[MRG] Support cross-talk and fine-calibration files

[hoechenberger]

PR Description

Adds support for Elekta/Neuromag/MEGIN cross-talk and fine-calibration files. Closes #495.

• mne_bids.write_cross_talk()
• mne_bids.write_fine_calibration()
• BIDSPath.cross_talk_fpath property*
• BIDSPath.fine_calibration_fpath property*
• CLI: mne_bids crosstalk_to_bids
• CLI: mne_bids calibration_to_bids

BIDS spec:
https://bids-specification.readthedocs.io/en/latest/99-appendices/06-meg-file-formats.html#neuromagelektamegin

Merge checklist

Maintainer, please confirm the following before merging:

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

[hoechenberger]

This is currently blocked by an upstream PR for bids-validator, bids-standard/bids-validator#1079

[sappelhoff]

API looks good to me, just two minor comments.

[codecov-commenter]

Codecov Report

❗ No coverage uploaded for pull request base (master@566cdbb). Click here to learn what that means.
The diff coverage is 91.66%.

@@            Coverage Diff            @@
##             master     #562   +/-   ##
=========================================
  Coverage          ?   92.72%           
=========================================
  Files             ?       17           
  Lines             ?     2267           
  Branches          ?        0           
=========================================
  Hits              ?     2102           
  Misses            ?      165           
  Partials          ?        0           

Impacted Files	Coverage Δ
mne_bids/config.py	91.17% <ø> (ø)
mne_bids/commands/mne_bids_calibration_to_bids.py	83.33% <83.33%> (ø)
mne_bids/commands/mne_bids_crosstalk_to_bids.py	83.33% <83.33%> (ø)
mne_bids/path.py	96.32% <100.00%> (ø)
mne_bids/write.py	95.80% <100.00%> (ø)

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[hoechenberger]

Hum, what's up with the CI now?!

[hoechenberger]

All tests pass locally for me and the error message(s) we see here in the CI don't make any sense to me…

[hoechenberger]

Should hopefully pass now after rebasing after #564 has been merged.

[hoechenberger]

The tests that are failing now use the stable bids-validator, which doesn't yet support the changes implemented here – only the master branch of bids-validator currently does. How should we deal with this? @sappelhoff?

[hoechenberger]

Ok so I've expanded the build matrix to use the stable and the development version of bids-validator on all platforms. All tests with the development version seem to pass now, so this should be good to merge.

[agramfort]

@hoechenberger it would be better to skip test if bids_validator does not have the correct version. Merging a PR with red CI is bad.

[hoechenberger]

Ugh now the tests are skipped on all platforms… because the bids-validator version number is not updated on GitHub master (is the same as in the latest stable release.) @sappelhoff is this intentional or do you think sb has just forgotten to update the version number?

[hoechenberger]

Ugh now the tests are skipped on all platforms… because the bids-validator version number is not updated on GitHub master (is the same as in the latest stable release.) @sappelhoff is this intentional or do you think sb has just forgotten to update the version number?

I've opened an issue upstream, bids-standard/bids-validator#1080

[hoechenberger]

bids-validator has been updated, and I've just restarted the CI jobs here and ensured that we're actually running the all tests (and not accidentally skipping some). All good, all green. Good to merge.

[sappelhoff]

@sappelhoff is this intentional or do you think sb has just forgotten to update the version number?

this is/was a known issue for a long time --> bids-standard/bids-validator#803

nobody got around to fixing it, and I am not sure whether your PR will persist, because I have no idea about the release process of bids-validator and what kinds of automations are in place that will overwrite/undo your changes - or break because of them 🙂

I pinged Ross (the maintainer) for that issue ... best case scenario, your simple fix was exactly what was needed --> let's hope for that.