DOC Add links to decomposition examples in docstrings and user guide by mmhamdy · Pull Request #26932 · scikit-learn/scikit-learn

mmhamdy · 2023-07-29T01:02:41Z

Reference Issues/PRs

What does this implement/fix? Explain your changes.

PR to add links to the examples mentioned in issue 26927 for the decomposition section. Links to examples were added to the user guide and API docs of the decomposition section:

examples/decomposition:

plot_faces_decomposition.py
plot_ica_blind_source_separation.py
plot_ica_vs_pca.py
plot_image_denoising.py
plot_incremental_pca.py
plot_kernel_pca.py
plot_pca_3d.py
plot_pca_iris.py
plot_pca_vs_fa_model_selection.py
plot_pca_vs_lda.py
plot_sparse_coding.py
plot_varimax_fa.py

other examples that are related to decomposition but found in different sections that were linked here:

examples/applications:

plot_digits_denoising.py
plot_topics_extraction_with_nmf_lda.py

examples/compose:

plot_compare_reduction.py

examples/release_highlights:

plot_release_highlights_1_1_0.py

github-actions · 2023-07-29T01:04:10Z

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adrinjalali · 2023-07-31T08:46:12Z

Having too many examples in the same PR makes it hard to review, could you please reduce this to PCA only?

mmhamdy · 2023-07-31T11:17:01Z

Linked examples are now limited to PCA only. Examples included are:

plot_faces_decomposition.py (The only example that has a demonstration for sparse PCA)
plot_incremental_pca.py
plot_kernel_pca.py
plot_pca_3d.py
plot_pca_iris.py
plot_pca_vs_fa_model_selection.py
plot_pca_vs_lda.py

adrinjalali · 2023-08-02T13:52:05Z

doc/modules/decomposition.rst


 .. topic:: Examples:

+    * :ref:`sphx_glr_auto_examples_decomposition_plot_pca_3d.py`


@glemaitre should we remove this? or merge it with plot_pca_iris?

ping @glemaitre

Indeed. This example is not super compiling as-is. I assume that we could do something similar on the iris dataset.

At the end, I am not a big fan of the 3d visualization. I think that having several 2-d visualization will be more helpful.

@mmhamdy do you need help removing this example? You can do git rm path/to/file to remove a file from the repo. And then remove all mentions of it from the codebase.

adrinjalali · 2023-08-02T13:58:10Z

sklearn/decomposition/_incremental_pca.py

+    For an examples of usage see:
+    - :ref:`sphx_glr_auto_examples_decomposition_plot_incremental_pca.py`


This example needs some improvements.

Like a more informative description?

sklearn/decomposition/_kernel_pca.py

adrinjalali · 2023-08-02T14:02:25Z

sklearn/decomposition/_pca.py

+    For examples of usage see:
+    - :ref:`sphx_glr_auto_examples_decomposition_plot_pca_iris.py`
+    - :ref:`sphx_glr_auto_examples_decomposition_plot_pca_3d.py`
+    - :ref:`sphx_glr_auto_examples_decomposition_plot_pca_vs_lda.py`
+    - :ref:`sphx_glr_auto_examples_decomposition_plot_pca_vs_fa_model_selection.py`


I think we should choose one really, instead of listing them all.

In this case, I think plot_pca_iris.py is a good and simple one.

PCA on iris would make sense. I think that we could improve this example greatly and merging with others.

adrinjalali · 2023-08-02T14:03:41Z

sklearn/decomposition/_sparse_pca.py

+    For an example of usage see:
+    - :ref:`sphx_glr_auto_examples_decomposition_plot_faces_decomposition.py`


This example is a good comparison between methods, not a usage example.

That's right. I can change "example of usage" to "example comparing sparse PCA to PCA"

Co-authored-by: Adrin Jalali <adrin.jalali@gmail.com>

mmhamdy · 2023-12-18T14:45:02Z

Hello @adrinjalali, so sorry for the delayed response. I've removed the 3d example and addressed the other comments.

adrinjalali

I'm happy with this as is, and do other improvements in other PRs. WDYT @glemaitre

glemaitre

LGTM. In order to avoid a 404 in the future, I made a redirection on the example that we removed. I also fixes a couple of rendering and typo issue.

glemaitre · 2024-01-10T14:10:05Z

Actually we should fix the unsupervised_learning.rst tutorial that uses some figures from the 3d examples. I will look at how we can rephrase this example with the iris example.

glemaitre · 2024-01-11T10:06:19Z

Enabling auto-merge after checking the artefacts.

…cikit-learn#26932) Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com> Co-authored-by: Adrin Jalali <adrin.jalali@gmail.com>

…26932) Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com> Co-authored-by: Adrin Jalali <adrin.jalali@gmail.com>

…cikit-learn#26932) Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com> Co-authored-by: Adrin Jalali <adrin.jalali@gmail.com>

DOC Add links to decomposition examples in docstrings and userguide

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github-actions bot added module:decomposition Documentation labels Jul 29, 2023

mmhamdy mentioned this pull request Jul 29, 2023

Add links to examples from the docstrings and user guides #26927

Closed

mmhamdy added 2 commits July 31, 2023 14:03

limit linked examples to only PCA

32bc538

remove linked example in dict learning

e31aa0b

Merge branch 'main' into main

cb73b06

adrinjalali reviewed Aug 2, 2023

View reviewed changes

glemaitre self-requested a review September 29, 2023 20:24

glemaitre and others added 4 commits September 29, 2023 22:26

Merge branch 'main' into main

b93dacb

remove 3d example and edit references

fa6330c

Merge branch 'main' of https://github.com/mmhamdy/scikit-learn into main

5aaaf06

Update sklearn/decomposition/_kernel_pca.py

c7d7d2e

Co-authored-by: Adrin Jalali <adrin.jalali@gmail.com>

adrinjalali approved these changes Jan 4, 2024

View reviewed changes

fixes

67270f3

glemaitre approved these changes Jan 10, 2024

View reviewed changes

glemaitre added 2 commits January 10, 2024 15:50

FIX rework the tutorial by creating figure.

89332d9

Merge remote-tracking branch 'origin' into pr/mmhamdy/26932

3e5337c

glemaitre enabled auto-merge (squash) January 11, 2024 10:06

glemaitre merged commit 55f4a3a into scikit-learn:main Jan 11, 2024

jeremiedbb pushed a commit that referenced this pull request Jan 17, 2024

DOC Add links to decomposition examples in docstrings and user guide (#…

2cc998c

…26932) Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com> Co-authored-by: Adrin Jalali <adrin.jalali@gmail.com>


		.. topic:: Examples:

		* :ref:`sphx_glr_auto_examples_decomposition_plot_pca_3d.py`

		For an examples of usage see:
		- :ref:`sphx_glr_auto_examples_decomposition_plot_incremental_pca.py`

		For an example of usage see:
		- :ref:`sphx_glr_auto_examples_decomposition_plot_faces_decomposition.py`

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mmhamdy commented Dec 18, 2023

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