Use :doi: and :arxiv: directives for references in the documentation (Issue #21088) #22603

JSchuerz · 2022-02-24T15:28:18Z

Reference Issues/PRs

What does this implement/fix? Explain your changes.

Towards #21088 I changed " https://arxiv.org/... " to " :arxiv:... " and " https://doi.org/... " to " :doi:... in the remaining files, wherethis has not yet been fixed.

Any other comments?

cmarmo

Thank you @JSchuerz for your pull request.
There is a lint error that should be fixed in order to allow the checks to run.

sklearn/semi_supervised/_self_training.py:122:89: E501 line too long (90 > 88 characters)

sklearn/decomposition/_pca.py

sklearn/metrics/_classification.py

doc/modules/semi_supervised.rst

Co-authored-by: Chiara Marmo <[email protected]>

sklearn/decomposition/_pca.py

cmarmo · 2022-02-27T00:08:37Z

Thanks @JSchuerz, all checks are green now.
For consistency with the previous introduced arxiv directives you might want to write:

doi:`My title, year, and authors. <doi-number-and-ref>`

without underscore at the end.

sklearn/linear_model/tests/test_logistic.py

cmarmo

Thanks @JSchuerz! I have some last comments.
Also, do you mind fixing the three DOI links in SpectralEmbedding?

scikit-learn/sklearn/manifold/_spectral_embedding.py

Lines 486 to 497 in 7a2a0f7

    
               - A Tutorial on Spectral Clustering, 2007 
        
                 Ulrike von Luxburg 
        
                 http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.165.9323 
        
               - On Spectral Clustering: Analysis and an algorithm, 2001 
        
                 Andrew Y. Ng, Michael I. Jordan, Yair Weiss 
        
                 http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.19.8100 
        
               - Normalized cuts and image segmentation, 2000 
        
                 Jianbo Shi, Jitendra Malik 
        
                 http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.160.2324

Almost done!

sklearn/manifold/_spectral_embedding.py

examples/inspection/plot_permutation_importance.py

Co-authored-by: Chiara Marmo <[email protected]>

benchmarks/bench_covertype.py

doc/modules/clustering.rst

cmarmo

Hi @JSchuerz, please do not add too much files to this PR as this makes hard to review it.
I have made some comments, but a number of links are not working now because apparently some reviews use the parameter DOI but they are not really registering it in the standardized system, so the explicit links works, but not the sphinx DOI directive.
May I ask you to choose only some submodules to fix and check their rendering to verify if the links are correct? Then reduce your PR to them? Thank you very much for your understanding.

benchmarks/bench_covertype.py

doc/modules/biclustering.rst

doc/modules/clustering.rst

doc/modules/manifold.rst

Co-authored-by: Chiara Marmo <[email protected]>

cmarmo

Thanks a lot @JSchuerz for your work. Indeed looking for Digital Identification Numbers on line is less straigthforward than I thought! :)
For your information you can check the DOIs at the official DOI page using the DOI resolver.

Please revert the following files, where no :doi: directive has been added

sklearn/manifold/_locally_linear.py
doc/modules/naive_bayes.rst

To do that you can run the command:

git checkout main <file-to-revert>

doc/modules/clustering.rst

sklearn/metrics/_classification.py

sklearn/manifold/_spectral_embedding.py

doc/modules/sgd.rst

JSchuerz · 2022-03-01T00:35:27Z

Thank you for referring me to the official DOI page. I checked all doi's and fixed them where necessary.
I also checked the rst files and made sure that the part of the reference which belongs to the link is consistent with the rest on the page.
If it is ok with you, I will not separate the PR?

JSchuerz · 2022-03-01T00:41:38Z

doc/modules/clustering.rst

@@ -563,7 +563,7 @@ graph, and SpectralClustering is initialized with `affinity='precomputed'`::

 * :arxiv:`"Preconditioned Spectral Clustering for Stochastic
   Block Partition Streaming Graph Challenge"
-   <1309.0238>`
+   <1708.07481>`


The arxiv number was indeed wrong.

cmarmo

If it is ok with you, I will not separate the PR?

After all your work (and mine! ;) ) let's keep it in one PR.

There is one check failing. You can fix it in synchronizing with main, as described here

Thanks for your work!

JSchuerz · 2022-03-01T11:54:43Z

All done! Thank you for reviewing my work!!!!! :)
I found two more working doi's and fixed them.

Interestingly for http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.19.8100 and http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.70.382 'official' doi's can be found here https://dl.acm.org/doi/10.5555/2980539.2980649 and here https://dl.acm.org/doi/10.5555/2976456.2976656 respectively. However, they do not work for the doi resolver. Any ideas how to proceed here?

If not I believe Issue #21088 is now completely fixed.

cmarmo · 2022-03-01T19:00:06Z

Interestingly for http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.19.8100 and http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.70.382 'official' doi's can be found here https://dl.acm.org/doi/10.5555/2980539.2980649 and here https://dl.acm.org/doi/10.5555/2976456.2976656 respectively. However, they do not work for the doi resolver. Any ideas how to proceed here?

If the DOIs are not resolved by doi.org they will not be linked by the :doi: directive, so please, keep the current links as is.

Thanks for your work, now we have to wait for a core-dev approval. Please be patient. Thanks!

jeremiedbb

just a couple remarks, otherwise LGTM. Thanks @JSchuerz and @cmarmo !

jeremiedbb · 2022-03-02T10:08:16Z

doc/modules/semi_supervised.rst

+       Computational Linguistics, Stroudsburg, PA, USA, 189-196.
+       :doi:`doi:10.3115/981658.981684 <10.3115/981658.981684>`


It would be nicer to put the link on the title of the paper

.. [1] :doi:`"Unsupervised word sense disambiguation rivaling supervised methods" <10.3115/981658.981684>` David Yarowsky, Proceedings of the 33rd annual meeting on Association for Computational Linguistics (ACL '95). Association for Computational Linguistics, Stroudsburg, PA, USA, 189-196.

examples/inspection/plot_permutation_importance.py

Co-authored-by: Jérémie du Boisberranger <[email protected]>

JSchuerz · 2022-03-02T13:43:13Z

All done!

JSchuerz and others added 4 commits Feb 23, 2022

:doi: and :arxiv: directives for references in the documentation

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:doi: and :arxiv: directives for references in the documentation

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Merge branch 'scikit-learn:main' into main

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Merge branch 'scikit-learn:main' into main

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cmarmo reviewed Feb 26, 2022

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JSchuerz and others added 12 commits Feb 26, 2022

Update sklearn/decomposition/_pca.py

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Co-authored-by: Chiara Marmo <[email protected]>

Update sklearn/metrics/_classification.py

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Co-authored-by: Chiara Marmo <[email protected]>

Update sklearn/metrics/_classification.py

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Co-authored-by: Chiara Marmo <[email protected]>

Merge branch 'scikit-learn:main' into main

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

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JSchuerz reviewed Feb 26, 2022

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Merge branch 'scikit-learn:main' into main

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Putting :doi: to beginning of reference

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minor changes citations

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Update examples/inspection/plot_permutation_importance.py

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Co-authored-by: Chiara Marmo <[email protected]>

Update sklearn/manifold/_spectral_embedding.py

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Co-authored-by: Chiara Marmo <[email protected]>

Also fixing <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=...>

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minor corrections

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Update doc/modules/clustering.rst

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Co-authored-by: Chiara Marmo <[email protected]>

Update doc/modules/biclustering.rst

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Co-authored-by: Chiara Marmo <[email protected]>

Update doc/modules/biclustering.rst

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wrong doi's

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cmarmo reviewed Feb 28, 2022

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JSchuerz added 3 commits Mar 1, 2022

Fixing doi's and sphinx links

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cmarmo approved these changes Mar 1, 2022

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Merge branch 'scikit-learn:main' into main

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Two more doi's found

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minor change

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jeremiedbb added Documentation and removed Waiting for Reviewer labels Mar 2, 2022

JSchuerz and others added 6 commits Mar 2, 2022

Merge branch 'main' into main

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Update examples/inspection/plot_permutation_importance.py

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Co-authored-by: Jérémie du Boisberranger <[email protected]>

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

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Merge branch 'scikit-learn:main' into main

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

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glemaitre merged commit 4a52eb6 into scikit-learn:main Mar 2, 2022
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Use :doi: and :arxiv: directives for references in the documentation (Issue #21088) #22603

Use :doi: and :arxiv: directives for references in the documentation (Issue #21088) #22603

JSchuerz commented Feb 24, 2022

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JSchuerz commented Mar 2, 2022

	- A Tutorial on Spectral Clustering, 2007
	Ulrike von Luxburg
	http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.165.9323

	- On Spectral Clustering: Analysis and an algorithm, 2001
	Andrew Y. Ng, Michael I. Jordan, Yair Weiss
	http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.19.8100

	- Normalized cuts and image segmentation, 2000
	Jianbo Shi, Jitendra Malik
	http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.160.2324

		Computational Linguistics, Stroudsburg, PA, USA, 189-196.
		:doi:`doi:10.3115/981658.981684 <10.3115/981658.981684>`

scikit-learn / scikit-learn Public

Use :doi: and :arxiv: directives for references in the documentation (Issue #21088) #22603

Use :doi: and :arxiv: directives for references in the documentation (Issue #21088) #22603

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JSchuerz commented Feb 24, 2022

Reference Issues/PRs

What does this implement/fix? Explain your changes.

Any other comments?

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