From 5221a8071ed36806376c5aed61c665ad245e7a94 Mon Sep 17 00:00:00 2001 From: David Collins Date: Wed, 22 Jan 2025 13:38:20 -0500 Subject: [PATCH 1/3] Fixup smoke test for FindClusters --- tests/testthat/test_find_clusters.R | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/tests/testthat/test_find_clusters.R b/tests/testthat/test_find_clusters.R index 0da9eb587..8e101a9cf 100644 --- a/tests/testthat/test_find_clusters.R +++ b/tests/testthat/test_find_clusters.R @@ -34,13 +34,17 @@ context("FindClusters") test_that("Smoke test for `FindClusters`", { test_case <- get_test_data() - # Spot check cluster assignments with using defaults. + # Validate cluster assignments using default parameters. results <- FindClusters(test_case)$seurat_clusters - expect_equal(results[[1]], factor(3, levels=0:5)) - expect_equal(results[[15]], factor(4, levels=0:5)) - expect_equal(results[[24]], factor(0, levels=0:5)) - expect_equal(results[[72]], factor(5, levels=0:5)) - expect_equal(results[[length(results)]], factor(2, levels=0:5)) + # Check that every cell was assigned to a cluster label. + expect_false(any(is.na(results))) + # Check that the expected cluster labels were assigned. + expect_equal(as.numeric(levels(results)), c(0, 1, 2, 3, 4, 5)) + # Check that the cluster sizes match the expected distribution. + expect_equal( + as.numeric(sort(table(results))), + c(9, 10, 10, 11, 20, 20) + ) # Check that every clustering algorithm can be run without errors. expect_no_error(FindClusters(test_case, algorithm = 1)) From 4f7659c56d623310579eb2cdc2e45173d7acf6e4 Mon Sep 17 00:00:00 2001 From: David Collins Date: Wed, 22 Jan 2025 13:46:39 -0500 Subject: [PATCH 2/3] Bump version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 25fda37bb..56c5a5f58 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: Seurat -Version: 5.2.0 +Version: 5.2.0.9001 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. Authors@R: c( From 63cf2c626403961fa3d10f1e347d4405b79713d8 Mon Sep 17 00:00:00 2001 From: David Collins Date: Wed, 22 Jan 2025 13:49:26 -0500 Subject: [PATCH 3/3] Update changelog --- NEWS.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/NEWS.md b/NEWS.md index b7d6e9359..a992acafb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# Unreleased + +## Changes +- Fixed `test_find_clusters.R` to accommodate variability in label assignments given by `FindClusters` across different systems ([#9641](https://github.com/satijalab/seurat/pull/9641)) + # Seurat 5.2.0 (2024-12-20) ## Changes