python-pynwb failed to build from source in Fedora rawhide/f37 https://koji.fedoraproject.org/koji/taskinfo?taskID=89887156 For details on the mass rebuild see: https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild Please fix python-pynwb at your earliest convenience and set the bug's status to ASSIGNED when you start fixing it. If the bug remains in NEW state for 8 weeks, python-pynwb will be orphaned. Before branching of Fedora 38, python-pynwb will be retired, if it still fails to build. For more details on the FTBFS policy, please visit: https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/
Created attachment 1902363 [details] build.log file build.log too big, will only attach last 32768 bytes
Created attachment 1902364 [details] root.log file root.log too big, will only attach last 32768 bytes
Created attachment 1902365 [details] state.log
Dear Maintainer, your package has an open Fails To Build From Source bug for Fedora 37. Action is required from you. PYC magic number has changed in Python 3.11.0b4, and all packages with Python bytecode need to be rebuilt. Most of them were rebuilt during the Fedora 37 mass rebuild, but since this package is FTBFS, we were hoping you could fix it and rebuild it manually, or it will cause subtle issues when used. Tracking bugzilla for all affected packages: https://bugzilla.redhat.com/show_bug.cgi?id=2107826 If you can fix your package to build, perform a build in koji, and if necessary, create an update in bodhi. If you are working on a fix, set the status to ASSIGNED to acknowledge this. If you have already fixed this issue, please close this Bugzilla report. Note that Fedora 37 is about to be branched very soon. If you fix this after branching, make sure to rebuild the package in both Rawhide (Fedora 38) and Fedora 37. ============================================== Following the policy for FTBFS packages [1], your package will be orphaned if this bug remains in a NEW state for more than 8 weeks (not sooner than 2022-09-27). A week before the mass branching of Fedora 38 according to the schedule [2], any packages not successfully rebuilt, at least on Fedora 36 will be retired regardless of the status of this bug. [1] https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/ [2] https://fedorapeople.org/groups/schedule/f-38/f-38-key-tasks.html
This bug appears to have been reported against 'rawhide' during the Fedora Linux 37 development cycle. Changing version to 37.
=================================== FAILURES =================================== _____ NWBFileTests.test_deprecate_simultaneous_recordings_on_add_stimulus ______ self = <tests.unit.test_icephys_metadata_tables.NWBFileTests testMethod=test_deprecate_simultaneous_recordings_on_add_stimulus> def test_deprecate_simultaneous_recordings_on_add_stimulus(self): """ Test that warnings are raised if the user tries to use a simultaneous_recordings table """ nwbfile = self.__get_icephysfile() device = self.__add_device(nwbfile) electrode = self.__add_electrode(nwbfile, device) stimulus = self.__get_stimulus(electrode=electrode) response = self.__get_response(electrode=electrode) # Make sure we warn if sweeptable is added on add_stimulus with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always") # Trigger all warnings nwbfile.add_stimulus(stimulus, use_sweep_table=True) > self.assertEqual(len(w), 1) E AssertionError: 2 != 1 tests/unit/test_icephys_metadata_tables.py:968: AssertionError __________ NWBFileTests.test_deprecate_sweepstable_on_add_acquistion ___________ self = <tests.unit.test_icephys_metadata_tables.NWBFileTests testMethod=test_deprecate_sweepstable_on_add_acquistion> def test_deprecate_sweepstable_on_add_acquistion(self): """ Test that warnings are raised if the user tries to use a sweeps table """ nwbfile = self.__get_icephysfile() device = self.__add_device(nwbfile) electrode = self.__add_electrode(nwbfile, device) stimulus = self.__get_stimulus(electrode=electrode) response = self.__get_response(electrode=electrode) # Make sure we warn if sweeptable is added on add_stimulus with warnings.catch_warnings(record=True) as w: nwbfile.add_acquisition(response, use_sweep_table=True) > self.assertEqual(len(w), 1) E AssertionError: 2 != 1 tests/unit/test_icephys_metadata_tables.py:1025: AssertionError _______________ NWBFileTests.test_deprecate_sweepstable_on_init ________________ self = <tests.unit.test_icephys_metadata_tables.NWBFileTests testMethod=test_deprecate_sweepstable_on_init> def test_deprecate_sweepstable_on_init(self): """ Test that warnings are raised if the user tries to use a sweeps table """ from pynwb.icephys import SweepTable with warnings.catch_warnings(record=True) as w: nwbfile = NWBFile( session_description='my first synthetic recording', identifier='EXAMPLE_ID', session_start_time=datetime.now(tzlocal()), sweep_table=SweepTable() ) device = self.__add_device(nwbfile) electrode = self.__add_electrode(nwbfile, device) stimulus = self.__get_stimulus(electrode=electrode) > self.assertEqual(len(w), 1) E AssertionError: 2 != 1 tests/unit/test_icephys_metadata_tables.py:1049: AssertionError _______ NWBFileTests.test_deprecate_sweeptable_on_add_stimulus_template ________ self = <tests.unit.test_icephys_metadata_tables.NWBFileTests testMethod=test_deprecate_sweeptable_on_add_stimulus_template> def test_deprecate_sweeptable_on_add_stimulus_template(self): """ Make sure we warn when using the sweep-table """ nwbfile = self.__get_icephysfile() local_electrode = nwbfile.create_icephys_electrode( name="elec0", description='a mock intracellular electrode', device=nwbfile.create_device(name='Heka ITC-1600') ) local_stimulus = VoltageClampStimulusSeries( name="ccss", data=[1, 2, 3, 4, 5], starting_time=123.6, rate=10e3, electrode=local_electrode, gain=0.02, sweep_number=np.uint64(15) ) local_stimulus2 = VoltageClampStimulusSeries( name="ccss2", data=[1, 2, 3, 4, 5], starting_time=123.6, rate=10e3, electrode=local_electrode, gain=0.02, sweep_number=np.uint64(15) ) with warnings.catch_warnings(record=True) as w: nwbfile.add_stimulus_template(local_stimulus, use_sweep_table=True) > self.assertEqual(len(w), 1) E AssertionError: 2 != 1 tests/unit/test_icephys_metadata_tables.py:1004: AssertionError =============================== warnings summary ===============================
=============================== warnings summary =============================== tests/unit/test_base.py: 8 warnings tests/unit/test_icephys_metadata_tables.py: 35 warnings /usr/lib/python3.11/site-packages/hdmf/utils.py:577: FutureWarning: VectorData.__init__: Using positional arguments for this method is discouraged and will be deprecated in a future major release. Please use keyword arguments to ensure future compatibility. warnings.warn(msg, FutureWarning) tests/unit/test_core.py: 1 warning tests/unit/test_ecephys.py: 15 warnings tests/unit/test_epoch.py: 5 warnings tests/unit/test_file.py: 16 warnings tests/unit/test_icephys_metadata_tables.py: 54 warnings tests/unit/test_misc.py: 15 warnings tests/unit/test_ophys.py: 11 warnings /usr/lib/python3.11/site-packages/hdmf/utils.py:577: FutureWarning: DynamicTable.__init__: Using positional arguments for this method is discouraged and will be deprecated in a future major release. Please use keyword arguments to ensure future compatibility. warnings.warn(msg, FutureWarning) tests/unit/test_ecephys.py: 15 warnings tests/unit/test_file.py: 1 warning /usr/lib/python3.11/site-packages/hdmf/utils.py:577: FutureWarning: DynamicTableRegion.__init__: Using positional arguments for this method is discouraged and will be deprecated in a future major release. Please use keyword arguments to ensure future compatibility. warnings.warn(msg, FutureWarning) tests/unit/test_icephys_metadata_tables.py: 32 warnings /usr/lib/python3.11/site-packages/hdmf/utils.py:577: FutureWarning: AlignedDynamicTable.__init__: Using positional arguments for this method is discouraged and will be deprecated in a future major release. Please use keyword arguments to ensure future compatibility. warnings.warn(msg, FutureWarning) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
It looks like this should be solved by updating to 2.1.0: https://github.com/NeurodataWithoutBorders/pynwb/blob/2.1.0/CHANGELOG.md#enhancements-and-minor-changes > Added support for HDMF 3.3.1. This is now the minimum version of HDMF supported. Importantly, HDMF 3.3 introduces warnings when the constructor of a class mapped to an HDMF-common data type or an autogenerated data type class is passed positional arguments instead of all keyword arguments. @rly (#1484)
FEDORA-2022-bf7b5c46a4 has been submitted as an update to Fedora 38. https://bodhi.fedoraproject.org/updates/FEDORA-2022-bf7b5c46a4
FEDORA-2022-bf7b5c46a4 has been pushed to the Fedora 38 stable repository. If problem still persists, please make note of it in this bug report.
FEDORA-2022-a55b64113d has been submitted as an update to Fedora 37. https://bodhi.fedoraproject.org/updates/FEDORA-2022-a55b64113d
FEDORA-2022-a55b64113d has been pushed to the Fedora 37 stable repository. If problem still persists, please make note of it in this bug report.