update devel w/main (#68)

* initial updates * update documentation and snapshots * Update cran-comments.md --------- Co-authored-by: Michael Stackhouse <[email protected]>
pharmaverse · Oct 9, 2024 · 3b52da7 · 3b52da7
1 parent 8f9e0c0
commit 3b52da7
Show file tree

Hide file tree

Showing 8 changed files with 23 additions and 28 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,12 +9,12 @@ 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

diff --git a/LICENSE b/LICENSE
diff --git a/R/init.R b/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

diff --git a/cran-comments.md b/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.

diff --git a/man/init.Rd b/man/init.Rd
diff --git a/tests/testthat/_snaps/R4.2/autos.md b/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
 
diff --git a/tests/testthat/_snaps/R4.2/init.md b/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

diff --git a/tests/testthat/_snaps/utils.md b/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