 
@@ -26,5 +26,3 @@ Bugs
 
 API changes
 ~~~~~~~~~~~
-
-

julearn-0.3.1.dev58/docs/changes/newsfragments/.gitignore

@@ -0,0 +1 @@
+!.gitignore

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/changes/newsfragments/151.bugfix

@@ -1 +1 @@
-Add ``BaseEstimator`` to ``ConfoundRemoval`` for Target by `Sami Hamdan`_
+Add ``BaseEstimator`` to ``ConfoundRemoval`` for Target by `Sami Hamdan`_

julearn-0.3.1.dev58/docs/changes/newsfragments/170.enh

@@ -0,0 +1 @@
+Make CBPM use sum by default by `Sami Hamdan`_

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/changes/newsfragments/232.misc

@@ -1 +1 @@
-Improve ``codespell`` support and fix typos in documentation by `Synchon Mandal`_
+Improve ``codespell`` support and fix typos in documentation by `Synchon Mandal`_

julearn-0.3.1.dev58/docs/changes/newsfragments/233.misc

@@ -0,0 +1 @@
+Adopt ``pre-commit`` for adding and managing git pre-commit hooks by `Synchon Mandal`_

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/changes/newsfragments/47.feature

@@ -1 +1 @@
-Add support for multiple grids in hyperparameter tuning by `Fede Raimondo`_
+Add support for multiple grids in hyperparameter tuning by `Fede Raimondo`_

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/changes/v0.2.5.inc

@@ -1,5 +1,5 @@
 .. NOTE: we are now using links to highlight new functions and classes.
-   Please follow the examples below like 
+   Please follow the examples below like
    :func:`julearn.api.run_cross_validation`, so the
    whats_new page will have a link to the function/class documentation.
 
@@ -21,7 +21,7 @@ Enhancements
 
 - Add information on updating the *What's new* section before releasing (by `Fede Raimondo`_).
 
-- Update docs to make it more uniform (by `Kaustubh Patil`_). 
+- Update docs to make it more uniform (by `Kaustubh Patil`_).
 
 - Refactor scoring to allow for registering and callable scorers (by `Sami Hamdan`_).
 
@@ -30,7 +30,7 @@ Enhancements
 - Add user facing `create_pipeline` function (by `Sami Hamdan`_).
 
 - Update default behavior of setting inner cv according to scikit-learn instead of using outer cv as default (by `Sami Hamdan`_).
-             
+
 - Add tests and more algorithms to `DynamicSelection` (by `Sami Hamdan`_ and `Shammi More`_).
 
 - Add CV schemes for stratifying based on the grouping variables, useful for regression problems. Check :class:`.ContinuousStratifiedGroupKFold` and :class:`.RepeatedContinuousStratifiedGroupKFold` (by `Fede Raimondo`_ and `Shammi More`_).
@@ -64,7 +64,7 @@ Bugs
 
 - Fix Bug of showing Warnings when using confound removal (:gh:`152` by `Sami Hamdan`_).
 
-- Fix Bug registered scorer not working in dictionary for scoring  ( by `Sami Hamdan`_). 
+- Fix Bug registered scorer not working in dictionary for scoring  ( by `Sami Hamdan`_).
 
 
 API changes
@@ -76,4 +76,3 @@ API changes
 - Inner `cv` needs to be provided using `search_params`. Deprecating `cv` in `model_params` (:gh:`146`  by `Sami Hamdan`_).
 
 - Add `n_jobs` and `verbose` to `run_cross_validation` (by `Sami Hamdan`_).
-

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/contributing.rst

@@ -31,6 +31,12 @@ Setting up the local development environment
 
    Now you can make your changes locally.
 
+#. Make sure you install git pre-commit hooks like so:
+
+   .. code-block:: bash
+
+       pre-commit install
+
 #. When making changes locally, it is helpful to ``git commit`` your work
    regularly. On one hand to save your work and on the other hand, the smaller
    the steps, the easier it is to review your work later. Please use `semantic
@@ -42,6 +48,14 @@ Setting up the local development environment
        git add .
        git commit -m "<prefix>: <summary of changes>"
 
+   In case, you want to commit some WIP (work-in-progress) code, please indicate
+   that in the commit message and use the flag ``--no-verify`` with
+   ``git commit`` like so:
+
+   .. code-block:: bash
+
+       git commit --no-verify -m "WIP: <summary of changes>"
+
 #. When you're done making changes, check that your changes pass our test suite.
    This is all included with ``tox``.
 

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/examples.rst

@@ -6,7 +6,7 @@ The following are a set of examples that use julearn.
 .. this needs to be done manually to avoid TOC issues
 .. see https://github.com/sphinx-gallery/sphinx-gallery/pull/944/
 
-.. toctree:: 
+.. toctree::
     :maxdepth: 2
     :caption: Contents:
 

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/index.rst

@@ -18,13 +18,13 @@ Welcome to julearn's documentation!
 What is Julearn?
 ----------------
 
-At the Applied Machine Learning (`AML`_) group, as part of the Institute of 
+At the Applied Machine Learning (`AML`_) group, as part of the Institute of
 Neuroscience and Medicine - Brain and Behaviour (`INM-7`_), we thought that
-using ML in research could be simpler. 
+using ML in research could be simpler.
 
 In the same way as `seaborn`_ provides an abstraction of `matplotlib`_'s
-functionality aiming for powerful data visualization with minor coding, we 
 built julearn on top of `scikit-learn`_.
+functionality aiming for powerful data visualization with minor coding, we
 
 Julearn is a library that provides users with the possibility of easy 
 testing ML models directly from `pandas`_ dataframes, while keeping the

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/links.inc

@@ -40,5 +40,3 @@
 
 
 .. _`DESlib`: https://github.com/scikit-learn-contrib/DESlib
-
-

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/redirect.html

@@ -6,4 +6,4 @@
     <meta http-equiv="refresh" content="0; url=./main/index.html">
     <link rel="canonical" href="https://juaml.github.io/julearn/main/index.html">
   </head>
-</html>
+</html>

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/selected_deeper_topics/CBPM.rst

@@ -8,4 +8,3 @@
 .. include:: ../auto_examples/99_docs/run_cbpm_docs.rst
    :start-after: sphx-glr-example-title
    :end-before: _sphx_glr_download_
-

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/selected_deeper_topics/confound_removal.rst

@@ -8,4 +8,3 @@
 .. include:: ../auto_examples/99_docs/run_confound_removal_docs.rst
    :start-after: sphx-glr-example-title
    :end-before: _sphx_glr_download_
-

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/selected_deeper_topics/cross_validation_splitter.rst

@@ -7,4 +7,4 @@
 
 .. include:: ../auto_examples/99_docs/run_cv_splitters_docs.rst
    :start-after: sphx-glr-example-title
-   :end-before: _sphx_glr_download_
+   :end-before: _sphx_glr_download_

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/selected_deeper_topics/hyperparameter_tuning.rst

@@ -7,4 +7,4 @@
 
 .. include:: ../auto_examples/99_docs/run_hyperparameters_docs.rst
    :start-after: sphx-glr-example-title
-   :end-before: _sphx_glr_download_
+   :end-before: _sphx_glr_download_

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/selected_deeper_topics/index.rst

@@ -1,5 +1,5 @@
 .. include:: ../links.inc
-    
+
 .. _selected_deeper_topics:
 
 Selected deeper topics

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/selected_deeper_topics/model_inspect.rst

@@ -8,4 +8,3 @@
 .. include:: ../auto_examples/99_docs/run_model_inspection_docs.rst
    :start-after: sphx-glr-example-title
    :end-before: _sphx_glr_download_
-

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/what_really_need_know/cross_validation.rst

@@ -86,4 +86,4 @@ See :ref:`model_evaluation_usage` for further details on the model evaluation.
 
       .. [#3] https://www.sciencedirect.com/science/article/pii/S1053811917305311
 
-      .. [#4] https://scikit-learn.org/stable/modules/cross_validation.html
+      .. [#4] https://scikit-learn.org/stable/modules/cross_validation.html

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/what_really_need_know/data.rst

@@ -6,4 +6,4 @@
 
 .. include:: ../auto_examples/99_docs/run_data_docs.rst
    :start-after: sphx-glr-example-title
-   :end-before: _sphx_glr_download_
+   :end-before: _sphx_glr_download_

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/what_really_need_know/model_comparison.rst

@@ -7,4 +7,4 @@
 
 .. include:: ../auto_examples/99_docs/run_model_comparison_docs.rst
    :start-after: sphx-glr-example-title
-   :end-before: _sphx_glr_download_
+   :end-before: _sphx_glr_download_

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/what_really_need_know/model_evaluation.rst

@@ -8,4 +8,3 @@
 .. include:: ../auto_examples/99_docs/run_model_evaluation_docs.rst
    :start-after: sphx-glr-example-title
    :end-before: _sphx_glr_download_
-

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/docs/what_really_need_know/pipeline.rst

@@ -7,4 +7,4 @@
 
 .. include:: ../auto_examples/99_docs/run_pipeline_docs.rst
    :start-after: sphx-glr-example-title
-   :end-before: _sphx_glr_download_
+   :end-before: _sphx_glr_download_

julearn-0.3.1.dev58/examples/01_model_comparison/README.rst

@@ -0,0 +1,4 @@
+Model Comparison
+================
+
+Examples that perform model comparisons.

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/examples/01_model_comparison/plot_simple_model_comparison.py

@@ -140,7 +140,7 @@ scores3.to_csv("/tmp/scores3.csv")
 
 from julearn.viz import plot_scores
 panel = plot_scores(scores1, scores2, scores3)
-# panel.show() 
+# panel.show()
 # uncomment the previous line show the plot
 # read the documentation for more information
 #  https://panel.holoviz.org/getting_started/build_app.html#deploying-panels
@@ -163,4 +163,4 @@ panel = plot_scores(scores1, scores2, scores3)
 #    scores2 = pd.read_csv("/tmp/scores2.csv")
 #    scores3 = pd.read_csv("/tmp/scores3.csv")
 #    panel = plot_scores(scores1, scores2, scores3, width=600)
-#    show(panel.get_root())
+#    show(panel.get_root())

julearn-0.3.1.dev58/examples/02_inspection/README.rst

@@ -0,0 +1,4 @@
+Inspection
+==========
+
+Examples that demonstrate how to inspect the models.

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/examples/02_inspection/run_binary_inspect_folds.py

@@ -66,4 +66,4 @@ cv_predictions = inspector.folds.predict()
 print(cv_predictions)
 
 ###############################################################################
-inspector.folds[0].model
+inspector.folds[0].model

julearn-0.3.1.dev58/examples/03_complex_models/README.rst

@@ -0,0 +1,4 @@
+Complex Models
+==============
+
+Examples that show how to build complex models.

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/examples/03_complex_models/run_example_pca_featsets.py

@@ -65,8 +65,8 @@ X_types = {
 }
 
 ###############################################################################
-# Create a pipeline to process the data and the fit a model. We must specify 
-# how each X_type will be used. For example if in the last step we do not 
+# Create a pipeline to process the data and the fit a model. We must specify
+# how each X_type will be used. For example if in the last step we do not
 # specify `apply_to=['continuous', 'categorical']`, then the pipeline will not
 # know what to do with the categorical features.
 creator = PipelineCreator(problem_type="regression")

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/examples/04_confounds/run_return_confounds.py

@@ -83,7 +83,7 @@ scores, model = run_cross_validation(
 )
 
 ###############################################################################
-# We can use the `preprocess` method of the `inspect` module to inspect the 
+# We can use the `preprocess` method of the `inspect` module to inspect the
 # transformations steps of the returned estimator.
 # By providing a step name to the `until` argument of the
 # `preprocess` method we return the transformed X and y up to
@@ -148,7 +148,7 @@ print(len(model.steps[-1][1].model.coef_))
 
 ###############################################################################
 # Lastly, you can also use the confound as a normal feature after confound
-# removal. 
+# removal.
 creator = PipelineCreator(problem_type="regression", apply_to="continuous")
 creator.add("confound_removal", keep_confounds=True)
 creator.add("pca")

julearn-0.3.1.dev58/examples/99_docs/README.rst

@@ -0,0 +1,4 @@
+Documentation
+=============
+
+Examples that show sections of the documentation

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/examples/99_docs/run_cbpm_docs.py

@@ -34,7 +34,7 @@ feature aggregation. Leveraging julearn's PipelineCreator, one can therefore
 easily apply the "cbpm" transformer as a preprocessing step, and then apply any
 sklearn-compatible estimator for the model building part.
 
-For example, to build a simple CBPM workflow, you can create a pipeline and 
+For example, to build a simple CBPM workflow, you can create a pipeline and
 run a cross-validation as follows:
 """
 

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/examples/99_docs/run_confound_removal_docs.py

@@ -239,7 +239,7 @@ print(scores)
 #   .. [#3] He, Tong, et al., `"Deep neural networks and kernel regression \
 #      achieve comparable accuracies for functional connectivity prediction \
 #      of behavior and demographics" <https://www.sciencedirect.com/science/\
-#      article/pii/S1053811919308675>`_, NeuroImage, Volume 206, 1 February 
+#      article/pii/S1053811919308675>`_, NeuroImage, Volume 206, 1 February
 #      2020, 116276
 #
 #   .. [#4] More, Shammi, et al., `"Confound Removal and Normalization in \

{julearn-0.3.1.dev50 → julearn-0.3.1.dev58}/examples/99_docs/run_cv_splitters_docs.py

@@ -21,7 +21,7 @@ surprise.
 Another important argument is that we want to have a good estimate of the
 variance of our model. This is important because we want to know how much the
 performance of our model will change if we train it on a different dataset.
-So which CV splitter we should use? As much as we would like to have an answer
+So which CV splitter should we use? As much as we would like to have an answer
 to this question, it is impossible for many reasons. According to Bengio and
 Grandvalet [#1]_, it is simply not possible to have an unbiased estimate of
 the variance of the generalization error.