Merge pull request #10 from pythonhealthdatascience/dev

Dev

Author: amyheather

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# 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]
+  workflow_dispatch:
+
+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")
+          )
+          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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -30,5 +30,7 @@ Suggests:
     mockery,
     patrick,
     scales,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    covr,
+    DT
 Config/testthat/edition: 3

R/validate_model_inputs.R

@@ -10,6 +10,7 @@ valid_inputs <- function(run_number, param) {
   check_run_number(run_number)
   check_all_param_names(param)
   check_param_values(param)
+  check_log_file_path(param)
 }
 
 
@@ -213,3 +214,23 @@ check_param_values <- function(param) {
     }
   }
 }
+
+#' Check logging file path
+#'
+#' @param param List containing parameters for the simulation.
+#'
+#' @return None. Throws an error if valid file path not provided, when
+#' log_to_file = TRUE.
+#' @export
+
+check_log_file_path <- function(param) {
+  log_to_file <- param[["log_to_file"]]
+  file_path <- param[["file_path"]]
+  if (isTRUE(log_to_file) && (is.null(file_path) || !nzchar(file_path))) {
+    stop(
+      "If 'log_to_file' is TRUE, you must provide a non-NULL, ",
+      "non-empty 'file_path'.",
+      call. = FALSE
+    )
+  }
+}

README.md

@@ -9,6 +9,7 @@
 [![R-CMD-check](https://github.com/pythonhealthdatascience/rdesrap_stroke/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pythonhealthdatascience/rdesrap_stroke/actions/workflows/R-CMD-check.yaml)
 [![Lint](https://github.com/pythonhealthdatascience/rdesrap_stroke/actions/workflows/lint.yaml/badge.svg)](https://github.com/pythonhealthdatascience/rdesrap_stroke/actions/workflows/lint.yaml)
 [![ORCID](https://img.shields.io/badge/ORCID_Amy_Heather-0000--0002--6596--3479-A6CE39?&logo=orcid&logoColor=white)](https://orcid.org/0000-0002-6596-3479)
+[![Codecov test coverage](https://codecov.io/gh/pythonhealthdatascience/rdesrap_stroke/graph/badge.svg)](https://app.codecov.io/gh/pythonhealthdatascience/rdesrap_stroke)
 <!-- badges: end -->
 </div>
 
@@ -91,6 +92,12 @@ bash run_rmarkdown.sh
 devtools::test()
 ```
 
+**Compute test coverage:**
+
+```{.r}
+devtools::test_coverage()
+```
+
 **Lint code:**
 
 ```{.r}