Docs, README overhaul & input dedup fix (Stage 7 of #301)#319
Merged
Conversation
- Restructure README: purpose up front, BIDS requirement stated, quick start with install, longitudinal as subsection, dev section consolidated, license corrected to LGPL-3.0-or-later - Add SVG output tree visualization with per-stage color coding - Complete data dictionary: add longitudinal metrics/QC/template sections, add missing cross-sectional entries (MNI-space T1w, ITK affine, pre-bandpass regressed BOLD), fix longitudinal anat xfm entities (longitudinal<->MNI, not longitudinal<->T1w) - Fix double-indexing when input dirs are nested (e.g. /data and /data/derivatives): deduplicate resolved roots in load_table - Remove --runner docker from all README examples (auto-detect)
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Final stage of the longitudinal refactor (#301). Docs polish and a small bug fix.
T1w<->longitudinal, actuallylongitudinal<->MNI152NLin6Asym)load_tablenow deduplicates resolved dataset roots, preventing double-indexing when one input dir is a subdirectory of another (e.g.,/dataand/data/derivatives)--runner dockerfrom all README examples (auto-detect is the default)Closes #301
Test plan
uv run pytest -m unitpasses (780 passed)uv run pre-commit run --files README.md docs/data_dictionary.mdcleanrbc longitudinal --helpoutput matches documented CLIrbc long --helpalias works