DOC Use :doi: and :arxiv: directives for references #21099

puhuk · 2021-09-21T15:22:56Z

To resolve issue #21088

Reference Issues/PRs

Fixes issue #21088

What does this implement/fix? Explain your changes.

To resolve issue #21088, correct references to use :doi: and :arxiv:

Any other comments?

To resolve issue scikit-learn#21088

ogrisel · 2021-09-23T12:45:22Z

doc/modules/kernel_approximation.rst

@@ -247,7 +247,7 @@ or store training examples.
      <https://www.robots.ox.ac.uk/~vgg/publications/2010/Sreekanth10/sreekanth10.pdf>`_
      Vempati, S. and Vedaldi, A. and Zisserman, A. and Jawahar, CV - 2010
    .. [PP2013] `"Fast and scalable polynomial kernels via explicit feature maps"
-      <https://doi.org/10.1145/2487575.2487591>`_
+      <:doi:`10.1145/2487575.2487591`>`_


Nesting backticks is invalid in restructured text format. See the rendered HTML page here:

https://153542-843222-gh.circle-artifacts.com/0/doc/modules/kernel_approximation.html

(you can access it via the ci/circleci: doc artifact entry of the continuous integration status report on the main github page of the PR).

Also, you can test the rendering of the website (without running all the examples) on your local machine with

cd doc EXAMPLES_PATTERN=disabled make html

see https://scikit-learn.org/dev/developers/contributing.html#documentation for the details and the list of dependencies.

Thanks for the feedback. Let me check and re-send the PR.

Note that I did the comment specifically for kernel_approximation but this is a general rule that applies for all the other links.

See the rendered HTML in the ci/circleci: doc artifact entry of the "checks" running on the PR.

doc/modules/kernel_approximation.rst

acse-srm3018 · 2021-09-27T18:19:11Z

Is this issue still open?
I want to take it!

puhuk · 2021-09-29T08:26:43Z

@ogrisel Could you review this PR :) Thanks in advance.

cmarmo

Thanks @puhuk. Please check how doi and arxiv directives should be used to correctly link to the references.

cmarmo · 2021-09-29T21:16:18Z

doc/about.rst

@@ -86,7 +86,7 @@ If you want to cite scikit-learn for its API or design, you may also want to con
 following paper:

  `API design for machine learning software: experiences from the scikit-learn
-  project <https://arxiv.org/abs/1309.0238>`_, Buitinck *et al.*, 2013.
+  project <:arxiv:`1309.0238`>`_, Buitinck *et al.*, 2013.


Suggested change

project <:arxiv:`1309.0238`>`_, Buitinck *et al.*, 2013.

project :arxiv:`1309.0238`, Buitinck *et al.*, 2013.

If you check the rendering of this pull request you see that the references are not displayed correctly. You might want to check scipy/#12858 to see how doi and arxiv directives should be used. My suggestion here is an example.

Thanks, let me check :)

cmarmo

Thanks @puhuk! The failing lint check is related to the doi_role.py file. scikit-learn recently adopted black formatting (see also the pull request checklist): the file needs to be reformatted with black doi_role.py.

cmarmo · 2021-10-06T18:12:45Z

doc/about.rst

+  API design for machine learning software: experiences from the scikit-learn
+  project, Buitinck *et al.*, 2013. :arxiv:`1309.0238`


I just realize that it is possible to give an explicit caption

scikit-learn/doc/sphinxext/doi_role.py

Lines 10 to 11 in fa7327b

You can also give an explicit caption, e.g.

:doi:`Basic local alignment search tool <10.1016/S0022-2836(05)80360-2>`.

Do you mind checking this solution that would be more consistent with other references?

Suggested change

API design for machine learning software: experiences from the scikit-learn

project, Buitinck *et al.*, 2013. :arxiv:`1309.0238`

:arxiv:`API design for machine learning software: experiences from the scikit-learn

project <1309.0238>`, Buitinck *et al.*, 2013.

Thanks!

@cmarmo Thanks for your advice! I reformatted and synced with other references.

Updated based on PR review

cmarmo

Thanks @puhuk! Almost there! It seems that some references went outside your radar.... :)
LGTM once they are fixed.

cmarmo · 2021-10-07T00:19:19Z

doc/modules/clustering.rst

@@ -1705,7 +1705,7 @@ cluster analysis.
 * Peter J. Rousseeuw (1987). "Silhouettes: a Graphical Aid to the
   Interpretation and Validation of Cluster Analysis". Computational
   and Applied Mathematics 20: 53–65.
-   `doi:10.1016/0377-0427(87)90125-7 <https://doi.org/10.1016/0377-0427(87)90125-7>`_.
+   :doi:`doi:10.1016/0377-0427(87)90125-7 <10.1016/0377-0427(87)90125-7>`


Do you mind adding an explicit caption here too? Thanks!

Sure, let me add :)

cmarmo · 2021-10-07T00:20:48Z

doc/modules/clustering.rst

@@ -1805,7 +1805,7 @@ number of points in cluster :math:`q`.
   `"A Dendrite Method for Cluster Analysis"
   <https://www.researchgate.net/publication/233096619_A_Dendrite_Method_for_Cluster_Analysis>`_.
   Communications in Statistics-theory and Methods 3: 1-27.
-   `doi:10.1080/03610927408827101 <https://doi.org/10.1080/03610927408827101>`_.
+   :doi:`doi:10.1080/03610927408827101 <10.1080/03610927408827101>`.


same as previous comment: the title of the article should be the text of the link.... there are some other similar cases in this file and in preprocessing.rst , with the doi directive.

puhuk · 2021-10-07T00:38:27Z

Thanks for quick feedback!
Let me check and update soon.

cmarmo

Thanks @puhuk! It seems to me that everything is good now.
Perhaps @lorentzenchr who opened the issue might want to have a look?

puhuk · 2021-10-07T23:50:42Z

@cmarmo Thanks for the review and your helps :)

@lorentzenchr If you have any feedback, please just let me know to reflect to this PR :)

jjerphan

Thank you, @puhuk.

This is a useful addition to the documentation setup.
Here are some minor suggestions.

jjerphan · 2021-10-08T06:50:44Z

doc/sphinxext/doi_role.py

+def doi_role(typ, rawtext, text, lineno, inliner, options={}, content=[]):
+    text = utils.unescape(text)
+    has_explicit_title, title, part = split_explicit_title(text)
+    full_url = "https://doi.org/" + part
+    if not has_explicit_title:
+        title = "DOI:" + part
+    pnode = nodes.reference(title, title, internal=False, refuri=full_url)
+    return [pnode], []
+
+
+def arxiv_role(typ, rawtext, text, lineno, inliner, options={}, content=[]):
+    text = utils.unescape(text)
+    has_explicit_title, title, part = split_explicit_title(text)
+    full_url = "https://arxiv.org/abs/" + part
+    if not has_explicit_title:
+        title = "arXiv:" + part
+    pnode = nodes.reference(title, title, internal=False, refuri=full_url)
+    return [pnode], []


Probably, those can be factorized together?

Maybe. Let me try and request review again.

jjerphan · 2021-10-08T06:52:29Z

doc/modules/permutation_importance.rst

+   .. [1] L. Breiman, :doi:`"Random Forests" <10.1023/A:1010933404324>`, Machine Learning, 45(1), 5-32,
+       2001.


For visual alignment.

Suggested change

.. [1] L. Breiman, :doi:`"Random Forests" <10.1023/A:1010933404324>`, Machine Learning, 45(1), 5-32,

2001.

.. [1] L. Breiman, :doi:`"Random Forests" <10.1023/A:1010933404324>`,

Machine Learning, 45(1), 5-32, 2001.

jjerphan · 2021-10-08T06:52:41Z

doc/modules/preprocessing.rst

+    * Perperoglou, A., Sauerbrei, W., Abrahamowicz, M. et al. :doi:`A review of
+      spline function procedures in R <10.1186/s12874-019-0666-3>`. BMC Med Res Methodol 19, 46 (2019).


Suggested change

* Perperoglou, A., Sauerbrei, W., Abrahamowicz, M. et al. :doi:`A review of

spline function procedures in R <10.1186/s12874-019-0666-3>`. BMC Med Res Methodol 19, 46 (2019).

* Perperoglou, A., Sauerbrei, W., Abrahamowicz, M. et al. :doi:`A review of

spline function procedures in R <10.1186/s12874-019-0666-3>`.

BMC Med Res Methodol 19, 46 (2019).

jjerphan · 2021-10-08T06:54:30Z

doc/modules/model_evaluation.rst

+  .. [Urbanowicz2015] Urbanowicz R.J.,  Moore, J.H. :doi:`ExSTraCS 2.0: description and evaluation of a scalable learning
+     classifier system <10.1007/s12065-015-0128-8>`, Evol. Intel. (2015) 8: 89.


Suggested change

.. [Urbanowicz2015] Urbanowicz R.J., Moore, J.H. :doi:`ExSTraCS 2.0: description and evaluation of a scalable learning

classifier system <10.1007/s12065-015-0128-8>`, Evol. Intel. (2015) 8: 89.

.. [Urbanowicz2015] Urbanowicz R.J., Moore, J.H. :doi:`ExSTraCS 2.0: description

and evaluation of a scalable learning classifier

system <10.1007/s12065-015-0128-8>`, Evol. Intel. (2015) 8: 89.

jjerphan · 2021-10-08T06:57:01Z

doc/modules/linear_model.rst

@@ -934,7 +934,7 @@ to warm-starting (see :term:`Glossary <warm_start>`).

    .. [6] Mark Schmidt, Nicolas Le Roux, and Francis Bach: `Minimizing Finite Sums with the Stochastic Average Gradient. <https://hal.inria.fr/hal-00860051/document>`_

-    .. [7] Aaron Defazio, Francis Bach, Simon Lacoste-Julien: `SAGA: A Fast Incremental Gradient Method With Support for Non-Strongly Convex Composite Objectives. <https://arxiv.org/abs/1407.0202>`_
+    .. [7] Aaron Defazio, Francis Bach, Simon Lacoste-Julien: :arxiv:`SAGA: A Fast Incremental Gradient Method With Support for Non-Strongly Convex Composite Objectives. <1407.0202>`


As this line gets modified, we can wrap it.

Suggested change

.. [7] Aaron Defazio, Francis Bach, Simon Lacoste-Julien: :arxiv:`SAGA: A Fast Incremental Gradient Method With Support for Non-Strongly Convex Composite Objectives. <1407.0202>`

.. [7] Aaron Defazio, Francis Bach, Simon Lacoste-Julien:

:arxiv:`SAGA: A Fast Incremental Gradient Method With Support for

Non-Strongly Convex Composite Objectives. <1407.0202>`

lorentzenchr · 2021-10-08T13:48:53Z

@cmarmo I won‘t have time.
@jjerphan Thanks for your review. If you approve, let us count it as +1 😏

jjerphan · 2021-10-11T06:05:47Z

doc/sphinxext/doi_role.py

+def reference_role(typ, rawtext, text, lineno, inliner, options={}, content=[]):
+    text = utils.unescape(text)
+    has_explicit_title, title, part = split_explicit_title(text)
+
+    if typ in ["arXiv", "arxiv"]:
+        full_url = "https://arxiv.org/abs/" + part
+        if not has_explicit_title:
+            title = "arXiv:" + part
+        pnode = nodes.reference(title, title, internal=False, refuri=full_url)
+        return [pnode], []
+
+    if typ in ["doi", "DOI"]:
+        full_url = "https://doi.org/" + part
+        if not has_explicit_title:
+            title = "DOI:" + part
+        pnode = nodes.reference(title, title, internal=False, refuri=full_url)
+        return [pnode], []


Can the logic be further simplified?

Suggested change

def reference_role(typ, rawtext, text, lineno, inliner, options={}, content=[]):

text = utils.unescape(text)

has_explicit_title, title, part = split_explicit_title(text)

if typ in ["arXiv", "arxiv"]:

full_url = "https://arxiv.org/abs/" + part

if not has_explicit_title:

title = "arXiv:" + part

pnode = nodes.reference(title, title, internal=False, refuri=full_url)

return [pnode], []

if typ in ["doi", "DOI"]:

full_url = "https://doi.org/" + part

if not has_explicit_title:

title = "DOI:" + part

pnode = nodes.reference(title, title, internal=False, refuri=full_url)

return [pnode], []

def reference_role(typ, rawtext, text, lineno, inliner, options={}, content=[]):

text = utils.unescape(text)

has_explicit_title, title, part = split_explicit_title(text)

typ = typ.lower()

full_url_prefixes = {

"arxiv": "https://arxiv.org/abs/",

"doi": "https://doi.org/",

}

title_prefixes = {

"arxiv": "arXiv:",

"doi": "DOI:",

}

full_url = f"{full_url_prefixes[typ]}{part}"

if not has_explicit_title:

title = f"{title_prefixes[typ]}{part}"

pnode = nodes.reference(title, title, internal=False, refuri=full_url)

return [pnode], []

@jjerphan sorry for stepping in. It seems to me that the optimization of this piece of code, taken from the scipy implementation, is outside the scope of this pull request, labeled as documentation and good first issue. Perhaps this might be kept for a further improvement in a follow-up pull request?

@cmarmo, Thanks for review. I like @jjerphan 's code even though it is out of scope for this PR. If you are ok let me recommit :)

puhuk · 2021-10-11T08:51:25Z

@cmarmo, @jjerphan
Sorry for bothering. But my PR has error with ci/circleci: linux-arm64.
There was no issue when build from local environment.
Could you tell me how can I resolve this.

jjerphan · 2021-10-11T12:24:46Z

Hi @puhuk,

The CI error is unrelated to the latest changes starting from 8b66236.

Between dabe843 and 8b66236, changes have been made on main on the CI script (by b2ee0f4) and might cause your PR to fail.

Can you try merging main in your branch?

To merge origin with local branch

puhuk · 2021-10-11T14:14:47Z

@jjerphan
I try with git merge origin but it fails again.
You mean merge the main repo of 'https://github.com/scikit-learn/scikit-learn' to my branch , right?

puhuk · 2021-10-11T15:57:02Z

@jjerphan It seems done Thanks! :)

jjerphan

Thanks @puhuk: it looks like there are references which could use those directives.

For instance (those lists might not be complete):

arXiv HTTP links

benchmarks/bench_plot_randomized_svd.py:55:    Halko, et al., 2009 https://arxiv.org/abs/0909.4061
doc/modules/sgd.rst:561:      <https://arxiv.org/pdf/1107.2490v2.pdf>`_
doc/modules/decomposition.rst:177:      <https://arxiv.org/pdf/1412.3510.pdf>`_
doc/modules/decomposition.rst:352:          <https://arxiv.org/pdf/1412.3510.pdf>`_
doc/modules/decomposition.rst:937:      <https://arxiv.org/pdf/1010.1763.pdf>`_
doc/modules/neural_networks_supervised.rst:372:       <https://arxiv.org/pdf/1412.6980v8.pdf>`_
doc/sphinxext/doi_role.py:27:        full_url = "https://arxiv.org/abs/" + part
doc/datasets/loading_other_datasets.rst:226:   <https://arxiv.org/pdf/1407.7722.pdf>`_,
examples/inspection/plot_partial_dependence.py:33:       Graphical Statistics, 24(1): 44-65 (https://arxiv.org/abs/1309.6392)
sklearn/cluster/_hierarchical_fast.pyx:454:# Implements MST-LINKAGE-CORE from https://arxiv.org/abs/1109.2378
sklearn/cluster/_hierarchical_fast.pyx:465:    by Daniel Mullner (https://arxiv.org/abs/1109.2378).
sklearn/cluster/_hierarchical_fast.pyx:486:        very efficiently. See https://arxiv.org/abs/1109.2378
sklearn/decomposition/_truncated_svd.py:120:    Halko, et al., 2009 (arXiv:909) https://arxiv.org/pdf/0909.4061.pdf
sklearn/ensemble/_hist_gradient_boosting/tests/test_gradient_boosting.py:444:    # "Remark 3" in https://arxiv.org/abs/1902.06931
sklearn/ensemble/_hist_gradient_boosting/splitting.pyx:503:                    # https://arxiv.org/abs/1603.02754
sklearn/ensemble/_hist_gradient_boosting/splitting.pyx:1040:    https://arxiv.org/abs/1603.02754
sklearn/ensemble/_hist_gradient_boosting/splitting.pyx:1079:    https://arxiv.org/abs/1603.02754
sklearn/ensemble/_hist_gradient_boosting/splitting.pyx:1119:    https://arxiv.org/abs/1603.02754
sklearn/linear_model/tests/test_logistic.py:2204:    https://arxiv.org/pdf/1706.10272.pdf
sklearn/linear_model/_sag.py:64:    https://arxiv.org/abs/1407.0202
sklearn/linear_model/_sag.py:238:    https://arxiv.org/abs/1407.0202
sklearn/linear_model/_sag_fast.pyx.tp:253:    https://arxiv.org/abs/1407.0202
sklearn/linear_model/_logistic.py:1374:        https://arxiv.org/abs/1407.0202
sklearn/utils/extmath.py:209:    Halko, et al., 2009 (arXiv:909) https://arxiv.org/pdf/0909.4061.pdf
sklearn/utils/extmath.py:351:      Halko, et al., 2009 https://arxiv.org/abs/0909.4061
sklearn/utils/extmath.py:543:      Halko, et al., 2009 https://arxiv.org/abs/0909.4061

DOI HTTP links

doc/modules/semi_supervised.rst:74:       https://doi.org/10.3115/981658.981684
doc/sphinxext/doi_role.py:8:    (``https://doi.org/10.1016/S0022-2836(05)80360-2``).
doc/sphinxext/doi_role.py:33:        full_url = "https://doi.org/" + part
examples/linear_model/plot_poisson_regression_non_normal_loss.py:35:    <http://dx.doi.org/10.2139/ssrn.3164764>`_
examples/linear_model/plot_tweedie_regression_insurance_claims.py:37:    <http://dx.doi.org/10.2139/ssrn.3164764>`_
examples/inspection/plot_permutation_importance.py:24:       2001. https://doi.org/10.1023/A:1010933404324
examples/release_highlights/plot_release_highlights_0_24_0.py:113:# <https://doi.org/10.3115/981658.981684>`_ can now be used with any
examples/kernel_approximation/plot_scalable_poly_kernels.py:226:# https://doi.org/10.1145/2487575.2487591
sklearn/decomposition/_pca.py:309:    <https://doi.org/10.1137/090771806>`_
sklearn/decomposition/_pca.py:314:    <https://doi.org/10.1016/j.acha.2010.02.003>`_.
sklearn/linear_model/tests/test_logistic.py:2199:    https://doi.org/10.1093/biostatistics%2Fkxg046
sklearn/manifold/_spectral_embedding.py:232:      https://doi.org/10.1137%2FS1064827500366124
sklearn/manifold/_spectral_embedding.py:327:        #     see https://doi.org/10.1007/s10208-015-9297-1
sklearn/metrics/_classification.py:866:       <https://doi.org/10.1093/bioinformatics/16.5.412>`_.
sklearn/preprocessing/_polynomial.py:841:            # penalties" https://doi.org/10.1214/ss/1038425655 advice
sklearn/semi_supervised/_self_training.py:123:    https://doi.org/10.3115/981658.981684
sklearn/inspection/_permutation_importance.py:216:             2001. https://doi.org/10.1023/A:1010933404324

Other DOI references

benchmarks/bench_covertype.py:29:   <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.139.2112>`_
benchmarks/bench_covertype.py:33:   <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.74.8513>`_
doc/modules/biclustering.rst:165:   <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.140.3011>`__.
doc/modules/biclustering.rst:248:   <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.135.1608>`__.
doc/modules/naive_bayes.rst:219:   <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.46.1529>`_
doc/modules/naive_bayes.rst:224:   <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.61.5542>`_
doc/modules/feature_selection.rst:310:      <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.24.4369&rep=rep1&type=pdf>`_.
doc/modules/manifold.rst:252:     <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.70.382>`_
doc/modules/manifold.rst:392:     <http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.4.3693>`_
doc/modules/sgd.rst:550:      <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.74.8513>`_
doc/modules/sgd.rst:565:      <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.124.4696>`_
doc/modules/sgd.rst:571:      <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.58.7377>`_
doc/modules/neighbors.rst:348:     <http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.91.8209>`_,
doc/modules/random_projection.rst:31:   `Random projection in dimensionality reduction: applications to image and text data. <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.24.5135&rep=rep1&type=pdf>`_
doc/modules/random_projection.rst:87:    <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.39.3334&rep=rep1&type=pdf>`_
doc/modules/linear_model.rst:717:    * David J. C. MacKay, `Bayesian Interpolation <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.27.9072&rep=rep1&type=pdf>`_, 1992.
doc/modules/linear_model.rst:765:    .. [4] Tristan Fletcher: `Relevance Vector Machines explained <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.651.8603&rep=rep1&type=pdf>`_
doc/modules/clustering.rst:432:   <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.76.8968&rep=rep1&type=pdf>`_
doc/modules/clustering.rst:532:   <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.165.9323>`_
doc/modules/clustering.rst:536:   <http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.160.2324>`_
doc/modules/clustering.rst:540:   <http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.33.1501>`_
doc/modules/clustering.rst:544:   <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.19.8100>`_
doc/modules/svm.rst:804:      <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.114.4288>`_,
doc/modules/model_evaluation.rst:832:     <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.157.5766&rep=rep1&type=pdf>`_,
examples/calibration/plot_compare_calibration.py:206:#        <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.29.3039&rep=rep1&type=pdf>`_
sklearn/cluster/_bicluster.py:306:      <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.140.3011>`__.
sklearn/cluster/_bicluster.py:461:      <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.135.1608>`__.
sklearn/cluster/_spectral.py:254:           <http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.160.2324>`_
sklearn/cluster/_spectral.py:258:           <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.165.9323>`_
sklearn/cluster/_spectral.py:489:           <http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.160.2324>`_
sklearn/cluster/_spectral.py:493:           <http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.165.9323>`_
sklearn/manifold/_locally_linear.py:298:        http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.70.382
sklearn/manifold/_locally_linear.py:664:        http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.70.382
sklearn/manifold/_spectral_embedding.py:491:      http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.165.9323
sklearn/manifold/_spectral_embedding.py:495:      http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.19.8100
sklearn/manifold/_spectral_embedding.py:499:      http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.160.2324
sklearn/mixture/_bayesian_mixture.py:320:       <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.36.2841&rep=rep1&type=pdf>`_
sklearn/semi_supervised/_label_propagation.py:544:    http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.115.3219
sklearn/svm/_classes.py:711:        <http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.41.1639>`_
sklearn/svm/_classes.py:968:        <http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.41.1639>`_
sklearn/svm/_classes.py:1170:        <http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.41.1639>`_
sklearn/svm/_classes.py:1358:        <http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.41.1639>`_
sklearn/tree/_reingold_tilford.py:161:    # http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.16.8757&rep=rep1&type=pdf
sklearn/random_projection.py:116:           http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.45.3654

Probably, creating dedicated Sphinx entries for them in subsequent PRs might be better because this is unrelated to this PR scope.

I would wait for maintainers' comments and/or approvals.

puhuk · 2021-10-12T16:31:01Z

@ogrisel, Hi. If you have any other feedback with this, please just let me know to update :)

jjerphan · 2021-10-12T20:26:03Z

@ogrisel, Hi. If you have any other feedback with this, please just let me know to update :)

I also think @cmarmo can provide authoritative feedback.

puhuk · 2021-10-18T11:39:05Z

Hi @ogrisel @cmarmo @jjerphan
This is reminder for review :)
It would be thanks to get feedback with this PR.

jjerphan

Let's keep this PR short and atomic: this LGTM!

As for the remarks in the latest message, I think they can be treated in another PR.

thomasjpfan

LGTM

thomasjpfan · 2021-10-19T19:49:19Z

doc/modules/clustering.rst

@@ -1804,8 +1803,7 @@ number of points in cluster :math:`q`.
 * Caliński, T., & Harabasz, J. (1974).
   `"A Dendrite Method for Cluster Analysis"
   <https://www.researchgate.net/publication/233096619_A_Dendrite_Method_for_Cluster_Analysis>`_.
-   Communications in Statistics-theory and Methods 3: 1-27.
-   `doi:10.1080/03610927408827101 <https://doi.org/10.1080/03610927408827101>`_.
+   :doi:`Communications in Statistics-theory and Methods 3: 1-27 <10.1080/03610927408827101>`.


The first link, https://www.researchgate.net/publication/233096619_A_Dendrite_Method_for_Cluster_Analysis gives free access to the paper while the doi does not have public access.

Since the version on main also has both links, I am okay with your change.

cmarmo · 2021-10-19T21:22:03Z

@thomasjpfan shall we just merge this one? Thanks!

DOC: use :doi: and :arxiv: directives for references

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To resolve issue scikit-learn#21088

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DOC: use :doi: and :arxiv: directives for references #21088

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Updates with issue scikit-learn#21088

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Resolve issue scikit-learn#21088

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Update for PR scikit-learn#21099

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thomasjpfan changed the title ~~DOC: use :doi: and :arxiv: directives for references~~ DOC Use :doi: and :arxiv: directives for references Oct 20, 2021

thomasjpfan merged commit 337e0d2 into scikit-learn:main Oct 20, 2021

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Release 1.0.1 #21404

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DOC Use :doi: and :arxiv: directives for references (scikit-learn#21099)

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ENH add 'cluster_qr' method to spectral segmentation #21148

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DOC Use :doi: and :arxiv: directives for references (#21099)

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DOC improve kernel PCA example #19945

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FIX/API Fix AIC/BIC in LassoLarsIC and introduce noise_variance #21481

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DOC Use :doi: and :arxiv: directives for references (scikit-learn#21099)

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	project <:arxiv:`1309.0238`>`_, Buitinck et al., 2013.
	project :arxiv:`1309.0238`, Buitinck et al., 2013.

		API design for machine learning software: experiences from the scikit-learn
		project, Buitinck et al., 2013. :arxiv:`1309.0238`

	You can also give an explicit caption, e.g.
	:doi:`Basic local alignment search tool <10.1016/S0022-2836(05)80360-2>`.

		.. [1] L. Breiman, :doi:`"Random Forests" <10.1023/A:1010933404324>`, Machine Learning, 45(1), 5-32,
		2001.

		* Perperoglou, A., Sauerbrei, W., Abrahamowicz, M. et al. :doi:`A review of
		spline function procedures in R <10.1186/s12874-019-0666-3>`. BMC Med Res Methodol 19, 46 (2019).

		.. [Urbanowicz2015] Urbanowicz R.J., Moore, J.H. :doi:`ExSTraCS 2.0: description and evaluation of a scalable learning
		classifier system <10.1007/s12065-015-0128-8>`, Evol. Intel. (2015) 8: 89.

DOC Use :doi: and :arxiv: directives for references #21099

DOC Use :doi: and :arxiv: directives for references #21099

Conversation

puhuk commented Sep 21, 2021

Reference Issues/PRs

What does this implement/fix? Explain your changes.

Any other comments?

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