Ticket-2524: corrected_fluorescence_traces to represent neuropil_corrected_trace instead of demixed_trace

[mikejhuang]

Changes made

• CorrectedFluorescenceTraces object now loads the corrected_fluorescence trace from a NeuropilCorrectedFile
• Created object NeuropilCorrectedFile which loads this file from LIMS and reads the hdf5 file to convert to a dataframe
• Created a DemixedTraces object to load the demixed_trace from a DemixedFile
• Modified cell_specimen to use the NeuropilCorrectedFile as the corrected_fluorscence and added demixed_trace and neuropil_trace to cell_specimen
• Modified the tests for cell_specimen incorporate the aforementioned changes.
• Added r and RMSE from the NeuropilCorrectedFile into cell_specimen and the nwbfile
• Created a NeuropilTraces object to load the neuropil_trace from a NeuropilFile

[CLAassistant]

All committers have signed the CLA.

[morriscb]

Okay, we can get everything loaded for r RMSE on the next ticket. One thing though, make sure to fix the linting on the test_cell_specimens.py file. I'll fix up the rest which we inherited from a while ago (no idea why they just recently showed up).

[danielsf]

@morriscb

"(no idea why they just recently showed up)"

To save ourselves a lot of agonizing work, the SDK CI was configured so that linting is only run on files when they are touched. We adopted PEP8 very late in the game and did not have the time to fix every file in the SDK. Thus, anyone unfortunate enough to have to touch ancient code gets hit with a bunch of linter errors that aren't their fault.

Just wanted to make sure you had that context.

[aamster]

@morriscb I fixed that in main so that I could deploy an internal module

I think you have to merge master into the release branch to make that go away.

[morriscb]

I think we can consider the adding the demix as an "addition" right now we are fixing the logic to return the correct data. Adding additional traces (which demix will be) is another issue.