release 2.9.8

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

@@ -38,22 +38,22 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-pandoc@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
 
-      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-tinytex@v2
+      - uses: r-lib/actions/setup-tinytex@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-r-dependencies@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           extra-packages: any::rcmdcheck, local::.
           needs: check
 
-      - uses: r-lib/actions/check-r-package@v2
+      - uses: r-lib/actions/check-r-package@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -4,12 +4,11 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
 
 permissions: read-all
 
@@ -26,17 +25,25 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-pandoc@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
 
-      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-r-dependencies@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
 
       - name: Build site
-        run: pkgdown::deploy_to_branch(new_process = FALSE, run_dont_run = TRUE)
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@65b5dfd4f5bcd3a7403bbc2959c144256167464e #v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/rhub.yaml

@@ -33,7 +33,7 @@ jobs:
 
     steps:
     # NO NEED TO CHECKOUT HERE
-    - uses: r-hub/actions/setup@v1
+    - uses: r-hub/actions/setup@e9663823ac5d540b7b2d93436945048a8f6fc4c1 #v1.6.6
       with:
         config: ${{ github.event.inputs.config }}
       id: rhub-setup
@@ -51,16 +51,16 @@ jobs:
       image: ${{ matrix.config.container }}
 
     steps:
-      - uses: r-hub/actions/checkout@v1
-      - uses: r-hub/actions/platform-info@v1
+      - uses: r-hub/actions/checkout@e9663823ac5d540b7b2d93436945048a8f6fc4c1 #v1.6.6
+      - uses: r-hub/actions/platform-info@e9663823ac5d540b7b2d93436945048a8f6fc4c1 #v1.6.6
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/actions/setup-deps@v1
+      - uses: r-hub/actions/setup-deps@e9663823ac5d540b7b2d93436945048a8f6fc4c1 #v1.6.6
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/actions/run-check@v1
+      - uses: r-hub/actions/run-check@e9663823ac5d540b7b2d93436945048a8f6fc4c1 #v1.6.6
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
@@ -76,20 +76,20 @@ jobs:
         config: ${{ fromJson(needs.setup.outputs.platforms) }}
 
     steps:
-      - uses: r-hub/actions/checkout@v1
-      - uses: r-hub/actions/setup-r@v1
+      - uses: r-hub/actions/checkout@e9663823ac5d540b7b2d93436945048a8f6fc4c1 #v1.6.6
+      - uses: r-hub/actions/setup-r@e9663823ac5d540b7b2d93436945048a8f6fc4c1 #v1.6.6
         with:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}
-      - uses: r-hub/actions/platform-info@v1
+      - uses: r-hub/actions/platform-info@e9663823ac5d540b7b2d93436945048a8f6fc4c1 #v1.6.6
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/actions/setup-deps@v1
+      - uses: r-hub/actions/setup-deps@e9663823ac5d540b7b2d93436945048a8f6fc4c1 #v1.6.6
         with:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}
-      - uses: r-hub/actions/run-check@v1
+      - uses: r-hub/actions/run-check@e9663823ac5d540b7b2d93436945048a8f6fc4c1 #v1.6.6
         with:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -4,9 +4,8 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
 
 permissions: read-all
 
@@ -19,11 +18,11 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - uses: r-lib/actions/setup-r-dependencies@bd49c52ffe281809afa6f0fecbf37483c5dd0b93 #v2.11.3
         with:
           extra-packages: any::covr, any::xml2
           needs: coverage
@@ -35,14 +34,16 @@ jobs:
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 #v5.5.1
         with:
-          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
-          file: ./cobertura.xml
-          plugin: noop
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
           disable_search: true
           token: ${{ secrets.CODECOV_TOKEN }}
 

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.9.7
-Date: 2025-06-18 23:41:37 UTC
-SHA: 43eb0047542d0bc739f6ea19bc95e008431f2119
+Version: 2.9.8
+Date: 2025-08-23 22:26:12 UTC
+SHA: 928ee2ce3c003194af3d7a6927dd8aec87ca4461

NEWS.md

@@ -15,6 +15,7 @@ MISC
 * compatibility fix for ggplot2 4.0.0 (reported: @teunbrand, #263,
   fixed: @zkamvar, #264)
 * CRAN maintenance: documentaiton fixes
+* internal code formatting has been applied with air
 
 poppr 2.9.6
 ===========
@@ -148,7 +149,7 @@ CRAN MAINTENANCE
 * The output from the `poppr()` function will no longer contain factor columns
   for the population names or the file names. This is due to R 4.0.0 changing
   behavior with the `stringsAsFactors` default in `data.frame()`. (See
-  <https://github.com/grunwaldlab/poppr/issue/212> for details).
+  <https://github.com/grunwaldlab/poppr/issues/212> for details).
 
 poppr 2.8.4
 ===========

README.md

@@ -2,6 +2,7 @@
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/grunwaldlab/poppr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/grunwaldlab/poppr/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/grunwaldlab/poppr/graph/badge.svg)](https://app.codecov.io/gh/grunwaldlab/poppr)
 <!-- badges: end -->
 
 ## What is *poppr*?

air.toml

@@ -0,0 +1,9 @@
+[format]
+line-width = 80
+indent-width = 2
+indent-style = "space"
+line-ending = "auto"
+persistent-line-breaks = true
+exclude = []
+default-exclude = true
+skip = []