[FIX] reorganize anat filename templates

[Remi-Gau]

fixes #1418

• split filename templates macro for anat into:
  • parametric suffixes
  • defacemask
  • non parametric suffixes
• add list of file collection suffixes in qMRI appendix

[codecov]

Codecov Report

Patch coverage has no change and project coverage change: +0.23 🎉

Comparison is base (134f532) 88.65% compared to head (6e7df7b) 88.88%.

❗ Current head 6e7df7b differs from pull request most recent head 268dc7b. Consider uploading reports for the commit 268dc7b to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1419      +/-   ##
==========================================
+ Coverage   88.65%   88.88%   +0.23%     
==========================================
  Files          11       11              
  Lines        1084     1080       -4     
==========================================
- Hits          961      960       -1     
+ Misses        123      120       -3     

Impacted Files	Coverage Δ
tools/schemacode/bidsschematools/render/text.py	97.47% <0.00%> (ø)
tools/schemacode/bidsschematools/render/utils.py	85.18% <0.00%> (ø)
...ools/schemacode/bidsschematools/types/namespace.py	91.09% <0.00%> (ø)
tools/schemacode/bidsschematools/schema.py	77.90% <0.00%> (+2.35%)	⬆️

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[Remi-Gau]

@sappelhoff I labelled this as a fix but I am 100% sure this is accurate because the schema was correct but it was our rendering of it that created some ambiguity.

Hence not sure if this should actually go in the changelog.

[sappelhoff]

thanks! I think it should go into the changelog, because what users mostly see is what we render.

[Remi-Gau]

thanks! I think it should go into the changelog, because what users mostly see is what we render.

good with me.
thanks!

[tsalo]

I like the overall change, but I have some suggestions to make it flow more nicely.

[Remi-Gau]

will have a closer look but it seems that I was being too conservative in my changes and that your suggestions really improve things.

[tsalo]

The changes look good to me. Thanks!

[Remi-Gau]

qmri appendix before

https://bids-specification.readthedocs.io/en/latest/appendices/qmri.html#inputs-are-file-collections

qmri appendix after

https://bids-specification--1419.org.readthedocs.build/en/1419/appendices/qmri.html#inputs-are-file-collections

[Remi-Gau]

anat section before

https://bids-specification.readthedocs.io/en/latest/modality-specific-files/magnetic-resonance-imaging-data.html#anatomy-imaging-data

anat section after

https://bids-specification--1419.org.readthedocs.build/en/1419/modality-specific-files/magnetic-resonance-imaging-data.html#anatomy-imaging-data

[Remi-Gau]

@effigies
added some screenshots and links to the relevant HTML to help reviewing.

let me know if you need something else.

[effigies]

Overall looks good, but I think I prefer the filename template to come before the suffix list. Other modalities continue to follow this convention, so I think it would make more sense to keep that as-is for now. A global reordering could be proposed separately (though I would vote against it).

[Remi-Gau]

Overall looks good, but I think I prefer the filename template to come before the suffix list. Other modalities continue to follow this convention, so I think it would make more sense to keep that as-is for now. A global reordering could be proposed separately (though I would vote against it).

good point

[Remi-Gau]

filename template to come before the suffix list.

@effigies

This is done.

[Remi-Gau]

it's been 5 days so I will merge this