[MAINT] use jinja in the macros

[Remi-Gau]

this is just a test to see if using jinja templates in the macros could help with our rendering of HTML / PDF

• closes [BUG] Glossary renderer is unaware of version (Markdown or PDF) #2069

[Remi-Gau]

unrelated: could be extracted in separate PR

[Remi-Gau]

unrelated: could be extracted in separate PR

[Remi-Gau]

• AFAICT using jinja templates already fixes: [BUG] Glossary renderer is unaware of version (Markdown or PDF) #2069

@oesteban

descriptions are back in pdf and still there in html:

[Remi-Gau]

a few oddities:

ordered list are a quote blocked in the html version:

or don't have the proper 'order' in pdf (item 1. appears twice)

[Remi-Gau]

Also see https://bids-specification--2083.org.readthedocs.build/en/2083/glossary.html#stimuluspresentation-metadata

or similarly:

• https://bids-specification--2083.org.readthedocs.build/en/2083/glossary.html#deidentificationmethodcodesequence-metadata

• https://bids-specification--2083.org.readthedocs.build/en/2083/glossary.html#genetics-metadata

[oesteban]

ordered list are a quote blocked in the html version:

I believe this is not a bug - we need to remove the indentation from the common principles yaml (it was added precisely because the current parser would otherwise render something funky).

bids-specification/src/schema/objects/common_principles.yaml

Lines 11 to 48 in 7f5e0a7

	data_type:
	display_name: Data type
	description: |
	A functional group of different types of data.
	Data files are contained in a directory named for the data type.
	In raw datasets, the data type directory is nested inside subject and (optionally) session directories.
	BIDS defines the following data types:
	1. `func` (task based and resting state functional MRI)
	2. `dwi` (diffusion weighted imaging)
	3. `fmap` (field inhomogeneity mapping data such as field maps)
	4. `anat` (structural imaging such as T1, T2, PD, and so on)
	5. `perf` (perfusion)
	6. `meg` (magnetoencephalography)
	7. `eeg` (electroencephalography)
	8. `ieeg` (intracranial electroencephalography)
	9. `beh` (behavioral)
	10. `pet` (positron emission tomography)
	11. `micr` (microscopy)
	12. `nirs` (near infrared spectroscopy)
	13. `motion` (motion)
	14. `mrs` (magnetic resonance spectroscopy)
	dataset:
	display_name: Dataset

[Remi-Gau]

ordered list are a quote blocked in the html version:

I believe this is not a bug - we need to remove the indentation from the common principles yaml (it was added precisely because the current parser would otherwise render something funky).

bids-specification/src/schema/objects/common_principles.yaml

Lines 11 to 48 in 7f5e0a7

	data_type:
	display_name: Data type
	description: |
	A functional group of different types of data.
	Data files are contained in a directory named for the data type.
	In raw datasets, the data type directory is nested inside subject and (optionally) session directories.
	BIDS defines the following data types:
	1. `func` (task based and resting state functional MRI)
	2. `dwi` (diffusion weighted imaging)
	3. `fmap` (field inhomogeneity mapping data such as field maps)
	4. `anat` (structural imaging such as T1, T2, PD, and so on)
	5. `perf` (perfusion)
	6. `meg` (magnetoencephalography)
	7. `eeg` (electroencephalography)
	8. `ieeg` (intracranial electroencephalography)
	9. `beh` (behavioral)
	10. `pet` (positron emission tomography)
	11. `micr` (microscopy)
	12. `nirs` (near infrared spectroscopy)
	13. `motion` (motion)
	14. `mrs` (magnetic resonance spectroscopy)
	dataset:
	display_name: Dataset

ha yeah good catch!

[Remi-Gau]

will probably focus refactoring by getting macros to use jinja first with 'no change in behavior' and then tackle remaining 'bugs' in a follow up PRs

also I would not mind have more explicit tests for some of this because working on this feels like flying blind.

[Remi-Gau]

I believe this is not a bug - we need to remove the indentation from the common principles yaml (it was added precisely because the current parser would otherwise render something funky).

to keep track of as well:

this may affect the rendering of the list in the common principles: