rename grabbids to layout, closes #228

[ltirrell]

Closes #228 by renaming bids/grabbids to bids/layout, but running creating a symlink from layout to grabbidsand keepinggrabbids in bids/__init__.py.

The README changes may not be the best, and no longer includes a pun.

[codecov-io]

Codecov Report

Merging #230 into master will decrease coverage by 0.16%.
The diff coverage is 50%.

@@            Coverage Diff             @@
##           master     #230      +/-   ##
==========================================
- Coverage   74.59%   74.42%   -0.17%     
==========================================
  Files          23       24       +1     
  Lines        2204     2209       +5     
  Branches      525      525              
==========================================
  Hits         1644     1644              
- Misses        409      414       +5     
  Partials      151      151

Flag	Coverage Δ
#unittests	74.42% <50%> (-0.17%)	⬇️

Impacted Files	Coverage Δ
bids/layout/bids_layout.py	59.6% <ø> (ø)
bids/reports/report.py	83.67% <ø> (ø)	⬆️
bids/reports/parsing.py	59.25% <ø> (ø)	⬆️
bids/version.py	0% <ø> (ø)	⬆️
bids/layout/bids_validator.py	91.02% <ø> (ø)
bids/variables/entities.py	87.64% <ø> (ø)	⬆️
bids/grabbids/__init__.py	0% <0%> (-100%)	⬇️
bids/layout/__init__.py	100% <100%> (ø)
bids/analysis/analysis.py	89.32% <100%> (ø)	⬆️

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[ltirrell]

tests failed when symlinking grabbids to layout. now aliasing the module name loosely based of this. also seems cleaner (i would guess symlinks would break in windows at the very least).

also added a DeprecationWarning when importing bids.grabbids directly. not sure if that's necessary, or should have an improved message.

the tutorial ipynb now imports from bids.layout instead.

[tyarkoni]

Great, thanks! @chrisfilo, you okay with renaming the grabbids module to layout?

[chrisgorgo]

Wouldn't this break a bunch of code doing from bids.grabbids import BIDSLayout or is the old syntax still supported?

[tyarkoni]

Old syntax is supported, with a deprecation warning, and we can eventually remove the old placeholder in a few releases.

[effigies]

I'd rather libraries not change the warnings registry. This makes it harder for programs to control their outputs.

[effigies]

Could we note in the warning text the version we're deprecating at (0.6.5 or 0.7), and when to expect its removal? This both helps downstream projects plan a transition path and lets pybids developers know when they can fully remove it.

[ltirrell]

How's this for a proposed change to those lines:

-warnings.simplefilter('always', DeprecationWarning)
-warnings.warn("grabbids has been renamed to layout", DeprecationWarning)
+warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.7", FutureWarning)

I could change the versions to whatever you think is best. FutureWarning shows up by default without changing the warning filter. I could also do that in another way

[effigies]

@tyarkoni Will the next version be 0.6.5 or 0.7?

And I would say we should remove in 1.0, unless that's expected within the next month. (I realize pybids is alpha, but the grabbids API has been around for a long time.)

[chrisgorgo]

works for me Best, Chris

…

On Thu, Aug 9, 2018 at 1:57 PM Chris Markiewicz ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In bids/grabbids/__init__.py <#230 (comment)>: > __all__ = ["BIDSLayout", "BIDSValidator"] + +warnings.simplefilter('always', DeprecationWarning) +warnings.warn("grabbids has been renamed to layout", DeprecationWarning) Could we note in the warning text the version we're deprecating at (0.6.5 or 0.7), and when to expect its removal? This both helps downstream projects plan a transition path and lets pybids developers know when they can fully remove it. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#230 (review)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOkpxcVjYGvp_61D6OmA8DwczLkaztsks5uPHfygaJpZM4V1GBA> .

[tyarkoni]

Thanks!