catalystneuro / neuroconv

Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.
https://neuroconv.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Enable zarr backend testing in data tests [1] #1056

Closed h-mayorquin closed 2 months ago

h-mayorquin commented 2 months ago

This enables zarr testing for running conversions with backend specified as a string (still missing the building a backend configuration part)

It also makes some metadata checks proper tests on their own which has two advantages:

h-mayorquin commented 2 months ago

@CodyCBakerPhD OK, we got the point were the failures are actually related to zarr, check out the video test failure:

https://github.com/catalystneuro/neuroconv/actions/runs/10744684959/job/29802201096?pr=1056

Does it ring any bell? I will dig into it but is a windows only error so it will have to wait a bit for me.

h-mayorquin commented 2 months ago

Note for myself to also add the documentation:

1019

CodyCBakerPhD commented 2 months ago

Don't believe I've seen this one myself, but from the message the path to the Zarr array (file): https://github.com/catalystneuro/neuroconv/actions/runs/10744684959/job/29802201096?pr=1056#step:31:3426

is not a valid Windows path (should have replaced the / with \\?)

h-mayorquin commented 2 months ago

@CodyCBakerPhD OK, this should be ready but it requires the fix on #1070 before (as does everything else).

The cause of the Windows error is here:

https://github.com/hdmf-dev/hdmf-zarr/issues/219

h-mayorquin commented 2 months ago

@CodyCBakerPhD this is ready to go.

CodyCBakerPhD commented 2 months ago

Coolio

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 97.67442% with 1 line in your changes missing coverage. Please review.

Project coverage is 90.40%. Comparing base (81a022d) to head (8590f2f). Report is 14 commits behind head on main.

Files with missing lines Patch % Lines
...c/neuroconv/tools/testing/data_interface_mixins.py 97.67% 1 Missing :warning:
Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/catalystneuro/neuroconv/pull/1056/graphs/tree.svg?width=650&height=150&src=pr&token=h63OQoWehP&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro)](https://app.codecov.io/gh/catalystneuro/neuroconv/pull/1056?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) ```diff @@ Coverage Diff @@ ## main #1056 +/- ## ========================================== + Coverage 90.32% 90.40% +0.08% ========================================== Files 129 129 Lines 7996 8029 +33 ========================================== + Hits 7222 7259 +37 + Misses 774 770 -4 ``` | [Flag](https://app.codecov.io/gh/catalystneuro/neuroconv/pull/1056/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/catalystneuro/neuroconv/pull/1056/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) | `90.40% <97.67%> (+0.08%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files with missing lines](https://app.codecov.io/gh/catalystneuro/neuroconv/pull/1056?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro) | Coverage Δ | | |---|---|---| | [...atainterfaces/behavior/video/videodatainterface.py](https://app.codecov.io/gh/catalystneuro/neuroconv/pull/1056?src=pr&el=tree&filepath=src%2Fneuroconv%2Fdatainterfaces%2Fbehavior%2Fvideo%2Fvideodatainterface.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro#diff-c3JjL25ldXJvY29udi9kYXRhaW50ZXJmYWNlcy9iZWhhdmlvci92aWRlby92aWRlb2RhdGFpbnRlcmZhY2UucHk=) | `93.63% <ø> (ø)` | | | [...c/neuroconv/tools/testing/data\_interface\_mixins.py](https://app.codecov.io/gh/catalystneuro/neuroconv/pull/1056?src=pr&el=tree&filepath=src%2Fneuroconv%2Ftools%2Ftesting%2Fdata_interface_mixins.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro#diff-c3JjL25ldXJvY29udi90b29scy90ZXN0aW5nL2RhdGFfaW50ZXJmYWNlX21peGlucy5weQ==) | `95.47% <97.67%> (+0.14%)` | :arrow_up: | ... and [4 files with indirect coverage changes](https://app.codecov.io/gh/catalystneuro/neuroconv/pull/1056/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=catalystneuro)