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Jan 30, 2023
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@thomasjpfan thomasjpfan commented Jan 29, 2023

This PR fixes Sphinx search by removing underscore.js, which is not required anymore.

We also need to cherry pick this fix onto 1.2.X to fix search on the stable site.

@thomasjpfan thomasjpfan added To backport PR merged in master that need a backport to a release branch defined based on the milestone. Quick Review For PRs that are quick to review labels Jan 29, 2023
@thomasjpfan thomasjpfan marked this pull request as draft January 30, 2023 01:31
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thomasjpfan commented Jan 30, 2023

There is another bug with the search. searchindex.js was not generated correctly. There is a big difference between the search index on 1.1 and 1.2:

I'll look more into it this week.

@thomasjpfan thomasjpfan removed the Quick Review For PRs that are quick to review label Jan 30, 2023
@thomasjpfan thomasjpfan changed the title DOC Fixes search by removing underscore.js DOC Fixes sphinx search on website Jan 30, 2023
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While debugging, I found that 6.1.3 does not generate the correct search index on Linux. With Sphinx pinned to 6.0.0, search works: https://output.circle-artifacts.com/output/job/0104e4ae-e96f-4b75-8fe1-85f52f267844/artifacts/0/doc/search.html?q=linear

I think pinning is a good for now to make sure the site is functional.

@thomasjpfan thomasjpfan marked this pull request as ready for review January 30, 2023 02:39
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Is removing underscore.js still something you want to do? I think yes, but wanted to double check.

Otherwise sticking with 6.0.0 for now looks like a pragmatic solution.

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Thank you for fixing the documentation, @thomasjpfan.

I agree with always pinning a version of sphinx.

Is there anything left to do? Should doc_min_dependencies also be adapted?
Also, must sphinx-gallery and sphinx-prompt be pinned as well?

@lesteve lesteve merged commit 6822e63 into scikit-learn:main Jan 30, 2023
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lesteve commented Jan 30, 2023

Merging thanks a lot!

The search works on CircleCI:
https://output.circle-artifacts.com/output/job/0104e4ae-e96f-4b75-8fe1-85f52f267844/artifacts/0/doc/search.html?q=neighbors

Is removing underscore.js still something you want to do? I think yes, but wanted to double check.

underscore.js is not needed anymore.

Is there anything left to do? Should doc_min_dependencies also be adapted?
Also, must sphinx-gallery and sphinx-prompt be pinned as well?

doc_min_dependencies uses an old sphinx which is not affected by this issue. Also we don't care too much about the search for doc_min_dependencies since this is not deployed anywhere.

Not sure why you want to pin sphinx-gallery and sphinx-prompt?

lesteve pushed a commit to lesteve/scikit-learn that referenced this pull request Jan 30, 2023
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lesteve commented Jan 30, 2023

I haved opened #25508 to backport this fix for the stable doc.

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Not sure why you want to pin sphinx-gallery and sphinx-prompt?

I do not know, but it might be that the generated documentation might slightly change and cause problem from one version of those tools to another.

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lesteve commented Jan 30, 2023

As a side-comment with lock files, package versions are actually pinned.

It is true that we don't necessarily think of checking the doc rendering when we update lock files and that also it's hard to know what to check until you realise that something is broken. To me pinning defensively seems a bit conservative ... maybe we can do it for some selected packages if we notice they kept causing issues?

ogrisel pushed a commit that referenced this pull request Jan 30, 2023
Co-authored-by: Thomas J. Fan <thomasjpfan@gmail.com>
thomasjpfan added a commit to thomasjpfan/scikit-learn that referenced this pull request Feb 3, 2023
AdarshPrusty7 added a commit to AdarshPrusty7/GSGP that referenced this pull request Mar 6, 2023
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* DOC Update date and contributors list for v1.2.1 (scikit-learn#25459)

* DOC Make MeanShift documentation clearer (scikit-learn#25305)

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* Finishes boolean and arithmetic creation

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* FIX fix faulty test in `cross_validate` that used the wrong estimator (scikit-learn#25456)

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* EFF Improve IsolationForest predict time (scikit-learn#25186)

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closes scikit-learn#25212

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* FIX make IsotonicRegression always predict NumPy arrays (scikit-learn#25500)



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* FEA Add Gamma deviance as loss function to HGBT (scikit-learn#22409)

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* MAINT Remove ReadonlyArrayWrapper from _loss module

* CLN Remove comments about Cython 3.0

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* FIX: documentation, and add code example

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---------

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* CLN Revert auto formatter

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* MAINT Use newest NumPy C API in tree._criterion

* FIX Use pointer for children

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* FIX Fixes check_array nonfinite checks with ArrayAPI specification

* DOC Adds PR number

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* MAINT Remove Cython compilation warnings ahead of Cython3.0 release (scikit-learn#25621)

* ENH Preserve DataFrame dtypes in transform for feature selectors (scikit-learn#25102)

* FIX report properly n_iter_ when warm_start=True (scikit-learn#25443)

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* FIX renormalization of y_pred inside log_loss (scikit-learn#25299)

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* DOC unify usage of 'w.r.t.' (scikit-learn#25683)

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* FIX Allow negative tol in SequentialFeatureSelector (scikit-learn#25664)

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* DOC Add scikit-learn-intelex to related projects (scikit-learn#23766)

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* FIX Raise appropriate attribute error in ensemble (scikit-learn#25668)

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* ENH Let csr_row_norms support multi-thread (scikit-learn#25598)

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* MAINT Parameter Validation for feature_selection.chi2 (scikit-learn#25719)

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* MAINT Parameters validation for sklearn.metrics.matthews_corrcoef (scikit-learn#25712)

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* MAINT parameter validation for sklearn.datasets.dump_svmlight_file (scikit-learn#25726)

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* MAINT Clean dead code in build helpers (scikit-learn#25661)

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* MAINT Remove redundant sparse square euclidian distances function (scikit-learn#25731)

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Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com>

* API Use grid_values instead of pdp_values in partial_dependence (scikit-learn#25732)

* MAINT remove np.product and inf/nan aliases in favor of canonical names (scikit-learn#25741)

* MAINT Parameters validation for metrics.label_ranking_loss (scikit-learn#25742)

Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com>

* MAINT Parameters validation for metrics.coverage_error (scikit-learn#25748)

* MAINT Parameters validation for metrics.dcg_score (scikit-learn#25749)

* MAINT replace cnp.ndarray with memory views in _fast_dict (scikit-learn#25754)

* MAINT Parameter Validation for feature_selection.f_regression (scikit-learn#25736)

Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com>

* MAINT Parameters validation for feature_selection.r_regression (scikit-learn#25734)

Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com>

* MAINT Parameter Validation for metrics.get_scorer (scikit-learn#25738)

Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com>

* DOC Move allowing pandas nullable dtypes to 1.2.2 (scikit-learn#25692)

* MAINT replace cnp.ndarray with memory views in sparsefuncs_fast (scikit-learn#25764)

* MAINT parameter validation for sklearn.datasets.fetch_covtype (scikit-learn#25759)

Co-authored-by: Jérémie du Boisberranger <34657725+jeremiedbb@users.noreply.github.com>

* MAINT Define centralized generic, but with explicit precision, types (scikit-learn#25739)

* CI Disable network when SciPy requires it (scikit-learn#25743)

* CI Open issue when arm wheel fails on CirrusCI (scikit-learn#25620)

* ENH Speed-up expected mutual information (scikit-learn#25713)

Co-authored-by: Kshitij Mathur <k.mathur68@gmail.com>
Co-authored-by: Guillaume Lemaitre <g.lemaitre58@gmail.com>
Co-authored-by: Omar Salman <omar.salman@arbisoft.com>

* FIX add retry mechanism to handle quotechar in read_csv (scikit-learn#25511)

* Merge Population Creation (#1)

---------

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jeremiedbb pushed a commit to jeremiedbb/scikit-learn that referenced this pull request Mar 7, 2023
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