AFNI enhancements & doctests #479
Conversation
BUG: Fixed afni.preprocess.to3D funcparams to not use the undocumented template for the argstr ENH: Adding tpattern reading functionality to To3D() BUG: Fixed bug for To3D() for output, To3D only returns AFNI output type (AFNI implementation) STYLE: fixed typo in documentation and made more PEP8-compliant BUG: Fixed file rename bug when copyfile is used for AFNI STYLE: Removed attempt to use base class for prefix and suffix inputs BUG: Fixed Refit() to correctly accept the output from To3D() ENH: Added more options for Refit()
…c FIRST or you get weird errors running the pipeline
…ile_*'. Contact mailing list about the add_traits() function and how it should be correctly implemented. Doctesting and pipeline testing pass the cmdline generation, but the pipeline fails to add the argstr for the pipeline run (causing failure)
BUG: Fixed all calls to super(AFNICommand, self) to super(CLASSNAME, self)
…enerated by the stdout, not by the json file handling
|
This looks very messy, could you try to create a new branch (from current
|
|
Sorry, @satra, I didn't see your reopen request… |
|
@chrisfilo I'll see what I can do. I didn't want to lose the conversation... |
|
After cherry picking you can delete this branch (locally), rename the new
|
|
@chrisfilo @satra I spent a couple of hours to cleaning up this. It's diverged from master quite a bit and I can't commit any more time to it. Sorry. Dave |
|
This has become very stale. After two years since the start of this effort it still has not been polished to the point of being able to submit. Abandoning this pull request. If it becomes relevant in the future, someone else can make an effort to incorporate it. |
@chrisfilo, @satra, @hjmjohnson,
Added 3dDeconvolve() and Zeropad(), more traited flags to Allineate() and others, updated style to conform better with PEP8 (http://www.python.org/dev/peps/pep-0008/) and increased doctest usage.
The doctest usage may or may not conflict with the web documentation style. If so, I can move the offending tests to a doctest file, but I'll need help integrating that into the Nipype testing infrastructure.
Cheers,
@dmwelch