[MRG + 1] Fix Sphinx errors #9420

balakmran · 2017-07-20T04:32:23Z

Reference Issue

Fixes #9417

What does this implement/fix? Explain your changes.

Fix warnings seen in doc build logs.

Previously modified with PR scikit-learn#6651

Old refers to new tag added with PR scikit-learn#7388

jnothman · 2017-07-20T04:33:52Z

Why WIP? What remains to be done before this should be reviewed for merge?

balakmran · 2017-07-20T04:35:28Z

I have few questions that I posted on the issue

pairwise metrics yet to be documented

…ear_model_plot_sparse_recovery.py. It is deprecated.

amueller · 2017-07-23T01:57:11Z

LGTM. why WIP, should be done now, right?

balakmran · 2017-07-23T02:59:47Z

/doc/modules/classes.rst:2: WARNING: Literal block expected; none found.
Should I add a new tag like api_ref at Line 1?

Citation [RH2007] is not referenced. (There were many)
Should I remove ref and replace with an asterisk (*)?

I posted these questions on the issue earlier.

jnothman

/doc/modules/classes.rst:2: WARNING: Literal block expected; none found. Should I add a new tag like api_ref at Line 1?

I don't understand this warning. Do you?

Citation [RH2007] is not referenced. (There were many) Should I remove ref and replace with an asterisk (*)?

Yes, I guess so

jnothman · 2017-07-23T12:33:12Z

sklearn/covariance/robust_covariance.py

+        ----------
+
+        .. [Rouseeuw1999] `A Fast Algorithm for the Minimum Covariance
+        Determinant Estimator, 1999, American Statistical Association and


Is this properly indented?

jnothman · 2017-07-23T12:33:20Z

sklearn/covariance/robust_covariance.py

+        ----------
+
+        .. [Rouseeuw1999] `A Fast Algorithm for the Minimum Covariance
+        Determinant Estimator, 1999, American Statistical Association and


Is this properly indented?

jnothman · 2017-07-23T12:34:29Z

sklearn/neighbors/lof.py

@@ -85,7 +85,7 @@ class LocalOutlierFactor(NeighborsBase, KNeighborsMixin, UnsupervisedMixin):

    p : integer, optional (default=2)
        Parameter for the Minkowski metric from
-        :ref:`sklearn.metrics.pairwise.pairwise_distances`. When p = 1, this is


I think this should work if you change :ref: to :func:, and I would much prefer that.

balakmran · 2017-07-23T19:40:26Z

Thanks, @jnothman for the review comments. Made necessary changes.

balakmran · 2017-07-23T19:42:08Z

/doc/modules/classes.rst:2: WARNING: Literal block expected; none found. Should I add a new tag like api_ref at Line 1?
I don't understand this warning. Do you?

I was unsure though. But I guess it was expecting a tag at the beginning of the file. ( .. _: )

jnothman · 2017-07-23T23:40:09Z

a tag is not a literal block as far as i can tell. is there anything amiss in the rendering?

…

On 24 Jul 2017 5:44 am, "Balakumaran Manoharan" ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In sklearn/neighbors/lof.py <#9420 (comment)> : > @@ -85,7 +85,7 @@ class LocalOutlierFactor(NeighborsBase, KNeighborsMixin, UnsupervisedMixin): p : integer, optional (default=2) Parameter for the Minkowski metric from - :ref:`sklearn.metrics.pairwise.pairwise_distances`. When p = 1, this is Done — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#9420 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAEz62bU5NPEz_uhdg20vfN6PqJI_LWLks5sQ6K7gaJpZM4Odl1m> .

jnothman · 2017-07-23T23:41:10Z

I've not confirmed the absence of warnings now, but the changes LGTM.

balakmran · 2017-07-24T05:58:00Z

How do I get the travis generated html docs URL?

jnothman · 2017-07-24T09:19:47Z

Tennis doesn't generate docs, circle does. The link under details is https://circleci.com/gh/scikit-learn/scikit-learn/12398?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-build-link. This will show logs etc. You can go straight to the rendered docs with http://scikit-learn.org/circle?12398. http://scikit-learn.org/circle?12398/_changed.html tries to list what's changed.

amueller · 2017-07-24T15:24:46Z

/doc/modules/classes.rst:2: WARNING: Literal block expected; none found.

I don't understand this error and it has been there forever. We should maybe investigate, but I don't think you should worry about it for this PR.

amueller · 2017-07-24T15:25:44Z

LGTM

amueller · 2017-07-24T15:31:58Z

there's still

/home/ubuntu/scikit-learn/doc/modules/calibration.rst:193: WARNING: Footnote [1] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/calibration.rst:196: WARNING: Footnote [2] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/calibration.rst:199: WARNING: Footnote [3] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/calibration.rst:205: WARNING: Footnote [5] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/covariance.rst:300: WARNING: Footnote [3] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/covariance.rst:302: WARNING: Footnote [4] is not referenced.

balakmran · 2017-07-24T18:09:35Z

Thank you @jnothman for the links.
Let me fix calibration and covariance @amueller

balakmran · 2017-07-25T10:14:47Z

Fixing few issues found from CircleCI rendered doc.

balakmran · 2017-07-25T10:33:14Z

sklearn/covariance/robust_covariance.py

+        References
+        ----------
+
+        .. [Rouseeuw1999] `A Fast Algorithm for the Minimum Covariance


@amueller @jnothman Why do I see a different number here? HTML Link

can you try removing the 1999 from the tag?

I think it's auto generating the number as the same tag has been used several times in the file.

balakmran · 2017-07-25T10:45:45Z

Verified all modified HTML links. Looks Good except Rouseeuw1999 link.

balakmran · 2017-07-25T23:23:03Z

sklearn/covariance/robust_covariance.py

        Estimator, 1999, American Statistical Association and the American
        Society for Quality, TECHNOMETRICS`
-    .. [Butler1993] `R. W. Butler, P. L. Davies and M. Jhun,
+    .. [ButlerDavies1993] `R. W. Butler, P. L. Davies and M. Jhun,


I still get wrong tag names after having them unique. Any idea?

jnothman · 2017-07-26T02:13:04Z

Hmm. The renumbering logic lives here: https://github.com/numpy/numpydoc/blob/master/numpydoc/numpydoc.py#L40. I've not looked at it, but if you find a bug, fixes to numpydoc are welcome. We've only recently adopted it and have some fixes to make before releasing scikit-learn using it in 0.20

balakmran · 2017-07-26T02:19:51Z

Ok, I can give it a try.
For now, what should I do with this PR?

jnothman · 2017-07-26T02:22:32Z

I'd be happy to merge this PR if that remains a numpydoc bug that we can fix before 0.20.

…

On 26 July 2017 at 12:19, Balakumaran Manoharan ***@***.***> wrote: Ok, I can give it a try. For now, what should I do with this PR? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#9420 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAEz6y5vKmf0rC4M4QxGqQr6xICYeVR6ks5sRqJJgaJpZM4Odl1m> .

amueller · 2017-07-26T15:28:53Z

most of the PR is independent of this issue, right?
Anyhow, I think this issue might be resolved by not naming references with numbers at the end.

balakmran · 2017-07-27T12:14:01Z

Hi @amueller Tried without numbers. No luck. Still seeing some random numbers appended at the end of the tag.

amueller · 2017-07-27T16:07:49Z

That's really weird....

amueller · 2017-07-27T16:09:36Z

I say open a new issue for that and let's merge this.

balakmran · 2017-07-27T19:56:26Z

Created an issue @amueller

jnothman · 2017-07-30T05:22:02Z

Thanks @bmanohar16

* Fix Rouseeuw1984 broken link * Change label vbgmm to bgmm Previously modified with PR scikit-learn#6651 * Change tag name Old refers to new tag added with PR scikit-learn#7388 * Remove prefix underscore to match tag * Realign to fit 80 chars * Link to metrics.rst. pairwise metrics yet to be documented * Remove tag as LSHForest is deprecated * Remove all references to randomized_l1 and sphx_glr_auto_examples_linear_model_plot_sparse_recovery.py. It is deprecated. * Fix few Sphinx warnings * Realign to 80 chars * Changes based on PR review * Remove unused ref in calibration * Fix link ref in covariance.rst * Fix linking issues * Differentiate Rouseeuw1999 tag within file. * Change all duplicate Rouseeuw1999 tags * Remove numbers from tag Rousseeuw

Balakumaran Manoharan added 4 commits July 19, 2017 19:47

Fix Rouseeuw1984 broken link

c7f133c

Change label vbgmm to bgmm

e697f7a

Previously modified with PR scikit-learn#6651

Change tag name

d411eaf

Old refers to new tag added with PR scikit-learn#7388

Remove prefix underscore to match tag

9054c97

Balakumaran Manoharan added 6 commits July 19, 2017 23:59

Realign to fit 80 chars

f0fa2a6

Link to metrics.rst.

272e3c7

pairwise metrics yet to be documented

Remove tag as LSHForest is deprecated

1c854cd

Remove all references to randomized_l1 and sphx_glr_auto_examples_lin…

920396b

…ear_model_plot_sparse_recovery.py. It is deprecated.

Fix few Sphinx warnings

ebd6728

Realign to 80 chars

84423d1

jnothman reviewed Jul 23, 2017

View reviewed changes

Changes based on PR review

7c499f2

balakmran changed the title ~~[WIP] Fix Sphinx errors~~ [MRG] Fix Sphinx errors Jul 23, 2017

amueller changed the title ~~[MRG] Fix Sphinx errors~~ [MRG + 1] Fix Sphinx errors Jul 24, 2017

Remove unused ref in calibration

dff16b1

Fix link ref in covariance.rst

65a617f

Fix linking issues

80ca198

balakmran commented Jul 25, 2017

View reviewed changes

Balakumaran Manoharan added 2 commits July 25, 2017 14:06

Differentiate Rouseeuw1999 tag within file.

65867f4

Change all duplicate Rouseeuw1999 tags

6fd0151

balakmran commented Jul 25, 2017

View reviewed changes

Remove numbers from tag Rousseeuw

460810d

balakmran mentioned this pull request Jul 27, 2017

numpydoc appends a randomized number at the end of references link tags #9459

Closed

jnothman merged commit 04be1a9 into scikit-learn:master Jul 30, 2017

balakmran deleted the sphinx-errors branch July 31, 2017 00:32

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[MRG + 1] Fix Sphinx errors #9420

[MRG + 1] Fix Sphinx errors #9420

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[MRG + 1] Fix Sphinx errors #9420

[MRG + 1] Fix Sphinx errors #9420

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balakmran commented Jul 20, 2017

Reference Issue

What does this implement/fix? Explain your changes.

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