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New --add_aux_var option

Paul McCarthy requested to merge bf/binarise-categorical into master
  • New --add_aux_var option, which ensures that auxillary/secondary variables used in processing rules will be imported, if they weren't already selected for import. For exmaple, the rule 41270 binariseCategorical(take=41280) would be skipped if 41280 were not imported. With --add_aux_vars, 41280 will be imported, even if explicitly excluded.
  • The FMRIB configuration profile is now maintained separately from the FUNPACK source code at fsl/funpack-fmrib-config>. This is so it can be updated independently of FUNPACK.
  • New utility script, refresh_showcase_schema.py to update built-in UKB schema. Only intended for use by me.
  • New documentation pages for the command-line interface, and FMRIB profile
  • Marked the broadcast_ feature in processing as deprecated. Alternative is for processing functions to implement their own parallelisation.

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