GNU bug report logs - #67630
Build python-phenograph.x86_64-linux on master is broken.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Subject: bug#67630: closed (Re: bug#67630: Build python-phenograph.x86_64-linux
 on master is broken.)
Date: Tue, 16 Jul 2024 18:57:03 +0000

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Your bug report

#67630: Build python-phenograph.x86_64-linux on master is broken.

which was filed against the guix package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 67630 <at> debbugs.gnu.org.

-- 
67630: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=67630
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Efraim Flashner <efraim <at> flashner.co.il>
To: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Cc: 67630-done <at> debbugs.gnu.org
Subject: Re: bug#67630: Build python-phenograph.x86_64-linux on master is
 broken.
Date: Tue, 16 Jul 2024 21:55:15 +0300

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This package appears to be building correctly now.

-- 
Efraim Flashner   <efraim <at> flashner.co.il>   רנשלפ םירפא
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From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
To: bug-guix <bug-guix <at> gnu.org>
Subject: Re: Build python-phenograph.x86_64-linux on master is broken.
Date: Mon, 04 Dec 2023 17:05:43 -0500

Hi,

cuirass <at> gnu.org (Cuirass) writes:

> <p>The build <b>python-phenograph.x86_64-linux</b> for specification <b>master</b> is
> broken. You can find the detailed information about this build <a
> href="https://ci.guix.gnu.org/build/2736972/details">here</a>.</p>
>
> https://ci.guix.gnu.org/build/2736972/details

The failure reads:

--8<---------------cut here---------------start------------->8---
=================================== FAILURES ===================================
___________________________ test_classify_generated ____________________________

cluster_dataset_generated = <tests.conftest.GeneratedClusterDataset object at 0x7ffdcfdb90f0>

    def test_classify_generated(cluster_dataset_generated):
        output, _ = classify(
            cluster_dataset_generated.train_set, cluster_dataset_generated.test_set
        )
        actual = cluster_dataset_generated.test_labels
>       assert all([p == a for p, a in zip(output, actual)])
E       assert False
E        +  where False = all([True, True, False])

tests/test_classify.py:9: AssertionError
----------------------------- Captured stdout call -----------------------------
Finding 30 nearest neighbors using minkowski metric and 'auto' algorithm
=============================== warnings summary ===============================
phenograph/cluster.py:13
  /tmp/guix-build-python-phenograph-1.5.7.drv-0/PhenoGraph-1.5.7/phenograph/cluster.py:13: DeprecationWarning: Please use `spmatrix` from the `scipy.sparse` namespace, the `scipy.sparse.base` namespace is deprecated.
    from scipy.sparse.base import spmatrix

tests/test_classify.py::test_classify_generated
tests/test_classify.py::test_classify_generated
tests/test_classify.py::test_classify_generated
tests/test_classify.py::test_classify_fixed
tests/test_classify.py::test_classify_fixed
tests/test_classify.py::test_classify_fixed
tests/test_classify.py::test_random_walk_probabilities_fixed
tests/test_classify.py::test_random_walk_probabilities_fixed
tests/test_classify.py::test_random_walk_probabilities_fixed
  /tmp/guix-build-python-phenograph-1.5.7.drv-0/PhenoGraph-1.5.7/phenograph/classify.py:43: DeprecationWarning: Please use `bicgstab` from the `scipy.sparse.linalg` namespace, the `scipy.sparse.linalg.isolve` namespace is deprecated.
    sp.linalg.isolve.bicgstab(Lu, b.T.todense(), atol="legacy") for b in B.T

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_classify.py::test_classify_generated - assert False
=================== 1 failed, 5 passed, 10 warnings in 3.48s ===================
--8<---------------cut here---------------end--------------->8---

The test is probably flaky and should be reported upstream and disabled
in our package meanwhile.

-- 
Thanks,
Maxim

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