Merge pull request #746 from joshua-d-campbell/master

Merging v2.12.2
compbiomed · Feb 5, 2024 · 14c9213 · 14c9213
2 parents 111cb1e + a31feba
commit 14c9213
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diff --git a/.github/workflows/BioC-check.yaml b/.github/workflows/BioC-check.yaml
@@ -33,42 +33,22 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
-          use-public-rspm: false
+          use-public-rspm: true
 
       - name: Install fftw3 on macOS
         if: runner.os == 'macOS'
         run: brew install fftw
 
-      - name: Manual Install
-        run: |
-          install.packages("BiocManager")
-          BiocManager::install("ggtree")
-          install.packages("remotes")
-          install.packages("magick")
-          remotes::install_version("assertive.properties", version = "0.0.5", repos = "http://cran.us.r-project.org", upgrade = "never")
-          remotes::install_version("assertive.types", version = "0.0.3", repos = "http://cran.us.r-project.org", upgrade = "never")
-          remotes::install_version("multipanelfigure", version = "2.1.2", repos = "http://cran.us.r-project.org", upgrade = "never")
-          BiocManager::install("celda")
-
-        shell: Rscript {0}
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
             any::rcmdcheck
-          cache: false
+          cache: true
 
       - name: Install XQuartz on macOS
         if: runner.os == 'macOS'
         run: brew install xquartz --cask
 
-      - name: Install Old Seurat
-        run: |
-          remotes::install_version("Matrix", version = "1.6.4", repos = "http://cran.us.r-project.org", upgrade = "never")
-          remotes::install_version("SeuratObject", version = "4.1.4", repos = "http://cran.us.r-project.org", upgrade = "never")
-          remotes::install_version("Seurat", version = "4.4.0", repos = "http://cran.us.r-project.org", upgrade = "never")
-        shell: Rscript {0}
-
       - name: Run BiocCheck
         run: |
           BiocManager::install("BiocCheck")

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -63,7 +63,7 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
-          use-public-rspm: false
+          use-public-rspm: true
 
       - name: Install fftw3 on Linux
         if: runner.os == 'Linux'
@@ -73,23 +73,9 @@ jobs:
         if: runner.os == 'macOS'
         run: brew install fftw
 
-      - name: Manual Install
-        run: |
-          install.packages("BiocManager")
-          BiocManager::install("ggtree")
-          install.packages("remotes")
-          install.packages("magick")
-          remotes::install_version("assertive.properties", version = "0.0.5", repos = "http://cran.us.r-project.org", upgrade = "never")
-          remotes::install_version("assertive.types", version = "0.0.3", repos = "http://cran.us.r-project.org", upgrade = "never")
-          remotes::install_version("multipanelfigure", version = "2.1.2", repos = "http://cran.us.r-project.org", upgrade = "never")
-          remotes::install_version("Matrix", version = "1.6.4", repos = "http://cran.us.r-project.org", upgrade = "never")
-          BiocManager::install("celda")
-
-        shell: Rscript {0}
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          cache: false
+          cache: true
           extra-packages: |
             any::rcmdcheck
           needs: check
@@ -98,13 +84,6 @@ jobs:
         if: runner.os == 'macOS'
         run: brew install xquartz --cask
 
-      - name: Install Old Seurat
-        run: |
-          remotes::install_version("Matrix", version = "1.6.4", repos = "http://cran.us.r-project.org", upgrade = "never")
-          remotes::install_version("SeuratObject", version = "4.1.4", repos = "http://cran.us.r-project.org", upgrade = "never")
-          remotes::install_version("Seurat", version = "4.4.0", repos = "http://cran.us.r-project.org", upgrade = "never")
-        shell: Rscript {0}
-
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_: false

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: singleCellTK
 Type: Package
 Title: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
-Version: 2.12.1
+Version: 2.12.2
 Authors@R: c(person(given="Yichen", family="Wang", email="wangych@bu.edu", role=c("aut"),
                     comment = c(ORCID = "0000-0003-4347-5199")),
              person(given="Irzam", family="Sarfraz", email="isarfraz@bu.edu", role=c("aut"),
@@ -139,6 +139,7 @@ Suggests:
     RColorBrewer,
     fastmap (>= 1.1.0),
     harmony,
+    SeuratObject,
     optparse
 VignetteBuilder: knitr
 URL: https://www.camplab.net/sctk/

diff --git a/NAMESPACE b/NAMESPACE
@@ -308,3 +308,4 @@ importFrom(stats,filter)
 importFrom(tibble,tibble)
 importFrom(tools,file_ext)
 importFrom(utils,head)
+importFrom(utils,packageVersion)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+Changes in Version 2.12.2 (2024-01-28)
+================================================================================
+* Added support for Seurat V5
+
 Changes in Version 2.12.1 (2024-01-10)
 ================================================================================
 * Updates to documentation