ENH: BrainSuite updates: Add interfaces for additional command line tools #1554

jason-wg · 2016-08-01T06:06:25Z

I have updated the BrainSuite Nipype interface to include classes for our BDP, SVReg and ThicknessPVC command line tools.

…s. Edited _gen_filename for Cortical Surface Extraction interfaces to produce outputs in required format for SVReg and BDP.

…terfaces. Ran make specs, and make-check-before-commit.

coveralls · 2016-08-01T06:14:45Z

Coverage increased (+0.05%) to 72.374% when pulling 56d5058 on jason-wg:master into 3ed411b on nipy:master.

jason-wg · 2016-08-29T20:31:40Z

@satra @chrisfilo
Can you please take a look at my code updates, or refer this PR to someone who is available to review my code?

Thanks!

satra · 2016-08-30T00:41:34Z

@jason-wg - quick observation - could you please try to get your code to be as close to PEP8 compliant as possible? as an example see: #1593

…online checker, removed all warnings, except for E501 Line Too Long

jason-wg · 2016-08-30T04:40:38Z

@satra
I've made formatting fixes for PEP8 compliance, except that many lines run over 80 characters.
Does this look fine to you?

coveralls · 2016-08-30T04:45:21Z

Coverage decreased (-0.02%) to 72.302% when pulling 04bb78c on jason-wg:master into 3ed411b on nipy:master.

satra · 2016-09-08T15:08:39Z

@jason-wg - could you please merge with current master, fix any conflicts and push?

…n regarding encoding comment and imports for Python 3 compatability.

coveralls · 2016-09-09T04:21:13Z

Coverage decreased (-0.03%) to 72.237% when pulling 6a1e80b on jason-wg:master into 0f9a620 on nipy:master.

coveralls · 2016-09-09T04:21:13Z

Coverage decreased (-0.06%) to 72.206% when pulling 6a1e80b on jason-wg:master into 0f9a620 on nipy:master.

… from most current code using make checks

coveralls · 2016-09-09T06:49:48Z

Coverage decreased (-0.03%) to 72.237% when pulling 15e51c3 on jason-wg:master into 0f9a620 on nipy:master.

coveralls · 2016-09-09T06:49:48Z

Coverage decreased (-0.03%) to 72.237% when pulling 15e51c3 on jason-wg:master into 0f9a620 on nipy:master.

coveralls · 2016-09-09T06:49:48Z

Coverage decreased (-0.03%) to 72.237% when pulling 15e51c3 on jason-wg:master into 0f9a620 on nipy:master.

jason-wg · 2016-09-09T07:41:03Z

@satra

A note regarding the failure that we see in the Travis CI build:
Per the log, a doctest fails: Doctest: nipype.interfaces.brainsuite.brainsuite.BDP ... FAIL
When I run the doctest to take a closer look, the failure message is: TraitError: Each element of the 'BVecBValPair' trait of a BDPInputSpec instance must be a value of type 'str', but a value of u'/directory/subdir/prefix.dwi.bvec' <type 'unicode'> was specified.

For reference, the line containing the failing doctest is here
bdp.inputs.BVecBValPair is of type traits.List, requiring string inputs.
Based on the code in the doctest, I expect that both the items in the List are in fact strings.

I have tried to identify the cause of this failure, and I have found that when I take out the import of unicode_literals from this line that was recently added to my code in 632c1f1 , then the doctest runs fine.

When I add doctests for any other traits.List fields, I get the same error, ... instance must be a value of type 'str', but a value of ... <type 'unicode'> was specified

I'm curious about why this error is appearing, so please do let me know if you have any insights on this.

As for my pull request, what do you suggest I do for my code?

satra · 2016-09-10T14:37:15Z

@jason-wg - you will need to: from ..traits_extension import Str

all strings are now unicode in nipype.

coveralls · 2016-09-10T18:55:48Z