Tolerant option for bids.layout

[tanguyduval]

No description provided.

[tanguyduval]

This issue solves #7
Tolerance on:

• dataset_description and .tsv files
• parse image modalities that are not in BIDS yet (but in extension proposal for instance)
• inconsistent data between subjects (currently it crashes if more images in one subject than another)

[Remi-Gau]

Nice.
Wouldn't it sense to have the inconsistency between subjects be the lowest level of tolerance: unless I am mistaken this does not make an invalid bids data set, where as the other 2 levels would.
Or am I missing something?

[tanguyduval]

@Remi-Gau agreed, I just tried an inconsistent dataset with bids validator and it gives no error. Only a warning in case of inconsistent data between subjects:

Warning 2: [Code 38] INCONSISTENT_SUBJECTS
Not all subjects contain the same files. Each subject should contain the same number of files with the same naming unless some files are known to be missing.

I'll change that.
Best

[tanguyduval]

@Remi-Gau this version accepts inconsistent data between subjects, even for files not officially in BIDS yet
tested on octave 5 and matlab.
Best

[Remi-Gau]

Thank. Will check things out during the weekend

[Remi-Gau]

• add tests to check warning VS error handling of the tolerant option of layout

[Remi-Gau]

If that's with everyone I will start mergin those old pull-requests that have not been "vetoed".

• bring the PR up to date with master
• clean up and refactor if needed
• create tests if needed or where easily possible
• wait for 24 hours after CI gives the green light (in case anyone has any final thoughts before merging)
• merge

[Remi-Gau]

On this one we would need some test to assert that a warning or an exception is thrown.

Not sure that our current framework allows this.

[Remi-Gau]

Good with me