Add a CRAN DOI badge to 'README.md' and update the documentation.

ropensci · Jun 22, 2024 · 2f3a27a · 2f3a27a
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diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
@@ -1,5 +1,6 @@
 # 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:
   push:
     branches: [main, master]
@@ -8,6 +9,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -29,7 +32,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +50,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,5 +1,6 @@
 # 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:
   push:
     branches: [main, master]
@@ -8,43 +9,54 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       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
diff --git a/.gitignore b/.gitignore
@@ -55,6 +55,6 @@ po/*~
 # End of https://www.toptal.com/developers/gitignore/api/r
 
 # Others
-.archive/
-pkgdown/
-revdep/
+/.archive/
+/pkgdown/
+/revdep/
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,34 +1,35 @@
-# -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v0.5.0
+# --------------------------------------------
+# CITATION file created with {cffr} R package
 # See also: https://docs.ropensci.org/cffr/
-# -----------------------------------------------------------
+# --------------------------------------------
 
 cff-version: 1.2.0
 message: 'To cite package "mctq" in publications use:'
 type: software
 license: MIT
-title: 'mctq: Tools to Process the Munich ChronoType Questionnaire (MCTQ)'
-version: 0.3.2.9000
-abstract: A complete toolkit to process the Munich ChronoType Questionnaire (MCTQ)
-  for its three versions (standard, micro, and shift). MCTQ is a quantitative and
-  validated tool to assess chronotypes using peoples' sleep behavior, originally presented
-  by Till Roenneberg, Anna Wirz-Justice, and Martha Merrow (2003, <doi:10.1177/0748730402239679>).
+title: 'mctq: Munich ChronoType Questionnaire Tools'
+version: 0.3.2.9001
+abstract: 'A complete toolkit for processing the Munich ChronoType Questionnaire (MCTQ)
+  in its three versions: standard, micro, and shift. The MCTQ is a quantitative and
+  validated tool used to assess chronotypes based on individuals'' sleep behavior.
+  It was originally presented by Till Roenneberg, Anna Wirz-Justice, and Martha Merrow
+  in 2003 (2003, <https://doi.org/10.1177/0748730402239679>).'
 authors:
 - family-names: Vartanian
   given-names: Daniel
   email: danvartan@gmail.com
   orcid: https://orcid.org/0000-0001-7782-759X
 preferred-citation:
   type: unpublished
-  title: 'mctq: tools to process the Munich ChronoType Questionnaire (MCTQ)'
+  title: 'mctq: Munich ChronoType Questionnaire tools'
   authors:
   - family-names: Vartanian
     given-names: Daniel
     email: danvartan@gmail.com
     orcid: https://orcid.org/0000-0001-7782-759X
-  year: '2023'
+  year: '2024'
   url: https://docs.ropensci.org/mctq/
-  notes: R package version 0.3.2.9000
+  notes: R package version 0.3.2.9001
 repository: https://bioconductor.org/
 repository-code: https://github.com/ropensci/mctq/issues/
 url: https://docs.ropensci.org/mctq/
@@ -44,11 +45,10 @@ references:
   url: https://www.R-project.org/
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2023'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
   version: '>= 4.2'
 - type: software
   title: checkmate
@@ -61,7 +61,7 @@ references:
     given-names: Michel
     email: michellang@gmail.com
     orcid: https://orcid.org/0000-0001-9754-0393
-  year: '2023'
+  year: '2024'
   version: '>= 2.2.0'
 - type: software
   title: cli
@@ -73,7 +73,7 @@ references:
   - family-names: Csárdi
     given-names: Gábor
     email: csardi.gabor@gmail.com
-  year: '2023'
+  year: '2024'
   version: '>= 3.6.1'
 - type: software
   title: dplyr
@@ -98,7 +98,7 @@ references:
     given-names: Davis
     email: davis@posit.co
     orcid: https://orcid.org/0000-0003-4777-038X
-  year: '2023'
+  year: '2024'
   version: '>= 1.1.2'
 - type: software
   title: hms
@@ -111,7 +111,7 @@ references:
     given-names: Kirill
     email: kirill@cynkra.com
     orcid: https://orcid.org/0000-0002-1416-3412
-  year: '2023'
+  year: '2024'
   version: '>= 1.1.3'
 - type: software
   title: lifecycle
@@ -122,12 +122,12 @@ references:
   authors:
   - family-names: Henry
     given-names: Lionel
-    email: lionel@rstudio.com
+    email: lionel@posit.co
   - family-names: Wickham
     given-names: Hadley
-    email: hadley@rstudio.com
+    email: hadley@posit.co
     orcid: https://orcid.org/0000-0003-4757-117X
-  year: '2023'
+  year: '2024'
   version: '>= 1.0.3'
 - type: software
   title: lubridate
@@ -143,7 +143,7 @@ references:
     given-names: Garrett
   - family-names: Wickham
     given-names: Hadley
-  year: '2023'
+  year: '2024'
   version: '>= 1.9.2'
 - type: software
   title: covr
@@ -155,19 +155,18 @@ references:
   - family-names: Hester
     given-names: Jim
     email: james.f.hester@gmail.com
-  year: '2023'
+  year: '2024'
   version: '>= 3.6.2'
 - type: software
   title: datasets
   abstract: 'R: A Language and Environment for Statistical Computing'
   notes: Suggests
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2023'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
   version: '>= 4.2.0'
 - type: software
   title: knitr
@@ -180,7 +179,7 @@ references:
     given-names: Yihui
     email: xie@yihui.name
     orcid: https://orcid.org/0000-0003-0645-5666
-  year: '2023'
+  year: '2024'
   version: '>= 1.43'
 - type: software
   title: mockr
@@ -192,7 +191,7 @@ references:
   - family-names: Müller
     given-names: Kirill
     email: kirill@cynkra.com
-  year: '2023'
+  year: '2024'
   version: '>= 0.2.1'
 - type: software
   title: readr
@@ -210,7 +209,7 @@ references:
     given-names: Jennifer
     email: jenny@posit.co
     orcid: https://orcid.org/0000-0002-6983-2759
-  year: '2023'
+  year: '2024'
   version: '>= 2.1.4'
 - type: software
   title: rlang
@@ -225,7 +224,7 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: hadley@posit.co
-  year: '2023'
+  year: '2024'
   version: '>= 1.1.1'
 - type: software
   title: rmarkdown
@@ -269,13 +268,13 @@ references:
     given-names: Richard
     email: rich@posit.co
     orcid: https://orcid.org/0000-0003-3925-190X
-  year: '2023'
+  year: '2024'
   version: '>= 2.23'
 - type: software
   title: spelling
   abstract: 'spelling: Tools for Spell Checking in R'
   notes: Suggests
-  url: https://docs.ropensci.org/spelling/
+  url: https://ropensci.r-universe.dev/spelling
   repository: https://CRAN.R-project.org/package=spelling
   authors:
   - family-names: Ooms
@@ -285,19 +284,18 @@ references:
   - family-names: Hester
     given-names: Jim
     email: james.hester@rstudio.com
-  year: '2023'
+  year: '2024'
   version: '>= 2.2.1'
 - type: software
   title: stats
   abstract: 'R: A Language and Environment for Statistical Computing'
   notes: Suggests
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2023'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
   version: '>= 4.2.0'
 - type: software
   title: testthat
@@ -309,7 +307,7 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: hadley@posit.co
-  year: '2023'
+  year: '2024'
   version: '>= 3.1.10'
 - type: software
   title: usethis
@@ -334,20 +332,20 @@ references:
     given-names: Andy
     email: andy.teucher@posit.co
     orcid: https://orcid.org/0000-0002-7840-692X
-  year: '2023'
+  year: '2024'
   version: '>= 2.2.2'
 - type: software
   title: utils
   abstract: 'R: A Language and Environment for Statistical Computing'
   notes: Suggests
   authors:
   - name: R Core Team
-  location:
-    name: Vienna, Austria
-  year: '2023'
   institution:
     name: R Foundation for Statistical Computing
+    address: Vienna, Austria
+  year: '2024'
   version: '>= 4.2.0'
 identifiers:
 - type: url
   value: https://github.com/ropensci/mctq/
+