omnideconv · pre-commit-ci · Nov 3, 2025 · Nov 3, 2025
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.1
+    rev: v0.4.3.9017
     hooks:
       - id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
@@ -13,7 +13,7 @@ repos:
       - id: deps-in-desc
         args: [--allow_private_imports]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
         exclude: '\.Rd'

diff --git a/R/DOT.R b/R/DOT.R
@@ -6,7 +6,6 @@ build_model_dot <- function() {
 }
 
 
-
 #' Deconvolute DOT
 #'
 #' @param single_cell_obj Single Cell Experiment

diff --git a/R/benchmarking.R b/R/benchmarking.R
@@ -121,9 +121,6 @@ plot_scatter <- function(spe = NULL, value1, value2, spe1 = NULL, spe2 = NULL, l
 }
 
 
-
-
-
 #' Compare Signatures
 #'
 #' @param signature1 signature

diff --git a/R/cluster.R b/R/cluster.R
@@ -66,7 +66,6 @@ cluster <- function(spe,
     cli::cli_alert_info(paste("Cluster resolution:", toString(clusres)))
 
 
-
     cli::cli_progress_step("Extracting data", msg_done = "Extracted data for clustering")
 
     # create seurat object
@@ -146,7 +145,6 @@ cluster <- function(spe,
   }
 
 
-
   cli::cli_progress_done()
 
   return(spe)
@@ -200,7 +198,6 @@ get_cluster_features <- function(spe,
   clusters <- colData(spe)[, clusterid]
 
 
-
   # Scores
   if (spmethod == "expression") {
     if (is.element("cpm", assayNames(spe)) && !is.null(spe@assays@data$cpm)) {

diff --git a/R/deconvolution_algorithms.R b/R/deconvolution_algorithms.R
@@ -285,8 +285,6 @@ deconvolute <- function(spatial_obj, signature = NULL, single_cell_obj = NULL,
   cli::cli_progress_step("testing parameter", msg_done = "parameter OK")
 
 
-
-
   if (is.null(spatial_obj)) {
     stop("Parameter 'spatial_obj' is missing or null, but is required.")
   }

diff --git a/R/preprocess.R b/R/preprocess.R
@@ -106,7 +106,6 @@ preprocess <- function(object, min_umi = 500, max_umi = NULL, assay = "counts",
   }
 
 
-
   cli::cli_progress_step(
     msg = "Checking for ENSEMBL Identifiers",
     msg_done = "Finished Preprocessing"

diff --git a/R/spatial_correlation.R b/R/spatial_correlation.R
@@ -96,7 +96,6 @@ spatialcorr <- function(spe,
   }
 
 
-
   # Select variables of interests
   # If variables is not provided but method is specified, the function selects variables based on those available in the dataset that start with the specified method.
   if (is.null(variables) && !is.null(method)) {

diff --git a/R/subset.R b/R/subset.R
@@ -124,10 +124,6 @@ subsetSCE <- function(sce, cell_type_col = "celltype_major", scenario = "even",
 }
 
 
-
-
-
-
 #' Isolate Regions within a SpatialExperiment Object
 #'
 #' Tailor a `SpatialExperiment` object to focus on specific areas by defining ranges in the spatial coordinates.

diff --git a/R/utils.R b/R/utils.R
@@ -305,7 +305,6 @@ checkENSEMBL <- function(names) {
 }
 
 
-
 #' Annotate Specific Spots within a SpatialExperiment Object
 #'
 #' This function allows for the annotation of specified spots within a `SpatialExperiment` object.

diff --git a/R/visualization.R b/R/visualization.R
@@ -479,7 +479,6 @@ plot_comparison <- function(spe, cell_type_1 = NULL, cell_type_2 = NULL,
 }
 
 
-
 #' Function to plot gene expression
 #'
 #' Generate Hex Plot of a SpatialExperiment containing deconvolution results
@@ -728,8 +727,6 @@ make_baseplot <- function(spe, df, to_plot, palette = "Mako", transform_scale =
   }
 
 
-
-
   # Check if plot is smoothed
   if (smooth) {
     smooth_suffix <- "smoothed"

diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
@@ -11,7 +11,6 @@ test_that("convert human to mouse with valid gene symbols", {
 })
 
 
-
 ad <- spe_to_ad(spe, assay = "counts")
 
 test_that("spe_to_ad returns an AnnData object", {

diff --git a/tests/testthat/test-signature.R b/tests/testthat/test-signature.R
@@ -21,7 +21,6 @@ test_that("Immunedeconv models works", {
 })
 
 
-
 # Test for input validation in build_model
 test_that("build_model requires non-null single_cell_obj", {
   expect_error(build_model(NULL, method = "rctd"), "Parameter 'single_cell_obj' missing or null, but is required")

diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
@@ -14,7 +14,6 @@ testthat::test_that("subsetSCE subsets the SingleCellExperiment correctly", {
 })
 
 
-
 testthat::test_that("Normalization works", {
   normalized <- spacedeconv::normalize(sce, method = "cpm", assay = "counts")
 

diff --git a/tests/testthat/test-visualization.R b/tests/testthat/test-visualization.R
@@ -23,8 +23,6 @@ test_that("Plot Umi Count works", {
 })
 
 
-
-
 test_that("Plot_post_abundant works", {
   p <- plot_most_abundant(spe, method = "estimate")
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,7 +6,6 @@ build_model_dot <- function() { @@
     }
     #' Deconvolute DOT
     #'
     #' @param single_cell_obj Single Cell Experiment
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -11,7 +11,6 @@ test_that("convert human to mouse with valid gene symbols", {
		})



		ad <- spe_to_ad(spe, assay = "counts")

		test_that("spe_to_ad returns an AnnData object", {
Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -14,7 +14,6 @@ testthat::test_that("subsetSCE subsets the SingleCellExperiment correctly", {
		})



		testthat::test_that("Normalization works", {
		normalized <- spacedeconv::normalize(sce, method = "cpm", assay = "counts")

Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -23,8 +23,6 @@ test_that("Plot Umi Count works", {
		})




		test_that("Plot_post_abundant works", {
		p <- plot_most_abundant(spe, method = "estimate")

Expand Down