Add option to skip BIDS validation

yarikoptic commented 4 years ago

takes time ;-) I might better do it once and not per each subject execution
does not yet play nicely with datalad yet. There is --ignoreSymlinks which might be of help (https://github.com/datalad-handbook/book/pull/562) if datalad is detected but sounds like an overkill and not yet sure what it does exactly based on its docstring (since no directories are symlinked but rather files):
```
--ignoreSymlinks      Skip any symlinked directories when validating a dataset
                                                                   [boolean]
```

fmriprep provides

  --skip_bids_validation, --skip-bids-validation
                        assume the input dataset is BIDS compliant and skip
                        the validation (default: False)

and I think it would be great if BIDSonym did that too ;-)

edit: filed https://github.com/bids-standard/bids-validator/issues/1050 to make it possible to make bids-validator more git-annex friendly but it would still require passing an option to it

yarikoptic commented 4 years ago

might be even worth adding an option to pass options into bids validator? (e.g. --version to discover what version of it is bundled within bidsonym container while effectively skipping validator ;) )

yarikoptic commented 4 years ago

May be @chrispycheng would be interested to submit a PR for this!?

PeerHerholz / BIDSonym

Add option to skip BIDS validation #35