Source: python-pomegranate
Version: 0.14.8-4
Severity: serious

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Dear maintainer,

your package has an autopkgtest regression with NumPy 1.26.
Hopefully relevent excerpt from the test log:

52s > ???
52s E ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
52s
52s pomegranate/kmeans.pyx:232: ValueError
52s =============================== warnings summary ===============================
52s ../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37
52s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.
fromtimestamp(timestamp, datetime.UTC).
52s EPOCH = datetime.datetime.utcfromtimestamp(0)
52s
52s tests/test_custom_distributions.py: 29600 warnings
52s tests/test_hmm.py: 375 warnings
52s /usr/lib/python3/dist-packages/joblib/parallel.py:1792: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this
operation. (Deprecated NumPy 1.25.)
52s res = func(*args, **kwargs)
52s
52s tests/test_custom_distributions.py: 40 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:223: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 400 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:232: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 200 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:345: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 200 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:359: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict(X), model2.predict(X))
52s
52s tests/test_custom_distributions.py: 200 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:373: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict_proba(X), model2.predict_proba(X))
52s
52s tests/test_custom_distributions.py: 200 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:387: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict_log_proba(X), model2.predict_log_proba(X))
52s
52s tests/test_custom_distributions.py: 200 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:402: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 2000 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:411: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 40 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:493: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 400 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:504: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 200 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:620: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 200 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:634: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict(X), model2.predict(X))
52s
52s tests/test_custom_distributions.py: 200 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:648: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict_proba(X), model2.predict_proba(X))
52s
52s tests/test_custom_distributions.py: 200 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:662: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict_log_proba(X), model2.predict_log_proba(X))
52s
52s tests/test_custom_distributions.py: 200 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:679: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 2000 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:690: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 10 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:700: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 30 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:705: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_equal(model1.predict(X), model2.predict(X))
52s
52s tests/test_custom_distributions.py: 30 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:710: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict_proba(X), model2.predict_proba(X))
52s
52s tests/test_custom_distributions.py: 30 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:715: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict_log_proba(X), model2.predict_log_proba(X))
52s
52s tests/test_custom_distributions.py: 10 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:724: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py::test_custom_normal_hmm_from_samples
52s tests/test_custom_distributions.py::test_custom_normal_hmm_from_samples
52s tests/test_custom_distributions.py::test_custom_normal_hmm_from_samples
52s tests/test_custom_distributions.py::test_custom_normal_hmm_from_samples
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:733: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 50 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:787: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 150 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:792: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict(X), model2.predict(X))
52s
52s tests/test_custom_distributions.py: 150 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:797: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict_proba(X), model2.predict_proba(X))
52s
52s tests/test_custom_distributions.py: 150 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:802: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.predict_log_proba(X), model2.predict_log_proba(X))
52s
52s tests/test_custom_distributions.py: 30 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:811: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s tests/test_custom_distributions.py: 20 warnings
52s /tmp/autopkgtest-lxc.qczb1z7m/downtmp/autopkgtest_tmp/tests/test_custom_distributions.py:820: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from
your array before performing this operation. (Deprecated NumPy 1.25.)
52s assert_array_almost_equal(model1.log_probability(X), model2.log_probability(X))
52s
52s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
52s =========================== short test summary info ============================
52s ERROR tests/test_kmeans.py::test_kmeans_from_samples - ValueError: The truth ...
52s ERROR tests/test_kmeans.py::test_kmeans_from_samples_parallel - ValueError: T...
52s ERROR tests/test_kmeans.py::test_kmeans_predict - ValueError: The truth value...
52s ERROR tests/test_kmeans.py::test_kmeans_predict_parallel - ValueError: The tr...
52s ERROR tests/test_kmeans.py::test_kmeans_predict_large - ValueError: The truth...
52s ERROR tests/test_kmeans.py::test_kmeans_predict_large_parallel - ValueError: ...
52s ERROR tests/test_kmeans.py::test_kmeans_fit - ValueError: The truth value of ...
52s ERROR tests/test_kmeans.py::test_kmeans_fit_parallel - ValueError: The truth ...
52s ERROR tests/test_kmeans.py::test_kmeans_multiple_init - ValueError: The truth...
52s ERROR tests/test_kmeans.py::test_kmeans_ooc_from_samples - ValueError: The tr...
52s ERROR tests/test_kmeans.py::test_kmeans_ooc_fit - ValueError: The truth value...
52s ERROR tests/test_kmeans.py::test_kmeans_minibatch_from_samples - ValueError: ...
52s ERROR tests/test_kmeans.py::test_kmeans_minibatch_fit - ValueError: The truth...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_from_samples - ValueError: The tr...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_from_samples_parallel - ValueErro...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_fit - ValueError: The truth value...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_fit_parallel - ValueError: The tr...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_fit_large - ValueError: The truth...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_fit_large_parallel - ValueError: ...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_predict - ValueError: The truth v...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_predict_parallel - ValueError: Th...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_large_predict - ValueError: The t...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_large_predict_parallel - ValueErr...
52s ERROR tests/test_kmeans.py::test_kmeans_nan_multiple_init - ValueError: The t...
52s ERROR tests/test_kmeans.py::test_kmeans_ooc_nan_from_samples - ValueError: Th...
52s ERROR tests/test_kmeans.py::test_kmeans_ooc_nan_fit - ValueError: The truth v...
52s ERROR tests/test_kmeans.py::test_kmeans_minibatch_nan_from_samples - ValueErr...
52s ERROR tests/test_kmeans.py::test_kmeans_minibatch_nan_fit - ValueError: The t...
52s =============== 570 passed, 37520 warnings, 28 errors in 12.06s ================


Cheers
Timo


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--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

Processing control commands:

tags -1 + patch

Bug #1067233 [src:python-pomegranate] python-pomegranate: autopkgtest regression with NumPy 1.26
Bug #1067294 [src:python-pomegranate] python-pomegranate: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13
Added tag(s) patch.
Added tag(s) patch.

--
1067233: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1067233
1067294: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1067294
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

Control: tags -1 + patch

Hi Maintainer

The attached patch fixes the test failures for me.

I noticed in this package's changelog that its only purpose is to work
with cnvkit. I have not tested whether cnvkit still functions with
this patch in place.

Regards
Graham

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--- SoupGate-Win32 v1.05
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Control: tag -1 pending

Hello,

Bug #1067233 in python-pomegranate reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/python-team/packages/python-pomegranate/-/commit/a9381a9a177cf18e72d60a67232f592744d3ac87

------------------------------------------------------------------------
Add patch from Graham Inggs to fix compat with NumPy 1.26+, thank you Graham! Closes: #1067233, #1067294
------------------------------------------------------------------------

(this message was generated automatically)
--
Greetings

https://bugs.debian.org/1067233

--- SoupGate-Win32 v1.05
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Processing control commands:

tag -1 pending

Bug #1067233 [src:python-pomegranate] python-pomegranate: autopkgtest regression with NumPy 1.26
Bug #1067294 [src:python-pomegranate] python-pomegranate: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13
Added tag(s) pending.
Added tag(s) pending.

--
1067233: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1067233
1067294: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1067294
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

--- SoupGate-Win32 v1.05
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This is a multi-part message in MIME format...

Your message dated Fri, 12 Apr 2024 11:21:17 +0000
with message-id <E1rvEy5-00FNqL-2o@fasolo.debian.org>
and subject line Bug#1067294: fixed in python-pomegranate 0.14.8-5
has caused the Debian Bug report #1067294,
regarding python-pomegranate: autopkgtest regression with NumPy 1.26
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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immediately.)


--
1067294: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1067294
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