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Fix and silence warnings#578

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t-b merged 13 commits into
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fix-and-silence-warnings
Sep 10, 2025
Merged

Fix and silence warnings#578
t-b merged 13 commits into
masterfrom
fix-and-silence-warnings

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@t-b t-b commented Aug 19, 2025 •
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@t-b t-b self-assigned this Aug 19, 2025
@t-b t-b force-pushed the fix-and-silence-warnings branch 3 times, most recently from eddfe48 to 9a9929f Compare August 27, 2025 13:48
@t-b t-b mentioned this pull request Aug 27, 2025
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t-b added 12 commits September 7, 2025 12:33
@t-b
pytest.ini: Ignore marshmallow warnings
3f2f3c3 
Created #575 to fix them.
@t-b
ipfx/bin/make_stimulus_ontology.py: Avoid unknown escape sequence
eaa1509 
This fixes the warning:

  /home/thomas/devel/ipfx/ipfx/bin/make_stimulus_ontology.py:26: DeprecationWarning: invalid escape sequence \d
    m = re.search("(.*)\d{6}$", scode)
@t-b
tests/test_ephys_extractor.py: Ignore divide by zero warnings
a55716f 
The whole purpose of the tests is to trigger that case.
@t-b
tests: Add missing timezone for NWB datetime entries
f9f4836 
This avoids warnings. The additional dependency is already required by
pynwb.
@t-b
test_XXX_nwb_data.py/test_nwb2_sink.py: Ignore DtypeConversionwarning
5fe2c4f 
This ignores the following and similiar warnings:

tests/dataset/test_mies_nwb_data.py: 2 warnings
  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/hdmf/build/objectmapper.py:267: DtypeConversionWarning: Spec 'CurrentClampSeries/sweep_number': Value with data type int64 is being converted to data type uint64 (min specification: uint32).
    warnings.warn(full_warning_msg, DtypeConversionWarning)

tests/attach_metadata/test_nwb2_sink.py: 10 warnings
tests/dataset/test_ephys_nwb_data.py: 6 warnings
tests/dataset/test_hbg_nwb_data.py: 3 warnings
tests/dataset/test_mies_nwb_data.py: 2 warnings
  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/hdmf/build/objectmapper.py:267: DtypeConversionWarning: Spec 'SweepTable/sweep_number': Value with data type int64 is being converted to data type uint64 (min specification: uint32).
    warnings.warn(full_warning_msg, DtypeConversionWarning)

tests/dataset/test_ephys_nwb_data.py: 6 warnings
tests/dataset/test_hbg_nwb_data.py: 3 warnings
tests/dataset/test_mies_nwb_data.py: 2 warnings
  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/hdmf/build/objectmapper.py:267: DtypeConversionWarning: Spec 'CurrentClampStimulusSeries/sweep_number': Value with data type int64 is being converted to data type uint64 (min specification: uint32).
    warnings.warn(full_warning_msg, DtypeConversionWarning)

Both int64 and uint64 are big enough for our number of sweeps. In addition
this test is using existing files so even fixing/upgrading IPNWB would not
solve the issue.
@t-b
ipfx: Avoid using deprecated pynwb interfaces
d05077a 
This fixes the following warnings:

  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/pynwb/base.py:87: DeprecationWarning: get_data_interface is deprecated and will be removed in PyNWB 4.0. Use get instead.
    warn('get_data_interface is deprecated and will be removed in PyNWB 4.0. Use get instead.', DeprecationWarning)

tests/test_mies_nwb_pipeline_output.py: 127 warnings
  /home/thomas/.venvs/ipfx-3.9/lib/python3.9/site-packages/pynwb/base.py:82: DeprecationWarning: add_data_interface is deprecated and will be removed in PyNWB 4.0. Use add instead.
    warn('add_data_interface is deprecated and will be removed in PyNWB 4.0. Use add instead.', DeprecationWarning)
@t-b
test_serialize: Silence pynwb warning
6c313a9 
pynwb 3.1.2 does currently always output a warning about a missing .nwb
ending in path even if path was not passed at all and is None.

This will be fixed in [1], ignore the warning until we require that
version.

We also drop the path argument to NWBHDF5IO as that is not needed.

[1]: NeurodataWithoutBorders/pynwb#2130
@t-b
tests/test_mies_nwb_pipeline_output.py: Silence warning about icephys…
45c3050 
…_filtering

This test uses existing files so even fixing/upgrading IPNWB would not
solve the issue.
@t-b
tests/attach_metadata/test_cli.py: Silence warning about icephys_filt…
59468f5 
…ering

This test uses existing files so even fixing/upgrading IPNWB would not
solve the issue.
@t-b
pytest.ini: Ignore scipy.misc warning for now
5b63dd2 
This is tracked in [1].

[1]: #576
@t-b
pytest.ini: Ignore pandas warning about ChainedAssignmentError
b0b1dba 
This is tracked in [1].

[1]: #577
@t-b
pytest.ini: Treat warnings as errors
05c14d1
@t-b t-b force-pushed the fix-and-silence-warnings branch from 9a9929f to 05c14d1 Compare September 7, 2025 10:34
@t-b t-b requested a review from gouwens September 7, 2025 10:34
@t-b t-b assigned gouwens and unassigned t-b Sep 7, 2025
@t-b t-b marked this pull request as ready for review September 7, 2025 10:35
@t-b

t-b commented Sep 9, 2025

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@gouwens Ready for review!

gouwens
gouwens approved these changes Sep 9, 2025
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It all looks good to me. I realized there was a way to avoid triggering one of the warnings by filtering out bad points first in the dv/dt calculation, so I fixed the underlying code and removed the filter (and pushed the commit).

@t-b

t-b commented Sep 10, 2025

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It all looks good to me. I realized there was a way to avoid triggering one of the warnings by filtering out bad points first in the dv/dt calculation, so I fixed the underlying code and removed the filter (and pushed the commit).

Perfect. That's even better than ignoring the warning.

@t-b t-b merged commit 745e4a3 into master Sep 10, 2025
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@t-b t-b deleted the fix-and-silence-warnings branch September 10, 2025 15:52
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Fix easy warnings in tests and ignore the rest

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