Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ENH] Define "phenotype" as a data type not nested inside subjects #2050

Open
wants to merge 1 commit into
base: master
Choose a base branch
from

Conversation

effigies
Copy link
Collaborator

Closes #1828. Please continue the conversation in that issue, and reserve this PR for discussing concrete changes.

@yarikoptic
Copy link
Collaborator

attn @bids-standard/bep036

15. `phenotype` (participant-level measurement and survey data)

For files that are subject- and session- specific, the data type directory
is nested inside those directories.
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Does this mean phenotype/ is permitted, but not required under the subject/[session/] directory? BEP036 is leaning into the aggregated model of tabular phenotypic data file storage at the root-level phenotype/ subdirectory.

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

To permit it, we would need a file rule where subject and session are optional, so this describes the current situation reasonably well, as it can't be subject- or session- specific.

I do not have a specific objection to permitting it to be used inside subject/session directories, but if BEP036 is not proposing it, it won't happen.

Happy to consider alternative wordings that make this clearer.

@effigies effigies force-pushed the feat/phenotype-datatype branch from f64abd7 to d85831e Compare March 3, 2025 14:39
@effigies effigies force-pushed the feat/phenotype-datatype branch from d85831e to f5a4863 Compare March 20, 2025 19:48
Copy link

codecov bot commented Mar 20, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.55%. Comparing base (fa58763) to head (f5a4863).

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #2050      +/-   ##
==========================================
+ Coverage   83.49%   83.55%   +0.05%     
==========================================
  Files          17       17              
  Lines        1509     1508       -1     
==========================================
  Hits         1260     1260              
+ Misses        249      248       -1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
  • 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Classify "phenotype/" as a datatype directory with no subject/session parent
3 participants