fine tuning after new cran release

.github/workflows/pkgdown.yaml

@@ -9,7 +9,9 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,8 +21,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage.yaml

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +17,45 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

.gitignore

@@ -1,3 +1,4 @@
 .Rproj.user
 inst/doc
 
+docs

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.8.4
-Date: 2024-05-17 21:26:07 UTC
-SHA: db8798a806b6f68a5ed8da147c9e96cc8ba4aec5
+Version: 0.8.5
+Date: 2024-10-29 16:16:45 UTC
+SHA: 895e49cdcda75d6030d4aac7407b13918dae8866

README.Rmd

@@ -24,6 +24,7 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/maraab23/ggseqplot/workflows/R-CMD-check/badge.svg)](https://github.com/maraab23/ggseqplot/actions)
 [![Codecov test coverage](https://codecov.io/gh/maraab23/ggseqplot/branch/main/graph/badge.svg)](https://app.codecov.io/gh/maraab23/ggseqplot?branch=main)
 [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/grand-total/ggseqplot)](https://cranlogs.r-pkg.org/badges/grand-total/ggseqplot)
+[![Codecov test coverage](https://codecov.io/gh/maraab23/ggseqplot/graph/badge.svg)](https://app.codecov.io/gh/maraab23/ggseqplot)
 <!-- badges: end -->
 
 The main goal of [`{ggseqplot}`](https://maraab23.github.io/ggseqplot/) is to 

README.md

@@ -12,6 +12,8 @@ status](https://www.r-pkg.org/badges/version/ggseqplot)](https://cran.r-project.
 coverage](https://codecov.io/gh/maraab23/ggseqplot/branch/main/graph/badge.svg)](https://app.codecov.io/gh/maraab23/ggseqplot?branch=main)
 [![CRAN
 Downloads](https://cranlogs.r-pkg.org/badges/grand-total/ggseqplot)](https://cranlogs.r-pkg.org/badges/grand-total/ggseqplot)
+[![Codecov test
+coverage](https://codecov.io/gh/maraab23/ggseqplot/graph/badge.svg)](https://app.codecov.io/gh/maraab23/ggseqplot)
 <!-- badges: end -->
 
 The main goal of [`{ggseqplot}`](https://maraab23.github.io/ggseqplot/)

_pkgdown.yml

@@ -1,39 +1,4 @@
-url: https://maraab23.github.io/ggseqplot
+url: ~
 template:
   bootstrap: 5
-  bslib:
-    base_font: {google: "Poppins"}
-    heading_font: {google: "Poppins"}
-    code_font: {google: "Fira Code"}
-figures:
-  fig.width: 8.000
-  fig.height: 4.94
 
-reference:
-- title: Summarization plots
-  contents:
-  - ggseqdplot
-  - ggseqeplot
-  - ggseqmsplot
-  - ggseqmtplot
-  - ggseqtrplot
-- title: Representation plots
-  contents:
-  - ggseqiplot
-  - ggseqfplot
-  - ggseqrplot
-  - ggseqrfplot
-
-
-navbar:
-  structure:
-    right: [twitter, github]
-  components:
-    twitter:
-      icon: fa-twitter
-      href: https://twitter.com/RaabM
-      aria-label: Twitter
-
-authors:
-  Marcel Raab:
-    href: https://marcelraab.de