datalad / datalad-neuroimaging

DataLad extension for neuroimaging research
http://datalad.org
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RF: use pytest, remove restriction on datalad version #110

Closed yarikoptic closed 1 year ago

yarikoptic commented 1 year ago

for the failing test -- we might be doomed to skip it for now, but we cannot really delay that long

yarikoptic commented 1 year ago

seems to be ok, besides that "gen4" issue . refs: https://github.com/datalad/datalad/pull/7001 (better but not complete), https://github.com/datalad/datalad/pull/7079 (ugly but works)

codecov[bot] commented 1 year ago

Codecov Report

Base: 85.58% // Head: 89.47% // Increases project coverage by +3.88% :tada:

Coverage data is based on head (337609a) compared to base (3e78e5b). Patch coverage: 97.95% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #110 +/- ## ========================================== + Coverage 85.58% 89.47% +3.88% ========================================== Files 23 24 +1 Lines 1214 1159 -55 ========================================== - Hits 1039 1037 -2 + Misses 175 122 -53 ``` | [Impacted Files](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad) | Coverage Δ | | |---|---|---| | [datalad\_neuroimaging/\_\_init\_\_.py](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad#diff-ZGF0YWxhZF9uZXVyb2ltYWdpbmcvX19pbml0X18ucHk=) | `100.00% <ø> (ø)` | | | [datalad\_neuroimaging/tests/test\_search.py](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad#diff-ZGF0YWxhZF9uZXVyb2ltYWdpbmcvdGVzdHMvdGVzdF9zZWFyY2gucHk=) | `84.72% <88.88%> (-1.70%)` | :arrow_down: | | [datalad\_neuroimaging/conftest.py](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad#diff-ZGF0YWxhZF9uZXVyb2ltYWdpbmcvY29uZnRlc3QucHk=) | `100.00% <100.00%> (ø)` | | | [datalad\_neuroimaging/extractors/tests/test\_bids.py](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad#diff-ZGF0YWxhZF9uZXVyb2ltYWdpbmcvZXh0cmFjdG9ycy90ZXN0cy90ZXN0X2JpZHMucHk=) | `100.00% <100.00%> (ø)` | | | [...neuroimaging/extractors/tests/test\_bids\_dataset.py](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad#diff-ZGF0YWxhZF9uZXVyb2ltYWdpbmcvZXh0cmFjdG9ycy90ZXN0cy90ZXN0X2JpZHNfZGF0YXNldC5weQ==) | `100.00% <100.00%> (ø)` | | | [...atalad\_neuroimaging/extractors/tests/test\_dicom.py](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad#diff-ZGF0YWxhZF9uZXVyb2ltYWdpbmcvZXh0cmFjdG9ycy90ZXN0cy90ZXN0X2RpY29tLnB5) | `93.61% <100.00%> (-0.93%)` | :arrow_down: | | [datalad\_neuroimaging/extractors/tests/test\_nidm.py](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad#diff-ZGF0YWxhZF9uZXVyb2ltYWdpbmcvZXh0cmFjdG9ycy90ZXN0cy90ZXN0X25pZG0ucHk=) | `100.00% <100.00%> (ø)` | | | [...talad\_neuroimaging/extractors/tests/test\_nifti1.py](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad#diff-ZGF0YWxhZF9uZXVyb2ltYWdpbmcvZXh0cmFjdG9ycy90ZXN0cy90ZXN0X25pZnRpMS5weQ==) | `93.33% <100.00%> (-1.12%)` | :arrow_down: | | [datalad\_neuroimaging/tests/test\_aggregation.py](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad#diff-ZGF0YWxhZF9uZXVyb2ltYWdpbmcvdGVzdHMvdGVzdF9hZ2dyZWdhdGlvbi5weQ==) | `100.00% <100.00%> (ø)` | | | [datalad\_neuroimaging/tests/test\_bids2scidata.py](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad#diff-ZGF0YWxhZF9uZXVyb2ltYWdpbmcvdGVzdHMvdGVzdF9iaWRzMnNjaWRhdGEucHk=) | `100.00% <100.00%> (+3.22%)` | :arrow_up: | | ... and [8 more](https://codecov.io/gh/datalad/datalad-neuroimaging/pull/110/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=datalad)

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bpoldrack commented 1 year ago

skipped also most of the tests on crippled fs

That seems a bit suspicious. Did they not pass before? The crippled FS run isn't new here, so what changed?

yarikoptic commented 1 year ago

I don't know and have no time to figure it dig out ATM given that they were even almost completely killed in datalad-deprecated. Figuring that out would be welcomed though! but given that tests already have some kind of skip on windows, I guess -- something which was not working reliably anyways -- for that the hint is that https://github.com/datalad/datalad-neuroimaging/actions/runs/3067753527 was the last ok run a month ago, was tested using datalad 0.16.7 and indeed a sample test

2022-09-16T12:15:30.4037902Z datalad_neuroimaging.extractors.tests.test_nidm.test_nidm ... ok

which started to fail was ok. So indeed might be some particular fix up (e.g. may be adding handling of gen4 metadata) was the one to worry about.

bpoldrack commented 1 year ago

Ok, let's proceed then. Guess switching the framework is more important.