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amueller opened this issue Jul 19, 2017 · 8 comments · Fixed by #9420
Closed

Fix remaining sphinx errors #9417

amueller opened this issue Jul 19, 2017 · 8 comments · Fixed by #9420
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Documentation Easy Well-defined and straightforward way to resolve

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@amueller
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Since we're now using upstream numpydoc, it should be fairly easy to fix the remaining errors in building the docs:

/home/ubuntu/scikit-learn/doc/modules/cross_validation.rst:287: WARNING: undefined label: time_series_cv (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/doc/modules/cross_validation.rst:287: WARNING: undefined label: group_cv (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/covariance/outlier_detection.py:docstring of sklearn.covariance.EllipticEnvelope.correct_covariance:4: WARNING: citation not found: Rouseeuw1984
/home/ubuntu/scikit-learn/sklearn/covariance/outlier_detection.py:docstring of sklearn.covariance.EllipticEnvelope.reweight_covariance:4: WARNING: citation not found: Rouseeuw1984
/home/ubuntu/scikit-learn/sklearn/covariance/robust_covariance.py:docstring of sklearn.covariance.MinCovDet.correct_covariance:4: WARNING: citation not found: Rouseeuw1984
/home/ubuntu/scikit-learn/sklearn/covariance/robust_covariance.py:docstring of sklearn.covariance.MinCovDet.reweight_covariance:4: WARNING: citation not found: Rouseeuw1984
/home/ubuntu/scikit-learn/doc/modules/generated/sklearn.linear_model.RandomizedLasso.rst:17: WARNING: undefined label: randomized_l1 (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/linear_model/randomized_l1.py:docstring of sklearn.linear_model.RandomizedLasso:25: WARNING: undefined label: randomized_l1 (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/linear_model/randomized_l1.py:docstring of sklearn.linear_model.RandomizedLasso:153: WARNING: undefined label: sphx_glr_auto_examples_linear_model_plot_sparse_recovery.py (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/doc/modules/generated/sklearn.linear_model.RandomizedLogisticRegression.rst:17: WARNING: undefined label: randomized_l1 (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/linear_model/randomized_l1.py:docstring of sklearn.linear_model.RandomizedLogisticRegression:27: WARNING: undefined label: randomized_l1 (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/linear_model/randomized_l1.py:docstring of sklearn.linear_model.RandomizedLogisticRegression:138: WARNING: undefined label: sphx_glr_auto_examples_linear_model_plot_sparse_recovery.py (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/doc/modules/generated/sklearn.linear_model.lasso_stability_path.rst:11: WARNING: undefined label: randomized_l1 (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/utils/deprecation.py:docstring of sklearn.linear_model.lasso_stability_path:67: WARNING: undefined label: sphx_glr_auto_examples_linear_model_plot_sparse_recovery.py (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/doc/modules/generated/sklearn.mixture.VBGMM.rst:22: WARNING: undefined label: vbgmm (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.GridSearchCV:46: WARNING: undefined label: multivalued_scorer_wrapping (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.RandomizedSearchCV:61: WARNING: undefined label: multivalued_scorer_wrapping (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/model_selection/_validation.py:docstring of sklearn.model_selection.cross_validate:42: WARNING: undefined label: multivalued_scorer_wrapping (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/model_selection/_validation.py:docstring of sklearn.model_selection.permutation_test_score:38: WARNING: undefined label: _scoring_parameter (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/model_selection/_validation.py:docstring of sklearn.model_selection.permutation_test_score:38: WARNING: undefined label: _scoring (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/doc/modules/generated/sklearn.neighbors.LSHForest.rst:21: WARNING: undefined label: approximate_nearest_neighbors (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/sklearn/neighbors/lof.py:docstring of sklearn.neighbors.LocalOutlierFactor:78: WARNING: undefined label: sklearn.metrics.pairwise.pairwise_distances (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/doc/modules/grid_search.rst:87: WARNING: undefined label: sphx_glr_auto_examples_model_selection_plot_multi_metric_evaluation (if the link has no caption the label must precede a section header)
/home/ubuntu/scikit-learn/doc/modules/grid_search.rst:186: WARNING: undefined label: sphx_glr_auto_examples_model_selection_plot_multi_metric_evaluation (if the link has no caption the label must precede a section header)
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amueller commented Jul 19, 2017 •
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/home/ubuntu/scikit-learn/doc/auto_examples/calibration/plot_compare_calibration.rst:51: WARNING: Footnote [1] is not referenced.
/home/ubuntu/scikit-learn/doc/auto_examples/covariance/plot_robust_vs_empirical_covariance.rst:51: WARNING: Footnote [2] is not referenced.
/home/ubuntu/scikit-learn/doc/auto_examples/covariance/plot_robust_vs_empirical_covariance.rst:54: WARNING: Footnote [3] is not referenced.
/home/ubuntu/scikit-learn/doc/auto_examples/ensemble/plot_adaboost_hastie_10_2.rst:19: WARNING: Footnote [1] is not referenced.
/home/ubuntu/scikit-learn/doc/auto_examples/ensemble/plot_adaboost_hastie_10_2.rst:22: WARNING: Footnote [2] is not referenced.
/home/ubuntu/scikit-learn/doc/auto_examples/ensemble/plot_adaboost_multiclass.rst:27: WARNING: Footnote [1] is not referenced.
/home/ubuntu/scikit-learn/doc/auto_examples/ensemble/plot_adaboost_regression.rst:16: WARNING: Footnote [1] is not referenced.
/home/ubuntu/scikit-learn/doc/auto_examples/ensemble/plot_ensemble_oob.rst:22: WARNING: Footnote [1] is not referenced.
/home/ubuntu/scikit-learn/doc/auto_examples/ensemble/plot_gradient_boosting_regularization.rst:23: WARNING: Footnote [1] is not referenced.
/home/ubuntu/scikit-learn/doc/auto_examples/ensemble/plot_isolation_forest.rst:27: WARNING: Footnote [1] is not referenced.
datasets/covtype.rst:5: WARNING: duplicate label covtype, other instance in /home/ubuntu/scikit-learn/doc/datasets/covtype.rst
/home/ubuntu/scikit-learn/doc/datasets/labeled_faces.rst:4: WARNING: duplicate label labeled_faces_in_the_wild, other instance in /home/ubuntu/scikit-learn/doc/datasets/index.rst
/home/ubuntu/scikit-learn/doc/datasets/mldata.rst:10: WARNING: duplicate label mldata, other instance in /home/ubuntu/scikit-learn/doc/datasets/index.rst
/home/ubuntu/scikit-learn/doc/datasets/olivetti_faces.rst:5: WARNING: duplicate label olivetti_faces, other instance in /home/ubuntu/scikit-learn/doc/datasets/index.rst
/home/ubuntu/scikit-learn/doc/datasets/rcv1.rst:5: WARNING: duplicate label rcv1, other instance in /home/ubuntu/scikit-learn/doc/datasets/index.rst
/home/ubuntu/scikit-learn/doc/datasets/twenty_newsgroups.rst:4: WARNING: duplicate label 20newsgroups, other instance in /home/ubuntu/scikit-learn/doc/datasets/index.rst
/home/ubuntu/scikit-learn/doc/developers/advanced_installation.rst:6: WARNING: Duplicate explicit target name: "pypi".
/home/ubuntu/scikit-learn/doc/developers/contributing.rst:5: WARNING: Duplicate explicit target name: "here".
/home/ubuntu/scikit-learn/doc/developers/contributing.rst:5: WARNING: Duplicate explicit target name: "project template".
/home/ubuntu/scikit-learn/doc/developers/tips.rst:5: WARNING: Duplicate explicit target name: "userscript".
/home/ubuntu/scikit-learn/doc/faq.rst:26: WARNING: Mismatch: both interpreted text role prefix and reference suffix.
/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:202: WARNING: Footnote [4] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/calibration.rst:205: WARNING: Footnote [5] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/classes.rst:2: WARNING: Literal block expected; none found.
/home/ubuntu/scikit-learn/doc/modules/classes.rst:2: WARNING: Literal block expected; none found.
/home/ubuntu/scikit-learn/doc/modules/classes.rst:2: WARNING: Literal block expected; none found.
/home/ubuntu/scikit-learn/doc/modules/classes.rst:2: WARNING: Literal block expected; none found.
/home/ubuntu/scikit-learn/doc/modules/cross_validation.rst:273: WARNING: malformed hyperlink target.
/home/ubuntu/scikit-learn/doc/modules/cross_validation.rst:509: WARNING: malformed hyperlink target.
/home/ubuntu/scikit-learn/doc/modules/cross_validation.rst:656: WARNING: malformed hyperlink target.
/home/ubuntu/scikit-learn/sklearn/covariance/outlier_detection.py:docstring of sklearn.covariance.EllipticEnvelope:76: WARNING: Footnote [1] is not referenced.
/home/ubuntu/scikit-learn/sklearn/datasets/lfw.py:docstring of sklearn.datasets.fetch_lfw_pairs:82: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/ubuntu/scikit-learn/sklearn/utils/deprecation.py:docstring of sklearn.datasets.load_mlcomp:19: WARNING: Inline strong start-string without end-string.
/home/ubuntu/scikit-learn/sklearn/utils/deprecation.py:docstring of sklearn.datasets.load_mlcomp:12: WARNING: Unknown target name: "set".
/home/ubuntu/scikit-learn/sklearn/linear_model/logistic.py:docstring of sklearn.linear_model.LogisticRegression:146: WARNING: Inline literal start-string without end-string.
docstring of sklearn.metrics.mutual_info_score:40: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/ubuntu/scikit-learn/sklearn/metrics/classification.py:docstring of sklearn.metrics.precision_recall_fscore_support:164: WARNING: Unexpected indentation.
/home/ubuntu/scikit-learn/sklearn/mixture/gaussian_mixture.py:docstring of sklearn.mixture.GaussianMixture:22: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.GridSearchCV:96: WARNING: Unexpected indentation.
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.GridSearchCV:157: WARNING: Undefined substitution referenced: "param_kernel|param_gamma|param_degree|split0_test_score".
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.GridSearchCV:157: WARNING: Undefined substitution referenced: "...".
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.GridSearchCV:157: WARNING: Undefined substitution referenced: "...".
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.GridSearchCV:157: WARNING: Undefined substitution referenced: "...".
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.GridSearchCV:157: WARNING: Undefined substitution referenced: "...".
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.RandomizedSearchCV:111: WARNING: Unexpected indentation.
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.RandomizedSearchCV:182: WARNING: Undefined substitution referenced: "...|rank_test_score".
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.RandomizedSearchCV:182: WARNING: Undefined substitution referenced: "...".
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.RandomizedSearchCV:182: WARNING: Undefined substitution referenced: "...".
/home/ubuntu/scikit-learn/sklearn/model_selection/_search.py:docstring of sklearn.model_selection.RandomizedSearchCV:182: WARNING: Undefined substitution referenced: "...".
/home/ubuntu/scikit-learn/sklearn/model_selection/_validation.py:docstring of sklearn.model_selection.cross_validate:51: WARNING: Unexpected indentation.
/home/ubuntu/scikit-learn/sklearn/multioutput.py:docstring of sklearn.multioutput.ClassifierChain:44: WARNING: Unexpected indentation.
/home/ubuntu/scikit-learn/doc/modules/linear_model.rst:1144: WARNING: Duplicate explicit target name: "f1".
/home/ubuntu/scikit-learn/doc/modules/linear_model.rst:1065: WARNING: Too many autonumbered footnote references: only 0 corresponding footnotes available.
/home/ubuntu/scikit-learn/doc/modules/linear_model.rst:1065: WARNING: Duplicate target name, cannot be used as a unique reference: "f1".
/home/ubuntu/scikit-learn/doc/modules/multiclass.rst:205: WARNING: Footnote [1] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/multiclass.rst:269: WARNING: Footnote [2] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/multiclass.rst:279: WARNING: Footnote [4] is not referenced.
/home/ubuntu/scikit-learn/doc/tutorial/statistical_inference/putting_together.rst.rst:19: WARNING: line number spec is out of range(1-63): '26-66'
/home/ubuntu/scikit-learn/doc/whats_new.rst:475: WARNING: Definition list ends without a blank line; unexpected unindent.
checking consistency... /home/ubuntu/scikit-learn/doc/datasets/kddcup99.rst: WARNING: document isn't included in any toctree
/home/ubuntu/scikit-learn/doc/documentation.rst: WARNING: document isn't included in any toctree
/home/ubuntu/scikit-learn/doc/includes/bigger_toc_css.rst: WARNING: document isn't included in any toctree
/home/ubuntu/scikit-learn/doc/modules/dp-derivation.rst: WARNING: document isn't included in any toctree
/home/ubuntu/scikit-learn/doc/themes/scikit-learn/static/ML_MAPS_README.rst: WARNING: document isn't included in any toctree
/home/ubuntu/scikit-learn/doc/modules/clustering.rst:1346: WARNING: Citation [RH2007] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/ensemble.rst:249: WARNING: Citation [GEW2006] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/outlier_detection.rst:129: WARNING: Citation [RD1999] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/outlier_detection.rst:175: WARNING: Citation [LTZ2008] is not referenced.
/home/ubuntu/scikit-learn/doc/modules/outlier_detection.rst:231: WARNING: Citation [BKNS2000] is not referenced.

@amueller amueller added Documentation Easy Well-defined and straightforward way to resolve Need Contributor labels Jul 19, 2017
@balakmran
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Working on the first set of warnings

@balakmran
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balakmran commented Jul 20, 2017 •
edited
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@amueller Comments for the 1st set,

time_series_cv and group_cv
Fixed with PR #9415

Rouseeuw1984
Fixing with this issue

randomized_l1 and sphx_glr_auto_examples_linear_model_plot_sparse_recovery.py
Tag removed with PR #9031. (Deprecated) What should I do?

vbgmm
Tag modified with PR #6651 in mixture.rst. Fixing it.

multivalued_scorer_wrapping
Refers to new tag added with PR #7388. Fixing it.

scoring_parameter and scoring
Remove prefix underscore. Fixing it.

approximate_nearest_neighbors
Tag removed with PR #9078. (Deprecated) What should I do?

sklearn.metrics.pairwise.pairwise_distances
Not seeing any documentation for pairwise. Only kernels were present in metrics.rst
Should I link it to metrics tag? or remove ref alone?

sphx_glr_auto_examples_model_selection_plot_multi_metric_evaluation
Fixed with PR #9410

@balakmran balakmran mentioned this issue Jul 20, 2017
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@amueller
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Thanks :)

If the example / tag is gone, remove the reference.

Wow there's really no docs for pairwise? Yeah maybe link to metrics.

@balakmran
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ok, Done. PR updated with new commits.

@balakmran
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Comments for 2nd set of warnings

/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.
Should I remove ref and replace with asterick (*)?

/sklearn/model_selection/_search.py
Unsure if this can be fixed. Documentation seems to be good.

Duplicate explicit target name
Seems legit.

/doc/modules/cross_validation.rst:273: WARNING: malformed hyperlink target.
/doc/modules/cross_validation.rst:509: WARNING: malformed hyperlink target.
/doc/modules/cross_validation.rst:656: WARNING: malformed hyperlink target.
Fixed with PR #9415

@amueller
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Should I remove ref and replace with asterick (*)?

Sounds good.
I would leave the rest alone for now.

@balakmran
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Okay

@balakmran balakmran mentioned this issue Jul 27, 2017
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[MRG + 1] Fix Sphinx errors balakmran/scikit-learn
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@amueller @balakmran