Port examples to sphinx_gallery #170

PicoCentauri · 2023-03-25T09:41:56Z

Fixes #167

As already stated in the issue this will allow easier maintance and gives these nice gallery view:

Also i fixed some warnings when generating the docs.

PicoCentauri · 2023-03-25T11:35:24Z

Somebody can help me with the linter? I ran black locally but still got an error in the ci...

EDIT: Should be fixed. My local version of black was not up to date.

PicoCentauri · 2023-03-27T09:47:28Z

I just saw that we can even use jupyterlite allowing running the examples in the browser. Should we try this?

rosecers

Overall this looks nice, but I caught a few conversion artifacts here and there. I have two other issues that should be ameliorated before merge --

Ordering of the gallery -- we previously had the examples in a specific order, can we preserve this for the gallery?
Sidebar contains all sub-headers, and should not.

I've built the docs at https://scikit-matter.readthedocs.io/en/sphinx_gallery/index.html if you'd like to see.

rosecers · 2023-03-27T19:48:02Z

examples/FeatureSelection-WHODataset.py

+
+# %%
+#
+# Scale and Center the Features and Targets


We've lost the relative importance of each header, can you fix it so that they are stacked like this?

Feature Selection on the WHO Dataset

Load the Dataset

Scale and Center the Features and Targets

Provide an estimated target for the feature selector

Compute the Selections for Each Selector Type

PCov-CUR

PCov-FPS

CUR

FPS

(For Comparison) Recursive Feature Addition

Plot our Results

Should be done in the latest version.

rosecers · 2023-03-27T19:48:25Z

examples/FeatureSelection-WHODataset.py

+
+# %%
+#
+# (For Comparison) Recurisive Feature Addition


Suggested change

# (For Comparison) Recurisive Feature Addition

# (For Comparison) Recursive Feature Addition

rosecers · 2023-03-27T19:51:57Z

examples/OrthogonalRegressionNonAnalytic.py

+
+plt.legend(bbox_to_anchor=(1, 1), loc="upper left")
+
+plt.show()


This figure is cut off in the build.

Should be done.

Now it looks all messed up

Ohh this looks nice 🤣.

Lets see how this looks in the new commit.

rosecers · 2023-03-27T19:52:37Z

examples/OrthogonalRegressionNonAnalytic.py

+)
+ax_wo_orth.set_xlabel("scaling in z direction")
+ax_wo_orth.legend(loc="upper right", bbox_to_anchor=(0.7, -0.2))
+plt.show()


Same with this one...

Should be done.

Lets see how this looks in the new commit.

examples/PCovR-WHODataset.py

rosecers · 2023-03-27T20:00:17Z

examples/PlotLFRE.py

+
+# %%
+#
+# load features


Same issue as last example

rosecers · 2023-03-27T20:00:56Z

examples/PlotPointwiseGFRE.py

+
+# %%
+#
+# load features


same as last two

rosecers · 2023-03-27T20:01:16Z

examples/PlotPointwiseGFRE.py

+#       \exp(-\gamma \|\mathbf{x}-\mathbf{x}'\|^2),\quad \gamma\in\mathbb{R}_+
+#
+# The projected RKHS features are computed using the eigendecomposition of the
+# positive-definite kernel matrix :math:`K``


prime mark is misplaced

skmatter/datasets/descr/nice_dataset.rst

docs/requirements.txt

rosecers · 2023-03-27T20:05:20Z

I just saw that we can even use jupyterlite allowing running the examples in the browser. Should we try this?

Feel free to put in an issue, I think that'd be great!

PicoCentauri · 2023-03-27T21:14:35Z

Thanks for the feedback. I will see what I can do.

Manual ordering always works.

PicoCentauri · 2023-03-28T06:21:41Z

I've built the docs at https://scikit-matter.readthedocs.io/en/sphinx_gallery/index.html if you'd like to see.

Thanks but you don't have to enable this manually the next time. In #161 we enabled that RTD builds the docs for each PR. For this one it is here: https://scikit-matter--170.org.readthedocs.build/en/170/. I will add a GH action in #172 for a direct link.

victorprincipe · 2023-03-30T15:56:29Z

Just went through the examples and made some typo/formatting fixes. Rest looks good.

PicoCentauri · 2023-03-30T16:10:31Z

Thanks @victorprincipe. All of them are super useful changes. I fixed another tiny formatting thing.

ceriottm · 2023-04-03T21:13:52Z

I don't see the nice gallery on the auto-built readthedocs page at https://scikit-matter--170.org.readthedocs.build/en/170/tutorials.html#

PicoCentauri · 2023-04-03T21:40:27Z

I don't see the nice gallery on the auto-built readthedocs page at https://scikit-matter--170.org.readthedocs.build/en/170/tutorials.html#

I had to remove the gallery view in order to keep the same structure as it was before. Sorry, if we want to have the gallery back I can look later how we can order it. But I think it will be not super easy to maintain the section titles.

ceriottm · 2023-04-04T20:01:07Z

Bummer. The gallery was really pretty.

PicoCentauri · 2023-04-04T21:25:13Z

Yes, I was also a fan of it.

rosecers · 2023-04-04T21:26:14Z

Is there no way to preserve order with the gallery?

…

On Tue, Apr 4, 2023, 16:25 Philip Loche ***@***.***> wrote: Yes, I was also a fan of it. — Reply to this email directly, view it on GitHub <#170 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALKVP3TXKCKCVRUIC72N6J3W7SGUJANCNFSM6AAAAAAWHNV6P4> . You are receiving this because your review was requested.Message ID: ***@***.***>

PicoCentauri · 2023-04-04T21:31:17Z

The only way I see is that we do subfolders for each current section and then we use sub-gallery-order.

PicoCentauri · 2023-04-05T15:48:39Z

Galleries are back. Let me know @rosecers and @ceriottm if this fine for you.

ceriottm · 2023-04-06T20:46:15Z

I like it a lot - it's also better to have separate pages, and I was finding the list of sub-headings of the notebooks rather confusing. IMO this is good to go.

rosecers

Looks good! Please squash before merging.

PicoCentauri · 2023-04-06T21:23:31Z

Thanks for your feedback! I can help you with rebasing your PR @ceriottm

PicoCentauri force-pushed the sphinx_gallery branch 3 times, most recently from 58332eb to b3c2039 Compare March 25, 2023 10:01

PicoCentauri force-pushed the sphinx_gallery branch 8 times, most recently from d836803 to 5a5ad37 Compare March 27, 2023 09:45

PicoCentauri requested review from rosecers and agoscinski March 27, 2023 09:47

PicoCentauri mentioned this pull request Mar 27, 2023

PCovR-WHODataset takes super long to compute #175

Closed

rosecers requested changes Mar 27, 2023

View reviewed changes

PicoCentauri force-pushed the sphinx_gallery branch 2 times, most recently from 6e6b9a8 to 9cf0239 Compare March 28, 2023 07:32

PicoCentauri mentioned this pull request Mar 28, 2023

Add an example of GCH for molecular materials #171

Merged

PicoCentauri force-pushed the sphinx_gallery branch 3 times, most recently from 8bb6c36 to 81a67bd Compare March 29, 2023 11:14

PicoCentauri force-pushed the sphinx_gallery branch 2 times, most recently from f1aa078 to 6834940 Compare March 30, 2023 16:09

PicoCentauri added 5 commits March 30, 2023 21:26

Port examples to sphinx_gallery

ed33dc3

Port examples to sphinx_gallery

6ce874b

Reintroduced ordering + fixing conversion typos

733da20

Fix rendering of plots and reverted comments

439aa06

Remove superflous markers

081b402

PicoCentauri force-pushed the sphinx_gallery branch from 6834940 to 26a68fc Compare March 30, 2023 19:28

Fixed typos and formatting problems.

ef1d0b7

PicoCentauri force-pushed the sphinx_gallery branch from 26a68fc to ef1d0b7 Compare March 30, 2023 19:31

PicoCentauri added 2 commits March 30, 2023 21:38

Extend linting to examples

9780a1c

Remove old notebook tests

4e9a98c

Merge branch 'main' into sphinx_gallery

5b73516

Add optional install for examples

7854bea

PicoCentauri force-pushed the sphinx_gallery branch from 34d4553 to 044248e Compare April 5, 2023 16:27

Bring back gallery

26d2332

PicoCentauri force-pushed the sphinx_gallery branch from 044248e to 26d2332 Compare April 5, 2023 16:39

rosecers self-requested a review April 6, 2023 20:54

rosecers approved these changes Apr 6, 2023

View reviewed changes

PicoCentauri merged commit 89073a9 into main Apr 6, 2023

PicoCentauri deleted the sphinx_gallery branch April 6, 2023 21:22

	# (For Comparison) Recurisive Feature Addition
	# (For Comparison) Recursive Feature Addition


		plt.legend(bbox_to_anchor=(1, 1), loc="upper left")

		plt.show()

Port examples to sphinx_gallery #170

Port examples to sphinx_gallery #170

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