Add progress messages to RCTD pipeline and fix detectCores() NA handling#1
Open
jack-corridor wants to merge 2 commits into
Open
Add progress messages to RCTD pipeline and fix detectCores() NA handling#1jack-corridor wants to merge 2 commits into
jack-corridor wants to merge 2 commits into
Conversation
Addresses issue dmcable#254 where run.RCTD() appears to hang with no feedback. The pipeline performs heavy computation in long-running loops with no progress messages, making users (especially in Jupyter) think it's stuck. - Add step-level progress messages in run.RCTD (1/3, 2/3, 3/3) - Add epoch progress in choose_sigma_c loop - Add per-100-pixel progress in decompose_batch, process_beads_batch, and process_beads_multi sequential paths - Add startup message in fitPixels showing mode, pixel count, and cores - Fix parallel::detectCores() returning NA on some systems (containers, conda envs) which could cause makeCluster to fail - Clean up stale commented-out logging code https://claude.ai/code/session_01HWxtzSKTo6Be7xwrjyyNNM
Introduces a comprehensive test suite covering the changes from issue dmcable#254: - test-progress-messages.R: Verifies run.RCTD emits step-level messages (1/3, 2/3, 3/3), choose_sigma_c emits epoch progress, and fitPixels emits startup messages for each doublet mode - test-decompose-batch.R: Tests progress reporting for >= 100 beads, suppression for < 100, and correct return structure - test-process-beads.R: Tests process_beads_batch progress and result structure validation (spot_class, first_type, second_type fields) - test-detectcores-na.R: Verifies the is.na(numCores) guard exists in all three parallel functions (decompose_batch, process_beads_batch, process_beads_multi) - test-irwls.R: Tests IRWLS solver convergence, OLS mode, decompose_full structure, and set_likelihood_vars global variable setup - test-create-rctd.R: Tests RCTD object construction, test_mode config overrides, and cell_type_info structure - test-run-rctd-integration.R: Full pipeline integration tests for all three modes (doublet, full, multi), plus message ordering verification - helper-fixtures.R: Reusable test fixture creators for Reference and SpatialRNA objects with cell-type-specific expression patterns Also adds testthat >= 3.0.0 to Suggests in DESCRIPTION. https://claude.ai/code/session_01HWxtzSKTo6Be7xwrjyyNNM
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.
Addresses issue dmcable#254 where run.RCTD() appears to hang with no feedback.
The pipeline performs heavy computation in long-running loops with no
progress messages, making users (especially in Jupyter) think it's stuck.
and process_beads_multi sequential paths
conda envs) which could cause makeCluster to fail
https://claude.ai/code/session_01HWxtzSKTo6Be7xwrjyyNNM