Package: src:bmtk Version: 1.1.1+ds-4 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202512/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:bmtk, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:317: python3.14 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: BSD License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. [... snipped ...] copying images... [ 53%] ../../../build/html/.doctrees/nbsphinx/tutorial_cell_placement_14_1.png copying images... 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The HTML pages are in build/html. make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp -r /<<PKGBUILDDIR>>/bmtk/tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bmtk/ I: pybuild base:317: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build; python3.14 -m pytest ============================= test session starts ============================== platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 rootdir: /<<PKGBUILDDIR>> plugins: typeguard-4.4.4 collected 354 items / 4 errors / 2 skipped ==================================== ERRORS ==================================== _ ERROR collecting .pybuild/cpython3_3.14/build/bmtk/tests/builder/auxi/test_node_params.py _ ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bmtk/tests/builder/auxi/test_node_params.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3.14/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ bmtk/tests/builder/auxi/test_node_params.py:8: in <module> from neuron import h /usr/lib/python3/dist-packages/neuron/__init__.py:120: in <module> raise ImportError(message) E ImportError: Python 3.14 is not supported by this NEURON installation (supported: 3.13). Either re-build NEURON with support for this version, use a supported version of Python, or try using nrniv -python so that NEURON can suggest a compatible version for you. _ ERROR collecting .pybuild/cpython3_3.14/build/bmtk/tests/simulator/bionet/test_iclamp.py _ ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bmtk/tests/simulator/bionet/test_iclamp.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3.14/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ bmtk/tests/simulator/bionet/test_iclamp.py:8: in <module> from neuron import h /usr/lib/python3/dist-packages/neuron/__init__.py:120: in <module> raise ImportError(message) E ImportError: Python 3.14 is not supported by this NEURON installation (supported: 3.13). Either re-build NEURON with support for this version, use a supported version of Python, or try using nrniv -python so that NEURON can suggest a compatible version for you. _ ERROR collecting .pybuild/cpython3_3.14/build/bmtk/tests/simulator/bionet/test_morphology.py _ ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bmtk/tests/simulator/bionet/test_morphology.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3.14/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ bmtk/tests/simulator/bionet/test_morphology.py:6: in <module> from neuron import h /usr/lib/python3/dist-packages/neuron/__init__.py:120: in <module> raise ImportError(message) E ImportError: Python 3.14 is not supported by this NEURON installation (supported: 3.13). Either re-build NEURON with support for this version, use a supported version of Python, or try using nrniv -python so that NEURON can suggest a compatible version for you. _ ERROR collecting .pybuild/cpython3_3.14/build/bmtk/tests/simulator/bionet/test_virtualcell.py _ ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bmtk/tests/simulator/bionet/test_virtualcell.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: /usr/lib/python3.14/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ bmtk/tests/simulator/bionet/test_virtualcell.py:6: in <module> from neuron import h /usr/lib/python3/dist-packages/neuron/__init__.py:120: in <module> raise ImportError(message) E ImportError: Python 3.14 is not supported by this NEURON installation (supported: 3.13). Either re-build NEURON with support for this version, use a supported version of Python, or try using nrniv -python so that NEURON can suggest a compatible version for you. =============================== warnings summary =============================== bmtk/tests/builder/bionet/test_swc_reader.py:5 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/bmtk/tests/builder/bionet/test_swc_reader.py:5: PytestDeprecationWarning: Module 'neuron' was found, but when imported by pytest it raised: ImportError('Python 3.14 is not supported by this NEURON installation (supported: 3.13). Either re-build NEURON with support for this version, use a supported version of Python, or try using nrniv -python so that NEURON can suggest a compatible version for you.') In pytest 9.1 this warning will become an error by default. You can fix the underlying problem, or alternatively overwrite this behavior and silence this warning by passing exc_type=ImportError explicitly. See https://docs.pytest.org/en/stable/deprecations.html#pytest-importorskip-default-behavior-regarding-importerror nrn = pytest.importorskip('neuron') # skip tests if neuron isn't installed on env. -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ ERROR bmtk/tests/builder/auxi/test_node_params.py ERROR bmtk/tests/simulator/bionet/test_iclamp.py ERROR bmtk/tests/simulator/bionet/test_morphology.py ERROR bmtk/tests/simulator/bionet/test_virtualcell.py !!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!! =================== 2 skipped, 1 warning, 4 errors in 2.20s ==================== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build; python3.14 -m pytest I: pybuild pybuild:308: cp -r /<<PKGBUILDDIR>>/bmtk/tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/bmtk/ I: pybuild base:317: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build; python3.13 -m pytest ============================= test session starts ============================== platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 rootdir: /<<PKGBUILDDIR>> plugins: typeguard-4.4.4 NEURON mechanisms not found in /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/bmtk/tests/simulator/bionet/components/mechanisms. collected 399 items / 1 skipped bmtk/tests/builder/auxi/test_edge_connectors.py .. [ 0%] bmtk/tests/builder/auxi/test_node_params.py ......s [ 2%] bmtk/tests/builder/bionet/test_swc_reader.py s [ 2%] bmtk/tests/builder/test_connection_map.py ....... [ 4%] bmtk/tests/builder/test_connector.py ..... [ 5%] bmtk/tests/builder/test_densenetwork.py ... [ 6%] bmtk/tests/builder/test_edge_iterator.py ... [ 7%] bmtk/tests/builder/test_edges_sorter.py ... [ 7%] bmtk/tests/builder/test_id_generator.py ...... [ 9%] bmtk/tests/builder/test_index_builders.py .. [ 9%] bmtk/tests/builder/test_iterator.py ........ [ 11%] bmtk/tests/builder/test_network.py ............ [ 14%] bmtk/tests/builder/test_network_mpi.py ssssssss [ 16%] bmtk/tests/builder/test_node_pool.py ..... [ 18%] bmtk/tests/builder/test_node_set.py ... [ 18%] bmtk/tests/builder/test_save_network.py ...... [ 20%] bmtk/tests/simulator/bionet/test_biograph.py ss [ 20%] bmtk/tests/simulator/bionet/test_gids.py . [ 21%] bmtk/tests/simulator/bionet/test_iclamp.py .................. [ 25%] bmtk/tests/simulator/bionet/test_morphology.py .....s.... [ 28%] bmtk/tests/simulator/bionet/test_nrn.py ....sss [ 29%] bmtk/tests/simulator/bionet/test_virtualcell.py sssssssss [ 32%] bmtk/tests/simulator/core/test_ecephys_module.py sssssss [ 33%] bmtk/tests/simulator/core/test_iclamp.py ..... [ 35%] bmtk/tests/simulator/core/test_io_tools.py .. [ 35%] bmtk/tests/simulator/core/test_pyfunction_cache.py ...... [ 37%] bmtk/tests/simulator/core/test_simulation_config.py .. [ 37%] bmtk/tests/simulator/core/test_simulation_config_validator.py ... [ 38%] bmtk/tests/simulator/filternet/lgnmodel/test_kernels.py ... [ 39%] bmtk/tests/simulator/filternet/lgnmodel/test_movie.py ..... [ 40%] bmtk/tests/simulator/filternet/lgnmodel/test_subclass_metrics.py ...... [ 41%] bmtk/tests/simulator/filternet/lgnmodel/test_transferfunction.py . [ 42%] bmtk/tests/simulator/filternet/lgnmodel/test_units.py .... [ 43%] bmtk/tests/simulator/filternet/lgnmodel/test_utils.py . [ 43%] bmtk/tests/simulator/filternet/test_default_setters.py ................. [ 47%] . [ 47%] bmtk/tests/simulator/filternet/test_filternet_movies.py . [ 48%] bmtk/tests/simulator/pointnet/test_multimeter_report.py ssss [ 49%] bmtk/tests/simulator/pointnet/test_pointgraph.py ss [ 49%] bmtk/tests/simulator/pointnet/test_pointnetwork.py sssssssssssssssss [ 53%] bmtk/tests/simulator/popnet/test_popgraph.py s [ 54%] bmtk/tests/simulator/utils/test_simulation_inputs.py ..... [ 55%] bmtk/tests/simulator/utils/test_simulation_reports.py .... [ 56%] bmtk/tests/utils/reports/compartment/test_compartment_reader.py .. [ 56%] bmtk/tests/utils/reports/compartment/test_compartment_writer.py ...... [ 58%] bmtk/tests/utils/reports/compartment/test_plotting.py ......... [ 60%] bmtk/tests/utils/reports/spike_trains/test_csv_adaptor.py .............. [ 64%] [ 64%] bmtk/tests/utils/reports/spike_trains/test_csv_adaptor_mpi.py .......... [ 66%] ...... [ 68%] bmtk/tests/utils/reports/spike_trains/test_plotting.py ................. [ 72%] ... [ 73%] bmtk/tests/utils/reports/spike_trains/test_sonata_adaptor.py ........... [ 75%] ................ [ 79%] bmtk/tests/utils/reports/spike_trains/test_sonata_adaptor_mpi.py ....... [ 81%] ............. [ 84%] bmtk/tests/utils/reports/spike_trains/test_spikes_buffer.py ............ [ 87%] ...... [ 89%] bmtk/tests/utils/reports/spike_trains/test_spikes_buffer_mpi.py ........ [ 91%] ........ [ 93%] bmtk/tests/utils/reports/spike_trains/test_spikes_core.py ..... [ 94%] bmtk/tests/utils/sonata/test_config.py ........... [ 97%] bmtk/tests/utils/sonata/test_config_validator.py .... [ 98%] bmtk/tests/utils/sonata/test_edge_stats.py ...... [100%] =============================== warnings summary =============================== .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/bmtk/builder/index_builders.py:205: FutureWarning: Series.fillna with 'method' is deprecated and will raise in a future version. Use obj.ffill() or obj.bfill() instead. i2r_table_df['range_end'] = i2r_table_df['range_end'].fillna(method='ffill') .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/bmtk/builder/index_builders.py:206: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method. The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy. For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object. i2r_table_df['range_end'].fillna(0, inplace=True) .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] .pybuild/cpython3_3.13/build/bmtk/tests/builder/test_index_builders.py::test_create_index[create_index_on_disk-indexer_args1] /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/bmtk/builder/index_builders.py:209: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy i2r_table_df['range_beg'][nans_mask] = i2r_table_df['range_end'][nans_mask] .pybuild/cpython3_3.13/build/bmtk/tests/simulator/core/test_simulation_config_validator.py::test_validate_network /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/bmtk/simulator/core/simulation_config_validator.py:30: DeprecationWarning: Subclassing validator classes is not intended to be part of their public API. A future version will make doing so an error, as the behavior of subclasses isn't guaranteed to stay the same between releases of jsonschema. Instead, prefer composition of validators, wrapping them in an object owned entirely by the downstream library. class SimulationConfigValidator(Draft4Validator): .pybuild/cpython3_3.13/build/bmtk/tests/simulator/filternet/lgnmodel/test_subclass_metrics.py::test_get_data_metrics[sus_sus-expected_val4] .pybuild/cpython3_3.13/build/bmtk/tests/simulator/filternet/lgnmodel/test_subclass_metrics.py::test_get_data_metrics[trans_sus-expected_val5] /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/bmtk/simulator/filternet/lgnmodel/cellmetrics.py:57: FutureWarning: The behavior of DataFrame.idxmax with all-NA values, or any-NA and skipna=False, is deprecated. In a future version this will raise ValueError exp_df['max_tf'] = sub_df.idxmax(axis=1).values # sub_df.idxmax(axis=1) .pybuild/cpython3_3.13/build/bmtk/tests/utils/sonata/test_edge_stats.py::test_edge_props_distribution .pybuild/cpython3_3.13/build/bmtk/tests/utils/sonata/test_edge_stats.py::test_edge_props_distribution .pybuild/cpython3_3.13/build/bmtk/tests/utils/sonata/test_edge_stats.py::test_edge_props_distribution .pybuild/cpython3_3.13/build/bmtk/tests/utils/sonata/test_edge_stats.py::test_edge_props_distribution .pybuild/cpython3_3.13/build/bmtk/tests/utils/sonata/test_edge_stats.py::test_nsyns_distribution .pybuild/cpython3_3.13/build/bmtk/tests/utils/sonata/test_edge_stats.py::test_nsyns_distribution .pybuild/cpython3_3.13/build/bmtk/tests/utils/sonata/test_edge_stats.py::test_nsyns_distribution /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/bmtk/utils/sonata/edge_stats.py:282: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` edges_df[edge_prop] = fill_val if edge_prop not in edges_df.columns else edges_df[edge_prop].fillna(fill_val) .pybuild/cpython3_3.13/build/bmtk/tests/utils/sonata/test_edge_stats.py::test_edge_stats_table /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/bmtk/utils/sonata/edge_stats.py:434: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` edges_df['nsyns'] = 1 if 'nsyns' not in edges_df.columns else edges_df['nsyns'].fillna(1) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================= 343 passed, 57 skipped, 29 warnings in 9.51s ================= dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13 make: *** [debian/rules:8: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 --------------------------------------------------------------------------------
