Merge pull request #173 from Oshlack/3.20-release

Prepare for 3.20 release
Oshlack · Oct 17, 2024 · 2239427 · 2239427
2 parents 4018ddc + 59e6561
commit 2239427
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diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
@@ -164,7 +164,7 @@ jobs:
         config:
           - {os: windows-latest}
           - {os: macOS-latest}
-          - {os: ubuntu-18.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-20.04, rspm: "https://packagemanager.posit.co/cran/__linux__/focal/latest"}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -191,6 +191,18 @@ jobs:
           extra-packages: any::rcmdcheck
           needs: check
 
+      # Fixes https://github.com/Bioconductor/bioconductor_docker/issues/22
+      - name: Manually install preprocessCore on Linux
+        if: runner.os == 'Linux'
+        run: |
+          install.packages(
+            "preprocessCore",
+            repos = BiocManager::repositories(),
+            type = "source",
+            configure.args = "--disable-threading"
+          )
+        shell: Rscript {0}
+
       - name: Session info
         run: |
           options(width = 100)
@@ -255,31 +267,26 @@ jobs:
 
   pkgdown:
     ## Build pkgdown site and push to gh-pages branch. Only runs if on the
-    ## devel branch and R-CMD-check-docker has completed successfully. Uses
-    ## the Bioconductor Docker image.
-    if: github.ref == 'refs/heads/devel'
+    ## devel branch and R-CMD-check-docker has completed successfully. Uses the
+    ## Bioconductor Docker image.
+    if: github.ref == 'refs/heads/devel' || github.base_ref == 'devel'
     needs: [get-bioc-release, get-bioc-version, R-CMD-check-docker]
     runs-on: ubuntu-latest
     container:
       image: ${{ needs.get-bioc-release.outputs.biocimage }}
       volumes:
         - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library
+    concurrency:
+      # Only restrict concurrency for non-PR jobs
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_BIOC_VERSION: ${{ needs.get-bioc-version.outputs.biocversion }}
 
     steps:
 
-      - name: Set git credentials
-        ## Assign commits to the GitHub Action user. This should happen
-        ## automatically but doesn't (maybe because of Docker).
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "GitHub Action"
-        shell: bash {0}
-
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install extra linux dependencies
         run: sudo apt-get update -y && sudo apt-get install -y libcurl4-openssl-dev devscripts qpdf

diff --git a/.github/workflows/dependabot.yaml b/.github/workflows/dependabot.yaml
@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -0,0 +1,85 @@
+# 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:
+  issue_comment:
+    types: [created]
+
+name: pr-commands.yaml
+
+permissions: read-all
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -30,3 +30,4 @@ docs/
 inst/doc
 doc
 Meta
+docs
diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,28 +1,27 @@
-Package: splatter
 Type: Package
+Package: splatter
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 1.29.0
-Date: 2024-05-01
-Authors@R:
-    c(person("Luke", "Zappia", role = c("aut", "cre"),
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0001-7744-8565", GitHub = "lazappi")),
-      person("Belinda", "Phipson", role = c("aut"),
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0002-1711-7454", GitHub = "bphipson")),
-      person("Christina", "Azodi", role = c("ctb"),
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0002-6097-606X", GitHub = "azodichr")),
-      person("Alicia", "Oshlack", role = c("aut"),
-      email = "[email protected]",
-      comment = c(ORCID = "0000-0001-9788-5690")))
+Version: 1.29.1
+Date: 2024-10-17
+Authors@R:c(
+    person("Luke", "Zappia", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-7744-8565", GitHub = "lazappi")),
+    person("Belinda", "Phipson", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0002-1711-7454", GitHub = "bphipson")),
+    person("Christina", "Azodi", , "[email protected]", role = "ctb",
+           comment = c(ORCID = "0000-0002-6097-606X", GitHub = "azodichr")),
+    person("Alicia", "Oshlack", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0001-9788-5690"))
+  )
 Description: Splatter is a package for the simulation of single-cell RNA
-    sequencing count data. It provides a simple interface for creating complex
-    simulations that are reproducible and well-documented. Parameters can be
-    estimated from real data and functions are provided for comparing real and
-    simulated datasets.
+    sequencing count data. It provides a simple interface for creating
+    complex simulations that are reproducible and well-documented.
+    Parameters can be estimated from real data and functions are provided
+    for comparing real and simulated datasets.
 License: GPL-3 + file LICENSE
-LazyData: FALSE
+URL: https://bioconductor.org/packages/splatter/,
+    https://github.com/Oshlack/splatter, http://oshlacklab.com/splatter/
+BugReports: https://github.com/Oshlack/splatter/issues
 Depends:
     R (>= 4.0),
     SingleCellExperiment
@@ -55,16 +54,16 @@ Suggests:
     GenomeInfoDb,
     GenomicRanges,
     ggplot2 (>= 3.4.0),
-    IRanges,
     igraph,
+    IRanges,
     knitr,
     limSolve,
     lme4,
     magick,
     mfa,
     phenopath,
-    progress,
     preprocessCore,
+    progress,
     pscl,
     rmarkdown,
     scales,
@@ -75,12 +74,12 @@ Suggests:
     spelling,
     testthat,
     VariantAnnotation,
-    zinbwave,
-biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
-    Software, ImmunoOncology
-URL: https://bioconductor.org/packages/splatter/, https://github.com/Oshlack/splatter
-BugReports: https://github.com/Oshlack/splatter/issues
-RoxygenNote: 7.3.1
+    zinbwave
+VignetteBuilder: 
+    knitr
+biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression,
+    Sequencing, Software, ImmunoOncology
 Encoding: UTF-8
-VignetteBuilder: knitr
 Language: en-GB
+LazyData: FALSE
+RoxygenNote: 7.3.2
diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,15 @@
 # DEVELOPMENT VERSION
 
-## Version 1.27.0 (2024-05-01)
+## Version 1.29.1 (2024-10-17)
+
+* Update roxygen2 version
+* Remove old CI config files
+* Add PR commands GitHub action
+* Re-configure pkgdown site
+* Add dependabot GitHub action
+* Update README
+
+## Version 1.29.0 (2024-05-01)
 
 Bioconductor 3.20 devel
-Original file line number
+Diff line change
@@ Expand Up / @@ -30,3 +30,4 @@ docs/ @@
     inst/doc
     doc
     Meta
+    docs