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Replace ic_electrode with icephys_electrode on NWBFile #1200

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merged 9 commits into from
Mar 3, 2020

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oruebel
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@oruebel oruebel commented Feb 29, 2020

Motivation

Fix #1181 . replace the use of ic prefix as it has an ambigious meaning in the icephys domain. Use the prefix icephys instead

Specifically, this PR:

  • Deprecate NWBFile.init(ic_electrodes ...) in favor of icephys_electrodes
  • Deprecate NWBFile.ic_electrodes property in favor of NWBFile.icephys_electrodes
  • Deprecate NWBFile.get/add/create_ic_electrode functions in favor NWBFile.get/add/create_icephys_electrode
  • Update tests to use the new functions
  • Add tests to check that the deprecation warnings are raised
  • Update icephys tutorial to use icephys_electrode instead of ic_electrode

Checklist

  • Have you checked our Contributing document?
  • Have you ensured the PR description clearly describes problem and the solution?
  • Is your contribution compliant with our coding style? This can be checked running flake8 from the source directory.
  • Have you checked to ensure that there aren't other open Pull Requests for the same change?
  • Have you included the relevant issue number using #XXX notation where XXX is the issue number?

@oruebel oruebel requested review from rly, t-b and ajtritt February 29, 2020 07:14
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codecov bot commented Feb 29, 2020

Codecov Report

Merging #1200 into dev will not change coverage.
The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##              dev    #1200   +/-   ##
=======================================
  Coverage   68.22%   68.22%           
=======================================
  Files          37       37           
  Lines        2316     2316           
  Branches      405      405           
=======================================
  Hits         1580     1580           
  Misses        667      667           
  Partials       69       69
Impacted Files Coverage Δ
src/pynwb/file.py 73.99% <ø> (ø) ⬆️

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t-b
t-b previously approved these changes Feb 29, 2020
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Fantastic!

src/pynwb/file.py Outdated Show resolved Hide resolved
tests/unit/test_icephys.py Outdated Show resolved Hide resolved
@oruebel
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oruebel commented Mar 3, 2020

@rly this should be good to go now

@oruebel oruebel merged commit 78537e3 into dev Mar 3, 2020
@oruebel oruebel deleted the enh/deprecate_ic_electrode branch March 3, 2020 03:16
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Avoid using ic as abbreviation for icephys
3 participants