[Debichem-devel] Bug#1114706: parmed: FTBFS with NumPy 2.3
roehling at debian.org
roehling at debian.org
Mon Sep 8 20:44:23 BST 2025
Source: parmed
Version: 4.3.0+dfsg-2
Severity: important
User: debian-python at lists.debian.org
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
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