Your message dated Fri, 23 Oct 2026 19:20:22 +0000
with message-id <[email protected]>
and subject line Bug#1149340: fixed in python-csb 1.2.5+dfsg-11
has caused the Debian Bug report #1149340,
regarding python-csb: FTBFS against python 3.15rc2 (several failing tests)
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1149340: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1149340
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:python-csb
Version: 1.2.5+dfsg-10
User: [email protected]
Usertags: python3.15
Tags: ftbfs, forky, sid
Severity: important
Hi!
While rebuilding the python related packages against the Python 3.15rc2 version
we found that python-csb fails to build from source:
https://debusine.debian.net/debian/r-python-python3.15/artifact/4856727/
From the log, the error seems to be:
======================================================================
ERROR: testRotationMatrix
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/numeric.TestMath.testRotationMatrix)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/numeric/__init__.py",
line 109, in testRotationMatrix
R2 = rotation_matrix([0, 0, 1], np.pi / 2.0)
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/numeric/__init__.py",
line 155, in rotation_matrix
axis = numpy.asfarray(axis) / norm(axis)
^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 778, in
__getattr__
raise AttributeError(
...<3 lines>...
)
AttributeError: `np.asfarray` was removed in the NumPy 2.0 release. Use
`np.asarray` with a proper dtype instead.
======================================================================
ERROR: testRead
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/bio/io/mrc.TestDensityMapReader.testRead)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/bio/io/mrc/__init__.py",
line 36, in testRead
density = self.reader.read()
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/bio/io/mrc.py",
line 248, in read
array = numpy.fromstring(map_data, numpy.float32, count)
ValueError: The binary mode of fromstring is removed, use frombuffer instead
======================================================================
ERROR: testReconstructHeader
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/bio/io/mrc.TestDensityMapWriter.testReconstructHeader)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/bio/io/mrc/__init__.py",
line 55, in setUp
self.density = self.reader.read()
~~~~~~~~~~~~~~~~^^
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/bio/io/mrc.py",
line 248, in read
array = numpy.fromstring(map_data, numpy.float32, count)
ValueError: The binary mode of fromstring is removed, use frombuffer instead
======================================================================
ERROR: testWriteDensity
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/bio/io/mrc.TestDensityMapWriter.testWriteDensity)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/bio/io/mrc/__init__.py",
line 55, in setUp
self.density = self.reader.read()
~~~~~~~~~~~~~~~~^^
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/bio/io/mrc.py",
line 248, in read
array = numpy.fromstring(map_data, numpy.float32, count)
ValueError: The binary mode of fromstring is removed, use frombuffer instead
======================================================================
ERROR: testFiveReplicas
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/statistics/samplers.TestReplicaHistory.testFiveReplicas)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/statistics/samplers/__init__.py",
line 899, in testFiveReplicas
assert(self._assertIdenticalProjTrajs(samples, swap_interval))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/statistics/samplers/__init__.py",
line 866, in _assertIdenticalProjTrajs
ok.append(True in [np.all(np.array(t1) == np.array(t2)) for t1 in trajs1
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: operands could not be broadcast together with shapes (85,) (75,)
======================================================================
ERROR: testFiveReplicasOffset
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/statistics/samplers.TestReplicaHistory.testFiveReplicasOffset)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/statistics/samplers/__init__.py",
line 909, in testFiveReplicasOffset
assert(self._assertIdenticalProjTrajs(samples, swap_interval, first_swap))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/statistics/samplers/__init__.py",
line 866, in _assertIdenticalProjTrajs
ok.append(True in [np.all(np.array(t1) == np.array(t2)) for t1 in trajs1
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: operands could not be broadcast together with shapes (103,) (73,)
======================================================================
ERROR: testFourReplicas
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/statistics/samplers.TestReplicaHistory.testFourReplicas)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/statistics/samplers/__init__.py",
line 889, in testFourReplicas
assert(self._assertIdenticalProjTrajs(samples, swap_interval))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/statistics/samplers/__init__.py",
line 866, in _assertIdenticalProjTrajs
ok.append(True in [np.all(np.array(t1) == np.array(t2)) for t1 in trajs1
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: operands could not be broadcast together with shapes (125,) (105,)
======================================================================
ERROR: testTwoReplicas
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/statistics/samplers.TestReplicaHistory.testTwoReplicas)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/statistics/samplers/__init__.py",
line 879, in testTwoReplicas
assert(self._assertIdenticalProjTrajs(samples, swap_interval))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/statistics/samplers/__init__.py",
line 866, in _assertIdenticalProjTrajs
ok.append(True in [np.all(np.array(t1) == np.array(t2)) for t1 in trajs1
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: operands could not be broadcast together with shapes (195,) (305,)
======================================================================
ERROR: runTest
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/core.TestDeepCopy.runTest)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/core/__init__.py",
line 21, in runTest
self.assertNotEquals(id(obj), id(copy))
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'TestDeepCopy' object has no attribute 'assertNotEquals'. Did
you mean: 'assertNotEqual'?
======================================================================
FAIL: testRecusionLimit
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/io.TestDumpLoad.testRecusionLimit)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/io/__init__.py",
line 528, in testRecusionLimit
with self.assertRaises(RuntimeError):
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
AssertionError: RuntimeError not raised
======================================================================
FAIL: testComparison
(build/reproducible-path/python-csb-1-2-5+dfsg/-pybuild/cpython3_3-14_csb/build/csb/test/cases/core.TestEnum.testComparison)
----------------------------------------------------------------------
Traceback (most recent call last):
File
"/build/reproducible-path/python-csb-1.2.5+dfsg/.pybuild/cpython3_3.14_csb/build/csb/test/cases/core/__init__.py",
line 73, in testComparison
self.assertFalse(self.enum.C == 66)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
AssertionError: True is not false
----------------------------------------------------------------------
Please note that while we ran into this error during the rebuild against Python
3.15, that doesn't mean that the root cause for the failure is necessarily the
new Python version.
Setting the severity to important for now. Once Python 3.15 is released and
later added to python3-defaults, this bug will become release critical.
--
Cheers,
Marga
--- End Message ---
--- Begin Message ---
Source: python-csb
Source-Version: 1.2.5+dfsg-11
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-csb, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated python-csb 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 23 Oct 2026 20:43:07 +0200
Source: python-csb
Architecture: source
Version: 1.2.5+dfsg-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1085900 1149340
Changes:
python-csb (1.2.5+dfsg-11) unstable; urgency=medium
.
* Fix Python3.12 string syntax
Closes: #1085900
* Exclude Python 3.15 from build (Closes: #1149340)
as well as fixing further NumPy issues
- replace numpy.asfarray (removed in numpy 2.0) with numpy.asarray
- replace binary numpy.fromstring with numpy.frombuffer
- fix failing test-suite assertions (replica exchange samplers,
enum comparison, pickling recursion limit)
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
* d/watch: version=5
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Remove Priority field (cme)
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* Reformat the Last-Update date as ISO YYYY-MM-DD.
* debputy lint --auto-fix (routine-update)
Checksums-Sha1:
b4a2485b90926edf350eeaf91b18bd0d982919e3 2267 python-csb_1.2.5+dfsg-11.dsc
4b11434539ed3a20d55c33a7fed04d636b48d1c5 14348
python-csb_1.2.5+dfsg-11.debian.tar.xz
7d9a8fbba251d20362c0fe95c9255d7e16f35777 9228
python-csb_1.2.5+dfsg-11_amd64.buildinfo
Checksums-Sha256:
e4cc18b9f998ea6aabce344c047eac852e22ae5a5adfb2c9429effda911771bd 2267
python-csb_1.2.5+dfsg-11.dsc
5389fb668b49b444e19ea6783e2f9954320353e2b64dbef9d4b039241ce10dbf 14348
python-csb_1.2.5+dfsg-11.debian.tar.xz
f06bc2b52f1d948981edee2e0e77fc1bae0b436a5e99df2924c75f97c465e0fa 9228
python-csb_1.2.5+dfsg-11_amd64.buildinfo
Files:
ae933ae5e51102ae2b9be48eef89feba 2267 science optional
python-csb_1.2.5+dfsg-11.dsc
ce6ae5b25d5ce80f2177af37096b4cdc 14348 science optional
python-csb_1.2.5+dfsg-11.debian.tar.xz
5b5a9301f89cbd519027212f8c38b067 9228 science optional
python-csb_1.2.5+dfsg-11_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=XPOi
-----END PGP SIGNATURE-----
pgpFvh4i4hnjB.pgp
Description: PGP signature
--- End Message ---
