From 4e3b975f7580ca3593921381b3369ed009f62459 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 6 Jul 2026 17:13:02 +0000
Subject: [PATCH 1/3] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/lorenzwalthert/precommit: v0.4.3.9015 → v0.4.3.9026](https://github.com/lorenzwalthert/precommit/compare/v0.4.3.9015...v0.4.3.9026)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 mode change 100755 => 100644 .pre-commit-config.yaml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
old mode 100755
new mode 100644
index 6ca9e4f..e7aa258
--- 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: v0.4.3.9015
+    rev: v0.4.3.9026
     hooks:
       - id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]

From f92c96155687c168f89cea68926db0459bfc4ded Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 6 Jul 2026 17:13:42 +0000
Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 R/dataset.R                     | 2 --
 R/simulator.R                   | 1 -
 tests/testthat/test_simulator.R | 2 --
 3 files changed, 5 deletions(-)

diff --git a/R/dataset.R b/R/dataset.R
index 39e0d1d..26e2633 100755
--- a/R/dataset.R
+++ b/R/dataset.R
@@ -151,8 +151,6 @@ generate_summarized_experiment <- function(annotation, count_matrix, tpm_matrix,
 }
 
 
-
-
 #' Build \link[SummarizedExperiment]{SummarizedExperiment} using local annotation and count matrix R objects
 #'
 #' @param annotation (mandatory) dataframe; needs columns 'ID' and 'cell_type'; 'ID' needs to be equal with cell_names in count_matrix
diff --git a/R/simulator.R b/R/simulator.R
index c9b0e1f..a6dd338 100755
--- a/R/simulator.R
+++ b/R/simulator.R
@@ -837,7 +837,6 @@ merge_simulations <- function(simulation_list) {
 }
 
 
-
 #' Create scaling vector from custom or pre-defined scaling factor
 #'
 #' @param data dataset
diff --git a/tests/testthat/test_simulator.R b/tests/testthat/test_simulator.R
index be14f20..df7560b 100755
--- a/tests/testthat/test_simulator.R
+++ b/tests/testthat/test_simulator.R
@@ -76,8 +76,6 @@ test_that("test different scaling factor calculations + mRNA bias removal from c
 })
 
 
-
-
 test_that("test census", {
   tpm <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol = 300), sparse = TRUE)
   tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm))

From e104d3014e1184fdb0afcf7988c18fea08593760 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]" <pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 6 Jul 2026 17:21:46 +0000
Subject: [PATCH 3/3] Roxygenize

---
 DESCRIPTION  | 2 +-
 man/SimBu.Rd | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 917c0a8..9b21732 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -14,7 +14,6 @@ Description: SimBu can be used to simulate bulk RNA-seq datasets with known cell
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE) 
-RoxygenNote: 7.3.3
 Imports: 
     basilisk,
     BiocParallel,
@@ -46,3 +45,4 @@ VignetteBuilder: knitr
 Config/testthat/edition: 3
 StagedInstall: no
 biocViews: Software, RNASeq, SingleCell
+Config/roxygen2/version: 8.0.0
diff --git a/man/SimBu.Rd b/man/SimBu.Rd
index 2ebcbcf..5bf93f2 100755
--- a/man/SimBu.Rd
+++ b/man/SimBu.Rd
@@ -43,4 +43,9 @@ Useful links:
 \author{
 \strong{Maintainer}: Alexander Dietrich \email{alex.dietrich@tum.de}
 
+Authors:
+\itemize{
+  \item Alexander Dietrich \email{alex.dietrich@tum.de}
+}
+
 }