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[Best Practices] Add check for TimeSeries unit follows CMIXF-12 convention #281

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[Best Practices] Add check for TimeSeries unit follows CMIXF-12 convention #281

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weiglszonja
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Motivation

WIP
Proposing a new check for TimeSeries that checks if unit formatting complies with the CMIXF-12 convention.
#208

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  • Have you ensured the PR description clearly describes the problem and solutions?
  • Have you checked to ensure that there aren't other open or previously closed Pull Requests for the same change?
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  • If this PR fixes an issue, is the first line of the PR description fix #XX where XX is the issue number?

@weiglszonja weiglszonja marked this pull request as draft October 3, 2022 13:41
@weiglszonja
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Double check what can and cannot be changed for units

weiglszonja
weiglszonja commented Oct 4, 2022
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nwbinspector/checks/time_series.py
Best Practice: :ref:`best_practice_units_of_measurement`
"""

# Early return for arbitrary units that are unknown or unavailable.
if time_series.unit == "a.u.":
return

lexer = CMIXFLexer()
tokens = lexer.tokenize(time_series.unit)
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lexer.tokenize() a generator object, when a bad character is found it immediately raises an error. e.g.

tokens = lexer.tokenize("ta")
next(tokens)

would return the recognized token value for unit t
Token(type='UNITC', value='t', lineno=1, index=0)

next(tokens)
would return:
{ValueError}Line 1: Bad character 'a'

weiglszonja
weiglszonja commented Oct 4, 2022
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docs/best_practices/time_series.rst
Comment on lines +105 to +107
* - :py:class:`~pynwb.retinotopy.AxisMap`
- "o"
- Degrees
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@weiglszonja weiglszonja Oct 4, 2022 •
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This is not TimeSeries but I thought could be good to include for example for representing degrees?

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CompassDirection is more typical for that as an example (be sure to include radians as well)

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Codecov Report

Merging #281 (8964521) into dev (06622b7) will increase coverage by 0.06%.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #281      +/-   ##
==========================================
+ Coverage   93.95%   94.02%   +0.06%     
==========================================
  Files          20       20              
  Lines        1026     1037      +11     
==========================================
+ Hits          964      975      +11     
  Misses         62       62
Flag Coverage Δ
unittests 94.02% <100.00%> (+0.06%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
nwbinspector/checks/time_series.py 97.77% <100.00%> (+0.71%) ⬆️

@CodyCBakerPhD CodyCBakerPhD added the category: new check a new best practices check to apply to all NWBFiles and their contents label Oct 4, 2022
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can we hold off on this? I don't know if we want to use CMIXF

@CodyCBakerPhD CodyCBakerPhD linked an issue Nov 9, 2022 that may be closed by this pull request
[Add Check]: units are in SI values #208
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@CodyCBakerPhD CodyCBakerPhD mentioned this pull request Dec 1, 2022
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[Add Check]: units are in SI values
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