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Testing

The tests in the tests folder use pytest and can be run locally as:

SKIP_LIMS=true TEST_INHOUSE=false pytest

This does not assume that you have access to AllenInstitute internal resources like LIMS or network shares.

Strategy for adopting newer NWB schema versions

The upstream source of NWB files for ipfx is MIES and IPNWB. We are at the moment using fixed versions of nwb-schema for IPNWB and pynwb for ipfx. This is done in order to reduce maintenance and friction between the two.

Steps for upgrading:

  • Choose a pynwb/nwb-schema version you want to adopt
  • Raise pynwb version in requirements.txt
  • Check if all tests still pass. In the past this always required patching the latest pynwb version, bringing that patch upstream and waiting for a new release.
  • Fix pynwb deprecations where appropriate
  • Upgrade the nwb-schema version used in IPNWB as documented there
  • Re-export the files Vip-IRES-Cre;Ai14(IVSCC)-226110.03.01.pxp and Vip-IRES-Cre;Ai14(IVSCC)-236654.04.02.pxp using the IPNWB/MIES version with the new nwb-schema to NWBv2
  • Add the files to tests/data and extend testdata in tests/test_run_feature_vector.py with them
  • Check if the tests still pass
  • Propose a PR