Bug 2275107
| Summary: | python-pynwb fails to build with pytest 8: Exception: DecompositionSeries/bands (processing/test_mod/LFPSpectralAnalysis/bands): missing data type VectorData (band_mean) | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Tomáš Hrnčiar <thrnciar> |
| Component: | python-pynwb | Assignee: | Sandro <gui1ty> |
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | unspecified | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | rawhide | CC: | bazanluis20, gui1ty, mhroncok, neuro-sig, thrnciar |
| Target Milestone: | --- | ||
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | Unspecified | ||
| Whiteboard: | |||
| Fixed In Version: | python-pynwb-2.7.0-3.fc41 | Doc Type: | If docs needed, set a value |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2024-05-29 16:21:02 UTC | Type: | Bug |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
| Bug Depends On: | |||
| Bug Blocks: | 2256331 | ||
Upstream is using pytest 8.2.1 in GH Actions: https://github.com/NeurodataWithoutBorders/pynwb/actions/runs/9281954184/job/25538951205 It looks like they are preparing a new release (2.8.0). I think waiting for that and checking again once that is out is the best way forward here. It turns it this now works with pytest 8.2.1 with the current release. FEDORA-2024-93aea91f86 (python-pynwb-2.7.0-3.fc41) has been submitted as an update to Fedora 41. https://bodhi.fedoraproject.org/updates/FEDORA-2024-93aea91f86 FEDORA-2024-93aea91f86 (python-pynwb-2.7.0-3.fc41) has been pushed to the Fedora 41 stable repository. If problem still persists, please make note of it in this bug report. |
python-pynwb fails to build with pytest 8. ====================================================================== ERROR: test_roundtrip (integration.hdf5.test_misc.TestDecompositionSeriesIO.test_roundtrip) Test whether the read Container has the same contents as the original Container and validate the file. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 60, in test_roundtrip self.read_container = self.roundtripContainer() ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 99, in roundtripContainer self.validate() File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 170, in validate raise Exception(err) Exception: DecompositionSeries/bands (processing/test_mod/LFPSpectralAnalysis/bands): missing data type VectorData (band_mean) ====================================================================== ERROR: test_roundtrip_export (integration.hdf5.test_misc.TestDecompositionSeriesIO.test_roundtrip_export) Test whether the test Container read from an exported file has the same contents as the original test Container ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 74, in test_roundtrip_export self.read_container = self.roundtripExportContainer() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 124, in roundtripExportContainer self.roundtripContainer(cache_spec=cache_spec) # self.read_nwbfile is now set ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 99, in roundtripContainer self.validate() File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 170, in validate raise Exception(err) Exception: DecompositionSeries/bands (processing/test_mod/LFPSpectralAnalysis/bands): missing data type VectorData (band_mean) ====================================================================== ERROR: test_eg_ref (integration.hdf5.test_misc.TestDecompositionSeriesWithSourceChannelsIO.test_eg_ref) Test that the electrode DynamicTableRegion references of the read ElectricalSeries have a group that ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/pynwb-2.5.0/tests/integration/hdf5/test_misc.py", line 182, in test_eg_ref read = self.roundtripContainer() ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 99, in roundtripContainer self.validate() File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 170, in validate raise Exception(err) Exception: DecompositionSeries/bands (acquisition/test_DS/bands): missing data type VectorData (band_name) ====================================================================== ERROR: test_roundtrip (integration.hdf5.test_misc.TestDecompositionSeriesWithSourceChannelsIO.test_roundtrip) Test whether the read Container has the same contents as the original Container and validate the file. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 60, in test_roundtrip self.read_container = self.roundtripContainer() ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 99, in roundtripContainer self.validate() File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 170, in validate raise Exception(err) Exception: DecompositionSeries/bands (acquisition/test_DS/bands): missing data type VectorData (band_name) ====================================================================== ERROR: test_roundtrip_export (integration.hdf5.test_misc.TestDecompositionSeriesWithSourceChannelsIO.test_roundtrip_export) Test whether the test Container read from an exported file has the same contents as the original test Container ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 74, in test_roundtrip_export self.read_container = self.roundtripExportContainer() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 124, in roundtripExportContainer self.roundtripContainer(cache_spec=cache_spec) # self.read_nwbfile is now set ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 99, in roundtripContainer self.validate() File "/builddir/build/BUILDROOT/python-pynwb-2.5.0-5.fc41.x86_64/usr/lib/python3.12/site-packages/pynwb/testing/testh5io.py", line 170, in validate raise Exception(err) Exception: DecompositionSeries/bands (acquisition/test_DS/bands): missing data type VectorData (band_name) ---------------------------------------------------------------------- Ran 161 tests in 59.679s FAILED (errors=5) ====================================================================== ERROR: test_read (back_compat.test_read.TestReadOldVersions.test_read) (file='1.5.1_imageseries_no_data.nwb') Test reading and validating all NWB files in the same folder as this file. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/pynwb-2.5.0/tests/back_compat/test_read.py", line 65, in test_read raise Exception("Unexpected validation error: %s: %s" % (f.name, e)) Exception: Unexpected validation error: 1.5.1_imageseries_no_data.nwb: ImageSeries/data (acquisition/test_imageseries): argument missing ====================================================================== ERROR: test_read (back_compat.test_read.TestReadOldVersions.test_read) (file='1.5.1_imageseries_no_unit.nwb') Test reading and validating all NWB files in the same folder as this file. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/pynwb-2.5.0/tests/back_compat/test_read.py", line 65, in test_read raise Exception("Unexpected validation error: %s: %s" % (f.name, e)) Exception: Unexpected validation error: 1.5.1_imageseries_no_unit.nwb: ImageSeries/data/unit (acquisition/test_imageseries/data): argument missing ====================================================================== ERROR: test_read (back_compat.test_read.TestReadOldVersions.test_read) (file='1.5.1_timeseries_no_data.nwb') Test reading and validating all NWB files in the same folder as this file. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/pynwb-2.5.0/tests/back_compat/test_read.py", line 65, in test_read raise Exception("Unexpected validation error: %s: %s" % (f.name, e)) Exception: Unexpected validation error: 1.5.1_timeseries_no_data.nwb: TimeSeries/data (acquisition/test_timeseries): argument missing ====================================================================== ERROR: test_read (back_compat.test_read.TestReadOldVersions.test_read) (file='1.5.1_timeseries_no_unit.nwb') Test reading and validating all NWB files in the same folder as this file. ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/pynwb-2.5.0/tests/back_compat/test_read.py", line 65, in test_read raise Exception("Unexpected validation error: %s: %s" % (f.name, e)) Exception: Unexpected validation error: 1.5.1_timeseries_no_unit.nwb: TimeSeries/data/unit (acquisition/test_timeseries/data): argument missing ---------------------------------------------------------------------- Ran 9 tests in 3.753s FAILED (errors=4) ====================================================================== 2024-04-02 17:56:40,368 - INFO - Ran 538 tests - FAILED (errors=9) https://docs.pytest.org/en/stable/changelog.html For the build logs, see: https://copr-be.cloud.fedoraproject.org/results/thrnciar/pytest/fedora-rawhide-x86_64/07248643-python-pynwb/ For all our attempts to build python-pynwb with pytest 8, see: https://copr.fedorainfracloud.org/coprs/thrnciar/pytest/package/python-pynwb/ Let us know here if you have any questions. Pytest 8 is planned to be included in Fedora 41. And this bugzilla is a heads up before we merge new pytest into rawhide. For more info see a Fedora Change proposal https://fedoraproject.org/wiki/Changes/Pytest_8 We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side.