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@knirirr knirirr commented Oct 29, 2025

There are still some warnings remaining.
Some have been hidden, for Pandas, and a link to an explanation has been provided.

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knirirr commented Oct 29, 2025

The first run of this triggered:

tests/test_clients/test_mw2isa.py:38: AssertionError
----------------------------- Captured stdout call -----------------------------
user options {'studyid': 'ST000367', 'outputdir': '/tmp/tmpdc446jk1', 'dl_option': 'no', 'validate_option': True}
Error: in main() method something went wrong
conversion failed

...which appears to be caused by the tests calling a live URL (http://www.metabolomicsworkbench.org/...) on line 1070 of isatools/net/mw2isa/init.py, which timed out.

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This should indeed be mocked to avoid such situations. I'll open a ticket.

@knirirr knirirr requested a review from proccaserra October 30, 2025 14:08
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Coverage Status

coverage: 82.314% (+0.004%) from 82.31%
when pulling 8976a8e on isatools_materials_test_deprecation
into 68ed2c4 on develop.

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looks good to me. opening an issue for the OLS service as discussed

@knirirr knirirr merged commit cbd152a into develop Oct 31, 2025
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@knirirr knirirr deleted the isatools_materials_test_deprecation branch October 31, 2025 10:46
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4 participants