ENH: Parse Boutiques output structure #3
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Adds support for dynamic parsing of boutiques output-files spec. Unfortunately, boutiques does not support specification of which input options will lead to the generation of specific output files, so _all_ output files are being specified. This will likely lead to some problems down the road, and might be worth suggesting to the boutiques team as a future enhancement of their schema.
Rather than assigning to self.inputs or self.outputs, BoutiqueInterface will actually generate subclasses of DynamicTraitedSpec (so that things like .help() might eventually work).
Generating an instance of BoutiqueInterface now allows for .help() to generate pretty help text using standard nipype machinery.
Better file handling (existence checking, output aggregating) for BoutiqueInterface
Adds example to BoutiqueInterface and makes some minor updates to input spec handling.
|
Alright, so I wasn't happy with the on-the-fly input/output assignment so I'm now creating new classes for I've added a descriptor (wrapping FSL's |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Adds support for dynamic parsing of
boutiquesoutput-files.Unfortunately,
boutiquesdoes not support specification of which input options will lead to the generation of specific output files, so all output files are being specified. This will likely lead to some problems down the road, and might be worth suggesting to theboutiquesteam as a future enhancement of their schema.