Merge branch 'dev'

.Rbuildignore

@@ -19,3 +19,4 @@ Dockerfile
 ^Meta$
 ^vignettes/*_files$
 ^vignettes/articles$
+^vignettes/figure/

.github/workflows/R-CMD-check.yaml

@@ -1,15 +1,13 @@
 # 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
-# on:
-#   push:
-#     branches: [main, master]
-#   pull_request:
-#     branches: [main, master]
 on:
-  release:
-    types: [published]
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
   workflow_dispatch:
 
+
 name: R-CMD-check
 
 permissions: read-all
@@ -25,11 +23,16 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
+          - {os: macos-latest, r: 'oldrel'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
+          - {os: windows-latest, r: 'oldrel'}
+          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          # - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
-
+          # - {os: ubuntu-20.04, r: 'release'}
+          # - {os: ubuntu-20.04, r: 'devel'}
+          # - {os: ubuntu-22.04, r: 'release'}
+          # - {os: ubuntu-22.04, r: 'devel'}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
@@ -47,7 +50,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck, local::.
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -15,7 +15,7 @@ permissions: read-all
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-latest
+    runs-on: macos-latest
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
@@ -31,15 +31,11 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-
-      - name: Install libcurl on Linux
-        if: runner.os == 'Linux'
-        run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev
-      # - uses: r-lib/actions/setup-r-dependencies@v2
-      #   with:
-      #     extra-packages: any::pkgdown, any::XML, local::.
-      #     needs: website
-      - uses: r-lib/actions/setup-renv@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

.gitignore

@@ -12,3 +12,4 @@ example
 /Meta/
 .vscode/
 results/
+docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scatools
 Title: scATAC Tools and Utilities For Copy Number Analysis
-Version: 0.1.2
+Version: 0.1.2.9000
 Authors@R: 
     person("Matthew", "Zatzman", , "[email protected]", role = c("aut", "cre"))
 Description: A collection of useful code for handling scATAC data.

NEWS.md

@@ -1,3 +1,5 @@
+# scatools (development version)
+
 # scatools 0.1.2
 
 * Replace `add_gc_cor`, `segment_cnv`, and `merge_segments` parallel backend to use `BiocParallel`