Please document how to run Python tests

[yurivict]

The Build/install page should explain how to run Python exension tests.

Running pytest in any of the directories test/, test/unit_distributed/ fails like this:

===>   py311-arbor-0.10.1 depends on file: /usr/local/bin/python3.11 - found
cd /usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/unit_distributed && /usr/bin/env -i HOME=/usr/ports/science/py-arbor/work-py311  PWD="${PWD}"  __MAKE_CONF=/nonexistent OSVERSION=1401500 PATH=/usr/local/libexec/ccache:/usr/ports/science/py-arbor/work-py311/.bin:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin TERM=xterm-256color NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/usr/ports/science/py-arbor/work-py311  XDG_CONFIG_HOME=/usr/ports/science/py-arbor/work-py311  XDG_CACHE_HOME=/usr/ports/science/py-arbor/work-py311/.cache  HOME=/usr/ports/science/py-arbor/work-py311 PATH=/usr/local/libexec/ccache:/usr/ports/science/py-arbor/work-py311/.bin:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/usr/ports/science/py-arbor/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/usr/ports/science/py-arbor/work-py311/stage PREFIX=/usr/local  LOCALBASE=/usr/local  CC="cc" CFLAGS="-O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing "  CPP="cpp" CPPFLAGS="-isystem /usr/local/include"  LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC -isystem /usr/local/include " 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" PYTHONPATH=/usr/ports/science/py-arbor/work-py311/stage/usr/local/lib/python3.11/site-packages /usr/local/bin/python3.11 -m pytest -k '' -rs -v -o addopts= -v
==================================================================================== test session starts ====================================================================================
platform freebsd14 -- Python 3.11.9, pytest-8.1.1, pluggy-1.5.0 -- /usr/local/bin/python3.11
cachedir: .pytest_cache
benchmark: 4.0.0 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/unit_distributed/.hypothesis/examples'))
Using --randomly-seed=2274967451
PyQt5 5.15.10 -- Qt runtime 5.15.14 -- Qt compiled 5.15.14
rootdir: /usr/ports/science/py-arbor/work-py311/arbor-0.10.1
configfile: pyproject.toml
plugins: mypy-plugins-3.1.2, timeout-2.1.0, time-machine-2.11.0, datadir-1.5.0, rerunfailures-11.1.2, flaky-3.8.1, benchmark-4.0.0, cov-5.0.0, hypothesis-6.98.18, mock-3.10.0, forked-1.6.0, randomly-3.12.0, asyncio-0.23.8, xdist-3.6.1, env-0.6.2, aspectlib-2.0.0, anyio-4.4.0, typeguard-4.3.0, qt-4.2.0, subprocess-1.5.2
asyncio: mode=Mode.STRICT
collected 0 items / 4 errors                                                                                                                                                                

========================================================================================== ERRORS ===========================================================================================
___________________________________________________________ ERROR collecting python/test/unit_distributed/test_contexts_arbmpi.py ___________________________________________________________
ImportError while importing test module '/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/unit_distributed/test_contexts_arbmpi.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.11/site-packages/_pytest/python.py:520: in importtestmodule
    mod = import_path(
/usr/local/lib/python3.11/site-packages/_pytest/pathlib.py:584: in import_path
    importlib.import_module(module_name)
/usr/local/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1204: in _gcd_import
    ???
<frozen importlib._bootstrap>:1176: in _find_and_load
    ???
<frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:690: in _load_unlocked
    ???
/usr/local/lib/python3.11/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
test_contexts_arbmpi.py:8: in <module>
    from .. import cases
E   ImportError: attempted relative import with no known parent package
___________________________________________________________ ERROR collecting python/test/unit_distributed/test_contexts_mpi4py.py ___________________________________________________________
ImportError while importing test module '/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/unit_distributed/test_contexts_mpi4py.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.11/site-packages/_pytest/python.py:520: in importtestmodule
    mod = import_path(
/usr/local/lib/python3.11/site-packages/_pytest/pathlib.py:584: in import_path
    importlib.import_module(module_name)
/usr/local/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1204: in _gcd_import
    ???
<frozen importlib._bootstrap>:1176: in _find_and_load
    ???
<frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:690: in _load_unlocked
    ???
/usr/local/lib/python3.11/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
test_contexts_mpi4py.py:8: in <module>
    from .. import cases
E   ImportError: attempted relative import with no known parent package
________________________________________________________ ERROR collecting python/test/unit_distributed/test_domain_decompositions.py ________________________________________________________
ImportError while importing test module '/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/unit_distributed/test_domain_decompositions.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.11/site-packages/_pytest/python.py:520: in importtestmodule
    mod = import_path(
/usr/local/lib/python3.11/site-packages/_pytest/pathlib.py:584: in import_path
    importlib.import_module(module_name)
/usr/local/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1204: in _gcd_import
    ???
<frozen importlib._bootstrap>:1176: in _find_and_load
    ???
<frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:690: in _load_unlocked
    ???
/usr/local/lib/python3.11/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
test_domain_decompositions.py:8: in <module>
    from .. import cases
E   ImportError: attempted relative import with no known parent package
______________________________________________________________ ERROR collecting python/test/unit_distributed/test_simulator.py ______________________________________________________________
ImportError while importing test module '/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/unit_distributed/test_simulator.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/local/lib/python3.11/site-packages/_pytest/python.py:520: in importtestmodule
    mod = import_path(
/usr/local/lib/python3.11/site-packages/_pytest/pathlib.py:584: in import_path
    importlib.import_module(module_name)
/usr/local/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1204: in _gcd_import
    ???
<frozen importlib._bootstrap>:1176: in _find_and_load
    ???
<frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
    ???
<frozen importlib._bootstrap>:690: in _load_unlocked
    ???
/usr/local/lib/python3.11/site-packages/_pytest/assertion/rewrite.py:178: in exec_module
    exec(co, module.__dict__)
test_simulator.py:7: in <module>
    from .. import cases
E   ImportError: attempted relative import with no known parent package
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
===================================================================================== 4 errors in 2.21s =====================================================================================
*** Error code 2

Version: 0.10.1
Python-3.11
FreeBSD 14.1

[thorstenhater]

Hi @yurivict,

there is a short comment on that, namely here
https://docs.arbor-sim.org/en/stable/contrib/test.html#python-tests
It has proven practical, however, to run the following from the cmake build dir
in the development cycle:

PYTHONPATH=`pwd`/python python3 -munittest discover -v -s ../python

[yurivict]

The above command fails after some tests succeeding:

cd /usr/ports/science/py-arbor/work-py311/.build &&  /usr/bin/env NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/usr/ports/science/py-arbor/work-py311  XDG_CONFIG_HOME=/usr/ports/science/py-arbor/work-py311  XDG_CACHE_HOME=/usr/ports/science/py-arbor/work-py311/.cache  HOME=/usr/ports/science/py-arbor/work-py311 PATH=/usr/local/libexec/ccache:/usr/ports/science/py-arbor/work-py311/.bin:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/usr/ports/science/py-arbor/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/usr/ports/science/py-arbor/work-py311/stage PREFIX=/usr/local  LOCALBASE=/usr/local  CC="cc" CFLAGS="-O2 -pipe  -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing "  CPP="cpp" CPPFLAGS="-isystem /usr/local/include"  LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -fPIC -isystem /usr/local/include " 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" PYTHONPATH=/usr/ports/science/py-arbor/work-py311/stage/usr/local/lib/python3.11/site-packages /usr/local/bin/python3.11 -munittest discover -v -s /usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python
test.unit.test_catalogues (unittest.loader._FailedTest.test.unit.test_catalogues) ... ERROR
test_spike_clearing (test.unit.test_clear_samplers.TestClearSamplers.test_spike_clearing) ... ok
test_context (test.unit.test_contexts.TestContexts.test_context) ... ok
test_context_allocation (test.unit.test_contexts.TestContexts.test_context_allocation) ... ok
test_default_allocation (test.unit.test_contexts.TestContexts.test_default_allocation) ... ok
test_default_context (test.unit.test_contexts.TestContexts.test_default_context) ... ok
test_exceptions_allocation (test.unit.test_contexts.TestContexts.test_exceptions_allocation) ... ok
test_set_allocation (test.unit.test_contexts.TestContexts.test_set_allocation) ... ok
test_iclamp (test.unit.test_decor.TestDecorClasses.test_iclamp) ... ok
test_domain_decomposition_exceptions (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_exceptions) ... ok
test_domain_decomposition_heterogenous_CPU (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_heterogenous_CPU) ... ok
test_domain_decomposition_heterogenous_GPU (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_heterogenous_GPU) ... skipped 'GPU not enabled'
test_domain_decomposition_hints (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_hints) ... ok
test_domain_decomposition_homogenous_CPU (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_homogenous_CPU) ... ok
test_domain_decomposition_homogenous_GPU (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_homogenous_GPU) ... skipped 'GPU not enabled'
test_event_generator_explicit_schedule (test.unit.test_event_generators.TestEventGenerator.test_event_generator_explicit_schedule) ... ok
test_event_generator_poisson_schedule (test.unit.test_event_generators.TestEventGenerator.test_event_generator_poisson_schedule) ... ok
test_event_generator_regular_schedule (test.unit.test_event_generators.TestEventGenerator.test_event_generator_regular_schedule) ... ok
test_gid_index_ctor_cell_member (test.unit.test_identifiers.TestCellMembers.test_gid_index_ctor_cell_member) ... ok
test_set_gid_index_cell_member (test.unit.test_identifiers.TestCellMembers.test_set_gid_index_cell_member) ... ok
test_fileio (test.unit.test_io.TestAccIo.test_fileio) ... ok
test_nameio (test.unit.test_io.TestAccIo.test_nameio) ... ok
test_pathio (test.unit.test_io.TestAccIo.test_pathio) ... ok
test_stringio (test.unit.test_io.TestAccIo.test_stringio) ... ok
test_fileio (test.unit.test_io.TestAscIo.test_fileio) ... ok
test_nameio (test.unit.test_io.TestAscIo.test_nameio) ... ok
test_pathio (test.unit.test_io.TestAscIo.test_pathio) ... ok
test_stringio (test.unit.test_io.TestAscIo.test_stringio) ... ok
test_serialize (test.unit.test_io.TestSerdes.test_serialize) ... ok
test_fileio (test.unit.test_io.TestSwcArborIo.test_fileio) ... ok
test_nameio (test.unit.test_io.TestSwcArborIo.test_nameio) ... ok
test_pathio (test.unit.test_io.TestSwcArborIo.test_pathio) ... ok
test_stringio (test.unit.test_io.TestSwcArborIo.test_stringio) ... ok
test_fileio (test.unit.test_io.TestSwcNeuronIo.test_fileio) ... ok
test_nameio (test.unit.test_io.TestSwcNeuronIo.test_nameio) ... ok
test_pathio (test.unit.test_io.TestSwcNeuronIo.test_pathio) ... ok
test_stringio (test.unit.test_io.TestSwcNeuronIo.test_stringio) ... ok
test_compose (test.unit.test_morphology.TestPlacePwlin.test_compose) ... ok
test_identity (test.unit.test_morphology.TestPlacePwlin.test_identity) ... ok
test_mpoint (test.unit.test_morphology.TestPlacePwlin.test_mpoint) ... ok
test_place_pwlin_id (test.unit.test_morphology.TestPlacePwlin.test_place_pwlin_id) ... ok
test_place_pwlin_isometry (test.unit.test_morphology.TestPlacePwlin.test_place_pwlin_isometry) ... ok
test_rotation (test.unit.test_morphology.TestPlacePwlin.test_rotation) ... ok
test_translation (test.unit.test_morphology.TestPlacePwlin.test_translation) ... ok
test_multiple_connections_rr_halt (test.unit.test_multiple_connections.TestMultipleConnections.test_multiple_connections_rr_halt) ... ok
test_multiple_connections_rr_no_halt (test.unit.test_multiple_connections.TestMultipleConnections.test_multiple_connections_rr_no_halt) ... ok
test_multiple_connections_uni (test.unit.test_multiple_connections.TestMultipleConnections.test_multiple_connections_uni) ... ok
test_probe_addr_metadata (test.unit.test_probes.TestCableProbes.test_probe_addr_metadata) ... ok
test_probe_addr_metadata (test.unit.test_probes.TestLifProbes.test_probe_addr_metadata) ... ok
test_probe_result (test.unit.test_probes.TestLifProbes.test_probe_result) ... ok
test_summary (test.unit.test_profiling.TestProfiling.test_summary) ... skipped 'run test only with profiling support'
test_support (test.unit.test_profiling.TestProfiling.test_support) ... ok
test_events_explicit_schedule (test.unit.test_schedules.TestExplicitSchedule.test_events_explicit_schedule) ... ok
test_exceptions_explicit_schedule (test.unit.test_schedules.TestExplicitSchedule.test_exceptions_explicit_schedule) ... ok
test_times_contor_explicit_schedule (test.unit.test_schedules.TestExplicitSchedule.test_times_contor_explicit_schedule) ... ok
test_events_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_events_poisson_schedule) ... ok
test_exceptions_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_exceptions_poisson_schedule) ... ok
test_freq_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_freq_poisson_schedule) ... ok
test_freq_seed_contor_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_freq_seed_contor_poisson_schedule) ... ok
test_freq_tstart_contor_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_freq_tstart_contor_poisson_schedule) ... ok
test_tstart_freq_seed_contor_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_tstart_freq_seed_contor_poisson_schedule) ... ok
test_tstop_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_tstop_poisson_schedule) ... ok
test_events_regular_schedule (test.unit.test_schedules.TestRegularSchedule.test_events_regular_schedule) ... ok
test_exceptions_regular_schedule (test.unit.test_schedules.TestRegularSchedule.test_exceptions_regular_schedule) ... ok
test_none_ctor_regular_schedule (test.unit.test_schedules.TestRegularSchedule.test_none_ctor_regular_schedule) ... ok
test_set_tstart_dt_tstop_regular_schedule (test.unit.test_schedules.TestRegularSchedule.test_set_tstart_dt_tstop_regular_schedule) ... ok
test_tstart_dt_tstop_ctor_regular_schedule (test.unit.test_schedules.TestRegularSchedule.test_tstart_dt_tstop_ctor_regular_schedule) ... ok
test_spikes_sorted (test.unit.test_spikes.TestSpikes.test_spikes_sorted) ... ok

======================================================================
ERROR: test.unit.test_catalogues (unittest.loader._FailedTest.test.unit.test_catalogues)
----------------------------------------------------------------------
ImportError: Failed to import test module: test.unit.test_catalogues
Traceback (most recent call last):
  File "/usr/local/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
    module = self._get_module_from_name(name)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
    __import__(name)
  File "/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/unit/test_catalogues.py", line 42, in <module>
    class TestCatalogues(unittest.TestCase):
  File "/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/unit/test_catalogues.py", line 47, in TestCatalogues
    @fixtures.dummy_catalogue()
     ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/fixtures.py", line 55, in decorator
    fixture = fixture_factory(*args, **kwargs)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/fixtures.py", line 40, in inject_fixture
    return func(*bound.args, **bound.kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/fixtures.py", line 173, in dummy_catalogue
    cat_path = _build_cat("dummy", path)
               ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/fixtures.py", line 40, in inject_fixture
    return func(*bound.args, **bound.kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/fixtures.py", line 161, in _build_cat
    _build_cat_local(name, path)
  File "/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/python/test/fixtures.py", line 120, in _build_cat_local
    raise _BuildCatError(
test.fixtures._BuildCatError: Tests can't build catalogue 'dummy' from '/usr/ports/science/py-arbor/work-py311/arbor-0.10.1/test/unit/dummy':
Traceback (most recent call last):
  File "/usr/local/bin/arbor-build-catalogue", line 318, in <module>
    sp.run(make_cmd, shell=True, check=True, capture_output = True, text = True)
  File "/usr/local/lib/python3.11/subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'make' returned non-zero exit status 2.
 Error:

c++: error: no input files
/bin/sh: -pipe: not found
/bin/sh: -fstack-protector-strong: not found
/bin/sh: -isystem: not found
/bin/sh: /usr/local/include: Permission denied
/bin/sh: -fno-strict-aliasing: not found
/bin/sh: -isystem: not found
/bin/sh: /usr/local/include: Permission denied
make[3]: *** [CMakeFiles/dummy-catalogue.dir/build.make:83: CMakeFiles/dummy-catalogue.dir/generated/dummy/dummy_catalogue.cpp.o] Error 126
make[2]: *** [CMakeFiles/Makefile2:83: CMakeFiles/dummy-catalogue.dir/all] Error 2
make[1]: *** [Makefile:91: all] Error 2


Building catalogue 'dummy' from mechanisms in /usr/ports/science/py-arbor/work-py311/arbor-0.10.1/test/unit/dummy
 * NMODL
   * dummy
Build log:
make[1]: Entering directory '/tmp/tmp_d0w1s6y/build'
[ 25%] modcc generating: /tmp/tmp_d0w1s6y/build/generated/dummy/dummy_catalogue.cpp;/tmp/tmp_d0w1s6y/build/generated/dummy/dummy_cpu.cpp
[ 50%] Building CXX object CMakeFiles/dummy-catalogue.dir/generated/dummy/dummy_catalogue.cpp.o
make[1]: Leaving directory '/tmp/tmp_d0w1s6y/build'



----------------------------------------------------------------------
Ran 68 tests in 0.064s

FAILED (errors=1, skipped=3)
*** Error code 1

[thorstenhater]

Does it still fail after traversing to the arbor checkout and using this instead:

PYTHONPATH=<path/to/build> python3 -munittest discover -v -s python

?
Reasoning: Some of our tests build a shared object plugin and it seems the
fixture is misbehaving such that artifact is not found

[thorstenhater]

Coming back to the error log, I'd also suspect something is off with the invocation:
Quoting the log

c++: error: no input files
/bin/sh: -pipe: not found
/bin/sh: -fstack-protector-strong: not found
/bin/sh: -isystem: not found
/bin/sh: /usr/local/include: Permission denied
/bin/sh: -fno-strict-aliasing: not found
/bin/sh: -isystem: not found
/bin/sh: /usr/local/include: Permission denied

Possibly skip the relevant tests (those loading plugins) and/or check whether you can build a
plugin like so (after make install; otherwise you'll have to adjust at least PYTHONPATH and PATH)

arbor-build-catalogue dummy [...]/test/unit/dummy/

Output should be similar to this

Building catalogue 'dummy' from mechanisms in [...]/test/unit/dummy
 * NMODL
   * dummy
Catalogue has been built and copied to [...]/dummy-catalogue.so

[yurivict]

I found the cause:

Tests fail to properly handle CXXFLAGS and CFLAGS passed in the environment.

Test environment in the FreeBSD port passes is:

NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/usr/ports/science/py-arbor/work-py311 XDG_CONFIG_HOME=/usr/ports/science/py-arbor/work-py311 XDG_CACHE_HOME=/usr/ports/science/py-arbor/work-py311/.cache HOME=/usr/ports/science/py-arbor/work-py311 PATH=/usr/local/libexec/ccache:/usr/ports/science/py-arbor/work-py311/.bin:/home/yuri/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/usr/ports/science/py-arbor/work-py311/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/usr/ports/science/py-arbor/work-py311/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -D_LIBCPP_HARDENING_MODE=_LIBCPP_HARDENING_MODE_NONE -isystem /usr/local/include " CCACHE_DIR="/var/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" PYTHONPATH=/usr/ports/science/py-arbor/work-py311/stage/usr/local/lib/python3.11/site-packages

Please fix this problem.

[thorstenhater]

Interesting. Arbor's installation records the values of CXX and CXXFLAGS during the build step and uses
them during building the dynamic libraries. From the path in your log /usr/local/bin/arbor-build-catalogue
we can assume this is post-installation. The error /bin/sh: -fstack-protector-strong: not found seems like
sh is trying to call -fstack-protector-strong like an executable or pass it to c++ as an input.

Is there an issue with quoting? Or a spurious newline? Also: how did you come to your conclusion?

[yurivict]

There is no issue with quoting when we call tests. The above environment looks correct.

The problem seems to be in how the test code treats CFLAGS/CXXFLAGS environment variables that contain spaces.

[thorstenhater]

So, I tried to reproduce this by a minimal example:

CXXFLAGS='-O2 -pipe -fstack-protector-strong'  python3 -munittest discover -v -s python

and all test pass

test_empty (test.unit.test_catalogues.TestCatalogues.test_empty) ... ok
test_nonexistent (test.unit.test_catalogues.TestCatalogues.test_nonexistent) ... ok
test_shared_catalogue (test.unit.test_catalogues.TestCatalogues.test_shared_catalogue) ... ok
test_simulation (test.unit.test_catalogues.TestCatalogues.test_simulation) ... ok
test_spike_clearing (test.unit.test_clear_samplers.TestClearSamplers.test_spike_clearing) ... ok
test_context (test.unit.test_contexts.TestContexts.test_context) ... ok
test_context_allocation (test.unit.test_contexts.TestContexts.test_context_allocation) ... ok
test_default_allocation (test.unit.test_contexts.TestContexts.test_default_allocation) ... ok
test_default_context (test.unit.test_contexts.TestContexts.test_default_context) ... ok
test_exceptions_allocation (test.unit.test_contexts.TestContexts.test_exceptions_allocation) ... ok
test_set_allocation (test.unit.test_contexts.TestContexts.test_set_allocation) ... ok
test_iclamp (test.unit.test_decor.TestDecorClasses.test_iclamp) ... ok
test_diffusion_different_radii_equal_length (test.unit.test_diffusion.TestDiffusion.test_diffusion_different_radii_equal_length) ... ok
test_diffusion_equal_radii_different_length (test.unit.test_diffusion.TestDiffusion.test_diffusion_equal_radii_different_length) ... ok
test_diffusion_equal_radii_equal_length (test.unit.test_diffusion.TestDiffusion.test_diffusion_equal_radii_equal_length) ... ok
test_diffusion_scaling_amount (test.unit.test_diffusion_scaling.TestDiffusionScaling.test_diffusion_scaling_amount) ... skipped 'SciPy not found'
test_diffusion_scaling_concentration (test.unit.test_diffusion_scaling.TestDiffusionScaling.test_diffusion_scaling_concentration) ... skipped 'SciPy not found'
test_domain_decomposition_exceptions (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_exceptions) ... ok
test_domain_decomposition_heterogenous_CPU (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_heterogenous_CPU) ... ok
test_domain_decomposition_heterogenous_GPU (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_heterogenous_GPU) ... skipped 'GPU not enabled'
test_domain_decomposition_hints (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_hints) ... ok
test_domain_decomposition_homogenous_CPU (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_homogenous_CPU) ... ok
test_domain_decomposition_homogenous_GPU (test.unit.test_domain_decompositions.TestDomain_Decompositions.test_domain_decomposition_homogenous_GPU) ... skipped 'GPU not enabled'
test_event_generator_explicit_schedule (test.unit.test_event_generators.TestEventGenerator.test_event_generator_explicit_schedule) ... ok
test_event_generator_poisson_schedule (test.unit.test_event_generators.TestEventGenerator.test_event_generator_poisson_schedule) ... ok
test_event_generator_regular_schedule (test.unit.test_event_generators.TestEventGenerator.test_event_generator_regular_schedule) ... ok
test_gid_index_ctor_cell_member (test.unit.test_identifiers.TestCellMembers.test_gid_index_ctor_cell_member) ... ok
test_set_gid_index_cell_member (test.unit.test_identifiers.TestCellMembers.test_set_gid_index_cell_member) ... ok
test_fileio (test.unit.test_io.TestAccIo.test_fileio) ... ok
test_nameio (test.unit.test_io.TestAccIo.test_nameio) ... ok
test_pathio (test.unit.test_io.TestAccIo.test_pathio) ... ok
test_stringio (test.unit.test_io.TestAccIo.test_stringio) ... ok
test_fileio (test.unit.test_io.TestAscIo.test_fileio) ... ok
test_nameio (test.unit.test_io.TestAscIo.test_nameio) ... ok
test_pathio (test.unit.test_io.TestAscIo.test_pathio) ... ok
test_stringio (test.unit.test_io.TestAscIo.test_stringio) ... ok
test_serialize (test.unit.test_io.TestSerdes.test_serialize) ... ok
test_fileio (test.unit.test_io.TestSwcArborIo.test_fileio) ... ok
test_nameio (test.unit.test_io.TestSwcArborIo.test_nameio) ... ok
test_pathio (test.unit.test_io.TestSwcArborIo.test_pathio) ... ok
test_stringio (test.unit.test_io.TestSwcArborIo.test_stringio) ... ok
test_fileio (test.unit.test_io.TestSwcNeuronIo.test_fileio) ... ok
test_nameio (test.unit.test_io.TestSwcNeuronIo.test_nameio) ... ok
test_pathio (test.unit.test_io.TestSwcNeuronIo.test_pathio) ... ok
test_stringio (test.unit.test_io.TestSwcNeuronIo.test_stringio) ... ok
test_compose (test.unit.test_morphology.TestPlacePwlin.test_compose) ... ok
test_identity (test.unit.test_morphology.TestPlacePwlin.test_identity) ... ok
test_mpoint (test.unit.test_morphology.TestPlacePwlin.test_mpoint) ... ok
test_place_pwlin_id (test.unit.test_morphology.TestPlacePwlin.test_place_pwlin_id) ... ok
test_place_pwlin_isometry (test.unit.test_morphology.TestPlacePwlin.test_place_pwlin_isometry) ... ok
test_rotation (test.unit.test_morphology.TestPlacePwlin.test_rotation) ... ok
test_translation (test.unit.test_morphology.TestPlacePwlin.test_translation) ... ok
test_multiple_connections_rr_halt (test.unit.test_multiple_connections.TestMultipleConnections.test_multiple_connections_rr_halt) ... ok
test_multiple_connections_rr_no_halt (test.unit.test_multiple_connections.TestMultipleConnections.test_multiple_connections_rr_no_halt) ... ok
test_multiple_connections_uni (test.unit.test_multiple_connections.TestMultipleConnections.test_multiple_connections_uni) ... ok
test_probe_addr_metadata (test.unit.test_probes.TestCableProbes.test_probe_addr_metadata) ... ok
test_probe_addr_metadata (test.unit.test_probes.TestLifProbes.test_probe_addr_metadata) ... ok
test_probe_result (test.unit.test_probes.TestLifProbes.test_probe_result) ... ok
test_summary (test.unit.test_profiling.TestProfiling.test_summary) ... skipped 'run test only with profiling support'
test_support (test.unit.test_profiling.TestProfiling.test_support) ... ok
test_events_explicit_schedule (test.unit.test_schedules.TestExplicitSchedule.test_events_explicit_schedule) ... ok
test_exceptions_explicit_schedule (test.unit.test_schedules.TestExplicitSchedule.test_exceptions_explicit_schedule) ... ok
test_times_contor_explicit_schedule (test.unit.test_schedules.TestExplicitSchedule.test_times_contor_explicit_schedule) ... ok
test_events_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_events_poisson_schedule) ... ok
test_exceptions_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_exceptions_poisson_schedule) ... ok
test_freq_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_freq_poisson_schedule) ... ok
test_freq_seed_contor_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_freq_seed_contor_poisson_schedule) ... ok
test_freq_tstart_contor_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_freq_tstart_contor_poisson_schedule) ... ok
test_tstart_freq_seed_contor_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_tstart_freq_seed_contor_poisson_schedule) ... ok
test_tstop_poisson_schedule (test.unit.test_schedules.TestPoissonSchedule.test_tstop_poisson_schedule) ... ok
test_events_regular_schedule (test.unit.test_schedules.TestRegularSchedule.test_events_regular_schedule) ... ok
test_exceptions_regular_schedule (test.unit.test_schedules.TestRegularSchedule.test_exceptions_regular_schedule) ... ok
test_none_ctor_regular_schedule (test.unit.test_schedules.TestRegularSchedule.test_none_ctor_regular_schedule) ... ok
test_set_tstart_dt_tstop_regular_schedule (test.unit.test_schedules.TestRegularSchedule.test_set_tstart_dt_tstop_regular_schedule) ... ok
test_tstart_dt_tstop_ctor_regular_schedule (test.unit.test_schedules.TestRegularSchedule.test_tstart_dt_tstop_ctor_regular_schedule) ... ok
test_dt_half_delay (test.unit.test_simulation.TestDelayNetwork.test_dt_half_delay) ... ok
test_zero_delay (test.unit.test_simulation.TestDelayNetwork.test_zero_delay) ... ok
test_spikes_sorted (test.unit.test_spikes.TestSpikes.test_spikes_sorted) ... ok

----------------------------------------------------------------------
Ran 78 tests in 0.091s

OK (skipped=5)

Adding some debug statements also shows that the environment variables are being passed into the
catalogue building phase. I am afraid I'll need more details or a minimal reproducer