Repository: scikit-learn/scikit-learn
Pull request: CI raise error for all kind of deprecation warnings in doc build
closes #27430

We are currently catching any deprecation warnings in the test and source code but not in our examples. This PRs intend to raise an error if there is any.

Since we are using lock file, we should not have warning until and if any when updating the lock files, then we should fix them.

It is expected to fail until we merge all the PRs fixing the deprecation warning in the examples.

Problem statement:
Catching deprecation warnings from examples
Up-to-now, we never check deprecation warnings that are raised when executing our examples.
I assume that we could scrap the RST generated file to find such warning:

```python
from pathlib import Path
from pprint import pprint

from sklearn.utils.fixes import VisibleDeprecationWarning

from conf import sphinx_gallery_conf

warning_types = (DeprecationWarning, FutureWarning, VisibleDeprecationWarning)

auto_examples_path = Path(sphinx_gallery_conf["gallery_dirs"][0])

example_raising_warnings = []
for example_filename in auto_examples_path.rglob("*.rst"):
    with open(example_filename, "r") as f:
        lines = f.readlines()
        for line in lines:
            if any([warning_type.__name__ in line for warning_type in warning_types]):
                example_raising_warnings.append(
                    f"{str(example_filename)}: {line.strip()}"
                )

pprint(example_raising_warnings, width=1_000)
```

What I am wondering is exactly how do we want to use it with the CI. Supposedly, it should be only CircleCI but should target only PRs?

Hints from issue discussion:
For instance this is the current output:

```shell
> python warning_scraping_from_generated_examples.py
/home/glemaitre/Documents/packages/scikit-learn/doc/conf.py:81: UserWarning:

jupyterlite_sphinx is not installed, you need to install it if you want JupyterLite links to appear in each example

['auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1119: FutureWarning:',
 'auto_examples/model_selection/plot_grid_search_stats.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1119: FutureWarning:',
 'auto_examples/mixture/plot_gmm_selection.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/mixture/plot_gmm_selection.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/mixture/plot_gmm_selection.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/mixture/plot_gmm_selection.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/mixture/plot_gmm_selection.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/mixture/plot_gmm_selection.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/release_highlights/plot_release_highlights_0_22_0.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/svm/_classes.py:32: FutureWarning:',
 'auto_examples/release_highlights/plot_release_highlights_0_22_0.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/svm/_classes.py:32: FutureWarning:',
 'auto_examples/release_highlights/plot_release_highlights_0_22_0.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/svm/_classes.py:32: FutureWarning:',
 'auto_examples/release_highlights/plot_release_highlights_0_22_0.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/svm/_classes.py:32: FutureWarning:',
 'auto_examples/release_highlights/plot_release_highlights_0_22_0.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/svm/_classes.py:32: FutureWarning:',
 'auto_examples/release_highlights/plot_release_highlights_0_22_0.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/svm/_classes.py:32: FutureWarning:',
 'auto_examples/cluster/plot_face_compress.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/preprocessing/_discretization.py:248: FutureWarning:',
 'auto_examples/cluster/plot_face_compress.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/preprocessing/_discretization.py:248: FutureWarning:',
 'auto_examples/preprocessing/plot_discretization_strategies.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/preprocessing/_discretization.py:248: FutureWarning:',
 'auto_examples/preprocessing/plot_discretization_strategies.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/preprocessing/_discretization.py:248: FutureWarning:',
 'auto_examples/preprocessing/plot_discretization_strategies.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/preprocessing/_discretization.py:248: FutureWarning:',
 'auto_examples/preprocessing/plot_discretization_strategies.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/preprocessing/_discretization.py:248: FutureWarning:',
 'auto_examples/preprocessing/plot_discretization_strategies.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/preprocessing/_discretization.py:248: FutureWarning:',
 'auto_examples/preprocessing/plot_discretization_strategies.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/preprocessing/_discretization.py:248: FutureWarning:',
 'auto_examples/linear_model/plot_ard.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/linear_model/_bayes.py:53: FutureWarning:',
 'auto_examples/linear_model/plot_ard.rst: /home/glemaitre/Documents/packages/scikit-learn/sklearn/linear_model/_bayes.py:53: FutureWarning:',
 'auto_examples/linear_model/plot_ard.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/linear_model/plot_ard.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/classification/plot_lda_qda.rst: /home/glemaitre/Documents/packages/scikit-learn/examples/classification/plot_lda_qda.py:30: MatplotlibDeprecationWarning:',
 'auto_examples/inspection/plot_partial_dependence.rst: /home/glemaitre/Documents/packages/scikit-learn/examples/inspection/plot_partial_dependence.py:113: FutureWarning:',
 'auto_examples/inspection/plot_partial_dependence.rst: /home/glemaitre/Documents/packages/scikit-learn/examples/inspection/plot_partial_dependence.py:117: FutureWarning:',
 'auto_examples/inspection/plot_partial_dependence.rst: /home/glemaitre/Documents/packages/scikit-learn/examples/inspection/plot_partial_dependence.py:117: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1119: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1119: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1119: FutureWarning:',
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 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
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 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
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 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_causal_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
 'auto_examples/inspection/plot_linear_model_coefficient_interpretation.rst: /home/glemaitre/mambaforge/envs/dev/lib/python3.10/site-packages/seaborn/_oldcore.py:1498: FutureWarning:',
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```
We should have it in the CI, the same way we have it for pytest/doctest I think. And when in a PR we do `[doc build]`, then these are triggered.
> We should have it in the CI, the same way we have it for pytest/doctest I think.

This is where it is tricky. We need to generate the documentation and it is never done on Azure.

On PRs, we can scrap the warnings from the example generated.

However, the only way to properly discover the warning is only when we run `[doc build]` that is almost never done. I would assume that if our nightly CRON job would execute trigger a full documentation build then we could catch those. Otherwise, it is unlikely.
We run those whenever the PR is merged as a part of the CI in `main` though.
Looking quickly at examples with warnings in https://github.com/scikit-learn/scikit-learn/issues/27430#issuecomment-1729444562, it seems like you need to special case the release highlights, since we probably don't care too much that old release highlights have warnings. 

Also I feel there may be some annoying situations where we will have to make the code in the example more complicated to be without warnings for the doc build and still run with the doc-min-depencies build, but maybe this is OK.
we probably don't care about warnings in doc-min-dependencies? 
> it seems like you need to special case the release highlights, since we probably don't care too much that old release highlights have warnings.

Yep this one I am not sure about. Up to today, we always tried to still make it work with a comment if required.

> Also I feel there may be some annoying situations where we will have to make the code in the example more complicated to be without warnings for the doc build and still run with the doc-min-depencies build, but maybe this is OK.

It will be case to case I assume. I could at this time to evaluate if we need to bump matplotlib for the mimimum doc to use the simplify code version. Having the lock file is indeed pretty handy to not savage all PRs.
> we probably don't care about warnings in doc-min-dependencies?

From experience, this is more that you need to use a new matplotlib functionality to make the new doc pass, and it will break the min doc CI. And then this is a big split to make it work between both. So to me, this is usually coming back to evaluate a bump to the matplotlib version for the min doc.

On the general comment that we "only" get a warning with old version, then I agree with you: I don't really care.

Commit message: [doc build][azure parallel] trigger documentation

Patch to review:
diff --git a/doc/conf.py b/doc/conf.py
index 1d4b061f9afb5..6dbbb1be670fd 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -692,6 +692,8 @@ def setup(app):
     ),
 )
 
+from sklearn.utils.fixes import VisibleDeprecationWarning
+
 warnings.filterwarnings(
     "ignore",
     category=UserWarning,
@@ -700,6 +702,11 @@ def setup(app):
         " non-GUI backend, so cannot show the figure."
     ),
 )
+# Raise warning as error in example to catch warnings when building the documentation
+# Since we are using lock files to build the documentation, we should not have any
+# warnings or fix them before to update the lock files.
+for warning_type in (FutureWarning, DeprecationWarning, VisibleDeprecationWarning):
+    warnings.filterwarnings("error", category=warning_type)
 
 # maps functions with a class name that is indistinguishable when case is
 # ignore to another filename


Code review comments:
diff_hunk: @@ -700,6 +702,11 @@ def setup(app):
         " non-GUI backend, so cannot show the figure."
     ),
 )
+# Raise warning as error in example to catch warnings when building the documentation
+# Since we are using lock files to build the documentation, we should not have any
+# warnings or fix them before to update the lock files.
path: doc/conf.py
text: @user1:
```suggestion
# warnings. Before updating the lock files, we need to fix them.
```