Your message dated Tue, 25 Nov 2025 10:09:56 +0000
with message-id <[email protected]>
and subject line Bug#1114706: fixed in parmed 4.3.0+dfsg-3
has caused the Debian Bug report #1114706,
regarding parmed: 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.
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--
1114706: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114706
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: parmed
Version: 4.3.0+dfsg-2
Severity: important
User: [email protected]
Usertags: numpy2.3
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for NumPy 2.3, parmed failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
test/test_parmed_tinker.py:5: in <module>
from utils import get_fn
test/utils.py:13: in <module>
from parmed import gromacs, openmm
parmed/__init__.py:23: in <module>
from . import amber, charmm, gromacs, dlpoly, namd, openmm, rosetta,
tinker, entos
parmed/amber/__init__.py:14: in <module>
from .netcdffiles import NetCDFTraj, NetCDFRestart
parmed/amber/netcdffiles.py:25: in <module>
from ..utils.netcdf import netcdf_file as NetCDFFile
parmed/utils/netcdf.py:46: in <module>
from numpy.compat import asbytes, asstr
E ModuleNotFoundError: No module named 'numpy.compat'
_ ERROR collecting
.pybuild/cpython3_3.13_parmed/build/test/test_parmed_topologyobjects.py _
ImportError while importing test module
'/build/reproducible-path/parmed-4.3.0+dfsg/.pybuild/cpython3_3.13_parmed/build/test/test_parmed_topologyobjects.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
test/test_parmed_topologyobjects.py:9: in <module>
from parmed.amber.readparm import AmberFormat
parmed/__init__.py:23: in <module>
from . import amber, charmm, gromacs, dlpoly, namd, openmm, rosetta,
tinker, entos
parmed/amber/__init__.py:14: in <module>
from .netcdffiles import NetCDFTraj, NetCDFRestart
parmed/amber/netcdffiles.py:25: in <module>
from ..utils.netcdf import netcdf_file as NetCDFFile
parmed/utils/netcdf.py:46: in <module>
from numpy.compat import asbytes, asstr
E ModuleNotFoundError: No module named 'numpy.compat'
_ ERROR collecting .pybuild/cpython3_3.13_parmed/build/test/test_parmed_unit.py
_
ImportError while importing test module
'/build/reproducible-path/parmed-4.3.0+dfsg/.pybuild/cpython3_3.13_parmed/build/test/test_parmed_unit.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
test/test_parmed_unit.py:4: in <module>
import utils
test/utils.py:13: in <module>
from parmed import gromacs, openmm
parmed/__init__.py:23: in <module>
from . import amber, charmm, gromacs, dlpoly, namd, openmm, rosetta,
tinker, entos
parmed/amber/__init__.py:14: in <module>
from .netcdffiles import NetCDFTraj, NetCDFRestart
parmed/amber/netcdffiles.py:25: in <module>
from ..utils.netcdf import netcdf_file as NetCDFFile
parmed/utils/netcdf.py:46: in <module>
from numpy.compat import asbytes, asstr
E ModuleNotFoundError: No module named 'numpy.compat'
_ ERROR collecting
.pybuild/cpython3_3.13_parmed/build/test/test_parmedtools_actions.py _
ImportError while importing test module
'/build/reproducible-path/parmed-4.3.0+dfsg/.pybuild/cpython3_3.13_parmed/build/test/test_parmedtools_actions.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
test/test_parmedtools_actions.py:8: in <module>
import parmed as pmd
parmed/__init__.py:23: in <module>
from . import amber, charmm, gromacs, dlpoly, namd, openmm, rosetta,
tinker, entos
parmed/amber/__init__.py:14: in <module>
from .netcdffiles import NetCDFTraj, NetCDFRestart
parmed/amber/netcdffiles.py:25: in <module>
from ..utils.netcdf import netcdf_file as NetCDFFile
parmed/utils/netcdf.py:46: in <module>
from numpy.compat import asbytes, asstr
E ModuleNotFoundError: No module named 'numpy.compat'
_ ERROR collecting
.pybuild/cpython3_3.13_parmed/build/test/test_parmedtools_parmlist.py _
ImportError while importing test module
'/build/reproducible-path/parmed-4.3.0+dfsg/.pybuild/cpython3_3.13_parmed/build/test/test_parmedtools_parmlist.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
test/test_parmedtools_parmlist.py:5: in <module>
from parmed import Structure, load_file
parmed/__init__.py:23: in <module>
from . import amber, charmm, gromacs, dlpoly, namd, openmm, rosetta,
tinker, entos
parmed/amber/__init__.py:14: in <module>
from .netcdffiles import NetCDFTraj, NetCDFRestart
parmed/amber/netcdffiles.py:25: in <module>
from ..utils.netcdf import netcdf_file as NetCDFFile
parmed/utils/netcdf.py:46: in <module>
from numpy.compat import asbytes, asstr
E ModuleNotFoundError: No module named 'numpy.compat'
____ ERROR collecting .pybuild/cpython3_3.13_parmed/build/test/test_vec3.py ____
ImportError while importing test module
'/build/reproducible-path/parmed-4.3.0+dfsg/.pybuild/cpython3_3.13_parmed/build/test/test_vec3.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.13/importlib/__init__.py:88: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
test/test_vec3.py:3: in <module>
from parmed import Vec3
parmed/__init__.py:23: in <module>
from . import amber, charmm, gromacs, dlpoly, namd, openmm, rosetta,
tinker, entos
parmed/amber/__init__.py:14: in <module>
from .netcdffiles import NetCDFTraj, NetCDFRestart
parmed/amber/netcdffiles.py:25: in <module>
from ..utils.netcdf import netcdf_file as NetCDFFile
parmed/utils/netcdf.py:46: in <module>
from numpy.compat import asbytes, asstr
E ModuleNotFoundError: No module named 'numpy.compat'
=============================== warnings summary ===============================
<frozen importlib._bootstrap>:488
<frozen importlib._bootstrap>:488: DeprecationWarning: builtin type
SwigPyPacked has no __module__ attribute
<frozen importlib._bootstrap>:488
<frozen importlib._bootstrap>:488: DeprecationWarning: builtin type
SwigPyObject has no __module__ attribute
<frozen importlib._bootstrap>:488
<frozen importlib._bootstrap>:488: DeprecationWarning: builtin type
swigvarlink has no __module__ attribute
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
ERROR test/test_format_conversions.py
ERROR test/test_openmm_amber.py
ERROR test/test_openmm_amber_forces.py
ERROR test/test_openmm_charmm.py
ERROR test/test_openmm_gromacs.py
ERROR test/test_openmm_reporters.py
ERROR test/test_parmed_amber.py
ERROR test/test_parmed_charmm.py
ERROR test/test_parmed_cif.py
ERROR test/test_parmed_dlpoly.py
ERROR test/test_parmed_entos.py
ERROR test/test_parmed_formats.py
ERROR test/test_parmed_genopen.py
ERROR test/test_parmed_geometry.py
ERROR test/test_parmed_gromacs.py
ERROR test/test_parmed_gromacs_cpp.py
ERROR test/test_parmed_misc.py
ERROR test/test_parmed_modeller.py
ERROR test/test_parmed_namd.py
ERROR test/test_parmed_netcdf.py
ERROR test/test_parmed_openmm.py
ERROR test/test_parmed_pandas.py
ERROR test/test_parmed_parameterset.py
ERROR test/test_parmed_rdkit.py
ERROR test/test_parmed_residue.py
ERROR test/test_parmed_rosetta.py
ERROR test/test_parmed_serialization.py
ERROR test/test_parmed_structure.py
ERROR test/test_parmed_structure_slicing.py
ERROR test/test_parmed_tinker.py
ERROR test/test_parmed_topologyobjects.py
ERROR test/test_parmed_unit.py
ERROR test/test_parmedtools_actions.py
ERROR test/test_parmedtools_parmlist.py
ERROR test/test_vec3.py
!!!!!!!!!!!!!!!!!!! Interrupted: 35 errors during collection !!!!!!!!!!!!!!!!!!!
======================== 3 warnings, 35 errors in 1.68s ========================
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd
/build/reproducible-path/parmed-4.3.0+dfsg/.pybuild/cpython3_3.13_parmed/build;
python3.13 -m pytest -k 'not test_download'
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13
returned exit code 13
make: *** [debian/rules:7: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-09-08T05:01:12Z
-------------------------------------------------------------------------------
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/2453405/
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/163624/
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: parmed
Source-Version: 4.3.0+dfsg-3
Done: Andrius Merkys <[email protected]>
We believe that the bug you reported is fixed in the latest version of
parmed, 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.
Andrius Merkys <[email protected]> (supplier of updated parmed 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, 25 Nov 2025 03:18:59 -0500
Source: parmed
Architecture: source
Version: 4.3.0+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Andrius Merkys <[email protected]>
Closes: 1114706
Changes:
parmed (4.3.0+dfsg-3) unstable; urgency=medium
.
* Backport upstream patch for gone numpy.compat (Closes: #1114706)
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