Merge branch 'develop'

.github/workflows/check_bash_style.yaml

@@ -0,0 +1,22 @@
+name: Check bash style
+
+on:
+  push:
+  pull_request:
+  schedule:
+  - cron: "0 0 16 * *"
+
+
+jobs:
+  check_bash_style:
+
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+
+      - name: Set up Git repository
+        uses: actions/checkout@v2
+
+      - name: Check bash scripts for style
+        run: shellcheck *.sh scripts/*.sh

.github/workflows/check_links.yaml

@@ -0,0 +1,19 @@
+on:
+  push:
+  pull_request:
+  schedule:
+  - cron: "0 0 12 * *"
+
+name: check-links
+
+jobs:
+  check-links:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: gaurav-nelson/github-action-markdown-link-check@v1
+        with:
+          config-file: 'mlc_config.json'

DESCRIPTION

@@ -18,11 +18,11 @@ Description: 'BEAST2' (<https://www.beast2.org>) is a widely used
     from an 'R' function call.
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Imports:
     ape,
     assertive,
-    beautier (>= 2.6.6),
+    beautier (>= 2.6.9),
     devtools,
     phangorn,
     rappdirs,
@@ -39,7 +39,7 @@ Suggests:
     spelling,
     testit,
     testthat (>= 2.1.0),
-    tracerer
+    tracerer (>= 2.2.3)
 URL: https://docs.ropensci.org/beastier/ (website)
     https://github.com/ropensci/beastier/
 BugReports: https://github.com/ropensci/beastier

NEWS.md

@@ -2,15 +2,16 @@
 
 Newest versions at top.
 
-## beastier 2.4.12 (unreleased)
+## beastier 2.4.12 (2023-09-25)
 
 ### NEW FEATURES
 
   * None
 
 ### MINOR IMPROVEMENTS
 
-  * None
+ * Use new CITATION style
+ * Did `usethis::use_package_doc()`
 
 ### BUG FIXES
 

inst/CITATION

@@ -1,18 +1,8 @@
-citHeader("To cite reports in publications, please use:")
-
-citEntry(entry = "article",
-  title="babette: BEAUti 2, BEAST 2 and Tracer for R",
-  author="Richèl JC Bilderbeek and Rampal S Etienne",
-  journal="Methods in Ecology and Evolution",
-  year="2018",
-  publisher="Wiley Online Library",
-  url="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13032",
-  textVersion = paste(
-    "Bilderbeek, Richèl JC, and Etienne, Rampal S.",
-    "babette: BEAUti 2, BEAST 2 and Tracer for R.",
-    "Methods in Ecology and Evolution (2018).",
-    "https://doi.org/10.1111/2041-210X.13032"
-  )
+bibentry(
+  bibtype = "Article",
+  author = "Richèl JC Bilderbeek and Rampal S Etienne",
+  title = "babette: BEAUti 2, BEAST 2 and Tracer for R",
+  journal = "Methods in Ecology and Evolution",
+  year = "2008",
+  url = "https://doi.org/10.1111/2041-210X.13032",
 )
-
-

scripts/build_cran.sh

@@ -3,19 +3,16 @@
 rm -rf build
 mkdir build
 
-cp -r ../R build
 cp -r ../inst build
 cp -r ../man build
+# cp -r ../Meta build
+cp -r ../R build
+# cp -r ../src build
 cp -r ../vignettes build
 cp ../DESCRIPTION build
 cp ../NAMESPACE build
 
-cd build
+cd build || exit 42
 R CMD build .
-R CMD check --as-cran $(ls *.tar.gz)
-
-
-if [[ $HOSTNAME == "N141CU" ]]; then
-  notify-send "Done building beastier"
-fi
-
+gz_files=$(ls ./*.tar.gz)
+R CMD check --as-cran "${gz_files}"