update workflows

Author: mpadge

.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:
@@ -31,10 +33,8 @@ jobs:
       ZENODO_TOKEN: ${{ secrets.ZENODO_TOKEN }}
       ZENODO_SANDBOX_TOKEN: ${{ secrets.ZENODO_SANDBOX_TOKEN }}
 
-
-
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -52,3 +52,4 @@ 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

@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -18,36 +20,47 @@ jobs:
       ZENODO_SANDBOX_TOKEN: ${{ secrets.ZENODO_SANDBOX_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")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        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 }}
+          files: ./cobertura.xml
+          plugins: 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

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: deposits
 Title: A universal client for depositing and accessing research data
     anywhere
-Version: 0.2.1.062
+Version: 0.2.1.063
 Authors@R: 
     person("Mark", "Padgham", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2172-5265"))

codemeta.json

@@ -7,7 +7,7 @@
   "codeRepository": "https://github.com/ropenscilabs/deposits",
   "issueTracker": "https://github.com/ropenscilabs/deposits/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.2.1.062",
+  "version": "0.2.1.063",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",