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[FIX] update highlighting of examples, JSON keys and values, and TSV headers or values in the schema #998

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merged 5 commits into from
Feb 4, 2022

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Remi-Gau
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@Remi-Gau Remi-Gau commented Feb 3, 2022

closes #746

make sure that that examples appear "as they should" be in JSON or TSV files

  • numeric examples appear for example like this 1
  • JSON keys or values when appearing in metadata descriptions appear with double quotes for example like "Key" or "n/a"
  • TSV column header or value appear without double quotes for example like 1 or like this n/a

I am sure I have missed some but this is a never ending battle (and I don't thing we want to automate or CI check this) so I suggest that this should close #746

@@ -201,7 +201,7 @@ reconstruction:
entity: rec
description: |
The `rec-<label>` key/value can be used to distinguish
different reconstruction algorithms (for example ones using motion
different reconstruction algorithms (for example `MoCo` for the ones using motion
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This feels like common enough occurrence in scanners output to add it by name as an example

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codecov bot commented Feb 3, 2022

Codecov Report

Merging #998 (7529d75) into master (2507964) will increase coverage by 1.07%.
The diff coverage is n/a.

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@@            Coverage Diff             @@
##           master     #998      +/-   ##
==========================================
+ Coverage   34.05%   35.13%   +1.07%     
==========================================
  Files           8        8              
  Lines         834      834              
==========================================
+ Hits          284      293       +9     
+ Misses        550      541       -9     
Impacted Files Coverage Δ
tools/schemacode/schemacode/_version.py 38.90% <0.00%> (+2.59%) ⬆️

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@@ -744,7 +744,7 @@ EffectiveEchoSpacing:
between lines in the phase-encoding direction,
defined based on the size of the reconstructed image in the phase direction.
It is frequently, but incorrectly, referred to as "dwell time"
(see `DwellTime` parameter below for actual dwell time).
(see `"DwellTime"` parameter for actual dwell time).
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removed the below because this might not make sense in all context if this description was used in a table where DwellTime does not appear

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Overall, I like these changes. Just two things:

  1. Including a leading underscore when referring to suffixes/specific files (e.g., _events.tsv) seems less readable to me.
  2. I'm not sure if you want to include quotes around fields when you're referring to the actual contents of the field, rather than the key. For example, in the RepetitionTimeExcitation description, we have:

Use RepetitionTimeExcitation (in combination with "RepetitionTimePreparation" if needed)

It seems like "RepetitionTimePreparation" should just be RepetitionTimePreparation in this case. That said, I don't feel strongly about this, so if you disagree then I'm happy to approve.

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src/schema/objects/metadata.yaml Outdated Show resolved Hide resolved
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Remi-Gau commented Feb 3, 2022

Overall, I like these changes. Just two things:

1. Including a leading underscore when referring to suffixes/specific files (e.g., `_events.tsv`) seems less readable to me.

2. I'm not sure if you want to include quotes around fields when you're referring to the actual contents of the field, rather than the key. For example, in the `RepetitionTimeExcitation` description, we have:

Use RepetitionTimeExcitation (in combination with "RepetitionTimePreparation" if needed)

It seems like "RepetitionTimePreparation" should just be RepetitionTimePreparation in this case. That said, I don't feel strongly about this, so if you disagree then I'm happy to approve.

Yeah In a way I agree but this adds another implicit rule about formatting that will be hard to keep track off and potentially confuse users, no?

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That's a fair point. Approved!

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it seems like you removed the leading underscores again based on a comment by Taylor. I think you missed two instances (see comments).

I also like events.tsv better than _events.tsv even though I know I've been using both in the past

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Co-authored-by: Stefan Appelhoff <[email protected]>
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Remi-Gau commented Feb 4, 2022

it seems like you removed the leading underscores again based on a comment by Taylor. I think you missed two instances (see comments).

I also like events.tsv better than _events.tsv even though I know I've been using both in the past

Thanks for catching those too!!

@sappelhoff sappelhoff merged commit e47283a into bids-standard:master Feb 4, 2022
Lestropie added a commit to Lestropie/bids-specification that referenced this pull request Apr 29, 2022
Resolves bids-standard#947 against:
- bids-standard#962 (21b7725)
- bids-standard#1044 (d9eeb6d)
- bids-standard#867 (5fe26e1)
- bids-standard#998 (e47283a)

Conflicts:
	src/02-common-principles.md
	src/schema/README.md
	src/schema/objects/entities.yaml
	src/schema/objects/metadata.yaml
@Remi-Gau Remi-Gau deleted the format_example branch August 17, 2022 07:23
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Remaining formatting issues in tables
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