Merge remote-tracking branch 'origin/main' into mebrooks/main

Author: jakub-jedrusiak

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

@@ -6,48 +6,56 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CODECOV_TOKEN: ${{ secrets.CODECOV_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
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3

DESCRIPTION

@@ -46,6 +46,8 @@ Description: Implementation of Multidimensional Top Scoring
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
+URL: https://github.com/jakub-jedrusiak/mtscr
+BugReports: https://github.com/jakub-jedrusiak/mtscr/issues
 RoxygenNote: 7.2.3
 Depends:
     R (>= 4.1.0)

README.Rmd

@@ -16,10 +16,10 @@ knitr::opts_chunk$set(
 # Multidimensional Top Scoring for Creativity Research <img src="./man/figures/mtscr-hex.svg" width="200" align="right"/> {#multidimensional-top-scoring-for-creativity-research}
 
 <!-- badges: start -->
-
-[![codecov](https://codecov.io/gh/jakub-jedrusiak/mtscr/branch/main/graph/badge.svg?token=N3UGHFK5QN)](https://app.codecov.io/gh/jakub-jedrusiak/mtscr) [![R-CMD-check](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml)
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![CRAN/METACRAN](https://img.shields.io/cran/v/mtscr)](https://CRAN.R-project.org/package=mtscr)
+[![R-CMD-check](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/jakub-jedrusiak/mtscr/graph/badge.svg)](https://app.codecov.io/gh/jakub-jedrusiak/mtscr)
 <!-- badges: end -->
 
 An R adaptation of Multidimensional Top Scoring method presented by Forthmann, Karwowski and Beaty ([2023](https://doi.org/10.1037/aca0000571)) using the code from the [OSF database](https://osf.io/7rgsp/). The code was adapted to use the [tidyverse](https://www.tidyverse.org/) framework for greater flexibility.

README.md

@@ -5,11 +5,12 @@
 
 <!-- badges: start -->
 
-[![codecov](https://codecov.io/gh/jakub-jedrusiak/mtscr/branch/main/graph/badge.svg?token=N3UGHFK5QN)](https://app.codecov.io/gh/jakub-jedrusiak/mtscr)
-[![R-CMD-check](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml)
 [![Lifecycle:
 stable](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![CRAN/METACRAN](https://img.shields.io/cran/v/mtscr)](https://CRAN.R-project.org/package=mtscr)
+[![R-CMD-check](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jakub-jedrusiak/mtscr/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/jakub-jedrusiak/mtscr/graph/badge.svg)](https://app.codecov.io/gh/jakub-jedrusiak/mtscr)
 <!-- badges: end -->
 
 An R adaptation of Multidimensional Top Scoring method presented by
@@ -57,6 +58,10 @@ library("mtscr")
 data("mtscr_creativity", package = "mtscr")
 
 mtscr_score(mtscr_creativity, id, item, SemDis_MEAN, top = 1:2)
+#> Warning in checkDepPackageVersion(dep_pkg = "TMB"): Package version inconsistency detected.
+#> glmmTMB was built with TMB version 1.9.11
+#> Current TMB version is 1.9.15
+#> Please re-install glmmTMB from source or restore original 'TMB' package (see '?reinstalling' for more information)
 #> # A tibble: 149 × 3
 #>    id    .creativity_score_top1 .creativity_score_top2
 #>    <chr>                  <dbl>                  <dbl>