Fix runModelingPipelineIntense() - #37
Merged
Merged
Conversation
eboyer221
requested review from
AbhirupaGhosh,
amcim,
epbrenner and
jananiravi
August 12, 2026 23:33
7 tasks
AbhirupaGhosh
approved these changes
Aug 13, 2026
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
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
What
runModelingPipelineIntense() is meant to run the whole modeling process from start to finish: first build the feature matrices from the data, then train all the models on them. The "build the matrices" step had been switched off (commented out).
Why it matters
Every step after the matrix-building step assumes those matrices already exist. With that step disabled, each later step fails because it can't find its input, and the function still prints "=== AMR-ML Pipeline Complete ===" at the end - so running the whole pipeline looks successful but actually produces nothing.
Fix
Turned the matrix-building step back on.
Testing
Added tests/testthat/test-run-modeling-pipeline-intense.R. Full test suite passes (205/205).
Found while reviewing #32. Split out from the "pipeline control flow" item in Issue #33 as its own PR, since this is a self-contained fix to a different, higher-level wrapper function than the other bugs in that item (see #36).