From 008bf01b07876351c0241fcf362e3ed306ffcd71 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 17:13:10 +0000
Subject: [PATCH 1/2] [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: v0.4.1 → v0.4.3.9026](https://github.com/lorenzwalthert/precommit/compare/v0.4.1...v0.4.3.9026)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v6.0.0)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ffb61523..76ba6095 100644
--- 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: v0.4.3.9026
     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'

From b450a8fa9ef802f77a4092bdf6f0d8d5e075e526 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 17:17:20 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 R/DOT.R                                        |  1 -
 R/benchmarking.R                               |  3 ---
 R/cluster.R                                    |  3 ---
 R/deconvolution_algorithms.R                   |  2 --
 R/preprocess.R                                 |  1 -
 R/spatial_correlation.R                        |  1 -
 R/subset.R                                     |  4 ----
 R/utils.R                                      |  1 -
 R/visualization.R                              |  3 ---
 docs/LICENSE-text.html                         |  3 +--
 docs/authors.html                              |  3 +--
 .../bootstrap-5.3.1/bootstrap.bundle.min.js    |  8 ++++----
 docs/deps/clipboard.js-2.0.11/clipboard.min.js |  2 +-
 docs/deps/jquery-3.6.0/jquery-3.6.0.js         |  8 ++++----
 docs/deps/jquery-3.6.0/jquery-3.6.0.min.js     | 18 ++++++++----------
 .../search-1.0.0/autocomplete.jquery.min.js    | 10 +++++-----
 docs/deps/search-1.0.0/fuse.min.js             | 10 +++++-----
 docs/deps/search-1.0.0/mark.min.js             |  2 +-
 tests/testthat/test-conversion.R               |  1 -
 tests/testthat/test-signature.R                |  1 -
 tests/testthat/test-utils.R                    |  1 -
 tests/testthat/test-visualization.R            |  2 --
 .../tmpdir/test-model_and_deconvolute.R        |  2 --
 23 files changed, 30 insertions(+), 60 deletions(-)

diff --git a/R/DOT.R b/R/DOT.R
index 4a0c5e4a..50012c21 100644
--- a/R/DOT.R
+++ b/R/DOT.R
@@ -11,7 +11,6 @@ build_model_dot <- function() {
 }
 
 
-
 #' Deconvolute with DOT
 #'
 #' Runs DOT deconvolution and returns the DOT weight matrix with column names
diff --git a/R/benchmarking.R b/R/benchmarking.R
index beb6fd2a..b0a950cc 100644
--- a/R/benchmarking.R
+++ b/R/benchmarking.R
@@ -123,9 +123,6 @@ plot_scatter <- function(spe = NULL, value1, value2, spe1 = NULL, spe2 = NULL, l
 }
 
 
-
-
-
 #' Compare Signatures
 #'
 #' Creates a scatterplot comparing two signature matrices across shared genes.
diff --git a/R/cluster.R b/R/cluster.R
index 12ffcaf6..0c9723e3 100644
--- a/R/cluster.R
+++ b/R/cluster.R
@@ -59,7 +59,6 @@ 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
@@ -139,7 +138,6 @@ cluster <- function(spe,
   }
 
 
-
   cli::cli_progress_done()
 
   return(spe)
@@ -199,7 +197,6 @@ 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
index a6790ac9..4f00ca5a 100644
--- a/R/deconvolution_algorithms.R
+++ b/R/deconvolution_algorithms.R
@@ -228,8 +228,6 @@ 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
index dbe9ed20..de580430 100644
--- a/R/preprocess.R
+++ b/R/preprocess.R
@@ -110,7 +110,6 @@ 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
index cd25bc90..c71b79fa 100644
--- a/R/spatial_correlation.R
+++ b/R/spatial_correlation.R
@@ -102,7 +102,6 @@ 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
index 858a2722..5c6060b4 100644
--- a/R/subset.R
+++ b/R/subset.R
@@ -117,10 +117,6 @@ subsetSCE <- function(sce, cell_type_col = "celltype_major", scenario = "even",
 }
 
 
-
-
-
-
 #' Subset a SpatialExperiment by Spatial Coordinates
 #'
 #' Filters a `SpatialExperiment` to spots that fall within the provided x/y ranges
diff --git a/R/utils.R b/R/utils.R
index 5fc3db10..7350f530 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -287,7 +287,6 @@ checkENSEMBL <- function(names) {
 }
 
 
-
 #' Annotate Specific Spots in a SpatialExperiment
 #'
 #' Adds a new `colData` column that marks selected spots with `value_pos` and all
diff --git a/R/visualization.R b/R/visualization.R
index afaafd91..27e6739a 100644
--- a/R/visualization.R
+++ b/R/visualization.R
@@ -491,7 +491,6 @@ plot_comparison <- function(spe, cell_type_1 = NULL, cell_type_2 = NULL,
 }
 
 
-
 #' Plot Gene Expression
 #'
 #' Generate a spatial hex plot for a single gene from a `SpatialExperiment`.
@@ -736,8 +735,6 @@ make_baseplot <- function(spe, df, to_plot, palette = "Mako", transform_scale =
   }
 
 
-
-
   # Check if plot is smoothed
   if (smooth) {
     smooth_suffix <- "smoothed"
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index fbe4bc88..d5fa1638 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -853,8 +853,7 @@ <h1>License</h1>
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
 &lt;https://www.gnu.org/licenses/why-not-lgpl.html&gt;.
-</pre
-          >
+</pre>
         </main>
       </div>
 
diff --git a/docs/authors.html b/docs/authors.html
index 0b3c1d81..604b995f 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -230,8 +230,7 @@ <h2 id="citation">Citation</h2>
   year = {2026},
   note = {R package version 1.0.0},
   url = {https://omnideconv.github.io/spacedeconv},
-}</pre
-            >
+}</pre>
           </div>
         </main>
         <aside class="col-md-3">
diff --git a/docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js b/docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
index 93896353..190b40dd 100644
--- a/docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
+++ b/docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
@@ -494,12 +494,12 @@
       parents(t, e) {
         const i = [];
         let n = t.parentNode.closest(e);
-        for (; n; ) (i.push(n), (n = n.parentNode.closest(e)));
+        for (; n;) (i.push(n), (n = n.parentNode.closest(e)));
         return i;
       },
       prev(t, e) {
         let i = t.previousElementSibling;
-        for (; i; ) {
+        for (; i;) {
           if (i.matches(e)) return [i];
           i = i.previousElementSibling;
         }
@@ -507,7 +507,7 @@
       },
       next(t, e) {
         let i = t.nextElementSibling;
-        for (; i; ) {
+        for (; i;) {
           if (i.matches(e)) return [i];
           i = i.nextElementSibling;
         }
@@ -1272,7 +1272,7 @@
     return me(t) && "fixed" !== xe(t).position ? t.offsetParent : null;
   }
   function $e(t) {
-    for (var e = fe(t), i = De(t); i && ke(i) && "static" === xe(i).position; )
+    for (var e = fe(t), i = De(t); i && ke(i) && "static" === xe(i).position;)
       i = De(i);
     return i &&
       ("html" === ue(i) || ("body" === ue(i) && "static" === xe(i).position))
diff --git a/docs/deps/clipboard.js-2.0.11/clipboard.min.js b/docs/deps/clipboard.js-2.0.11/clipboard.min.js
index 261894f8..4c2488b2 100644
--- a/docs/deps/clipboard.js-2.0.11/clipboard.min.js
+++ b/docs/deps/clipboard.js-2.0.11/clipboard.min.js
@@ -373,7 +373,7 @@
             e.oMatchesSelector ||
             e.webkitMatchesSelector),
           (t.exports = function (t, e) {
-            for (; t && 9 !== t.nodeType; ) {
+            for (; t && 9 !== t.nodeType;) {
               if ("function" == typeof t.matches && t.matches(e)) return t;
               t = t.parentNode;
             }
diff --git a/docs/deps/jquery-3.6.0/jquery-3.6.0.js b/docs/deps/jquery-3.6.0/jquery-3.6.0.js
index de7f5d06..d629ac0c 100644
--- a/docs/deps/jquery-3.6.0/jquery-3.6.0.js
+++ b/docs/deps/jquery-3.6.0/jquery-3.6.0.js
@@ -2408,7 +2408,7 @@
                 : argument > length
                   ? length
                   : argument;
-            for (; --i >= 0; ) {
+            for (; --i >= 0;) {
               matchIndexes.push(i);
             }
             return matchIndexes;
@@ -2416,7 +2416,7 @@
 
           gt: createPositionalPseudo(function (matchIndexes, length, argument) {
             var i = argument < 0 ? argument + length : argument;
-            for (; ++i < length; ) {
+            for (; ++i < length;) {
               matchIndexes.push(i);
             }
             return matchIndexes;
@@ -8099,7 +8099,7 @@
           }
         }
 
-        for (index = timers.length; index--; ) {
+        for (index = timers.length; index--;) {
           if (
             timers[index].elem === this &&
             (type == null || timers[index].queue === type)
@@ -8141,7 +8141,7 @@
         }
 
         // Look for any active animations, and finish them
-        for (index = timers.length; index--; ) {
+        for (index = timers.length; index--;) {
           if (timers[index].elem === this && timers[index].queue === type) {
             timers[index].anim.stop(true);
             timers.splice(index, 1);
diff --git a/docs/deps/jquery-3.6.0/jquery-3.6.0.min.js b/docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
index 3bc59377..c7a57951 100644
--- a/docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
+++ b/docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
@@ -1202,11 +1202,11 @@
             return e;
           }),
           lt: ve(function (e, t, n) {
-            for (var r = n < 0 ? n + t : t < n ? t : n; 0 <= --r; ) e.push(r);
+            for (var r = n < 0 ? n + t : t < n ? t : n; 0 <= --r;) e.push(r);
             return e;
           }),
           gt: ve(function (e, t, n) {
-            for (var r = n < 0 ? n + t : n; ++r < t; ) e.push(r);
+            for (var r = n < 0 ? n + t : n; ++r < t;) e.push(r);
             return e;
           }),
         },
@@ -3123,13 +3123,11 @@
         l,
         c = e.cloneNode(!0),
         f = ie(e);
-      if (
-        !(
-          y.noCloneChecked ||
-          (1 !== e.nodeType && 11 !== e.nodeType) ||
-          S.isXMLDoc(e)
-        )
-      )
+      if (!(
+        y.noCloneChecked ||
+        (1 !== e.nodeType && 11 !== e.nodeType) ||
+        S.isXMLDoc(e)
+      ))
         for (a = ve(c), r = 0, i = (o = ve(e)).length; r < i; r++)
           ((s = o[r]),
             (u = a[r]),
@@ -4031,7 +4029,7 @@
               r = Y.get(this);
             if (t) r[t] && r[t].stop && a(r[t]);
             else for (t in r) r[t] && r[t].stop && it.test(t) && a(r[t]);
-            for (t = n.length; t--; )
+            for (t = n.length; t--;)
               n[t].elem !== this ||
                 (null != i && n[t].queue !== i) ||
                 (n[t].anim.stop(o), (e = !1), n.splice(t, 1));
diff --git a/docs/deps/search-1.0.0/autocomplete.jquery.min.js b/docs/deps/search-1.0.0/autocomplete.jquery.min.js
index d61cc03a..675c7bdb 100644
--- a/docs/deps/search-1.0.0/autocomplete.jquery.min.js
+++ b/docs/deps/search-1.0.0/autocomplete.jquery.min.js
@@ -918,7 +918,7 @@
     function g(a) {
       var b;
       if (!this._callbacks) return this;
-      for (a = a.split(l); (b = a.shift()); ) delete this._callbacks[b];
+      for (a = a.split(l); (b = a.shift());) delete this._callbacks[b];
       return this;
     }
     function h(a) {
@@ -962,8 +962,8 @@
     function e() {
       if (!h) {
         ((n = !1), (h = !0));
-        for (var a = m.length, b = setTimeout(d); a; ) {
-          for (i = m, m = []; i && ++l < a; ) i[l].run();
+        for (var a = m.length, b = setTimeout(d); a;) {
+          for (i = m, m = []; i && ++l < a;) i[l].run();
           ((l = -1), (a = m.length));
         }
         ((i = null), (l = -1), (h = !1), clearTimeout(b));
@@ -1069,8 +1069,8 @@
       if (!p) {
         var a = e(g);
         p = !0;
-        for (var b = o.length; b; ) {
-          for (n = o, o = []; ++q < b; ) n && n[q].run();
+        for (var b = o.length; b;) {
+          for (n = o, o = []; ++q < b;) n && n[q].run();
           ((q = -1), (b = o.length));
         }
         ((n = null), (p = !1), f(a));
diff --git a/docs/deps/search-1.0.0/fuse.min.js b/docs/deps/search-1.0.0/fuse.min.js
index e365a6a0..6aea40b7 100644
--- a/docs/deps/search-1.0.0/fuse.min.js
+++ b/docs/deps/search-1.0.0/fuse.min.js
@@ -626,7 +626,7 @@ var e, t;
               },
               x = this.pattern.length;
             if (x > 32) {
-              for (var L = 0, S = x % 32, w = x - S; L < w; )
+              for (var L = 0, S = x % 32, w = x - S; L < w;)
                 (b(this.pattern.substr(L, 32), L), (L += 32));
               if (S) {
                 var _ = x - 32;
@@ -699,7 +699,7 @@ var e, t;
                           ignoreLocation: p,
                         });
                         if (((x = Math.min(O, x)), (S = m + k), w))
-                          for (var j = 0; j < k; ) ((_[m + j] = 1), (j += 1));
+                          for (var j = 0; j < k;) ((_[m + j] = 1), (j += 1));
                       }
                       S = -1;
                       for (
@@ -707,7 +707,7 @@ var e, t;
                         P < k;
                         P += 1
                       ) {
-                        for (var N = 0, D = E; N < D; ) {
+                        for (var N = 0, D = E; N < D;) {
                           var z = R(t, {
                             errors: P,
                             currentLocation: b + D,
@@ -1232,13 +1232,13 @@ var e, t;
           i < o;
           i += 1
         ) {
-          for (var c = n[i], a = !1, s = -1; !a && ++s < H; ) {
+          for (var c = n[i], a = !1, s = -1; !a && ++s < H;) {
             var u = G[s],
               h = u.isMultiMatch(c);
             h && (r.push(new u(h, t)), (a = !0));
           }
           if (!a)
-            for (s = -1; ++s < H; ) {
+            for (s = -1; ++s < H;) {
               var f = G[s],
                 l = f.isSingleMatch(c);
               if (l) {
diff --git a/docs/deps/search-1.0.0/mark.min.js b/docs/deps/search-1.0.0/mark.min.js
index 6e24d637..577e2b3e 100644
--- a/docs/deps/search-1.0.0/mark.min.js
+++ b/docs/deps/search-1.0.0/mark.min.js
@@ -930,7 +930,7 @@
             value: function (e) {
               if (e) {
                 if (3 === e.nodeType)
-                  for (; e.nextSibling && 3 === e.nextSibling.nodeType; )
+                  for (; e.nextSibling && 3 === e.nextSibling.nodeType;)
                     ((e.nodeValue += e.nextSibling.nodeValue),
                       e.parentNode.removeChild(e.nextSibling));
                 else this.normalizeTextNode(e.firstChild);
diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
index 04677b00..a7ba7690 100644
--- 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
index dc54095a..11308174 100644
--- 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
index eb9df281..afd9b81e 100644
--- 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
index 09b70192..fa759977 100644
--- 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")
 
diff --git a/tests/testthat/tmpdir/test-model_and_deconvolute.R b/tests/testthat/tmpdir/test-model_and_deconvolute.R
index 59085199..7698c9ca 100644
--- a/tests/testthat/tmpdir/test-model_and_deconvolute.R
+++ b/tests/testthat/tmpdir/test-model_and_deconvolute.R
@@ -2,8 +2,6 @@ spe <- readRDS(system.file("testdata", "spe.rds", package = "spacedeconv"))
 sce <- readRDS(system.file("testdata", "sce.rds", package = "spacedeconv"))
 
 
-
-
 test_that("quanTIseq model and deconvolution in one step works", {
   deconv <- spacedeconv::build_and_deconvolute(
     single_cell_obj = sce,