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DOCTEST: Use legacy float array printing for now #556

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Merged
merged 6 commits into from
Oct 5, 2017
Merged

DOCTEST: Use legacy float array printing for now #556

merged 6 commits into from
Oct 5, 2017

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effigies
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In numpy's pre-release, float arrays now have different printing strategies. Adding #doctest: +NORMALIZE_WHITESPACE doesn't resolve the issue, so for the moment we need to use their option to revert printing behavior to keep doctests from breaking.

Using .. testsetup:: should avoid visual changes to the docs.

Introduced in numpy/numpy@710e032

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Coverage Status

Coverage remained the same at 96.271% when pulling a2bc501 on effigies:fix/numpy_print_doctests into dbe74e1 on nipy:master.

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codecov-io commented Sep 27, 2017 •
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Codecov Report

Merging #556 into master will decrease coverage by <.01%.
The diff coverage is 80%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #556      +/-   ##
==========================================
- Coverage   94.34%   94.33%   -0.01%     
==========================================
  Files         177      177              
  Lines       24670    24680      +10     
  Branches     2634     2635       +1     
==========================================
+ Hits        23275    23283       +8     
- Misses        920      921       +1     
- Partials      475      476       +1
Impacted Files Coverage Δ
nibabel/__init__.py 90.69% <100%> (+0.22%) ⬆️
nibabel/nicom/dwiparams.py 71.69% <100%> (+0.54%) ⬆️
nibabel/affines.py 100% <100%> (ø) ⬆️
nibabel/quaternions.py 98.05% <100%> (+0.01%) ⬆️
nibabel/nifti1.py 91.14% <100%> (+0.01%) ⬆️
nibabel/casting.py 85.83% <100%> (+0.06%) ⬆️
nibabel/testing/__init__.py 94.79% <50%> (-1.95%) ⬇️

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@effigies
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@matthew-brett I think you'll know more about how to deal with this error than I do. Is this an issue on matplotlib's end, or some buildbot that needs fixing?

THESE PACKAGES DO NOT MATCH THE HASHES FROM THE REQUIREMENTS FILE. If you have updated the package versions, please update the hashes. Otherwise, examine the package contents carefully; someone may have tampered with them.
    matplotlib from https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com/matplotlib-2.1.0rc1+104.g4792425-cp27-cp27mu-manylinux1_x86_64.whl#sha256=0b50fa1925772cf0b6d7a386774c9f7671c758bdc3c2472e06f0e319da841848:
        Expected sha256 0b50fa1925772cf0b6d7a386774c9f7671c758bdc3c2472e06f0e319da841848
             Got        b49660821b0a93fd9c1dd8c0aafd5489b86524edd907e032f9347eebb84f47f1

matthew-brett
matthew-brett reviewed Sep 27, 2017
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Some hopeful suggestions.

nibabel/nifti1.py Outdated
@@ -9,6 +9,12 @@
''' Read / write access to NIfTI1 image format

NIfTI1 format defined at http://nifti.nimh.nih.gov/nifti-1/

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Can we make this two separate strings, so the user doesn't get this testsetup in the docstring help?

nibabel/nicom/dwiparams.py Outdated
@@ -18,6 +18,11 @@

B ~ (q_est . q_est.T) / norm(q_est)

.. testsetup::
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Can we put this in a separate docstring? See comment below.

nibabel/quaternions.py Outdated
@@ -23,6 +23,12 @@
>>> M = quat2mat(q) # from this module
>>> vec = np.array([1, 2, 3]).reshape((3,1)) # column vector
>>> tvec = np.dot(M, vec)

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Ditto.

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Hopefully this works. I don't know all the rules to doctests.

@effigies effigies force-pushed the fix/numpy_print_doctests branch from b803ac6 to dab6331 Compare September 27, 2017 17:40
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Coverage Status

Coverage remained the same at 96.271% when pulling dab6331 on effigies:fix/numpy_print_doctests into dbe74e1 on nipy:master.

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Is there some way to do a package-wide pre-doctest setup so we can have this in one place? Hard to google.

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I don't know how to set up project wide doctest initialization - other than writing a specific nibabel plugin for the doctests / nose.

@effigies effigies mentioned this pull request Oct 2, 2017
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@effigies effigies force-pushed the fix/numpy_print_doctests branch from dab6331 to 600f7f2 Compare October 2, 2017 23:47
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effigies commented Oct 3, 2017

I think I've resolved this. If there's a setup_test() function, that will get run before doctests (see doctest fixtures). At least locally, I was able to write this function in one place nibabel.testing and import it in others. We'll see if it does what we want with the pre-release installed.

@effigies effigies force-pushed the fix/numpy_print_doctests branch from b72634f to 26dfee3 Compare October 3, 2017 01:53
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Coverage Status

Coverage decreased (-0.003%) to 96.268% when pulling b72634f on effigies:fix/numpy_print_doctests into dbe74e1 on nipy:master.

@effigies effigies force-pushed the fix/numpy_print_doctests branch from b27efce to 70afacb Compare October 3, 2017 02:09
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Coverage Status

Coverage decreased (-0.003%) to 96.268% when pulling 70afacb on effigies:fix/numpy_print_doctests into dbe74e1 on nipy:master.

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effigies commented Oct 4, 2017

@matthew-brett Does this look reasonable?

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Thanks - looks good - in it goes.

@matthew-brett matthew-brett merged commit fa76141 into nipy:master Oct 5, 2017
@matthew-brett matthew-brett mentioned this pull request Oct 5, 2017
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@effigies effigies deleted the fix/numpy_print_doctests branch October 6, 2017 16:01
@effigies effigies mentioned this pull request Jan 11, 2018
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