[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args: ["--maxkb=200"]
@@ -13,7 +13,7 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.27.2
+    rev: v8.30.0
     hooks:
       - id: gitleaks
   - repo: local
@@ -24,15 +24,15 @@ repos:
         language: fail
         files: "(conda-meta|pyvenv.cfg|renv/library)"
   - repo: https://github.com/crate-ci/typos
-    rev: v1.34.0
+    rev: v1
     hooks:
       - id: typos
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.2
+    rev: v0.14.10
     hooks:
       - id: ruff-format
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9012
+    rev: v0.4.3.9020
     hooks:
       - id: style-files
       - id: parsable-R

modules/cell-type-consensus/resources/usr/bin/assign-consensus-celltypes.R

@@ -296,7 +296,6 @@ expressed_markers <- intersect(all_markers, expressed_genes)
 # if no markers are found, fill in columns with NA
 if (length(expressed_markers) == 0) {
   (
-
     gene_exp_df <- data.frame(
       barcodes = rownames(sce),
       library_id = library_id,
@@ -305,7 +304,6 @@ if (length(expressed_markers) == 0) {
       validation_group_annotation = NA,
       validation_group_ontology = NA
     )
-
   )
 } else {
   # get logcounts from sce for expressed genes

modules/cell-type-neuroblastoma-04/resources/usr/bin/assign-labels.R

@@ -88,10 +88,11 @@ stopifnot(
 #'
 #' @returns Wide data frame with ontologies and family labels for the given annotation type
 prep_for_annotation <- function(
-    df,
-    annot_type,
-    ontology_df,
-    label_map_df) {
+  df,
+  annot_type,
+  ontology_df,
+  label_map_df
+) {
   df |>
     dplyr::rename(label = annot_type) |>
     ####### Join in the family labels

modules/merge-sce/resources/usr/bin/sce_to_anndata.R

@@ -162,7 +162,6 @@ if (opt$is_merged) {
 message("Formatting done")
 
 
-
 # export sce as anndata object
 # this function will also remove any R-specific object types from the SCE metadata
 #   before converting to AnnData

modules/simulate-sce/resources/usr/bin/sce-to-anndata.R

@@ -61,7 +61,6 @@ format_merged_sce <- function(sce) {
 }
 
 
-
 # CZI compliance function ------------------------------------------------------
 
 # this function applies any necessary reformatting or changes needed to make