Merge pull request #34 from alephnull7/master

Use `windowSize` to determine `sizeThreshold`

.github/workflows/create-release.yaml

@@ -2,28 +2,32 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    paths: ["CHANGELOG.md"]
+    branches:
+      - master
+      - main
+    paths:
+      - 'CHANGELOG.md'
 
 name: create-release
 
 jobs:
-  release-documentation:
+  create-release:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       CHANGELOG: "CHANGELOG.md"
       DESCRIPTION: "DESCRIPTION"
-    outputs:
-      version: ${{ steps.extract-version.outputs.version }}
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
 
       - name: Extract release version from first level 4 heading
         id: extract-version
         run: |
           version=$(grep -oP '####[^0-9]*\K\d+\.\d+\.\d+' -m 1 $CHANGELOG)
           echo "version=$version" >> $GITHUB_ENV
-          echo "version=$version" >> $GITHUB_OUTPUT
           echo "Version: $version"
 
       - name: Get current UTC timestamp
@@ -62,19 +66,10 @@ jobs:
           git add ./R/*.R
           git add DESCRIPTION
           git add CHANGELOG.md
-          git commit -m "Updated documentation for release" || echo "No changes to commit"
+          git commit -m "Update documentation for version" || echo "No changes to commit"
           git pull --ff-only
           git push origin
 
-  release-build:
-    runs-on: ubuntu-latest
-    needs: release-documentation
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CHANGELOG: "CHANGELOG.md"
-    steps:
-      - uses: actions/checkout@v3
-
       - uses: r-lib/actions/setup-tinytex@v2
       - run: |
           tlmgr --version
@@ -117,8 +112,7 @@ jobs:
       - name: Make release properties
         id: release-fields
         run: |
-          version="${{ needs.release-documentation.outputs.version }}"
-          echo "version=$version" >> $GITHUB_ENV
+          version="${{ env.version }}"
           echo "Version: $version"
           tag="v${version}"
           echo "tag=$tag" >> $GITHUB_ENV

.github/workflows/prepare-pull-request.yaml

@@ -0,0 +1,131 @@
+# 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:
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - ready_for_review
+
+name: prepare-pull-request
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-tinytex@v2
+      - run: |
+          tlmgr --version
+          tlmgr update --self
+
+      - name: Install additional LaTeX packages
+        run: |
+          tlmgr install preprint
+          tlmgr install listings
+          tlmgr install tcolorbox
+          tlmgr install pgf
+          tlmgr install environ
+          tlmgr install tikzfill
+          tlmgr install pdfcol
+          tlmgr install grfext
+          tlmgr list --only-installed
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          build_args: 'c("--compact-vignettes=gs+qpdf")'
+
+  document:
+    runs-on: ubuntu-latest
+    needs: R-CMD-check
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE DESCRIPTION
+          git commit -m "Update documentation" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin
+
+  line-break-fix:
+    runs-on: ubuntu-latest
+    needs: document
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up dos2unix
+        run: sudo apt-get install dos2unix
+
+      - name: Run dos2unix
+        run: |
+          find ./R -type f -name "*.R" -exec dos2unix {} \;
+          find ./tests/testthat -type f -name "*.R" -exec dos2unix {} \;
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add ./R/*.R
+          git add ./tests/testthat/*.R
+          git commit -m "Conversion of R files from CRLF to LF" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin

CHANGELOG.md

@@ -1,6 +1,6 @@
 CHANGELOG
 ---------
-#### Version 1.0.8 (2024.02.23)
+#### Version 1.0.8 (2024.02.25)
 * Handling of GenBank features with multiple qualifiers of the same name
 * Coverage summaries added to `verbose` output files
 * Parameters `syntenyLineType` and `regionsCheck` for `PACVr.complete()` have been combined into `IRCheck`

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PACVr
 Version: 1.0.8
-Date: 2024-02-23
+Date: 2024-02-25
 Title: Plastome Assembly Coverage Visualization
 Authors@R: c(person("Gregory", "Smith", role=c("ctb")),
              person("Nils", "Jenke", role=c("ctb")),

R/IRoperations.R

@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.23.0220"
+#version="2024.02.25.0307"
 
 checkIREquality <- function(gbkSeq, regions, dir, sample_name) {
   if ("IRb" %in% regions[, 4] && "IRa" %in% regions[, 4]) {

R/PACVr.R

@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.23.0220"
+#version="2024.02.25.0307"
 
 PACVr.read.gb <- function(gbkFile) {
   gbkRaw <- getGbkRaw(gbkFile)

R/customizedRCircos.R

@@ -1,7 +1,7 @@
 #!/usr/bin/env RScript
 #contributors=c("Gregory Smith", "Nils Jenke", "Michael Gruenstaeudl")
 #email="m_gruenstaeudl@fhsu.edu"
-#version="2024.02.23.0220"
+#version="2024.02.25.0307"
 
 
 # The following R functions were taken from the R package RCircos and then modified.