Closes #66: remove nulls before setting autos

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: envsetup
 Title: Support the Setup of the R Environment for Clinical Trial Programming Workflows
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: c(
     person("Nicholas", "Masel", email = "[email protected]", role = c("aut", "cre")),
     person("Mike", "Stackhouse", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0001-6030-723X")),
@@ -9,15 +9,15 @@ Authors@R: c(
     person("Atorus Research LLC", role = "cph")
   )
 Description: The purpose of this package is to support the setup the R environment.  
-    The two main features are `autos`, to automatically source files and/or 
-    directories into your environment, and `paths` to consistently set path objects 
+    The two main features are 'autos', to automatically source files and/or 
+    directories into your environment, and 'paths' to consistently set path objects 
     across projects for input and output. Both are implemented using a configuration 
     file to allow easy, custom configurations that can be used for multiple 
     or all projects.
-License: Apache License 2.0 | file LICENSE
+License: Apache License 2.0
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports: 
     config,
     fs,

NEWS.md

@@ -1,8 +1,11 @@
+# envsetup 0.2.1
+
+- `set_autos()` will how handle NULL hierarchical paths (#66)
+
 # envsetup 0.2.0
 
 - `library()` will no longer actively reset autos, instead placing newly attached packages in the correct position that respects existing autos (#59)
 
-
 # envsetup 0.1.0
 
 - Minor updates to prepare for initial CRAN release (#55)

R/autos.R

@@ -24,6 +24,11 @@ set_autos <- function(autos, envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON"))
     stop("Paths for autos in your envsetup configuration file must be named", call.=FALSE)
   }
 
+  # remove NULL before further processing
+  # NULL is expected for hierarchical paths when running in an environment
+  # after the first level of the hierarchy
+  autos <- autos[!vapply(autos, is.null, FALSE)]
+
   for (i in seq_along(autos)) {
     cur_autos <- autos[[i]]
 
@@ -291,4 +296,4 @@ library <- function(..., pos = NULL) {
       pos <- min(grep("^package:", search()))
   }
   base::library(..., pos = pos)
-}
+}

R/init.R

@@ -1,6 +1,6 @@
 #' Initialize the R environment with envsetup
 #'
-#' @param project Character. The path to the project directory. Defaults to the current working directory.
+#' @param project Character. The path to the project directory.
 #' @param config_path Character. The path of the config file. Defaults to NULL.
 #' @param create_paths Logical indicating if missing paths should be created. Defaults to NULL.
 #' @export
@@ -36,7 +36,7 @@
 #' init(project = tmpdir,
 #'      config_path = file.path(tmpdir, "hierarchy.yml"),
 #'      create_paths = TRUE)
-init <- function(project = getwd(), config_path = NULL, create_paths = NULL) {
+init <- function(project, config_path = NULL, create_paths = NULL) {
 
   create_config <- FALSE
   config_found <- FALSE

cran-comments.md

@@ -1,3 +1,10 @@
+## Resubmission
+This is a resubmission.  In this version I have:
+
+* Corrected quotations in the description.
+* Removed the LICENSE file, as there are no additional restrictions.
+* Removed the default write path in R/init.R.
+
 ## envsetup 0.1.0
 
 Tested on RHEL 7, RHEL 8, GitHub Action and RHub.

tests/testthat/_snaps/R4.2/autos.md

@@ -2,6 +2,7 @@
 
     Code
       suppressMessages(rprofile(custom_name))
-    Warning <simpleWarning>
+    Condition
+      Warning:
       The projects autos has named environments DEV, QA, PROD that do not match with the envsetup_environ parameter or ENVSETUP_ENVIRON environment variable bad_name
 

tests/testthat/_snaps/R4.2/init.md

@@ -2,7 +2,7 @@
 
     Code
       init(init_tmpdir, config_path, create_paths = FALSE)
-    Message <rlang_message>
+    Message
       v Configuration file found!
       i The following paths in your configuration do not exist:
         /DEV/username/project1/data
@@ -21,7 +21,7 @@
 
     Code
       init(init_tmpdir, config_path, create_paths = FALSE)
-    Message <rlang_message>
+    Message
       v Configuration file found!
       i The following paths in your configuration do not exist:
         /DEV/username/project1/data
@@ -40,7 +40,7 @@
 
     Code
       init(init_tmpdir, config_path, create_paths = FALSE)
-    Message <rlang_message>
+    Message
       v Configuration file found!
       i The following paths in your configuration do not exist:
         /DEV/username/project1/data

tests/testthat/_snaps/R4.4/autos.md

@@ -0,0 +1,8 @@
+# Autos warns user when ENVSETUP_ENVIRON does not match named environments in autos
+
+    Code
+      suppressMessages(rprofile(custom_name))
+    Condition
+      Warning:
+      The projects autos has named environments DEV, QA, PROD that do not match with the envsetup_environ parameter or ENVSETUP_ENVIRON environment variable bad_name
+

tests/testthat/_snaps/R4.4/init.md

@@ -0,0 +1,57 @@
+# init creates a .Rprofile
+
+    Code
+      init(init_tmpdir, config_path, create_paths = FALSE)
+    Message
+      v Configuration file found!
+      i The following paths in your configuration do not exist:
+        /DEV/username/project1/data
+        /PROD/project1/data
+        /DEV/username/project1/programs
+        /PROD/project1/programs
+        /DEV/username/project1/functions
+        /PROD/project1/functions
+        /DEV/username/project1/output
+        /PROD/project1/output
+      i All path objects will not work since directories are missing.
+      v .Rprofile created
+      v envsetup initialization complete
+
+# init initializes an .Rprofile correcty when one does not exist
+
+    Code
+      init(init_tmpdir, config_path, create_paths = FALSE)
+    Message
+      v Configuration file found!
+      i The following paths in your configuration do not exist:
+        /DEV/username/project1/data
+        /PROD/project1/data
+        /DEV/username/project1/programs
+        /PROD/project1/programs
+        /DEV/username/project1/functions
+        /PROD/project1/functions
+        /DEV/username/project1/output
+        /PROD/project1/output
+      i All path objects will not work since directories are missing.
+      v .Rprofile created
+      v envsetup initialization complete
+
+# init initializes an .Rprofile correcty when one does exist
+
+    Code
+      init(init_tmpdir, config_path, create_paths = FALSE)
+    Message
+      v Configuration file found!
+      i The following paths in your configuration do not exist:
+        /DEV/username/project1/data
+        /PROD/project1/data
+        /DEV/username/project1/programs
+        /PROD/project1/programs
+        /DEV/username/project1/functions
+        /PROD/project1/functions
+        /DEV/username/project1/output
+        /PROD/project1/output
+      i All path objects will not work since directories are missing.
+      v .Rprofile updated
+      v envsetup initialization complete
+

tests/testthat/_snaps/utils.md

@@ -2,15 +2,15 @@
 
     Code
       validate_config(config::get(file = path))
-    Message <rlang_message>
+    Message
       v paths are specified as part of your configuration
       i no hierarchical paths found
 
 # validate_config, hierarchy paths return correct messages
 
     Code
       validate_config(config::get(file = path))
-    Message <rlang_message>
+    Message
       v paths are specified as part of your configuration
       v hierarchal paths found for:
         data
@@ -21,7 +21,7 @@
 
     Code
       validate_config(config::get(file = path))
-    Message <rlang_message>
+    Message
       v paths are specified as part of your configuration
       v hierarchal paths found for:
         data
@@ -35,6 +35,6 @@
 
     Code
       validate_config(config::get(file = path))
-    Message <rlang_message>
+    Message
       i no paths are specified as part of your configuration, skipping path valiation
 

tests/testthat/man/_envsetup_testthat_null.yml

@@ -0,0 +1,33 @@
+default:
+  project_path: !expr Sys.setenv(ENVSETUP_PROJECT_PATH = Sys.getenv("testpath"));
+                      Sys.getenv("testpath")
+  paths:
+    data: !expr list(
+      DEV = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "DEV", "data"),
+      QA = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "QA", "data"),
+      PROD = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "PROD", "data")
+      )
+    programs: !expr list(
+      DEV = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "DEV", "programs"),
+      QA = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "QA", "programs"),
+      PROD = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "PROD", "programs")
+      )
+    functions: !expr list(
+      DEV = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "DEV", "functions"),
+      QA = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "QA", "functions"),
+      PROD = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "PROD", "functions")
+      )
+    output: !expr list(
+      DEV = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "DEV", "output"),
+      QA = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "QA", "output"),
+      PROD = file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "PROD", "output")
+      )
+  autos:
+    projects: !expr NULL
+    global: !expr file.path(Sys.getenv("ENVSETUP_PROJECT_PATH"), "global", "functions")
+    envre: !expr file.path(
+      Sys.getenv("ENVSETUP_PROJECT_PATH"),
+      "PROD",
+      "functions",
+      "envre.R"
+      )

tests/testthat/test-autos.R

@@ -8,6 +8,7 @@ file.copy(testthat::test_path("man/testdir/DEV"), tmpdir, recursive = TRUE)
 file.copy(testthat::test_path("man/testdir/global"), tmpdir, recursive = TRUE)
 file.copy(testthat::test_path("man/testdir/PROD"), tmpdir, recursive = TRUE)
 file.copy(testthat::test_path("man/testdir/QA"), tmpdir, recursive = TRUE)
+dir.create(file.path(tmpdir, "returns_null"))
 
 custom_name <- config::get(
   file = testthat::test_path("man/_envsetup_testthat.yml")
@@ -125,3 +126,15 @@ test_that("Autos warns user when ENVSETUP_ENVIRON does not match named environme
 
   expect_snapshot(suppressMessages(rprofile(custom_name)), variant = r_version())
 })
+
+
+#' @editor Nick Masel
+#' @editDate 2024-10-24
+detach_autos()
+Sys.setenv(ENVSETUP_ENVIRON = "QA")
+null_test <- config::get(
+  file = testthat::test_path("man/_envsetup_testthat_null.yml")
+)
+test_that("NULL paths do not throw an error", {
+  expect_no_error(set_autos(null_test$autos))
+})