Add custom extensions

[ageorgou]

As far as I can see, the test failures are:

1. pep8 style check
2. epochs test because of recent API change; for this PR, I think we should fix pynwb to 1.1.2, and then make the necessary update in #11.
3. epochs test because of a numpy problem? (only in some jobs, like this one!) We should verify what version we use locally.

The signatures tests are skipped. I examined @alessandrofelder's results manually (eliminating expected or previously checked discrepancies due to renaming, precision changes etc), and it generally looks okay, except for the following:

• The following need to be checked to make sure the values match:
  1. n ROI and Zstack acquisitions, field_of_view
  2. zplane_pockels (before in /general/optophysiology/zplane_pockels, now in /general/silverlab_optophysiology/pockels)
  3. In /stimulus/presentation/air_puff, timestamps
• Video frame rate: used to be seconds, now should be fps (probably changed in http://docs.mikeboers.com/pyav/7.0.0/development/changelog.html#v0-4-0)
• We now include cycles_per_trial ~and timestamps_reference_time~, which don't seem to exist in the previous extensions.

The only other big thing that has changed is the structure of the ImageSegmentation processing module. I believe we check that through Matlab, though?

A few other minor things are due to schema changs (missing decriptions, experimenter and related publications are now vectors).

[alessandrofelder]

Great, some comments:

• Previous had /stimulus/presentation/air_puff/num_samples, which is missing in new
• I have programmatically checked values for pockels,field_of_view and they match exactly
• I have programmatically checked and air_puff/timestamps values, and the match with tol 1e-7
• num_cycles_per_trial seemed to exist at some point? See Line 10 in RunUsingNwb.m. Not sure about timestamps_reference_time
• Yes, we have tested the ImageSegmentation (to some extent at least: x_start, y_start, z_start and pixel_time_offsets) in MatLab

See this commit on AnalysisPipeline repo for programmatical checks

[ageorgou]

My mistake - timestamps_reference_time comes from pynwb, presumably added since NWB1.

[codecov-io]

Codecov Report

:exclamation: No coverage uploaded for pull request base (adapt-to-updated-libs@56e6ce6). Click here to learn what that means. The diff coverage is 14.28%.

@@                   Coverage Diff                   @@
##             adapt-to-updated-libs     #18   +/-   ##
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  Coverage                         ?   25.9%           
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  Files                            ?      12           
  Lines                            ?    1490           
  Branches                         ?     240           
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  Hits                             ?     386           
  Misses                           ?    1086           
  Partials                         ?      18

Impacted Files	Coverage Δ
src/silverlabnwb/generate_extended_schema.py	0% <0%> (ø)
src/silverlabnwb/nwb_file.py	38.99% <30.76%> (ø)

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[ageorgou]

@alessandrofelder If you don't have any comments about my changes, I think we can merge this now.

[alessandrofelder]

No further comments, thanks for reviewing!