Merge pull request #848 from jiajic/suite

hotfix access to GiottoClass generics

.github/workflows/pkgdown.yaml

@@ -1,16 +1,16 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+name: pkgdown
+
 on:
   push:
-    branches: [main, master]
+    branches: [suite]
   pull_request:
-    branches: [main, master]
+    branches: [suite]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
-
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -22,17 +22,22 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repo for workflow access
+        uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v2
+      - name: Setup R environment
+        uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Set up dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          dependencies: '"hard"' # do not use suggested dependencies
+          extra-packages: any::pkgdown, local::., any::kableExtra
           needs: website
 
       - name: Build site

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.0.1
+Version: 4.0.2
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre")),
@@ -31,7 +31,8 @@ Depends:
     base (>= 3.5.0),
     utils (>= 3.5.0),
     R (>= 3.5.0),
-    methods
+    methods,
+    GiottoClass (>= 0.1.1)
 Imports:
     BiocParallel,
     BiocSingular,
@@ -41,9 +42,8 @@ Imports:
     dbscan (>= 1.1-3),
     ggplot2 (>= 3.1.1),
     ggrepel,
-    GiottoUtils (>= 0.1.0.1),
-    GiottoClass (>= 0.1.0.1),
-    GiottoVisuals (>= 0.1.0.1),
+    GiottoUtils (>= 0.1.1),
+    GiottoVisuals (>= 0.1.1),
     igraph (>= 1.2.4.1),
     jsonlite,
     limma,
@@ -89,6 +89,7 @@ Suggests:
     hdf5r,
     htmlwidgets,
     jackstraw,
+    kableExtra,
     knitr,
     MAST,
     miniUI,

NEWS.md

@@ -1,4 +1,8 @@
 
+# Giotto Suite 4.0.2 (2023/12/21)
+
+## Changes
+* Move *GiottoClass* back to depends to fix access to some generics
 
 # Giotto Suite 4.0.1 (2023/12/16)