[MRG] DOC Fix warnings in examples by adrinjalali · Pull Request #12654 · scikit-learn/scikit-learn

adrinjalali · 2018-11-22T16:29:27Z

Fixe or suppresses many warnings in examples, including matplotlib complaining about the non-gui backend.

…iclass.py

…ate_selection.py

…_20newsgroups.py

rth

Very nice! A few comments are below, overall LGTM.

In general, I don't think it's such a big issue to have e.g. a ConvergenceWarning in an example if a few are remaining. That's a real use case, and it's better to show that to user rather than hide it (just for the sake of having no warnings in sphinx log).

examples/calibration/plot_calibration_curve.py

examples/cluster/plot_adjusted_for_chance_measures.py

examples/exercises/plot_cv_diabetes.py

examples/linear_model/plot_lasso_model_selection.py

rth · 2018-12-28T12:47:30Z

examples/linear_model/plot_sgd_early_stopping.py

 estimator_dict = {
    'No stopping criterion':
-    linear_model.SGDClassifier(tol=None, n_iter_no_change=3),
+    linear_model.SGDClassifier(tol=-np.inf, n_iter_no_change=3),


Why not None (or just remove it altogether since it's the default)?

Had it -inf cause that's the default now, but changed to 1e-3 which is the new default. Not passing it causes a warning.

rth · 2018-12-28T12:48:37Z

examples/linear_model/plot_sparse_logistic_regression_20newsgroups.py


-t0 = time.clock()
+warnings.filterwarnings("ignore", category=ConvergenceWarning,
+                        module="sklearn")


I would argue that it's better to show the convergence warning to user rather than hide it.

My idea here is to be explicit in the code that we know the model is not converging, but we know what we're doing. I'd say if such a usecase happens in production, the user should explicitly have this in the code.

…rn into examples/warnings

jnothman · 2019-01-02T21:21:32Z

LGTM, though tests are failing.

adrinjalali · 2019-01-02T22:38:46Z

yep, the tests fail due to #12906, they used to pass though.

adrinjalali · 2019-01-17T10:05:09Z

Tests finally pass, [hopefully final] reviews welcome :)

jnothman · 2019-01-17T10:41:23Z

Thanks @adrinjalali

jnothman · 2019-01-17T12:24:59Z

Hmm... this has broken Circle with the following TeX error:


! Package pdftex.def Error: File `modules/../auto_examples/svm/images/sphx_glr_
plot_iris_001.png' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.16846 ...vm/images/sphx_glr_plot_iris_001}.png}}
                                                  \end{figure}^^M
!  ==> Fatal error occurred, no output PDF file produced!

Any idea what the cause is, or does it need investigation?

jnothman · 2019-01-17T12:27:15Z

Ah, I see. File name changed.

adrinjalali · 2019-01-17T12:27:37Z

yep examples/svm/plot_iris.py → examples/svm/plot_svm_iris.py

jnothman · 2019-01-17T12:32:06Z

Fixing in 486f8fc

Fixe or suppresses many warnings in examples, including matplotlib complaining about the non-gui backend.

This reverts commit 492d014.

Fixe or suppresses many warnings in examples, including matplotlib complaining about the non-gui backend.

adrinjalali added 30 commits November 22, 2018 13:05

fix normed->density deprecated matplotlib parameter

ce41bc1

fix example/svm/plot_iris.py warnings

dbc2f26

fix warnings in examples/svm/plot_svm_nonlinear.py

15ac45b

fix warning in examples/svm/plot_svm_regression.py

6f2a87d

rename two plot_iris files to avoid conflict

6f82ec5

ignore matplotlib frontend engine warning

9172621

fix matplotlib warning in examples/plot_johnson_lindenstrauss_bound.py

6c22b26

fix warnings in examples/applications/plot_out_of_core_classification.py

71a8c3a

fix warnings in examples/calibration/plot_calibration_curve.py

ed1d41b

fix matplotlib warnings in examples/calibration/plot_calibration.py

b87b025

fix matplotlib warnings in examples/calibration/plot_calibration_mult…

fd6cc59

…iclass.py

fix warnings in examples/classification/plot_classifier_comparison.py

60c6b87

fix warnings in examples/cluster/plot_coin_segmentation.py

f001039

fix warnings in examples/cluster/plot_coin_ward_segmentation.py

55b95a7

fix warnings in examples/cluster/plot_affinity_propagation.py

3f8322d

fix warning in examples/cluster/plot_dbscan.py

fcefd89

fix warnings in examples/cluster/plot_adjusted_for_chance_measures.py

b5f520b

fix warning in examples/cluster/plot_feature_agglomeration_vs_univari…

e508e0f

…ate_selection.py

fix warning in examples/cluster/plot_kmeans_digits.py

56f92a5

fix warnings in examples/compose/plot_compare_reduction.py

9dc891d

fix warning in examples/decomposition/plot_sparse_coding.py

4f53c53

fix warning in examples/decomposition/plot_faces_decomposition.py

c044b12

fix warning in examples/exercises/plot_cv_diabetes.py

9892f67

fix warning in examples/linear_model/plot_sgd_separating_hyperplane.py

266760f

fix warnings in examples/linear_model/plot_sgd_weighted_samples.py

208f92d

fix warnings in examples/linear_model/plot_sgd_comparison.py

776c127

fix warning in examples/linear_model/plot_lasso_model_selection.py

545d777

fix import warning position

54d505f

fix warnings in examples/linear_model/plot_sparse_logistic_regression…

c0ac016

…_20newsgroups.py

fix warnings in examples/linear_model/plot_sgd_early_stopping.py

641564c

Merge remote-tracking branch 'upstream/master' into examples/warnings

be3ecad

adrinjalali mentioned this pull request Dec 20, 2018

[MRG] circle-ci should only run/build plot_* files #12797

Merged

adrinjalali mentioned this pull request Dec 28, 2018

MNT CI run all examples if some code is changed #12880

Closed

rth approved these changes Dec 28, 2018

View reviewed changes

adrinjalali mentioned this pull request Jan 2, 2019

change double backtick to single backtick do take advantage of default role? #12535

Closed

adrinjalali added 4 commits January 2, 2019 15:21

add a comment for EPSILON

207f218

change tol to 1e-3

b8beddc

Merge branch 'examples/warnings' of github.com:adrinjalali/scikit-lea…

94d200c

…rn into examples/warnings

Merge remote-tracking branch 'upstream/master' into examples/warnings

09ff1fe

adrinjalali mentioned this pull request Jan 2, 2019

AttributeError: 'PrettyPrinter' object has no attribute '_indent_at_name' #12906

Closed

adrinjalali added 2 commits January 12, 2019 13:27

Merge remote-tracking branch 'upstream/master' into examples/warnings

f385836

Merge remote-tracking branch 'upstream/master' into examples/warnings

8fdf909

jnothman approved these changes Jan 17, 2019

View reviewed changes

jnothman merged commit 69c8967 into scikit-learn:master Jan 17, 2019

adrinjalali deleted the examples/warnings branch January 17, 2019 10:42

thomasjpfan pushed a commit to thomasjpfan/scikit-learn that referenced this pull request Feb 7, 2019

DOC Fix warnings in examples (scikit-learn#12654)

df4ce74

Fixe or suppresses many warnings in examples, including matplotlib complaining about the non-gui backend.

xhluca pushed a commit to xhluca/scikit-learn that referenced this pull request Apr 28, 2019

DOC Fix warnings in examples (scikit-learn#12654)

492d014

Fixe or suppresses many warnings in examples, including matplotlib complaining about the non-gui backend.

xhluca pushed a commit to xhluca/scikit-learn that referenced this pull request Apr 28, 2019

Revert "DOC Fix warnings in examples (scikit-learn#12654)"

6da99a6

This reverts commit 492d014.

xhluca pushed a commit to xhluca/scikit-learn that referenced this pull request Apr 28, 2019

Revert "DOC Fix warnings in examples (scikit-learn#12654)"

f9ace00

This reverts commit 492d014.

koenvandevelde pushed a commit to koenvandevelde/scikit-learn that referenced this pull request Jul 12, 2019

DOC Fix warnings in examples (scikit-learn#12654)

2af76e8

Fixe or suppresses many warnings in examples, including matplotlib complaining about the non-gui backend.

This was referenced Jul 12, 2019

deprecation warnings in coin examples #11554

Closed

[MRG] Fixed warnings mentioned in #11554 #11670

Closed

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