Handling of supplementary `source` / `code` folders with arbitrary content

[JuliaSprenger]

When supplementary folders are present in the current structure the validation fails as these are unexpected. This implies that additional material can only be provided outside of the AnDO structure, e.g. a code folder needs to be located one level above the sub-<subject-id> folder.

This is inconsistent with the BIDS specifications, that allow to have a code folder with arbitrary content at the same level as the sub-<subject-id> and participants.csv, see https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#code

[SylvainTakerkart]

yep, I agree this is a probem at the moment... however, we should be careful not to get into a mode where we re-implement step by step the bids validator... so let's think about whether it's easy or not to handle this; if it's trivial, let's implement it! if not, let's get together, discuss and decide what to do...

[Remi-Gau]

Allowed folders:

• code
• sourcedata
• derivatives
• stimuli
• phenotype

Also check if there is a .bidsignore file to maybe anticipate how the validator will react https://github.com/bids-standard/bids-validator#bidsignore

[Remi-Gau]

other things I am getting "false positive" errors by the checker when working with datalad dataset:

• .git
• .datalad
• .gitignore
• .gitattributes
• .gitmodules

[Remi-Gau]

Getting false positive for those files too

• samples.tsv
• README
• LICENSE