move paths to an environment w/in envsetup

.github/workflows/test-coverage.yaml

@@ -1,62 +1,50 @@
-# 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
+name: test-coverage
+
 on:
   push:
-    branches: [main, master]
+    branches: [main]
   pull_request:
-
-name: test-coverage.yaml
-
-permissions: read-all
+    branches: [main]
 
 jobs:
-  test-coverage:
+  coverage:
     runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    permissions:
+      contents: write
 
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::covr, any::xml2
-          needs: coverage
+      - name: Install system dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
 
-      - 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@v4
-        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 }}
-          file: ./cobertura.xml
-          plugin: noop
-          disable_search: true
-          token: ${{ secrets.CODECOV_TOKEN }}
-
-      - name: Show testthat output
-        if: always()
+      - name: Install dependencies
         run: |
-          ## --------------------------------------------------------------------
-          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          Rscript -e 'install.packages(c("remotes", "covr", " testthat", "DT", "htmltools"))'
+          Rscript -e 'remotes::install_deps(dependencies = TRUE)'
 
-      - name: Upload test results
-        if: failure()
-        uses: actions/upload-artifact@v4
+
+      - name: Run coverage and generate badge
+        run: |
+          mkdir -p coverage
+          Rscript -e '
+            cov <- covr::package_coverage(type = "tests")
+            covr::to_cobertura(cov, "coverage/cobertura.xml")
+            covr::report(cov, file = "coverage/coverage.html")
+            pct <- round(covr::percent_coverage(cov))
+            col <- if (pct >= 90) "brightgreen" else if (pct >= 75) "orange" else "red"
+            url <- sprintf("https://img.shields.io/badge/coverage-%s%%25-%s.svg", pct, col)
+            download.file(url, "coverage/badge.svg", quiet = TRUE)
+          '
+
+      - name: Deploy badge and reports to gh-pages
+        uses: peaceiris/actions-gh-pages@v3
         with:
-          name: coverage-test-failures
-          path: ${{ runner.temp }}/package
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./coverage
+          publish_branch: gh-pages
+          destination_dir: _xml_coverage_reports/

NAMESPACE

@@ -3,6 +3,7 @@
 export(build_from_config)
 export(detach_autos)
 export(envsetup_environment)
+export(get_path)
 export(init)
 export(read_path)
 export(rprofile)

R/envsetup.R

@@ -6,7 +6,8 @@
       mustWork = TRUE
     ),
     envsetup.rprofile.path = system.file(".Rprofile", package = "envsetup"),
-    envsetup.renviron.path = system.file(".Renviron", package = "envsetup")
+    envsetup.renviron.path = system.file(".Renviron", package = "envsetup"),
+    envsetup.path.environment = .GlobalEnv
   )
 
   toset <- !(names(op.envsetup) %in% names(op))

R/paths.R

@@ -1,7 +1,74 @@
-#' Path environment
+#' Environment Setup Environment
+#'
+#' A dedicated environment object used to store and manage path configurations
+#' and other setup variables for the envsetup package. This environment provides
+#' an isolated namespace for storing path objects that can be retrieved using
+#' the package's path management functions.
+#'
+#' @format An environment object created with \code{new.env()}.
+#'
+#' @details
+#' This environment serves as the default storage location for path objects
+#' when using envsetup package functions. It helps maintain clean separation
+#' between user workspace and package-managed paths.
+#'
+#' @examples
+#' # Store a path in the envsetup environment
+#' assign("project_root", "/path/to/project", envir = envsetup_environment)
+#'
+#' # List objects in the environment
+#' ls(envir = envsetup_environment)
+#'
+#' # Check if the environment exists and is an environment
+#' exists("envsetup_environment")
+#' is.environment(envsetup_environment)
+#'
+#' @seealso \code{\link{get_path}}, \code{\link[base]{new.env}}
+#'
 #' @export
 envsetup_environment <- new.env()
 
+#' Get Path Object from Environment
+#'
+#' Retrieves a path object from the specified environment using non-standard
+#' evaluation. The function uses `substitute()` to capture the unevaluated
+#' expression and `get()` to retrieve the corresponding object.
+#'
+#' @param path An unquoted name of the path object to retrieve from the environment.
+#' @param envir The environment to search for the path object. Defaults to the
+#'   value of `getOption("envsetup.path.environment")`.
+#'
+#' @return The path object stored in the specified environment under the given name.
+#'
+#' @examples
+#' # Create a custom environment and store some paths
+#' path_env <- new.env()
+#' assign("data_dir", "/home/user/data", envir = path_env)
+#' assign("output_dir", "/home/user/output", envir = path_env)
+#'
+#' # Set up the option to use our custom environment
+#' options(envsetup.path.environment = path_env)
+#'
+#' # Retrieve paths using the function
+#' data_path <- get_path(data_dir)
+#' output_path <- get_path(output_dir)
+#'
+#' print(data_path)    # "/home/user/data"
+#' print(output_path)  # "/home/user/output"
+#'
+#' # Using with a different environment
+#' temp_env <- new.env()
+#' assign("temp_dir", "/tmp/analysis", envir = temp_env)
+#' temp_path <- get_path(temp_dir, envir = temp_env)
+#' print(temp_path)    # "/tmp/analysis"
+#'
+#' @seealso \code{\link[base]{get}}, \code{\link[base]{substitute}}
+#'
+#' @export
+get_path <- function(path, envir = getOption("envsetup.path.environment")){
+  base::get(substitute(path), envir)
+}
+
 #' Read path
 #'
 #' Check each environment for the file and return the path to the first.
@@ -57,10 +124,11 @@ envsetup_environment <- new.env()
 read_path <- function(lib,
                       filename,
                       full.path = TRUE,
-                      envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON")) {
+                      envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON"),
+                      envir = getOption("envsetup.path.environment")) {
 
   # lib can be a object in a different environment
-  # get this directly from envsetup:paths
+  # get this directly from envsetup_environment
   lib_arg <- quo_get_expr(enquo(lib))
 
   if (is_string(lib_arg)) {
@@ -70,7 +138,7 @@ read_path <- function(lib,
     ), call. = FALSE)
   }
 
-  read_lib <- base::get(toString(lib_arg), "envsetup:paths")
+  read_lib <- base::get(toString(lib_arg), envir)
 
   restricted_paths <- read_lib
 
@@ -166,7 +234,8 @@ read_path <- function(lib,
 #'
 #' # save data in data folder using write_path
 #' saveRDS(mtcars, write_path(data, "mtcars.rds"))
-write_path <- function(lib, filename = NULL, envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON")) {
+write_path <- function(lib, filename = NULL, envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON"),
+                       envir = getOption("envsetup.path.environment")) {
   # examine lib to ensure it's not a string
   # if it's a string, you end up with an incorrect path
   lib_arg <- quo_get_expr(enquo(lib))
@@ -178,7 +247,7 @@ write_path <- function(lib, filename = NULL, envsetup_environ = Sys.getenv("ENVS
     ), call. = FALSE)
   }
 
-  write_path <- base::get(toString(lib_arg), "envsetup:paths")
+  write_path <- base::get(toString(lib_arg), envir)
   path <- write_path
 
   if (length(write_path) > 1 && envsetup_environ == "") {

R/rprofile.R

@@ -23,32 +23,23 @@
 #' writeLines(hierarchy, file.path(tmpdir, "hierarchy.yml"))
 #'
 #' rprofile(config::get(file = file.path(tmpdir, "hierarchy.yml")))
-rprofile <- function(config, overwrite = TRUE) {
-  if ("envsetup:paths" %in% search()) {
-    detach("envsetup:paths", character.only = TRUE)
-  }
+rprofile <- function(config,
+                     envir = getOption("envsetup.path.environment"), 
+                     overwrite = TRUE) {
 
   # remove autos and pass everything else to "envsetup:paths"
   config_minus_autos <- config
   config_minus_autos$autos <- NULL
 
-  # attach after package to allow functions from package to be used in config
-  if (any(search() == "package:envsetup")) {
-    pos <- which(search() == "package:envsetup") + 1
-  } else {
-    (pos <- 2L)
-  }
-
-  attach(config_minus_autos$paths,
-    name = "envsetup:paths",
-    pos = pos
-  )
+  walk2(names(config_minus_autos$paths),
+        config_minus_autos$paths,
+        assign,
+        envir = envir)
 
-  message("Attaching paths to envsetup:paths")
+  message(paste0("Assigned paths to ", envnames::environment_name(envir)))
 
   # store config with a standard name in a standard location
-  # this will allow `envsetup::library()` to re-attach autos
-  assign("auto_stored_envsetup_config", config, pos)
+  assign("auto_stored_envsetup_config", config, envir = envir)
 
   # If autos exist, set them
   if (!is.null(config$autos)) {