cleanup and snakenull for handling missing entities #149
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TODOs:
** this has an open request already: khanlab/snakebids#293 |
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oh no, i think i triggered CI when i accidentally closed and then reopened this PR. I guess that's another 436min of processing :/ |
Updated 'snakebids.yml' to introduce 'snakenull' feature and modify wildcards for acquisitions.
Updated configuration to replace 'acq' with 'acquisition' for clarity and consistency.
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Snakenull is a new snakebids feature described here: khanlab/snakebids#470 in response to the issue raised here khanlab/snakebids#469
It adds flexibility to input datasets. For example, if run-X exists in some subjects but not others, it will keep the
runentity as a wildcard, and infill X assnakenullfor all cases that didn't already have it defined. Note that the default behaviour is still to have snakenull disabled, so here we enable it (globally, but we could just as easily enable it for a given pybids_input) in your snakebids.yml config file.Also note that for this build to work, we will need to include snakenull in our dependencies. Currently I'm working with a local build and my test runs are working. To deploy correctly, we can either wait until this feature is merged and specify its new version number as our snakebids requirement, or we can use
git+to point to the branch (this would be a temporary fix as the branch will be deleted once merged).This PR also clean up some files that should never have been included (.vscode, __pycache__, and .snakemake - which were most likely committed by mistake during development and testing)