Add coverage report to repo

m-path-io · Oct 16, 2024 · ebfc498 · ebfc498
1 parent 236927d
commit ebfc498
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diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,61 @@
+# 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]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/R/timestamps_to_datetime.R b/R/timestamps_to_datetime.R
@@ -83,13 +83,13 @@ timestamps_to_datetime <- function(x, tz_offset = NULL, force_tz = NULL) {
   out <- as.POSIXct(x, origin = "1970-01-01", tz = "UTC")
 
   if (!is.null(force_tz)) {
-    if (!requireNamespace("lubridate", quietly = TRUE)) {
+    if (!requireNamespace("lubridate", quietly = TRUE)) { #nocov start
       cli_abort(c(
         paste0("Package `lubridate` is needed for this function to work."),
         i = paste0("Please install it using `install.packages(\"lubridate\")`")),
         call = call
       )
-    }
+    } #nocov end
 
     out <- lubridate::force_tz(out, tzone = force_tz)
   }

diff --git a/R/write_mpath.R b/R/write_mpath.R
@@ -61,9 +61,7 @@ write_mpath <- function(
     "accountCode",
     "questionListName",
     "questionListLabel",
-    "fromProtocolName",
-    "recording_recording_filename",
-    "recording_recording_metadata"
+    "fromProtocolName"
   )
 
   # Find which columns are lists of strings

diff --git a/README.Rmd b/README.Rmd
@@ -18,6 +18,7 @@ options(tibble.print_min = 5, tibble.print_max = 5)
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/m-path-io/mpathr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/m-path-io/mpathr/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/m-path-io/mpathr/graph/badge.svg)](https://app.codecov.io/gh/m-path-io/mpathr)
 <!-- badges: end -->
 
 ## Overview

diff --git a/README.md b/README.md
@@ -6,6 +6,8 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/m-path-io/mpathr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/m-path-io/mpathr/actions/workflows/R-CMD-check.yaml)
+[![Codecov test
+coverage](https://codecov.io/gh/m-path-io/mpathr/graph/badge.svg)](https://app.codecov.io/gh/m-path-io/mpathr)
 <!-- badges: end -->
 
 ## Overview
@@ -46,20 +48,20 @@ data <- read_mpath(
 
 print(data)
 #> # A tibble: 2,221 × 100
-#>   connectionId legacyCode  code       alias initials accountCode scheduledBeepId sentBeepId
-#>          <int> <chr>       <chr>      <chr> <chr>    <chr>                 <int>      <int>
-#> 1       234609 !9v48@jp7a7 !byyo kjyt abc   Ver      jp7a7                    -1   19355815
-#> 2       234609 !9v48@jp7a7 !byyo kjyt abc   Ver      jp7a7              28626776   19369681
-#> 3       234609 !9v48@jp7a7 !byyo kjyt abc   Ver      jp7a7              28626777   19370288
-#> 4       234609 !9v48@jp7a7 !byyo kjyt abc   Ver      jp7a7              28626781   19375253
-#> 5       234609 !9v48@jp7a7 !byyo kjyt abc   Ver      jp7a7              28626782   19377280
+#>   connectionId legacyCode  code       alias initials accountCode scheduledBeepId
+#>          <int> <chr>       <chr>      <chr> <chr>    <chr>                 <int>
+#> 1       234609 !9v48@jp7a7 !byyo kjyt abc   Ver      jp7a7                    -1
+#> 2       234609 !9v48@jp7a7 !byyo kjyt abc   Ver      jp7a7              28626776
+#> 3       234609 !9v48@jp7a7 !byyo kjyt abc   Ver      jp7a7              28626777
+#> 4       234609 !9v48@jp7a7 !byyo kjyt abc   Ver      jp7a7              28626781
+#> 5       234609 !9v48@jp7a7 !byyo kjyt abc   Ver      jp7a7              28626782
 #> # ℹ 2,216 more rows
-#> # ℹ 92 more variables: reminderForOriginalSentBeepId <int>, questionListName <chr>,
-#> #   questionListLabel <lgl>, fromProtocolName <chr>, timeStampScheduled <int>, timeStampSent <int>,
-#> #   timeStampStart <int>, timeStampStop <int>, originalTimeStampSent <int>, timeZoneOffset <int>,
-#> #   deltaUTC <dbl>, consent_yesno_yesno <int>, gender_multipleChoice_index <int>,
-#> #   gender_multipleChoice_string <chr>, gender_multipleChoice_likert <int>, age_open <chr>,
-#> #   SWLS_intro_basic <int>, SWLS_1_multipleChoice_index <int>, …
+#> # ℹ 93 more variables: sentBeepId <int>, reminderForOriginalSentBeepId <int>,
+#> #   questionListName <chr>, questionListLabel <chr>, fromProtocolName <chr>,
+#> #   timeStampScheduled <int>, timeStampSent <int>, timeStampStart <int>,
+#> #   timeStampStop <int>, originalTimeStampSent <int>, timeZoneOffset <int>,
+#> #   deltaUTC <dbl>, consent_yesno_yesno <int>,
+#> #   gender_multipleChoice_index <int>, gender_multipleChoice_string <chr>, …
 ```
 
 ## Getting help

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,5 +1,6 @@
 BFI
 CMD
+Codecov
 ESM
 Github
 JSON