scipy 1.10 is now available in experimental.
scikit-learn fails debci tests using it.

We are considering uploading scipy 1.10 to unstable in order to
included it in the forthcoming stable release.  If we proceed with
that, then this bug will become Severity: serious.

test_search.py is affected
A sample from the failing test log is
E       assert -2147483648 == 3

/usr/lib/python3/dist-packages/sklearn/model_selection/tests/test_search.py:1630: AssertionError

Full log:
https://ci.debian.net/data/autopkgtest/unstable/amd64/s/scikit-learn/30693526/log.gz

There appear to be at least 2 separate failures here, both known and
probably fixed upstream.  So yes, 'new upstream version' is the first
thing to try, but we'll need to check what _that_ breaks.

https://github.com/scikit-learn/scikit-learn/issues/23626
https://github.com/scikit-learn/scikit-learn/issues/24424

Am Thu, Jan 26, 2023 at 07:51:23PM +0000 schrieb Rebecca N. Palmer:

Sure.  Thus I uploaded to experimental first.  I hope we can get
some enlightenment from

https://qa.debian.org/excuses.php?experimental=1&package=scikit-learn

soon (at the time of writing this is empty since the package was
just uploaded).  At least autopkgtest is passing.  I'll check
Debian Med related packages manually later.

Kind regards
    Andreas.

scikit-learn looks like it should manageable.

I've uploaded scipy 1.10 to unstable now.

Drew

Hi Drew

I think python3-scipy should declare a Breaks on python3-skbio less
than the version in unstable (0.5.8-3).
This should sort out the autopkgtest regressions of emperor,
python-skbio itself, q2-metadata and q2-quality-control, which are all
passing in unstable, and allow scipy and python-skbio to migrate
together.

Python-cooler seems to have a different failure, and I don't see a bug
filed for it.

Regards
Graham

Ok, I'll add that with the gammapy patch.

cooler seems to be fixed in experimental, I guess it just needs to be
uploaded to unstable.

Drew

Am Tue, Feb 07, 2023 at 09:05:28AM +0100 schrieb Drew Parsons:

Thanks a lot.

I'll do so

Thanks for the hint

     Andreas.

scikit-learn continues to fail with scipy 1.11 from experimental

648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/linear_model/tests/test_quantile.py::test_incompatible_solver_for_sparse_input[interior-point]
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/linear_model/tests/test_quantile.py::test_linprog_failure
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/linear_model/tests/test_quantile.py::test_warning_new_default
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/metrics/tests/test_dist_metrics.py::test_cdist_bool_metric[X_bool0-Y_bool0-kulsinski]
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/metrics/tests/test_dist_metrics.py::test_cdist_bool_metric[X_bool1-Y_bool1-kulsinski]
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/metrics/tests/test_dist_metrics.py::test_pdist_bool_metrics[X_bool0-kulsinski]
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/metrics/tests/test_dist_metrics.py::test_pdist_bool_metrics[X_bool1-kulsinski]
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/metrics/tests/test_pairwise.py::test_pairwise_boolean_distance[kulsinski]
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/neighbors/tests/test_neighbors.py::test_kneighbors_brute_backend[float64-kulsinski]
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/neighbors/tests/test_neighbors.py::test_radius_neighbors_brute_backend[kulsinski]
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/preprocessing/tests/test_data.py::test_power_transformer_yeojohnson_any_input[X3]
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/tests/test_base.py::test_clone_sparse_matrices
648s FAILED ../../../../usr/lib/python3/dist-packages/sklearn/tests/test_common.py::test_estimators[PowerTransformer()-check_fit2d_1sample]
648s = 13 failed, 24496 passed, 2459 skipped, 2 deselected, 116 xfailed, 43 xpassed, 2600 warnings in 577.48s (0:09:37) =

scipy 1.11 is currently in experimental but I'd like to upload soon to
unstable to resolve Bug#1061605, which would make this bug serious.

It's likely fixed in the newer upstream releases.

scipy 1.11 is now uploaded to unstable,
so bumping this bug severity to serious.

We believe that the bug you reported is fixed in the latest version of
scikit-learn, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1029701@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated scikit-learn package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Sat, 17 Feb 2024 14:59:42 +0100
Source: scikit-learn
Architecture: source
Version: 1.4.1.post1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers <debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 1003165 1008369 1018635 1027208 1029701 1046775 1049646 1059206
Changes:
 scikit-learn (1.4.1.post1+dfsg-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream version
     Closes: #1029701, #1008369, #1027208, #1003165
   * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
   * Build-Depends: python3-sphinx-copybutton
   * Support loong64
     Closes: #1059206
   * Drop nose from Build-/Test-Depends
     Closes: #1018635
   * Fix clean target
     Closes: #1046775, #1049646
   * Work around unknown key 'recommender' in sphinx
   * Exclude minimized jquery JS from source and use symlink to Debian
     packaged min.js instead (crossing fingers that the version plays nicely)
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