Merge pull request #138 from mrc-ide/mrc-5052

FIx code coverage and restore 100%

.github/workflows/test-coverage.yaml

@@ -36,6 +36,7 @@ jobs:
       - name: Test coverage
         run: |
           covr::codecov(
+            token = "${{ secrets.CODECOV_TOKEN }}",
             quiet = FALSE,
             clean = FALSE,
             install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hipercow
 Title: High Performance Computing
-Version: 1.0.31
+Version: 1.0.32
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Wes", "Hinsley", role = "aut"),

R/envvars.R

@@ -161,12 +161,12 @@ envvars_apply <- function(envvars, envir) {
 }
 
 envvars_export <- function(envvars, path) {
+  lines <- character(0)
   if (!is.null(envvars)) {
     vars <- envvars[!envvars$secret, ]
-    writeLines(sprintf("%s=%s", vars$name, vars$value), path)
-  } else {
-    file.create(path)
+    lines <- sprintf("%s=%s", vars$name, vars$value)
   }
+  writeLines(lines, path)
 }
 
 

R/task-create.R

@@ -542,11 +542,11 @@ task_export_envvars <- function(root, dst, envvars, inherit_envvars) {
     envvars_export(envvars, dst)
   } else {
     src <- file.path(path_task(root$path$tasks, inherit_envvars), RENVIRON)
+    lines <- character(0)
     if (fs::file_exists(src)) {
-      fs::file_copy(src, dst)
-    } else {
-      fs::file_create(dst)
+      lines <- readLines(src)
     }
+    writeLines(lines, dst)
   }
 }
 

drivers/windows/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hipercow.windows
 Title: DIDE HPC Support for Windows
-Version: 1.0.31
+Version: 1.0.32
 Authors@R: c(person("Rich", "FitzJohn", role = c("aut", "cre"),
                     email = "[email protected]"),
              person("Wes", "Hinsley", role = "aut"),