Your message dated Tue, 09 Sep 2025 21:04:25 +0000
with message-id <[email protected]>
and subject line Bug#1114696: fixed in brian 2.9.0-1
has caused the Debian Bug report #1114696,
regarding brian: FTBFS with NumPy 2.3
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
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1114696: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114696
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: brian
Version: 2.8.0.4-1
Severity: important
User: [email protected]
Usertags: numpy2.3
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for NumPy 2.3, brian failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
Message: "No numerical integration method specified for group 'neurongroup_1',
using method 'euler' (took 0.00s, trying other methods took 0.00s)."
Arguments: ()
____________________ test_synapse_creation_generator_random ____________________
self = <brian2.codegen.runtime.cython_rt.cython_rt.CythonCodeObject object at
0x7f4c7f5816a0>
block = 'run'
def run_block(self, block):
compiled_code = self.compiled_code[block]
if compiled_code:
try:
> return compiled_code.main(self.namespace)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/codegen/runtime/cython_rt/cython_rt.py:199:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.cython/brian_extensions/_cython_magic_880208a1063c6c8dc24a4e1c2f9ce43c.pyx:214:
in _cython_magic_880208a1063c6c8dc24a4e1c2f9ce43c.main
???
.cython/brian_extensions/_cython_magic_880208a1063c6c8dc24a4e1c2f9ce43c.pyx:63:
in _cython_magic_880208a1063c6c8dc24a4e1c2f9ce43c._rand
???
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
attr = 'NPY_OWNDATA'
def __getattr__(attr):
# Warn for expired attributes
import warnings
if attr == "linalg":
import numpy.linalg as linalg
return linalg
elif attr == "fft":
import numpy.fft as fft
return fft
elif attr == "dtypes":
import numpy.dtypes as dtypes
return dtypes
elif attr == "random":
import numpy.random as random
return random
elif attr == "polynomial":
import numpy.polynomial as polynomial
return polynomial
elif attr == "ma":
import numpy.ma as ma
return ma
elif attr == "ctypeslib":
import numpy.ctypeslib as ctypeslib
return ctypeslib
elif attr == "exceptions":
import numpy.exceptions as exceptions
return exceptions
elif attr == "testing":
import numpy.testing as testing
return testing
elif attr == "matlib":
import numpy.matlib as matlib
return matlib
elif attr == "f2py":
import numpy.f2py as f2py
return f2py
elif attr == "typing":
import numpy.typing as typing
return typing
elif attr == "rec":
import numpy.rec as rec
return rec
elif attr == "char":
import numpy.char as char
return char
elif attr == "array_api":
raise AttributeError("`numpy.array_api` is not available from "
"numpy 2.0 onwards", name=None)
elif attr == "core":
import numpy.core as core
return core
elif attr == "strings":
import numpy.strings as strings
return strings
elif attr == "distutils":
if 'distutils' in __numpy_submodules__:
import numpy.distutils as distutils
return distutils
else:
raise AttributeError("`numpy.distutils` is not available from "
"Python 3.12 onwards", name=None)
if attr in __future_scalars__:
# And future warnings for those that will change, but also give
# the AttributeError
warnings.warn(
f"In the future `np.{attr}` will be defined as the "
"corresponding NumPy scalar.", FutureWarning, stacklevel=2)
if attr in __former_attrs__:
raise AttributeError(__former_attrs__[attr], name=None)
if attr in __expired_attributes__:
raise AttributeError(
f"`np.{attr}` was removed in the NumPy 2.0 release. "
f"{__expired_attributes__[attr]}",
name=None
)
if attr == "chararray":
warnings.warn(
"`np.chararray` is deprecated and will be removed from "
"the main namespace in the future. Use an array with a string "
"or bytes dtype instead.", DeprecationWarning, stacklevel=2)
import numpy.char as char
return char.chararray
> raise AttributeError(f"module {__name__!r} has no attribute {attr!r}")
E AttributeError: module 'numpy' has no attribute 'NPY_OWNDATA'
/usr/lib/python3/dist-packages/numpy/__init__.py:795: AttributeError
The above exception was the direct cause of the following exception:
@pytest.mark.standalone_compatible
def test_synapse_creation_generator_random():
G1 = NeuronGroup(10, "v:1")
G2 = NeuronGroup(20, "v:1")
G1.v = "i"
G2.v = "10 + i"
SG1 = G1[:5]
SG2 = G2[10:]
# connect based on pre-/postsynaptic state variables
S2 = Synapses(SG1, SG2)
> S2.connect(j="k for k in sample(N_post, p=1.0*int(v_pre > 2))")
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/tests/test_subgroup.py:461:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/core/base.py:346: in
device_override_decorated_function
return func(*args, **kwds)
^^^^^^^^^^^^^^^^^^^
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/synapses/synapses.py:1627:
in connect
self._add_synapses_generator(
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/synapses/synapses.py:2122:
in _add_synapses_generator
codeobj()
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/codegen/codeobject.py:131:
in __call__
return self.run()
^^^^^^^^^^
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/codegen/codeobject.py:159:
in run
return self.run_block("run")
^^^^^^^^^^^^^^^^^^^^^
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <brian2.codegen.runtime.cython_rt.cython_rt.CythonCodeObject object at
0x7f4c7f5816a0>
block = 'run'
def run_block(self, block):
compiled_code = self.compiled_code[block]
if compiled_code:
try:
return compiled_code.main(self.namespace)
except Exception as exc:
message = (
"An exception occured during the execution of the "
f"'{block}' block of code object '{self.name}'.\n"
)
> raise BrianObjectException(message, self.owner) from exc
E brian2.core.base.BrianObjectException: Error encountered with
object named 'synapses'.
E Object was created here (most recent call only, full details in
debug log):
E File '/usr/lib/python3/dist-packages/_pytest/python.py', line
157, in pytest_pyfunc_call
E result = testfunction(**testargs)
E
E An exception occured during the execution of the 'run' block of
code object 'synapses_synapses_create_generator_codeobject'.
E (See above for original error message and traceback.)
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/codegen/runtime/cython_rt/cython_rt.py:205:
BrianObjectException
=============================== warnings summary ===============================
../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1474
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:1474:
PytestConfigWarning: Unknown config option: timeout
self._warn_or_fail_if_strict(f"Unknown config option: {key}\n")
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/tests/test_complex_examples.py::test_cuba
FAILED
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/tests/test_poissoninput.py::test_poissoninput
FAILED
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/tests/test_poissoninput.py::test_poissoninput_refractory
FAILED
../debian/tmp/usr/lib/python3.13/dist-packages/brian2/tests/test_subgroup.py::test_synapse_creation_generator_random
4 failed, 33 passed, 1 skipped, 244 deselected, 1 warning in 154.65s (0:02:34)
ERROR: 1/4 test suite(s) did not complete successfully (see above).
make[1]: *** [debian/rules:58: execute_after_dh_auto_install] Error 1
make[1]: Leaving directory '/build/reproducible-path/brian-2.8.0.4'
make: *** [debian/rules:32: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-09-07T21:21:16Z
-------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/debian/developers-roehling.numpy/artifact/2448433/
About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.
You can find the build task here:
https://debusine.debian.net/debian/developers-roehling.numpy/work-request/163207/
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Cheers
Timo
--- End Message ---
--- Begin Message ---
Source: brian
Source-Version: 2.9.0-1
Done: Michael R. Crusoe <[email protected]>
We believe that the bug you reported is fixed in the latest version of
brian, 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.
Michael R. Crusoe <[email protected]> (supplier of updated brian 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: Tue, 09 Sep 2025 15:32:14 +0200
Source: brian
Architecture: source
Version: 2.9.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 1114696
Changes:
brian (2.9.0-1) unstable; urgency=medium
.
* Team upload.
* New upstream version. Support NumPy 2.3+ (Closes: #1114696)
* Standards-Version: 4.7.2 (routine-update)
* d/patches: refreshed; removed rm-setuptools-dep.patch, it is no
longer needed.
* Fixed links to external docs to instead point to the packaged -docs.
* d/control: add missing pytest plugins.
* d/rules: respect Debian Policy 4.9.1 and use DEB_BUILD_OPTION_PARALLEL to
set the level of pytest parallelism via PYTEST_XDIST_AUTO_NUM_WORKERS.
* Exclude far fewer tests
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Files:
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