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catalystneuro / buzsaki-lab-to-nwb

BSD 3-Clause "New" or "Revised" License
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Add environment.yml and requirements.txt for Tingley septal conversion #46

Closed h-mayorquin closed 2 years ago

h-mayorquin commented 2 years ago

This is to discuss how (or if) we should store the requirements.txt (for pip) and the environment.yml (for conda). I added the frozen version of the state of the repos just after I ran the conversion.

Right now, they just stand as an indicator of what libraries the environment that I used in dandi had. I am not sure this will be sufficient to reproduce the environment as I have not tested it but maybe this should be enough?

Let me know what you think.

CodyCBakerPhD commented 2 years ago

In general I would think all we really need is (a) version of nwb-conversion-tools, and (b) version of spikeextractors. Those are the API's that have the most changes related to debugs, function calls, etc.

While the full frozen state would indeed be required to perfectly (100%) ensure reproducibility of original files, this might be overkill for our purposes.

h-mayorquin commented 2 years ago

In general I would think all we really need is (a) version of nwb-conversion-tools, and (b) version of spikeextractors. Those are the API's that have the most changes related to debugs, function calls, etc.

While the full frozen state would indeed be required to perfectly (100%) ensure reproducibility of original files, this might be overkill for our purposes.

@CodyCBakerPhD The changes that we used in both nwb-conversion-tools and spikeextractors are not included in any tagged version of them, aren't they? (i.e. the latest additions to cellexplorersortingextractor in spikeextractors).

CodyCBakerPhD commented 2 years ago

@h-mayorquin No, probably not; you can pin it to the commit hash of the version state used successfully to run the conversion though (example: https://github.com/catalystneuro/nwb-conversion-tools/blob/main/requirements-full.txt#L13-L14)

h-mayorquin commented 2 years ago

@h-mayorquin No, probably not; you can pin it to the commit hash of the version state used successfully to run the conversion though (example: https://github.com/catalystneuro/nwb-conversion-tools/blob/main/requirements-full.txt#L13-L14)

@CodyCBakerPhD The latest commit follows your suggestion above to only have the pinned versions of nwb-conversion-tools and spikeextractors.

CodyCBakerPhD commented 2 years ago

@h-mayorquin Looks great!