Fix the R-CMD-check and add Quarto to render README.md

.Rbuildignore

@@ -1,6 +1,8 @@
 ^\.github$
 ^\.lintr$
+^.quarto$
 ^\.Rproj\.user$
+^_quarto\.yml$
 ^_pkgdown\.yml$
 ^CITATION\.cff$
 ^CODE_OF_CONDUCT\.md$
@@ -15,4 +17,4 @@
 ^man-roxygen$
 ^Meta$
 ^pkgdown$
-^README\.Rmd$
+^README\.qmd$

.github/CONTRIBUTING.md

@@ -6,13 +6,13 @@ First of all, thanks for considering contributing to `lubritime`! 👍 It's peop
 
 `lubritime` is an open source project, maintained by people who care. We are not directly funded to do so.
 
-[repo]: https://github.com/giperbio/lubritime
-[issues]: https://github.com/giperbio/lubritime/issues
-[discussions]: https://github.com/giperbio/lubritime/discussions
-[new_issue]: https://github.com/giperbio/lubritime/issues/new
-[new_discussion]: https://github.com/giperbio/lubritime/discussions/new
-[website]: https://giperbio.github.io/lubritime
-[citation]: https://giperbio.github.io/lubritime/authors.html
+[repo]: https://github.com/danielvartan/lubritime
+[issues]: https://github.com/danielvartan/lubritime/issues
+[discussions]: https://github.com/danielvartan/lubritime/discussions
+[new_issue]: https://github.com/danielvartan/lubritime/issues/new
+[new_discussion]: https://github.com/danielvartan/lubritime/discussions/new
+[website]: https://danielvartan.github.io/lubritime
+[citation]: https://danielvartan.github.io/lubritime/authors.html
 [email]: mailto:[email protected]
 
 ## Code of conduct

.github/workflows/check-standard.yaml

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -29,7 +31,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +49,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.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 +17,46 @@ 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 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 }}
+          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

@@ -1,59 +1,21 @@
-# Created by https://www.toptal.com/developers/gitignore/api/r
-# Edit at https://www.toptal.com/developers/gitignore?templates=r
+# See <https://git-scm.com/docs/gitignore> to learn more.
 
-### R ###
-# History files
-.Rhistory
+*.knit.md
 .Rapp.history
-
-# Session Data files
 .RData
-
-# User-specific files
+.Renviron
+.Rhistory
 .Ruserdata
+*.utf8.md
 
-# Example code in package build process
-*-Ex.R
-
-# Output files from R CMD build
-/*.tar.gz
-
-# Output files from R CMD check
 /*.Rcheck/
-
-# RStudio files
 .Rproj.user/
-
-# produced vignettes
-vignettes/*.html
-vignettes/*.pdf
-
-# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
-.httr-oauth
-
-# knitr and R markdown default cache directories
 *_cache/
 /cache/
-
-# Temporary files created by R markdown
-*.utf8.md
-*.knit.md
-
-# R Environment Variables
-.Renviron
-
-# pkgdown site
 docs/
-
-# translation temp files
-po/*~
-
-### R.Bookdown Stack ###
-# R package: bookdown caching files
-/*_files/
-
-# End of https://www.toptal.com/developers/gitignore/api/r
-
-# Others
-.archive/
 pkgdown/
+revdep/
+vignettes/*.html
+vignettes/*.pdf
+
+/.quarto/