Tests do not run in PEP517 out-of-source build (gentoo)

[mschubert]

When trying to run the tests of a locally built wheel, I run into errors in the collection phase. The steps are, roughly:

1. Build the wheel (works fine)
2. Install the wheel in a temporary location (works fine)
3. Run the tests (errors on test collection)

# build wheel
python3.12 -m gpep517 build-wheel --prefix=/my_dir/usr --backend setuptools.build_meta --output-fd 3 --wheel-dir /my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0-python3_12/wheel

# install wheel
python3.12 -m gpep517 install-wheel --destdir=/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0-python3_12/install --interpreter=/my_dir/usr/bin/python3.12 --prefix=/my_dir/usr --optimize=all /my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0-python3_12/wheel/bx_python-0.12.0-cp312-cp312-linux_x86_64.whl

# run tests
# cd into dir
python3.12 -m pytest -vv -ra -l -Wdefault -Werror::pytest.PytestUnhandledCoroutineWarning --color=yes -o console_output_style=count -o tmp_path_retention_count=0 -o tmp_path_retention_policy=failed -p no:cov -p no:flake8 -p no:flakes -p no:pylint -p no:markdown -p no:sugar -p no:xvfb -p no:pytest-describe -p no:plus -p no:tavern -p no:salt-factories

The relevant sections are:

ImportError while importing test module _epo
Hint: make sure your test modules/packages have valid Python names.
E   ModuleNotFoundError: No module named 'bx.align._epo'
# or:
E   ModuleNotFoundError: No module named 'bx.align.sitemask._cpg'
# or:
E   ModuleNotFoundError: No module named 'bx.arrays.array_tree'
# or:
E   ModuleNotFoundError: No module named 'bx.bbi.bigwig_file'
# or:
E   ModuleNotFoundError: No module named 'bx.bitset'
# and others

E   ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import)

This always worked fine with other packages, so I'm not sure what's going wrong here.

Detailed log here (including package versions)

2024-07-16 09:58:34,058 gpep517 INFO The backend produced /my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0-python3_12/wheel/bx_python-0.12.0-cp312-cp312-linux_x86_64.whl
 /my_dir/*   Installing bx_python-0.12.0-cp312-cp312-linux_x86_64.whl to /my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0-python3_12/install
python3.12 -m gpep517 install-wheel --destdir=/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0-python3_12/install --interpreter=/my_dir/usr/bin/python3.12 --prefix=/my_dir/usr --optimize=all /my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0-python3_12/wheel/bx_python-0.12.0-cp312-cp312-linux_x86_64.whl
2024-07-16 09:58:35,223 gpep517 INFO Installing /my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0-python3_12/wheel/bx_python-0.12.0-cp312-cp312-linux_x86_64.whl into /my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0-python3_12/install
2024-07-16 09:58:36,175 gpep517 INFO Installation complete
>>> Source compiled.
>>> Test phase: sci-biology/bx-python-0.12.0
 /my_dir/* python3_12: running distutils-r1_run_phase python_test
python3.12 -m pytest -vv -ra -l -Wdefault -Werror::pytest.PytestUnhandledCoroutineWarning --color=yes -o console_output_style=count -o tmp_path_retention_count=0 -o tmp_path_retention_policy=failed -p no:cov -p no:flake8 -p no:flakes -p no:pylint -p no:markdown -p no:sugar -p no:xvfb -p no:pytest-describe -p no:plus -p no:tavern -p no:salt-factories
============================= test session starts ==============================
platform linux -- Python 3.12.4, pytest-8.2.2, pluggy-1.5.0 -- /my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0-python3_12/install/my_dir/usr/bin/python3.12
cachedir: .pytest_cache
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/.hypothesis/examples'))
rootdir: /my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0
configfile: pytest.ini
testpaths: lib, script_tests/
plugins: asyncio-0.23.7, hypothesis-6.103.2, pkgcore-0.12.27, typeguard-4.3.0
asyncio: mode=Mode.STRICT
collecting ... collected 62 items / 18 errors

==================================== ERRORS ====================================
__________________ ERROR collecting lib/bx/align/epo_tests.py __________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/align/epo_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/align/epo_tests.py:9: in <module>
    from bx.align._epo import (
E   ModuleNotFoundError: No module named 'bx.align._epo'
__________________ ERROR collecting lib/bx/align/lav_tests.py __________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/align/lav_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/align/lav_tests.py:7: in <module>
    import bx.align.lav as lav
lib/bx/align/lav.py:11: in <module>
    import bx.seq
lib/bx/seq/__init__.py:7: in <module>
    from bx.seq.core import *  # noqa: F40
lib/bx/seq/core.py:11: in <module>
    from . import (
lib/bx/seq/nib.py:30: in <module>
    from . import _nib
E   ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/__init__.py)
___________ ERROR collecting lib/bx/align/sitemask/sitemask_tests.py ___________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/align/sitemask/sitemask_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/align/sitemask/sitemask_tests.py:9: in <module>
    from bx.align.sitemask import cpg
lib/bx/align/sitemask/cpg.py:6: in <module>
    from ._cpg import (
E   ModuleNotFoundError: No module named 'bx.align.sitemask._cpg'
______________ ERROR collecting lib/bx/arrays/array_tree_tests.py ______________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/arrays/array_tree_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/arrays/array_tree_tests.py:11: in <module>
    from bx.arrays.array_tree import (
E   ModuleNotFoundError: No module named 'bx.arrays.array_tree'
_________________ ERROR collecting lib/bx/bbi/bigwig_tests.py __________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/bbi/bigwig_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/bbi/bigwig_tests.py:12: in <module>
    from bx.bbi.bigwig_file import BigWigFile
E   ModuleNotFoundError: No module named 'bx.bbi.bigwig_file'
___________________ ERROR collecting lib/bx/bitset_tests.py ____________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/bitset_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/bitset_tests.py:7: in <module>
    import bx.bitset
E   ModuleNotFoundError: No module named 'bx.bitset'
______________ ERROR collecting lib/bx/intervals/cluster_tests.py ______________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/intervals/cluster_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1310: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:995: in exec_module
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
lib/bx/intervals/__init__.py:7: in <module>
    from bx.intervals.intersection import *  # noqa: F40
E   ModuleNotFoundError: No module named 'bx.intervals.intersection'
___________ ERROR collecting lib/bx/intervals/intersection_tests.py ____________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/intervals/intersection_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1310: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:995: in exec_module
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
lib/bx/intervals/__init__.py:7: in <module>
    from bx.intervals.intersection import *  # noqa: F40
E   ModuleNotFoundError: No module named 'bx.intervals.intersection'
__________________ ERROR collecting lib/bx/misc/bgzf_tests.py __________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/misc/bgzf_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/misc/bgzf_tests.py:1: in <module>
    import bx.misc.bgzf
E   ModuleNotFoundError: No module named 'bx.misc.bgzf'
_______________ ERROR collecting lib/bx/misc/seekbzip2_tests.py ________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/misc/seekbzip2_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/misc/seekbzip2_tests.py:10: in <module>
    from bx.misc import seekbzip2
lib/bx/misc/seekbzip2.py:7: in <module>
    from ._seekbzip2 import SeekBzip2
E   ModuleNotFoundError: No module named 'bx.misc._seekbzip2'
______________ ERROR collecting lib/bx/motif/io/transfac_tests.py ______________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/motif/io/transfac_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/motif/io/transfac_tests.py:5: in <module>
    from bx.motif.io import transfac
lib/bx/motif/io/transfac.py:5: in <module>
    from bx.motif.pwm import FrequencyMatrix
lib/bx/motif/pwm.py:19: in <module>
    from . import _pwm
E   ImportError: cannot import name '_pwm' from 'bx.motif' (/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/motif/__init__.py)
__________________ ERROR collecting lib/bx/motif/pwm_tests.py __________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/motif/pwm_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/motif/pwm_tests.py:6: in <module>
    from bx.motif import pwm
lib/bx/motif/pwm.py:19: in <module>
    from . import _pwm
E   ImportError: cannot import name '_pwm' from 'bx.motif' (/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/motif/__init__.py)
__________________ ERROR collecting lib/bx/seq/fasta_tests.py __________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/fasta_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1310: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:995: in exec_module
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
lib/bx/seq/__init__.py:7: in <module>
    from bx.seq.core import *  # noqa: F40
lib/bx/seq/core.py:11: in <module>
    from . import (
lib/bx/seq/nib.py:30: in <module>
    from . import _nib
E   ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/__init__.py)
___________________ ERROR collecting lib/bx/seq/nib_tests.py ___________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/nib_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1310: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:995: in exec_module
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
lib/bx/seq/__init__.py:7: in <module>
    from bx.seq.core import *  # noqa: F40
lib/bx/seq/core.py:11: in <module>
    from . import (
lib/bx/seq/nib.py:30: in <module>
    from . import _nib
E   ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/__init__.py)
__________________ ERROR collecting lib/bx/seq/qdna_tests.py ___________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/qdna_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1310: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:995: in exec_module
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
lib/bx/seq/__init__.py:7: in <module>
    from bx.seq.core import *  # noqa: F40
lib/bx/seq/core.py:11: in <module>
    from . import (
lib/bx/seq/nib.py:30: in <module>
    from . import _nib
E   ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/__init__.py)
___________________ ERROR collecting lib/bx/seq/seq_tests.py ___________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/seq_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1310: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:995: in exec_module
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
lib/bx/seq/__init__.py:7: in <module>
    from bx.seq.core import *  # noqa: F40
lib/bx/seq/core.py:11: in <module>
    from . import (
lib/bx/seq/nib.py:30: in <module>
    from . import _nib
E   ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/__init__.py)
_________________ ERROR collecting lib/bx/seq/twobit_tests.py __________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/twobit_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1310: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
<frozen importlib._bootstrap_external>:995: in exec_module
    ???
<frozen importlib._bootstrap>:488: in _call_with_frames_removed
    ???
lib/bx/seq/__init__.py:7: in <module>
    from bx.seq.core import *  # noqa: F40
lib/bx/seq/core.py:11: in <module>
    from . import (
lib/bx/seq/nib.py:30: in <module>
    from . import _nib
E   ImportError: cannot import name '_nib' from partially initialized module 'bx.seq' (most likely due to a circular import) (/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seq/__init__.py)
_________________ ERROR collecting lib/bx/seqmapping_tests.py __________________
ImportError while importing test module '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx/seqmapping_tests.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../../../../../usr/lib/python3.12/site-packages/_pytest/python.py:492: in importtestmodule
    mod = import_path(
../../../../../../../usr/lib/python3.12/site-packages/_pytest/pathlib.py:591: in import_path
    importlib.import_module(module_name)
../../../../../../../usr/lib/python3.12/importlib/__init__.py:90: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1387: in _gcd_import
    ???
<frozen importlib._bootstrap>:1360: in _find_and_load
    ???
<frozen importlib._bootstrap>:1331: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:935: in _load_unlocked
    ???
../../../../../../../usr/lib/python3.12/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
lib/bx/seqmapping_tests.py:13: in <module>
    import bx.seqmapping
lib/bx/seqmapping.py:31: in <module>
    from ._seqmapping import (
E   ModuleNotFoundError: No module named 'bx._seqmapping'
=============================== warnings summary ===============================
lib/bx_extras/pyparsing.py:65
  /my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0/lib/bx_extras/pyparsing.py:65: DeprecationWarning: module 'sre_constants' is deprecated
    import sre_constants

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
ERROR lib/bx/align/epo_tests.py
ERROR lib/bx/align/lav_tests.py
ERROR lib/bx/align/sitemask/sitemask_tests.py
ERROR lib/bx/arrays/array_tree_tests.py
ERROR lib/bx/bbi/bigwig_tests.py
ERROR lib/bx/bitset_tests.py
ERROR lib/bx/intervals/cluster_tests.py
ERROR lib/bx/intervals/intersection_tests.py
ERROR lib/bx/misc/bgzf_tests.py
ERROR lib/bx/misc/seekbzip2_tests.py
ERROR lib/bx/motif/io/transfac_tests.py
ERROR lib/bx/motif/pwm_tests.py
ERROR lib/bx/seq/fasta_tests.py
ERROR lib/bx/seq/nib_tests.py
ERROR lib/bx/seq/qdna_tests.py
ERROR lib/bx/seq/seq_tests.py
ERROR lib/bx/seq/twobit_tests.py
ERROR lib/bx/seqmapping_tests.py
!!!!!!!!!!!!!!!!!!! Interrupted: 18 errors during collection !!!!!!!!!!!!!!!!!!!
======================== 1 warning, 18 errors in 1.93s =========================
 * ERROR: sci-biology/bx-python-0.12.0::science failed (test phase):
 *   pytest failed with python3.12
 * 
 * Call stack:
 *     ebuild.sh, line  136:  Called src_test
 *   environment, line 3896:  Called distutils-r1_src_test
 *   environment, line 1948:  Called _distutils-r1_run_foreach_impl 'python_test'
 *   environment, line  745:  Called python_foreach_impl 'distutils-r1_run_phase' 'python_test'
 *   environment, line 3501:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test'
 *   environment, line 3058:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test'
 *   environment, line 3056:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_test'
 *   environment, line 1194:  Called distutils-r1_run_phase 'python_test'
 *   environment, line 1871:  Called python_test
 *   environment, line 3783:  Called distutils-r1_python_test
 *   environment, line 1809:  Called epytest
 *   environment, line 2485:  Called die
 * The specific snippet of code:
 *       [[ ${ret} -ne 0 ]] && die -n "pytest failed with ${EPYTHON}";
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/bx-python-0.12.0::science'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/bx-python-0.12.0::science'`.
 * The complete build log is located at '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/temp/build.log'.
 * The ebuild environment file is located at '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/temp/environment'.
 * Working directory: '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0'
 * S: '/my_dir/var/tmp/portage/sci-biology/bx-python-0.12.0/work/bx-python-0.12.0'

[nsoranzo]

Thanks for reporting the issue!
@mr-c Maybe you have suggestions from the Debian packaging?

[mschubert]

The issue here seems to be that -m gpep517 (at least in Gentoo ebuilds) does not allow in-source builds. The pytest.ini and test_data are in the sources, while the compiled (or installed) package is in a separate directory.

I could get most tests to run by linking pytest.ini and test_data into the built directory and calling pytest from there.

Now, only the following two fail:

lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_file_lzo
lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_binned_array_writer

both with:

compress = comp_types[comp_type][0]
E       KeyError: 'lzo'

[nsoranzo]

I could get most tests to run by linking pytest.ini and test_data into the built directory and calling pytest from there.

That's good progress, thanks for your work on that!

Now, only the following two fail:

lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_file_lzo
lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_binned_array_writer

both with:

compress = comp_types[comp_type][0]
E       KeyError: 'lzo'

That's likely due to missing python-lzo, which is not strictly required by bx-python but it's need for these tests to pass, see https://github.com/bxlab/bx-python/blob/main/tox.ini#L16

[mschubert]

Oh yes, that makes sense. Thank you!

I edited the title for the PEP517 tests, please feel free to leave open or close as you prefer.

[nsoranzo]

@mschubert Sorry for late reply here, if there's anything that we can do here that would make your life easier let us know!