Merge pull request #341 from Olink-Proteomics/optimization_develop_li…

…nt_covr_test

Update covr and lintr CI workflows
arrow does not work on MacOC for now apache/arrow#40667

.github/workflows/lint.yaml

@@ -1,41 +1,39 @@
 # 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
-      - optimization
-      - optimization_develop
-  pull_request:
-    branches:
-      - main
-      - optimization
-      - optimization_develop
+  [push]
 
 name: lint
 
 jobs:
   lint:
     runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v3
         with:
-          fetch-depth: 0
-
+          fetch-depth: 2
+      
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          working-directory: OlinkAnalyze
-          extra-packages: lintr
+          packages: any::pak
+
+      - name: install OA
+        run: |
+          pak::pkg_install(c("local::OlinkAnalyze", "lintr", "devtools"))
+        shell: Rscript {0}
 
       - name: Lint
         run: |
-          pkgload::load_all(path = "OlinkAnalyze")
-          lintr::lint_package()
+          options(lintr.github_annotation_project_dir = "OlinkAnalyze")
+          devtools::load_all(path = "OlinkAnalyze")
+          lintr::lint_package(path = "OlinkAnalyze")
         shell: Rscript {0}
         env:
           LINTR_ERROR_ON_LINT: true

.github/workflows/test-coverage.yaml

@@ -1,16 +1,7 @@
 # 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
-      - optimization
-      - optimization_develop
-  pull_request:
-    branches:
-      - main
-      - optimization
-      - optimization_develop
+  [push]
 
 name: test-coverage
 
@@ -21,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
         with:
-          fetch-depth: 0
+          fetch-depth: 2
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -39,13 +30,20 @@ jobs:
             path = "OlinkAnalyze",
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
           )
         shell: Rscript {0}
-
+        
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
           find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package