[Bug 1931183] Review Request: python-spikeextractors - Python module for extracting recorded and spike sorted extracellular data from different file types and formats

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https://bugzilla.redhat.com/show_bug.cgi?id=1931183



--- Comment #25 from Andy Mender <andymenderunix@xxxxxxxxx> ---
(In reply to Ankur Sinha (FranciscoD) from comment #24)
> OK, so more deps:
> 
> - exdir
> - hdf5storage (surprised this isn't in Fedora yet)
> - MEArec
> - shybrid
> 
> We can disable their tests and proceed in the meantime, and then keep
> packaging them up and enabling the tests. I'll start with exdir next.
> 
> About the buggy tests, we should report them upstream first and see what
> they say. If they're not trivial and upstream can't fix them (or suggest a
> workaround/fix) soon, these can also be disabled with a comment that
> includes the issue URL. You could take a quick look to see if it's something
> obvious (like a change in py3.10 perhaps) and see if it's possible to submit
> a patch?
> 
> Cheers,

A quick update:
- I forgot to mention last time, but because the test cases run as
unittest-style methods from a test class, it's not possible to silence only
specific tests. This was supposedly fixed upstream in pytest (compatibility
with unittest), but I couldn't get it to work with the suggested workaround.

- spikeextractors was now merged into spikeinterface:
https://github.com/SpikeInterface/spikeinterface
  Not sure how this impacts your use case, but the old project will be used for
bug fixes only and submitting new issues is already blocked:
https://github.com/SpikeInterface/spikeextractors

- The exdir unit test still fails on the same assert call as before, because it
somehow fails to recognize the exdir module.

- The value issues in the tests look like something related to h5py or overall
compatibility on the line Python - numpy - h5py.

I think it might be worth opening a new review request for spikeinterface
instead, since that's the umbrella project and perhaps it's also packaged a
little differently. At least I see the test layout is different:
https://github.com/SpikeInterface/spikeinterface/tree/master/spikeinterface/extractors/tests

I would hold off with opening extra review requests for spikeextractors
dependencies as these may no longer be needed :).


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