MRG: Deprecate silently adding a leading period to an extension in BIDSPath

[hoechenberger]

This works in main:

# %%
from mne_bids import BIDSPath

bp_1 = BIDSPath(extension='vhdr')
bp_2 = BIDSPath(extension='.vhdr')

assert bp_1 == bp_2

With this PR, it warns:

FutureWarning: extension should start with a period ".", but got: "vhdr". Prepending "." to form: ".vhdr". This will raise an exception starting with MNE-BIDS 0.12.

This is part of my journey to try and make MNE-BIDS less clever.

Merge checklist

Maintainer, please confirm the following before merging.
If applicable:

• All comments are resolved
• This is not your own PR
• All CIs are happy
• PR title starts with [MRG]
• whats_new.rst is updated
• New contributors have been added to CITATION.cff
• PR description includes phrase "closes <#issue-number>"

[adam2392]

Yay for less magic :)

[codecov]

Codecov Report

Merging #1061 (4241aa4) into main (388616f) will increase coverage by 1.25%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #1061      +/-   ##
==========================================
+ Coverage   93.95%   95.20%   +1.25%     
==========================================
  Files          25       25              
  Lines        3836     3840       +4     
==========================================
+ Hits         3604     3656      +52     
+ Misses        232      184      -48     

Impacted Files	Coverage Δ
mne_bids/path.py	97.58% <100.00%> (+0.01%)	⬆️
mne_bids/stats.py	92.85% <100.00%> (ø)
mne_bids/utils.py	95.74% <0.00%> (+0.53%)	⬆️
mne_bids/write.py	97.17% <0.00%> (+1.91%)	⬆️
mne_bids/dig.py	98.27% <0.00%> (+9.65%)	⬆️

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[sappelhoff]

failures are due to recent changes in the NIRS validator: https://github.com/bids-standard/bids-validator/pull/952

I don't know if for better or worse -- @rob-luke could you have a look, please?

[sappelhoff]

it's funny how the windows job with the NIRS validator passes 🤯 ... ubuntu and macos don't

now I am re-running after a potential fix has been pushed upstream

EDIT: okay, not such a mystery after all ... in the windows log it says:

SKIPPED [1] mne_bids\tests\test_write.py:1722: requires Rob's NIRS branch of bids-validator

so apparently it doesn't properly detect that it DOES have rob's validator and skips the test. no need to fix IMHO because nirs will soon be merged (within the next 3 weeks probably)

[sappelhoff]

thanks! Makes sense to me. Also BIDS says:

Note that the left-most period is included in the file extension.

https://bids-specification.readthedocs.io/en/latest/02-common-principles.html