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Test failures of No module named 'hdmf.array' #1541

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kabilar opened this issue Nov 26, 2024 · 0 comments
Open

Test failures of No module named 'hdmf.array' #1541

kabilar opened this issue Nov 26, 2024 · 0 comments

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@kabilar
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kabilar commented Nov 26, 2024

Only the ubuntu-latest, 3.9, dev-deps CI workflow has 14 failures of No module named 'hdmf.array'. See latest run.

Error logs from latest run 
=================================== FAILURES ===================================
____________________________ test_validate_severity ____________________________
dandi/cli/tests/test_cmd_validate.py:33: in test_validate_severity
    assert r.exit_code == 0
E   assert 1 == 0
E    +  where 1 = <Result SystemExit(1)>.exit_code
------------------------------ Captured log setup ------------------------------
INFO     dandi:organize.py:838 Loading metadata from 1 files
INFO     dandi:organize.py:1079 Organized 1 paths. Visit /tmp/pytest-of-runner/pytest-0/organized_nwb_dir0/
------------------------------ Captured log call -------------------------------
DEBUG    dandi:base.py:134 Caught exception No module named 'hdmf.array'
_____________________________ test_validate_ignore _____________________________
dandi/cli/tests/test_cmd_validate.py:49: in test_validate_ignore
    assert "DANDI.NO_DANDISET_FOUND" in r.output
E   assert 'DANDI.NO_DANDISET_FOUND' in "Error: No module named 'hdmf.array'\n"
E    +  where "Error: No module named 'hdmf.array'\n" = <Result SystemExit(1)>.output
------------------------------ Captured log call -------------------------------
DEBUG    dandi:base.py:134 Caught exception No module named 'hdmf.array'
_______________________ test_validate_nwb_path_grouping ________________________
dandi/cli/tests/test_cmd_validate.py:60: in test_validate_nwb_path_grouping
    assert r.exit_code == 0
E   assert 1 == 0
E    +  where 1 = <Result SystemExit(1)>.exit_code
------------------------------ Captured log setup ------------------------------
INFO     dandi:organize.py:838 Loading metadata from 2 files
INFO     dandi:organize.py:1079 Organized 2 paths. Visit /tmp/pytest-of-runner/pytest-0/organized_nwb_dir1/
------------------------------ Captured log call -------------------------------
DEBUG    dandi:base.py:134 Caught exception No module named 'hdmf.array'
_____________________________ test_smoke[command1] _____________________________
dandi/cli/tests/test_command.py:18: in test_smoke
    assert r.exit_code == 0, f"Exited abnormally. out={r.stdout}"
E   AssertionError: Exited abnormally. out=Error: No module named 'hdmf.array'
E     
E   assert 1 == 0
E    +  where 1 = <Result SystemExit(1)>.exit_code
------------------------------ Captured log call -------------------------------
DEBUG    dandi:base.py:134 Caught exception No module named 'hdmf.array'
____________________________ test_validate_simple1 _____________________________
dandi/tests/test_files.py:325: in test_validate_simple1
    errors = dandi_file(simple1_nwb).get_validation_errors(
dandi/files/bases.py:512: in get_validation_errors
    from nwbinspector import Importance, inspect_nwbfile, load_config
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/__init__.py:6: in <module>
    from ._nwb_inspection import (
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/_nwb_inspection.py:12: in <module>
    from hdmf_zarr import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/__init__.py:1: in <module>
    from .backend import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/backend.py:24: in <module>
    from .zarr_utils import BuilderZarrReferenceDataset, BuilderZarrTableDataset
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/zarr_utils.py:14: in <module>
    from hdmf.array import Array
E   ModuleNotFoundError: No module named 'hdmf.array'
_______________________ test_validate_simple1_no_subject _______________________
dandi/tests/test_files.py:332: in test_validate_simple1_no_subject
    errors = dandi_file(simple1_nwb).get_validation_errors()
dandi/files/bases.py:512: in get_validation_errors
    from nwbinspector import Importance, inspect_nwbfile, load_config
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/__init__.py:6: in <module>
    from ._nwb_inspection import (
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/_nwb_inspection.py:12: in <module>
    from hdmf_zarr import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/__init__.py:1: in <module>
    from .backend import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/backend.py:24: in <module>
    from .zarr_utils import BuilderZarrReferenceDataset, BuilderZarrTableDataset
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/zarr_utils.py:14: in <module>
    from hdmf.array import Array
E   ModuleNotFoundError: No module named 'hdmf.array'
____________________________ test_validate_simple2 _____________________________
dandi/tests/test_files.py:342: in test_validate_simple2
    errors = dandi_file(
dandi/files/bases.py:512: in get_validation_errors
    from nwbinspector import Importance, inspect_nwbfile, load_config
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/__init__.py:6: in <module>
    from ._nwb_inspection import (
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/_nwb_inspection.py:12: in <module>
    from hdmf_zarr import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/__init__.py:1: in <module>
    from .backend import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/backend.py:24: in <module>
    from .zarr_utils import BuilderZarrReferenceDataset, BuilderZarrTableDataset
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/zarr_utils.py:14: in <module>
    from hdmf.array import Array
E   ModuleNotFoundError: No module named 'hdmf.array'
__________________________ test_validate_simple2_new ___________________________
dandi/tests/test_files.py:351: in test_validate_simple2_new
    errors = dandi_file(
dandi/files/bases.py:512: in get_validation_errors
    from nwbinspector import Importance, inspect_nwbfile, load_config
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/__init__.py:6: in <module>
    from ._nwb_inspection import (
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/_nwb_inspection.py:12: in <module>
    from hdmf_zarr import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/__init__.py:1: in <module>
    from .backend import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/backend.py:24: in <module>
    from .zarr_utils import BuilderZarrReferenceDataset, BuilderZarrTableDataset
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/zarr_utils.py:14: in <module>
    from hdmf.array import Array
E   ModuleNotFoundError: No module named 'hdmf.array'
_____________________ test_validate_simple3_no_subject_id ______________________
dandi/tests/test_files.py:359: in test_validate_simple3_no_subject_id
    errors = dandi_file(simple3_nwb).get_validation_errors()
dandi/files/bases.py:512: in get_validation_errors
    from nwbinspector import Importance, inspect_nwbfile, load_config
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/__init__.py:6: in <module>
    from ._nwb_inspection import (
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/_nwb_inspection.py:12: in <module>
    from hdmf_zarr import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/__init__.py:1: in <module>
    from .backend import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/backend.py:24: in <module>
    from .zarr_utils import BuilderZarrReferenceDataset, BuilderZarrTableDataset
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/zarr_utils.py:14: in <module>
    from hdmf.array import Array
E   ModuleNotFoundError: No module named 'hdmf.array'
_____________________________ test_validate_bogus ______________________________
dandi/tests/test_files.py:377: in test_validate_bogus
    errors = dandi_file(path).get_validation_errors()
dandi/files/bases.py:512: in get_validation_errors
    from nwbinspector import Importance, inspect_nwbfile, load_config
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/__init__.py:6: in <module>
    from ._nwb_inspection import (
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/_nwb_inspection.py:12: in <module>
    from hdmf_zarr import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/__init__.py:1: in <module>
    from .backend import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/backend.py:24: in <module>
    from .zarr_utils import BuilderZarrReferenceDataset, BuilderZarrTableDataset
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/zarr_utils.py:14: in <module>
    from hdmf.array import Array
E   ModuleNotFoundError: No module named 'hdmf.array'
_____________________________ test_upload_download _____________________________
dandi/tests/test_upload.py:39: in test_upload_download
    new_dandiset.upload()
dandi/tests/fixtures.py:561: in upload
    upload(
dandi/upload.py:431: in upload
    for v in process_path(dfile):
dandi/upload.py:264: in process_path
    validation_statuses = dfile.get_validation_errors()
dandi/files/bases.py:512: in get_validation_errors
    from nwbinspector import Importance, inspect_nwbfile, load_config
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/__init__.py:6: in <module>
    from ._nwb_inspection import (
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/_nwb_inspection.py:12: in <module>
    from hdmf_zarr import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/__init__.py:1: in <module>
    from .backend import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/backend.py:24: in <module>
    from .zarr_utils import BuilderZarrReferenceDataset, BuilderZarrTableDataset
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/zarr_utils.py:14: in <module>
    from hdmf.array import Array
E   ModuleNotFoundError: No module named 'hdmf.array'
------------------------------ Captured log setup ------------------------------
DEBUG    dandi:dandiapi.py:198 POST http://localhost:8000/api/dandisets/
DEBUG    dandi:dandiapi.py:262 Response: 200
------------------------------ Captured log call -------------------------------
DEBUG    dandi:dandiapi.py:198 GET http://localhost:8000/api/info/
DEBUG    dandi:dandiapi.py:262 Response: 200
DEBUG    dandi:dandiapi.py:494 Using api key from DANDI_API_KEY environment variable
DEBUG    dandi:dandiapi.py:198 GET http://localhost:8000/api/auth/token
DEBUG    dandi:dandiapi.py:262 Response: 200
DEBUG    dandi:dandiset.py:128 Found identifier 000226 in top level 'identifier'
INFO     dandi:upload.py:214 Found 2 files to consider
_________________________ test_upload_invalid_metadata _________________________
dandi/tests/test_upload.py:278: in test_upload_invalid_metadata
    new_dandiset.upload()
dandi/tests/fixtures.py:561: in upload
    upload(
dandi/upload.py:431: in upload
    for v in process_path(dfile):
dandi/upload.py:264: in process_path
    validation_statuses = dfile.get_validation_errors()
dandi/files/bases.py:512: in get_validation_errors
    from nwbinspector import Importance, inspect_nwbfile, load_config
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/__init__.py:6: in <module>
    from ._nwb_inspection import (
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/_nwb_inspection.py:12: in <module>
    from hdmf_zarr import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/__init__.py:1: in <module>
    from .backend import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/backend.py:24: in <module>
    from .zarr_utils import BuilderZarrReferenceDataset, BuilderZarrTableDataset
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/zarr_utils.py:14: in <module>
    from hdmf.array import Array
E   ModuleNotFoundError: No module named 'hdmf.array'
------------------------------ Captured log setup ------------------------------
DEBUG    dandi:dandiapi.py:198 POST http://localhost:8000/api/dandisets/
DEBUG    dandi:dandiapi.py:262 Response: 200
------------------------------ Captured log call -------------------------------
DEBUG    dandi:dandiapi.py:198 GET http://localhost:8000/api/info/
DEBUG    dandi:dandiapi.py:262 Response: 200
DEBUG    dandi:dandiapi.py:494 Using api key from DANDI_API_KEY environment variable
DEBUG    dandi:dandiapi.py:198 GET http://localhost:8000/api/auth/token
DEBUG    dandi:dandiapi.py:262 Response: 200
DEBUG    dandi:dandiset.py:128 Found identifier 000247 in top level 'identifier'
INFO     dandi:upload.py:214 Found 2 files to consider
___________________________ test_validate_nwb_error ____________________________
dandi/tests/test_validate.py:16: in test_validate_nwb_error
    assert len([i for i in validation_result if i.severity]) > 0
dandi/tests/test_validate.py:16: in <listcomp>
    assert len([i for i in validation_result if i.severity]) > 0
dandi/validate.py:161: in validate
    yield from df.get_validation_errors(
dandi/files/bases.py:512: in get_validation_errors
    from nwbinspector import Importance, inspect_nwbfile, load_config
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/__init__.py:6: in <module>
    from ._nwb_inspection import (
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/_nwb_inspection.py:12: in <module>
    from hdmf_zarr import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/__init__.py:1: in <module>
    from .backend import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/backend.py:24: in <module>
    from .zarr_utils import BuilderZarrReferenceDataset, BuilderZarrTableDataset
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/zarr_utils.py:14: in <module>
    from hdmf.array import Array
E   ModuleNotFoundError: No module named 'hdmf.array'
_____________________ test_validate_bids[ieeg_epilepsyNWB] _____________________
dandi/tests/test_validate.py:54: in test_validate_bids
    for i in validation_result:
dandi/validate.py:161: in validate
    yield from df.get_validation_errors(
dandi/files/bids.py:223: in get_validation_errors
    return NWBAsset.get_validation_errors(
dandi/files/bases.py:512: in get_validation_errors
    from nwbinspector import Importance, inspect_nwbfile, load_config
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/__init__.py:6: in <module>
    from ._nwb_inspection import (
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/nwbinspector/_nwb_inspection.py:12: in <module>
    from hdmf_zarr import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/__init__.py:1: in <module>
    from .backend import ZarrIO
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/backend.py:24: in <module>
    from .zarr_utils import BuilderZarrReferenceDataset, BuilderZarrTableDataset
/opt/hostedtoolcache/Python/3.9.20/x64/lib/python3.9/site-packages/hdmf_zarr/zarr_utils.py:14: in <module>
    from hdmf.array import Array
E   ModuleNotFoundError: No module named 'hdmf.array'
------------------------------ Captured log call -------------------------------
WARNING  bids-schema:validator.py:341 No BIDS reference root provided.
INFO     bids-schema:validator.py:292 SUCCESS: All files are BIDS valid and no BIDS-required files are missing.

---------- coverage: platform linux, python 3.9.20-final-0 -----------
Coverage XML written to file coverage.xml

============================= slowest 10 durations =============================
54.81s call     dandi/tests/test_dandiapi.py::test_rename_type_mismatch[subdir1/apple.txt/core.dat]
50.71s setup    dandi/cli/tests/test_service_scripts.py::test_reextract_metadata
19.20s call     dandi/tests/test_metadata.py::test_bids_nwb_metadata_integration
9.43s call     dandi/tests/test_dandiapi.py::test_get_dandiset_published_other_version[True]
9.39s call     dandi/tests/test_dandiapi.py::test_get_dandiset_published_other_version[False]
8.64s call     dandi/tests/test_download.py::test_download_000027[https://dandiarchive.org/dandiset/000027/0.210831.2033]
8.14s call     dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
7.96s call     dandi/tests/test_download.py::test_download_newest_version
7.54s call     dandi/tests/test_dandiapi.py::test_publish_and_manipulate
6.94s call     dandi/tests/test_upload.py::test_upload_bids_zarr
=========================== short test summary info ============================
FAILED dandi/cli/tests/test_cmd_validate.py::test_validate_severity - assert 1 == 0
 +  where 1 = <Result SystemExit(1)>.exit_code
FAILED dandi/cli/tests/test_cmd_validate.py::test_validate_ignore - assert 'DANDI.NO_DANDISET_FOUND' in "Error: No module named 'hdmf.array'\n"
 +  where "Error: No module named 'hdmf.array'\n" = <Result SystemExit(1)>.output
FAILED dandi/cli/tests/test_cmd_validate.py::test_validate_nwb_path_grouping - assert 1 == 0
 +  where 1 = <Result SystemExit(1)>.exit_code
FAILED dandi/cli/tests/test_command.py::test_smoke[command1] - AssertionError: Exited abnormally. out=Error: No module named 'hdmf.array'
  
assert 1 == 0
 +  where 1 = <Result SystemExit(1)>.exit_code
FAILED dandi/tests/test_files.py::test_validate_simple1 - ModuleNotFoundError: No module named 'hdmf.array'
FAILED dandi/tests/test_files.py::test_validate_simple1_no_subject - ModuleNotFoundError: No module named 'hdmf.array'
FAILED dandi/tests/test_files.py::test_validate_simple2 - ModuleNotFoundError: No module named 'hdmf.array'
FAILED dandi/tests/test_files.py::test_validate_simple2_new - ModuleNotFoundError: No module named 'hdmf.array'
FAILED dandi/tests/test_files.py::test_validate_simple3_no_subject_id - ModuleNotFoundError: No module named 'hdmf.array'
FAILED dandi/tests/test_files.py::test_validate_bogus - ModuleNotFoundError: No module named 'hdmf.array'
FAILED dandi/tests/test_upload.py::test_upload_download - ModuleNotFoundError: No module named 'hdmf.array'
FAILED dandi/tests/test_upload.py::test_upload_invalid_metadata - ModuleNotFoundError: No module named 'hdmf.array'
FAILED dandi/tests/test_validate.py::test_validate_nwb_error - ModuleNotFoundError: No module named 'hdmf.array'
FAILED dandi/tests/test_validate.py::test_validate_bids[ieeg_epilepsyNWB] - ModuleNotFoundError: No module named 'hdmf.array'
ERROR dandi/cli/tests/test_service_scripts.py::test_reextract_metadata - ModuleNotFoundError: No module named 'hdmf.array'
= 14 failed, 694 passed, 1 skipped, 3 xfailed, 13 xpassed, 1 error in 778.37s (0:12:58) =
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@kabilar