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Tests fail: cannot import name 'neighlist' from partially initialized module 'kliff.neighbor' #81

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yurivict opened this issue Oct 7, 2022 · 1 comment
Open

Tests fail: cannot import name 'neighlist' from partially initialized module 'kliff.neighbor' #81

yurivict opened this issue Oct 7, 2022 · 1 comment

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@yurivict
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yurivict commented Oct 7, 2022

Describe the bug

===>  Testing for py39-kliff-0.4.1
===>   py39-kliff-0.4.1 depends on package: py39-pytest>=7,1 - found
===>   py39-kliff-0.4.1 depends on file: /usr/local/bin/python3.9 - found
cd /disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1 && /usr/bin/env XDG_DATA_HOME=/disk-samsung/freebsd-ports/science/py-kliff/work-py39  XDG_CONFIG_HOME=/disk-samsung/freebsd-ports/science/py-kliff/work-py39  XDG_CACHE_HOME=/disk-samsung/freebsd-ports/science/py-kliff/work-py39/.cache  HOME=/disk-samsung/freebsd-ports/science/py-kliff/work-py39 PATH=/usr/local/libexec/ccache:/disk-samsung/freebsd-ports/science/py-kliff/work-py39/.bin:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/disk-samsung/freebsd-ports/science/py-kliff/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local  LOCALBASE=/usr/local  CC="cc" CFLAGS="-O2 -pipe -fno-omit-frame-pointer  -fstack-protector-strong -fno-strict-aliasing "  CPP="cpp" CPPFLAGS="-fno-omit-frame-pointer"  LDFLAGS=" -fstack-protector-strong " LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fno-omit-frame-pointer -fstack-protector-strong -fno-strict-aliasing -fno-omit-frame-pointer  "  MANPREFIX="/usr/local" CCACHE_DIR="/tmp/.ccache" BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 0644"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -m 0644"  BSD_INSTALL_MAN="install  -m 444" /usr/local/bin/python3.9 -m pytest -k '' -rs -v -o addopts= 
==================================================================================== test session starts =====================================================================================
platform freebsd13 -- Python 3.9.13, pytest-7.1.3, pluggy-1.0.0 -- /usr/local/bin/python3.9
cachedir: .pytest_cache
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/.hypothesis/examples')
rootdir: /disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1
plugins: forked-1.4.0, hypothesis-6.55.0, cov-2.9.0, rerunfailures-10.1, xdist-2.5.0, typeguard-2.13.3
collected 9 items / 9 errors                                                                                                                                                                 

=========================================================================================== ERRORS ===========================================================================================
__________________________________________________________________________ ERROR collecting tests/test_neighbor.py ___________________________________________________________________________
ImportError while importing test module '/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/tests/test_neighbor.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.9/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_neighbor.py:6: in <module>
    from kliff.neighbor import NeighborList
kliff/neighbor/__init__.py:1: in <module>
    from .neighbor import NeighborList, assemble_forces, assemble_stress
kliff/neighbor/neighbor.py:7: in <module>
    from kliff.neighbor import neighlist as nl  # C extension
E   ImportError: cannot import name 'neighlist' from partially initialized module 'kliff.neighbor' (most likely due to a circular import) (/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/kliff/neighbor/__init__.py)
_______________________________________________________________________ ERROR collecting tests/test_scipy_optimize.py ________________________________________________________________________
ImportError while importing test module '/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/tests/test_scipy_optimize.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.9/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_scipy_optimize.py:5: in <module>
    from kliff.calculators import Calculator
kliff/calculators/__init__.py:3: in <module>
    from .calculator import Calculator
kliff/calculators/calculator.py:8: in <module>
    from kliff.models.model import Model
kliff/models/__init__.py:1: in <module>
    from kliff.models.kim import KIMModel
kliff/models/kim.py:14: in <module>
    from kliff.neighbor import assemble_forces, assemble_stress
kliff/neighbor/__init__.py:1: in <module>
    from .neighbor import NeighborList, assemble_forces, assemble_stress
kliff/neighbor/neighbor.py:7: in <module>
    from kliff.neighbor import neighlist as nl  # C extension
E   ImportError: cannot import name 'neighlist' from partially initialized module 'kliff.neighbor' (most likely due to a circular import) (/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/kliff/neighbor/__init__.py)
___________________________________________________________________ ERROR collecting tests/calculators/test_calculator.py ____________________________________________________________________
ImportError while importing test module '/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/tests/calculators/test_calculator.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.9/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/calculators/test_calculator.py:8: in <module>
    from kliff.models import KIMModel
kliff/models/__init__.py:1: in <module>
    from kliff.models.kim import KIMModel
kliff/models/kim.py:14: in <module>
    from kliff.neighbor import assemble_forces, assemble_stress
kliff/neighbor/__init__.py:1: in <module>
    from .neighbor import NeighborList, assemble_forces, assemble_stress
kliff/neighbor/neighbor.py:7: in <module>
    from kliff.neighbor import neighlist as nl  # C extension
E   ImportError: cannot import name 'neighlist' from partially initialized module 'kliff.neighbor' (most likely due to a circular import) (/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/kliff/neighbor/__init__.py)
___________________________________________________________________ ERROR collecting tests/descriptors/test_bispectrum.py ____________________________________________________________________
ImportError while importing test module '/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/tests/descriptors/test_bispectrum.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.9/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/descriptors/test_bispectrum.py:6: in <module>
    from kliff.descriptors import Bispectrum
kliff/descriptors/__init__.py:1: in <module>
    from .bispectrum.bispectrum import Bispectrum
kliff/descriptors/bispectrum/bispectrum.py:4: in <module>
    from kliff.descriptors.bispectrum import bs  # C extension
E   ImportError: cannot import name 'bs' from 'kliff.descriptors.bispectrum' (/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/kliff/descriptors/bispectrum/__init__.py)
___________________________________________________________________ ERROR collecting tests/descriptors/test_descriptor.py ____________________________________________________________________
ImportError while importing test module '/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/tests/descriptors/test_descriptor.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.9/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/descriptors/test_descriptor.py:8: in <module>
    from kliff.descriptors.descriptor import Descriptor, DescriptorError, load_fingerprints
kliff/descriptors/__init__.py:1: in <module>
    from .bispectrum.bispectrum import Bispectrum
kliff/descriptors/bispectrum/bispectrum.py:4: in <module>
    from kliff.descriptors.bispectrum import bs  # C extension
E   ImportError: cannot import name 'bs' from 'kliff.descriptors.bispectrum' (/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/kliff/descriptors/bispectrum/__init__.py)
________________________________________________________________ ERROR collecting tests/descriptors/test_symmetry_function.py ________________________________________________________________
ImportError while importing test module '/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/tests/descriptors/test_symmetry_function.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.9/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/descriptors/test_symmetry_function.py:12: in <module>
    from kliff.descriptors import SymmetryFunction
kliff/descriptors/__init__.py:1: in <module>
    from .bispectrum.bispectrum import Bispectrum
kliff/descriptors/bispectrum/bispectrum.py:4: in <module>
    from kliff.descriptors.bispectrum import bs  # C extension
E   ImportError: cannot import name 'bs' from 'kliff.descriptors.bispectrum' (/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/kliff/descriptors/bispectrum/__init__.py)
_________________________________________________________________________ ERROR collecting tests/models/test_kim.py __________________________________________________________________________
ImportError while importing test module '/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/tests/models/test_kim.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.9/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/models/test_kim.py:7: in <module>
    from kliff.models.kim import KIMComputeArguments, KIMModel
kliff/models/__init__.py:1: in <module>
    from kliff.models.kim import KIMModel
kliff/models/kim.py:14: in <module>
    from kliff.neighbor import assemble_forces, assemble_stress
kliff/neighbor/__init__.py:1: in <module>
    from .neighbor import NeighborList, assemble_forces, assemble_stress
kliff/neighbor/neighbor.py:7: in <module>
    from kliff.neighbor import neighlist as nl  # C extension
E   ImportError: cannot import name 'neighlist' from partially initialized module 'kliff.neighbor' (most likely due to a circular import) (/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/kliff/neighbor/__init__.py)
____________________________________________________________________ ERROR collecting tests/models/test_lennard_jones.py _____________________________________________________________________
ImportError while importing test module '/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/tests/models/test_lennard_jones.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.9/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/models/test_lennard_jones.py:9: in <module>
    from kliff.models.lennard_jones import LennardJones, LJComputeArguments
kliff/models/__init__.py:1: in <module>
    from kliff.models.kim import KIMModel
kliff/models/kim.py:14: in <module>
    from kliff.neighbor import assemble_forces, assemble_stress
kliff/neighbor/__init__.py:1: in <module>
    from .neighbor import NeighborList, assemble_forces, assemble_stress
kliff/neighbor/neighbor.py:7: in <module>
    from kliff.neighbor import neighlist as nl  # C extension
E   ImportError: cannot import name 'neighlist' from partially initialized module 'kliff.neighbor' (most likely due to a circular import) (/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/kliff/neighbor/__init__.py)
___________________________________________________________________________ ERROR collecting tests/uq/test_mcmc.py ___________________________________________________________________________
ImportError while importing test module '/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/tests/uq/test_mcmc.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.9/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/uq/test_mcmc.py:10: in <module>
    from kliff.models import KIMModel
kliff/models/__init__.py:1: in <module>
    from kliff.models.kim import KIMModel
kliff/models/kim.py:14: in <module>
    from kliff.neighbor import assemble_forces, assemble_stress
kliff/neighbor/__init__.py:1: in <module>
    from .neighbor import NeighborList, assemble_forces, assemble_stress
kliff/neighbor/neighbor.py:7: in <module>
    from kliff.neighbor import neighlist as nl  # C extension
E   ImportError: cannot import name 'neighlist' from partially initialized module 'kliff.neighbor' (most likely due to a circular import) (/disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/kliff/neighbor/__init__.py)
====================================================================================== warnings summary ======================================================================================
kliff/__init__.py:11
  /disk-samsung/freebsd-ports/science/py-kliff/work-py39/kliff-0.4.1/kliff/__init__.py:11: UserWarning: 'PyTorch' not found. All kliff machine learning modules (e.g. NeuralNetwork) are not imported. Ignore this if you want to use kliff to train physics-based models.
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 9 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
================================================================================ 1 warning, 9 errors in 1.81s ================================================================================
*** Error code 2

To Reproduce
Run pytest.

Additional context
Add any other context about the problem here. For example,

  • Operating system (Linux/Mac/Win) and version: FreeBSD 13.1 STABLE
  • Python version: 3.9
@mjwen
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mjwen commented Oct 10, 2022

Sees a kimpy bug. Will investigate there openkim/kimpy#16

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