update workflows

jakub-jedrusiak · Sep 26, 2024 · a9d5a60 · a9d5a60
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,40 +1,52 @@
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-#
-# See https://github.com/r-lib/actions/tree/master/examples#readme for
-# additional example workflows available for the R community.
-
-name: R
-
+# 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" ]
+    branches: [main, master]
   pull_request:
-    branches: [ "main" ]
+    branches: [main, master]
+
+name: R-CMD-check.yaml
 
-permissions:
-  contents: read
+permissions: read-all
 
 jobs:
-  build:
-    runs-on: macos-latest
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
     strategy:
+      fail-fast: false
       matrix:
-        r-version: ['3.6.3', '4.1.1']
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up R ${{ matrix.r-version }}
-        uses: r-lib/actions/setup-r@f57f1301a053485946083d7a45022b278929a78a
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          r-version: ${{ matrix.r-version }}
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-      - name: Check
-        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        shell: Rscript {0}
+          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
@@ -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: ${{ runner.temp }}/package
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
diff --git a/README.Rmd b/README.Rmd
@@ -16,10 +16,10 @@ knitr::opts_chunk$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.

diff --git a/README.md b/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>