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Audit warning filter #1534

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Audit warning filter #1534

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@asmacdo asmacdo commented Nov 21, 2024 •
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I've tested locally with python 3.9 and 3.12.

I ran the tests with tox -e 39 and tox -e 312. Since this was sufficient for both, I figure lets let the automation run to see where we are-- I'm surprised that we dont need more filters tbh.

FWIW, there were ~20 warnings when I was testing without the error in filterwarnings. I was quite surprised that adding this in removed all but 1 of those warnings (the one filtered here). (I had expected that those warnings would be promoted to errors).

Warnings without `filterwarnings == error`

============================================================ warnings summary =============================================================
dandi/tests/test_download.py::test_DownloadDirectory_basic
dandi/tests/test_download.py::test_DownloadDirectory_basic
/usr/lib64/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=753514) is multi-threaded, use of fork() may lead to deadlocks in the child.
self.pid = os.fork()

dandi/tests/test_fixtures.py: 20 warnings
dandi/tests/test_organize.py: 20 warnings
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/joblib/externals/loky/backend/fork_exec.py:38: DeprecationWarning: This process (pid=753514) is multi-threaded, use of fork() may lead to deadlocks in the child.
pid = os.fork()

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/ecephys.py:223: DeprecationWarning: use pynwb.misc.Units or NWBFile.units instead
warnings.warn("use pynwb.misc.Units or NWBFile.units instead", DeprecationWarning)

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/ecephys.py:257: DeprecationWarning: use pynwb.misc.Units or NWBFile.units instead
warnings.warn("use pynwb.misc.Units or NWBFile.units instead", DeprecationWarning)

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/icephys.py:22: UserWarning: Unit 'A' for CurrentClampSeries 'ccs' is ignored and will be set to 'volts' as per NWB 2.1.0.
warnings.warn(

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/icephys.py:22: UserWarning: Unit 'A' for CurrentClampStimulusSeries 'ccss' is ignored and will be set to 'amperes' as per NWB 2.1.0.
warnings.warn(

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/icephys.py:226: UserWarning: Stimulus description 'NA' for IZeroClampSeries 'izcs' is ignored and will be set to 'N/A' as per NWB 2.3.0.
warnings.warn(

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/icephys.py:22: UserWarning: Unit 'A' for IZeroClampSeries 'izcs' is ignored and will be set to 'volts' as per NWB 2.1.0.
warnings.warn(

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/icephys.py:341: DeprecationWarning: Use of SweepTable is deprecated. Use the IntracellularRecordingsTable instead. See also the NWBFile.add_intracellular_recordings function.
warnings.warn("Use of SweepTable is deprecated. Use the IntracellularRecordingsTable "

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/ophys.py:116: DeprecationWarning: The 'manifold' argument is deprecated in favor of 'origin_coords' and 'grid_spacing'.
warnings.warn("The 'manifold' argument is deprecated in favor of 'origin_coords' and 'grid_spacing'.",

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/ophys.py:119: DeprecationWarning: The 'conversion' argument is deprecated in favor of 'origin_coords' and 'grid_spacing'.
warnings.warn("The 'conversion' argument is deprecated in favor of 'origin_coords' and 'grid_spacing'.",

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/ophys.py:122: DeprecationWarning: The 'unit' argument is deprecated in favor of 'origin_coords_unit' and 'grid_spacing_unit'.
warnings.warn("The 'unit' argument is deprecated in favor of 'origin_coords_unit' and 'grid_spacing_unit'.",

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/core.py:48: UserWarning: ImageSeries 'test_iS': The number of frame indices in 'starting_frame' should have the same length as 'external_file'.
warn(error_msg)

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/core.py:48: UserWarning: ImageSeries 'test_iS': Format must be 'external' when external_file is specified.
warn(error_msg)

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/image.py:106: UserWarning: TwoPhotonSeries 'test_2ps': Length of data does not match length of timestamps. Your data may be transposed. Time should be on the 0th dimension
warnings.warn(

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/icephys.py:22: UserWarning: Unit 'A' for VoltageClampSeries 'vcs' is ignored and will be set to 'amperes' as per NWB 2.1.0.
warnings.warn(

dandi/tests/test_organize.py::test_organize_nwb_test_data[1-dry]
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/pynwb/icephys.py:22: UserWarning: Unit 'A' for VoltageClampStimulusSeries 'vcss' is ignored and will be set to 'volts' as per NWB 2.1.0.
warnings.warn(

dandi/tests/test_pynwb_utils.py::test_nwb_has_external_links
/home/austin/devel/dandi-cli/.tox/py3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:264: DtypeConversionWarning: Spec 'TimeSeries/timestamps': Value with data type int64 is being converted to data type float64 as specified.
warnings.warn(full_warning_msg, DtypeConversionWarning)

@asmacdo
Remove filter warnings to begin audit
9ff476e
@asmacdo
Add filterwarnings for test_nwb_has_external_links
02dae51 
Fixes all warnings for 3.12

_______________________________________________________ test_nwb_has_external_links _______________________________________________________
.tox/py3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1107: in __add_datasets
    data, dtype = self.convert_dtype(spec, attr_value)
.tox/py3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:264: in convert_dtype
    warnings.warn(full_warning_msg, DtypeConversionWarning)
E   hdmf.build.warnings.DtypeConversionWarning: Spec 'TimeSeries/timestamps': Value with data type int64 is being converted to data type float64 as specified.
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codecov bot commented Nov 21, 2024 •
edited
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.53%. Comparing base (ca1f575) to head (02dae51).
Report is 3 commits behind head on master.

Additional details and impacted files 
@@           Coverage Diff           @@
##           master    #1534   +/-   ##
=======================================
  Coverage   88.53%   88.53%           
=======================================
  Files          78       78           
  Lines       10691    10691           
=======================================
  Hits         9465     9465           
  Misses       1226     1226
Flag Coverage Δ
unittests 88.53% <ø> (ø)

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@asmacdo
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asmacdo commented Nov 21, 2024

FWIW, the no-longer-filtered warnings show up as noise in the test run on CI (its a very noisy run , but do NOT cause failures. @yarikoptic is it sufficient to filter only warnings that are escalated to failures, or are we aiming to slightly reduce the noise?

Some warnings in CI logs https://github.com/dandi/dandi-cli/actions/runs/11946325336/job/33300465114?pr=1534

/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/icephys.py:22: UserWarning: Unit 'A' for CurrentClampStimulusSeries 'ccss' is ignored and will be set to 'amperes' as per NWB 2.1.0.
warnings.warn(
/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/core.py:48: UserWarning: ImageSeries 'test_iS': The number of frame indices in 'starting_frame' should have the same length as 'external_file'.
warn(error_msg)
/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/core.py:48: UserWarning: ImageSeries 'test_iS': Format must be 'external' when external_file is specified.
warn(error_msg)
/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/image.py:106: UserWarning: TwoPhotonSeries 'test_2ps': Length of data does not match length of timestamps. Your data may be transposed. Time should be on the 0th dimension
warnings.warn(
/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/icephys.py:22: UserWarning: Unit 'A' for VoltageClampStimulusSeries 'vcss' is ignored and will be set to 'volts' as per NWB 2.1.0.
warnings.warn(
/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/icephys.py:22: UserWarning: Unit 'A' for CurrentClampSeries 'ccs' is ignored and will be set to 'volts' as per NWB 2.1.0.
warnings.warn(
/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/core.py:48: UserWarning: ImageSeries 'test_iS': The number of frame indices in 'starting_frame' should have the same length as 'external_file'.
warn(error_msg)
/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/core.py:48: UserWarning: ImageSeries 'test_iS': Format must be 'external' when external_file is specified.
warn(error_msg)
/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/icephys.py:22: UserWarning: Unit 'A' for VoltageClampSeries 'vcs' is ignored and will be set to 'amperes' as per NWB 2.1.0.
warnings.warn(
/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/icephys.py:226: UserWarning: Stimulus description 'NA' for IZeroClampSeries 'izcs' is ignored and will be set to 'N/A' as per NWB 2.3.0.
warnings.warn(
/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pynwb/icephys.py:22: UserWarning: Unit 'A' for IZeroClampSeries 'izcs' is ignored and will be set to 'volts' as per NWB 2.1.0.
warnings.warn(

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@asmacdo