[WIP] Add AnDO Generator

INT-NIT / BEP032tools

Software tools supporting the BIDS Extension Proposal (BEP) dedicated to adding support for electrophysiological data recorded in animal models (BEP032)

MIT License

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[WIP] Add AnDO Generator #49

Closed JuliaSprenger closed 3 years ago

JuliaSprenger commented 3 years ago

This PR is still work in progress, but open to comments regarding the general approach already.

It aims at providing a mechanism to set up an AnDO compatible folder structure independent of the input format used for defining the experiment, subject and session infos.

TODOs:

[x] integrate with existing code that generates the AnDO structure from a table
[x] add generator tests to set of tests run by CI (see #53)
[x] review check_Path function for raw/meta/derived folders (-> fix failing test)
[ ] test usability from external diglab2ando module -> add dictionary based Generator interface (postponed to future PR)

SylvainTakerkart commented 3 years ago

sooo @JuliaSprenger, shall we merge at this point, or do you prefer to continue this PR?

JuliaSprenger commented 3 years ago

I would like to integrate the new code into the existing csv -> ando code, to not have different pieces of code for the same purpose. I will keep you updated here.

JuliaSprenger commented 3 years ago

@Slowblitz The tests are failing for dataset7, which according to your tests should not be a valid AnDO dataset. However, I am not sure exactly why this dataset is not considered valid. Maybe I am missing a detail here?

Slowblitz commented 3 years ago

@SylvainTakerkart , checks are passing now !

SylvainTakerkart commented 3 years ago

@SylvainTakerkart , checks are passing now !

ok, good ;)

@Slowblitz @JuliaSprenger let me know explicitly when you need something to be reviewed, or when I can merge...

JuliaSprenger commented 3 years ago

Ready to merge from my side. I think it makes sense to merge this first and do potential improvement in the DigLab2AnDO context in a separate PR, since this one is already quite old and big.

SylvainTakerkart commented 3 years ago

ok!!! Merging!!