diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 5e9a7e5..97a755d 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.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/
diff --git a/NAMESPACE b/NAMESPACE
index df3a59d..096d65e 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/envsetup.R b/R/envsetup.R
index 76c5ce0..2ce4e18 100644
--- a/R/envsetup.R
+++ b/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))
diff --git a/R/paths.R b/R/paths.R
index d41fae2..0b4f340 100644
--- a/R/paths.R
+++ b/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 == "") {
diff --git a/R/rprofile.R b/R/rprofile.R
index 653b49c..863368a 100644
--- a/R/rprofile.R
+++ b/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)) {
diff --git a/README.Rmd b/README.Rmd
index 212f332..cc9db02 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -15,33 +15,84 @@ knitr::opts_chunk$set(
# envsetup 
+
+[
](https://pharmaverse.org)
+[](https://github.com/pharmaverse/envsetup/actions/workflows/R-CMD-check.yaml)
+[](https://pharmaverse.github.io/envsetup/)
+[](https://pharmaverse.github.io/envsetup/_xml_coverage_reports/coverage.html)
+
+
+
+
+
+[](https://www.repostatus.org/#active)
+[](https://github.com/pharmaverse/envsetup/tree/main)
+[](https://github.com/pharmaverse/envsetup/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
+
+
+
-
-[](https://pharmaverse.org)
-
-[](https://app.codecov.io/gh/pharmaverse/envsetup?branch=main)
+# Overview
-
+The `envsetup` package helps you manage R project environments by
+providing a flexible configuration system that adapts to different
+deployment stages (development, testing, production) without requiring
+code changes.
-## Overview
+## Why Use envsetup?
-The purpose of this package is to support the setup of the R environment. The two main features are:
+When working on R projects, you often need to:
+- Point to different data sources across environments
-- `autos` to automatically source files and/or directories into your environment
+- Use different output directories
-- `paths` to consistently set path objects across projects for I/O
+- Load environment-specific functions
-Both are implemented using a configuration file to allow easy, custom configurations that can be used for multiple or all projects.
+- Maintain consistent code across environments like dev, qa, and prod
+Instead of hardcoding paths or manually changing configurations,
+`envsetup` uses YAML configuration files to manage these differences
+automatically.
-## Installation
+## Basic Concepts
-```{r eval = FALSE}
-install.packages("envsetup")
+The `envsetup` package works with two main components:
+
+1. **PATHS**: Manages file system locations (data, output, programs)
+2. **AUTOS**: Automatically sources R scripts from specified
+ directories
+
+## Your First Configuration
+
+Here's the simplest possible `_envsetup.yml` configuration:
+
+``` yaml
+default:
+ paths:
+ data: "/path/to/your/data"
+ output: "/path/to/your/output"
+```
+
+## Quick Start Example
+
+```{r eval=FALSE}
+library(envsetup)
+
+# Load your configuration
+envsetup_config <- config::get(file = "_envsetup.yml")
+
+# Apply the configuration
+rprofile(envsetup_config)
+
+# Now you can use the configured paths
+print(data) # Points to your data directory
+print(output) # Points to your output directory
```
+## Installation
+
### Development version
```{r eval = FALSE}
@@ -49,18 +100,18 @@ install.packages("envsetup")
devtools::install_github("pharmaverse/envsetup")
```
+## What's Next?
-## Usage
+In the following guides, you'll learn:
-1. Create the _envsetup.yml configuration file to specify your autos and paths and store centrally. See `vignette("config")` for more details on how to create your config.
-2. Create or update your `.Rprofile` to read in the config and call `rprofile()`
+- How to set up basic path configurations
-```{r eval = FALSE}
-library(envsetup)
+- Managing multiple environments
-# read configuration
-envsetup_config <- config::get(file = "path/to/_envsetup.yml")
+- Advanced path resolution
-# pass configuration to rprofile() to setup the environment
-rprofile(envsetup_config)
-```
+- Automatic script sourcing
+
+- Real-world examples and best practices
+
+Let's start with basic path configuration in the next section.
diff --git a/README.md b/README.md
index 5bb25c8..c2210d9 100644
--- a/README.md
+++ b/README.md
@@ -3,33 +3,98 @@
# envsetup
-
+
[](https://pharmaverse.org)
-
-[](https://app.codecov.io/gh/pharmaverse/envsetup?branch=main)
-
+[](https://github.com/pharmaverse/envsetup/actions/workflows/R-CMD-check.yaml)
+[](https://pharmaverse.github.io/envsetup/)
+[](https://pharmaverse.github.io/envsetup/_xml_coverage_reports/coverage.html)
+
+
+
+
+
+[](https://www.repostatus.org/#active)
+[](https://github.com/pharmaverse/envsetup/tree/main)
+[](https://github.com/pharmaverse/envsetup/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
+
+
-## Overview
+# Overview
-The purpose of this package is to support the setup of the R
-environment. The two main features are:
+The `envsetup` package helps you manage R project environments by
+providing a flexible configuration system that adapts to different
+deployment stages (development, testing, production) without requiring
+code changes.
-- `autos` to automatically source files and/or directories into your
- environment
+## Why Use envsetup?
-- `paths` to consistently set path objects across projects for I/O
+When working on R projects, you often need to:
-Both are implemented using a configuration file to allow easy, custom
-configurations that can be used for multiple or all projects.
+- Point to different data sources across environments
-## Installation
+- Use different output directories
+
+- Load environment-specific functions
+
+- Maintain consistent code across environments like dev, qa, and prod
+
+Instead of hardcoding paths or manually changing configurations,
+`envsetup` uses YAML configuration files to manage these differences
+automatically.
+
+## Basic Concepts
+
+The `envsetup` package works with two main components:
+
+1. **PATHS**: Manages file system locations (data, output, programs)
+2. **AUTOS**: Automatically sources R scripts from specified
+ directories
+
+## Your First Configuration
+
+Hereโs the simplest possible `_envsetup.yml` configuration:
+
+``` yaml
+default:
+ paths:
+ data: "/path/to/your/data"
+ output: "/path/to/your/output"
+```
+
+## Quick Start Example
``` r
-install.packages("envsetup")
+library(envsetup)
+
+# Load your configuration
+envsetup_config <- config::get(file = "_envsetup.yml")
+
+# Apply the configuration
+rprofile(envsetup_config)
+
+# Now you can use the configured paths
+print(data) # Points to your data directory
+print(output) # Points to your output directory
```
+## Installation
+
### Development version
``` r
@@ -37,20 +102,18 @@ install.packages("envsetup")
devtools::install_github("pharmaverse/envsetup")
```
-## Usage
+## Whatโs Next?
-1. Create the \_envsetup.yml configuration file to specify your autos
- and paths and store centrally. See `vignette("config")` for more
- details on how to create your config.
-2. Create or update your `.Rprofile` to read in the config and call
- `rprofile()`
+In the following guides, youโll learn:
-``` r
-library(envsetup)
+- How to set up basic path configurations
-# read configuration
-envsetup_config <- config::get(file = "path/to/_envsetup.yml")
+- Managing multiple environments
-# pass configuration to rprofile() to setup the environment
-rprofile(envsetup_config)
-```
+- Advanced path resolution
+
+- Automatic script sourcing
+
+- Real-world examples and best practices
+
+Letโs start with basic path configuration in the next section.
diff --git a/man/envsetup_environment.Rd b/man/envsetup_environment.Rd
index 77ffb3c..c7bf617 100644
--- a/man/envsetup_environment.Rd
+++ b/man/envsetup_environment.Rd
@@ -3,14 +3,39 @@
\docType{data}
\name{envsetup_environment}
\alias{envsetup_environment}
-\title{Path environment}
+
+\title{Environment Setup Environment}
\format{
-An object of class \code{environment} of length 0.
+An environment object created with \code{new.env()}.
}
\usage{
envsetup_environment
}
\description{
-Path 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.
+}
+\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}}
+
}
\keyword{datasets}
diff --git a/man/get_path.Rd b/man/get_path.Rd
new file mode 100644
index 0000000..3367276
--- /dev/null
+++ b/man/get_path.Rd
@@ -0,0 +1,48 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/paths.R
+\name{get_path}
+\alias{get_path}
+\title{Get Path Object from Environment}
+\usage{
+get_path(path, envir = getOption("envsetup.path.environment"))
+}
+\arguments{
+\item{path}{An unquoted name of the path object to retrieve from the environment.}
+
+\item{envir}{The environment to search for the path object. Defaults to the
+value of \code{getOption("envsetup.path.environment")}.}
+}
+\value{
+The path object stored in the specified environment under the given name.
+}
+\description{
+Retrieves a path object from the specified environment using non-standard
+evaluation. The function uses \code{substitute()} to capture the unevaluated
+expression and \code{get()} to retrieve the corresponding object.
+}
+\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}}
+}
diff --git a/man/read_path.Rd b/man/read_path.Rd
index e646ced..ab8d075 100644
--- a/man/read_path.Rd
+++ b/man/read_path.Rd
@@ -8,7 +8,8 @@ read_path(
lib,
filename,
full.path = TRUE,
- envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON")
+ envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON"),
+ envir = getOption("envsetup.path.environment")
)
}
\arguments{
diff --git a/man/rprofile.Rd b/man/rprofile.Rd
index 1de3c31..867dbfd 100644
--- a/man/rprofile.Rd
+++ b/man/rprofile.Rd
@@ -4,7 +4,7 @@
\alias{rprofile}
\title{Function used to pass through code to the .Rprofile}
\usage{
-rprofile(config, overwrite = TRUE)
+rprofile(config, envir = getOption("envsetup.path.environment"))
}
\arguments{
\item{config}{configuration object from config::get()}
diff --git a/man/write_path.Rd b/man/write_path.Rd
index cecfc1d..d1421bc 100644
--- a/man/write_path.Rd
+++ b/man/write_path.Rd
@@ -7,7 +7,8 @@
write_path(
lib,
filename = NULL,
- envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON")
+ envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON"),
+ envir = getOption("envsetup.path.environment")
)
}
\arguments{
diff --git a/tests/testthat/test-autos.R b/tests/testthat/test-autos.R
index 558df55..98b2a70 100644
--- a/tests/testthat/test-autos.R
+++ b/tests/testthat/test-autos.R
@@ -172,6 +172,15 @@ test_that("Autos validation from yml happens correctly", {
expect_warning(set_autos(list(x = "/bad/path/")),
"An autos path specified in your envsetup configuration file does not exist")
+
+
+ withr::local_envvar(c("ENVSETUP_ENVIRON" = ""))
+
+ expect_error(
+ set_autos(list(project = c(DEV="path1", PROD="path2"))),
+ "The envsetup_environ parameter or ENVSETUP_ENVIRON environment variable must be used if hierarchical autos are set."
+ )
+
})
# Detatch and re-setup for QA now
diff --git a/tests/testthat/test-paths.R b/tests/testthat/test-paths.R
index 1231a0a..5761e64 100644
--- a/tests/testthat/test-paths.R
+++ b/tests/testthat/test-paths.R
@@ -21,6 +21,22 @@ test_that("read_path will return the correct path if the object exists in anothe
rm(data)
})
+test_that("read_path checks fire as expected", {
+ expect_error(
+ read_path("data", "iris.csv"),
+ "The lib argument should be an object containing the paths for all environments of a directory, not a string."
+ )
+
+ withr::local_envvar(ENVSETUP_ENVIRON = "dev")
+
+ expect_warning(
+ read_path(data, "iris.csv"),
+ "The path has named environments DEV, QA, PROD that do not match with the envsetup_environ parameter or ENVSETUP_ENVIRON environment variable"
+ )
+
+
+})
+
test_that("write_path will return the correct path if the object exists in another environment", {
data <- function() {
stop()
@@ -31,6 +47,52 @@ test_that("write_path will return the correct path if the object exists in anoth
rm(data)
})
+test_that("write_path checks fire as expected", {
+ expect_error(
+ write_path("data", "iris.csv"),
+ "The lib argument should be an object containing the paths for all environments of a directory, not a string."
+ )
+ expect_error(
+ write_path(data, "iris.csv", envsetup_environ = ""),
+ "The envsetup_environ parameter or ENVSETUP_ENVIRON environment variable must be used if hierarchical paths are set."
+ )
+
+ withr::local_envvar(ENVSETUP_ENVIRON = "dev")
+
+ expect_warning(
+ write_path(data, "iris.csv"),
+ "The path has named environments DEV, QA, PROD that do not match with the envsetup_environ parameter or ENVSETUP_ENVIRON environment variable"
+ )
+
+
+})
+
+test_that("build_from_config checks fire as expected", {
+ build_tmpdir <- tempdir()
+ withr::defer(unlink(build_tmpdir))
+
+ hierarchy <- "default:
+ path:
+ data: !expr list(DEV = '/demo/DEV/username/project1/data',
+ PROD = '/demo/PROD/project1/data')
+ output: !expr list(DEV = '/demo/DEV/username/project1/output',
+ PROD = '/demo/PROD/project1/output')
+ programs: !expr list(DEV = '/demo/DEV/username/project1/programs',
+ PROD = '/demo/PROD/project1/programs')
+ docs: !expr list(DEV = 'docs',
+ PROD = 'docs')"
+
+ writeLines(hierarchy, file.path(build_tmpdir, "hierarchy.yml"))
+
+ config <- config::get(file = file.path(build_tmpdir, "hierarchy.yml"))
+
+ expect_message(
+ build_from_config(config, build_tmpdir),
+ "No paths are specified as part of your configuration. Update your config file to add paths."
+ )
+
+})
+
test_that("build_from_config builds the correct directories", {
build_tmpdir <- tempdir()
withr::defer(unlink(build_tmpdir))
@@ -63,6 +125,7 @@ test_that("build_from_config builds the correct directories", {
expect_true(dir.exists(file.path(build_tmpdir, "docs")))
})
+
#' @editor Aidan Ceney
#' @editDate 2022-05-12
test_that("1.1", {
@@ -150,3 +213,20 @@ test_that("write_path works with unset envsetup_environ and non-hierarhical path
readin <- write_path(data)
expect_equal(readin, paste0(tmpdir, "/DEV/data"))
})
+
+#' @editor Nick Masel
+#' @editDate 2025-07-16
+test_that("path environment option will store and retrieve paths from envsetup environment", {
+ withr::local_options(
+ envsetup.path.environment = envsetup_environment
+ )
+
+ expect_message(rprofile(envsetup_config), "^Assigned paths to package\\:envsetup\\$envsetup_environment")
+
+ expect_equal(getOption("envsetup.path.environment"), envsetup_environment)
+
+ expect_equal(all(c("auto_stored_envsetup_config", "data", "programs", "functions", "output") %in% ls(envir = envsetup_environment)), TRUE)
+
+ expect_equal(get_path(data), envsetup_environment$data)
+})
+
diff --git a/tests/testthat/test-rprofile.R b/tests/testthat/test-rprofile.R
index 1011f40..e23e417 100644
--- a/tests/testthat/test-rprofile.R
+++ b/tests/testthat/test-rprofile.R
@@ -18,7 +18,8 @@ rootpath_dev <- "DEV"
rootpath_qa <- "QA"
rootpath_prod <- "PROD"
-
+#' @editor Nick Masel
+#' @editDate 2025-07-17
test_that("rprofile stores the configuration", {
config_tmpdir <- tempdir()
withr::defer(unlink(file.path(config_tmpdir, ".Rprofile")))
@@ -38,12 +39,7 @@ test_that("rprofile stores the configuration", {
rprofile(custom_name)
- stored_config <- base::get(
- "auto_stored_envsetup_config",
- pos = which(search() == "envsetup:paths")
- )
-
- expect_equal(custom_name, stored_config)
+ expect_equal(custom_name, auto_stored_envsetup_config)
})
@@ -52,8 +48,6 @@ test_that("rprofile stores the configuration", {
test_that("1.1", {
rprofile(envsetup_config)
- withr::defer(detach(envsetup:paths))
-
expected <- list()
folder <- "data"
expected$DEV <- file.path(tmpdir, rootpath_dev, folder)
@@ -70,8 +64,6 @@ test_that("2.1", {
Sys.setenv(ENVSETUP_ENVIRON = "DEV")
rprofile(envsetup_config)
- withr::defer(detach(envsetup:paths))
-
expect_equal(c(test_dev()), c("Test of dev autos"))
})
@@ -89,7 +81,5 @@ test_that("3.1", {
read_path(data, "iris.csv", full.path = TRUE, envsetup_environ = "DEV")
)
- withr::defer(detach(envsetup:paths))
-
expect_equal(tidyr::as_tibble(iris)$Petal.Length, readin$Petal.Length)
})