fix codecov

Author: timcadman

.github/workflows/dsBaseClient_test_suite.yaml

@@ -231,36 +231,29 @@ jobs:
           R -q -e "library(opalr); opal <- opal.login('administrator', 'datashield_test&', url='http://localhost:8080/'); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)"
         working-directory: dsBaseClient/tests/testthat/data_files
 
-      - name: Run dsBase tests with JUnit report
+      - name: Run dsBase tests with coverage & JUnit report
         run: |
           R -q -e "devtools::reload();"
-          R -q -e '
-            output_file <- file("test_console_output_dsbase.txt");
-            sink(output_file, split = TRUE);
-            junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results_dsbase.xml"));
-            progress_rep <- testthat::ProgressReporter$new(max_failures = 999999);
-            multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep));
-            options("datashield.return_errors" = FALSE, "default_driver" = "${{ env.DS_DRIVER }}");
-            testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ matrix.filter }}", reporter = multi_rep, stop_on_failure = FALSE)' || R_EXIT=$?
-          cat test_console_output_dsbase.txt
-          exit "${R_EXIT:-0}"
-        working-directory: dsBaseClient
-
-      - name: Generate dsBase coverage report
-        run: |
           R -q -e '
             write.csv(
               covr::coverage_to_list(
                 covr::package_coverage(
-                  type = "none",
+                  type = c("none"),
                   code = c('"'"'
+                    output_file <- file("test_console_output_dsbase.txt");
+                    sink(output_file, split = TRUE);
+                    junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results_dsbase.xml"));
+                    progress_rep <- testthat::ProgressReporter$new(max_failures = 999999);
+                    multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep));
                     options("datashield.return_errors" = FALSE, "default_driver" = "${{ env.DS_DRIVER }}");
-                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ matrix.filter }}", reporter = "silent", stop_on_failure = FALSE)'"'"'
+                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ matrix.filter }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
                   )
                 )
               ),
               "coveragelist.csv"
-            )'
+            )' || R_EXIT=$?
+          cat test_console_output_dsbase.txt
+          exit "${R_EXIT:-0}"
         working-directory: dsBaseClient
 
       - name: Upload shard results
@@ -746,36 +739,29 @@ jobs:
         run: grep "Caused by:" armadillo_home/logs/stdout.log | sort -u
         working-directory: dsBaseClient
 
-      - name: Run dsBase tests with JUnit report
+      - name: Run dsBase tests with coverage & JUnit report
         run: |
           R -q -e "devtools::reload();"
-          R -q -e '
-            output_file <- file("test_console_output_dsbase.txt");
-            sink(output_file, split = TRUE);
-            junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results_dsbase.xml"));
-            progress_rep <- testthat::ProgressReporter$new(max_failures = 999999);
-            multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep));
-            options("datashield.return_errors" = FALSE, "default_driver" = "${{ env.DS_DRIVER }}");
-            testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ matrix.filter }}", reporter = multi_rep, stop_on_failure = FALSE)' || R_EXIT=$?
-          cat test_console_output_dsbase.txt
-          exit "${R_EXIT:-0}"
-        working-directory: dsBaseClient
-
-      - name: Generate dsBase coverage report
-        run: |
           R -q -e '
             write.csv(
               covr::coverage_to_list(
                 covr::package_coverage(
-                  type = "none",
+                  type = c("none"),
                   code = c('"'"'
+                    output_file <- file("test_console_output_dsbase.txt");
+                    sink(output_file, split = TRUE);
+                    junit_rep <- testthat::JunitReporter$new(file = file.path(getwd(), "test_results_dsbase.xml"));
+                    progress_rep <- testthat::ProgressReporter$new(max_failures = 999999);
+                    multi_rep <- testthat::MultiReporter$new(reporters = list(progress_rep, junit_rep));
                     options("datashield.return_errors" = FALSE, "default_driver" = "${{ env.DS_DRIVER }}");
-                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ matrix.filter }}", reporter = "silent", stop_on_failure = FALSE)'"'"'
+                    testthat::test_package("${{ env.PROJECT_NAME }}", filter = "${{ matrix.filter }}", reporter = multi_rep, stop_on_failure = FALSE)'"'"'
                   )
                 )
               ),
               "coveragelist.csv"
-            )'
+            )' || R_EXIT=$?
+          cat test_console_output_dsbase.txt
+          exit "${R_EXIT:-0}"
         working-directory: dsBaseClient
 
       - name: Upload shard results