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Merged
ohagen merged 2 commits into from
Aug 13, 2025
Merged

messed up workflow... changes should be on development branch #75

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a10f1ce
updating testthat calls
ohagen Aug 12, 2025
88dd7ce
base::.BaseNamespaceEnv instead of baseenv()
ohagen Aug 12, 2025
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11 changes: 6 additions & 5 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -22,13 +22,14 @@ LazyData: false
Depends: R (>= 3.5.0)
Imports: Rcpp (>= 0.12.16), Matrix, methods, utils, raster, gdistance, stringr, tools, grDevices
Suggests:
knitr,
markdown,
testthat (>= 2.1.0),
rmarkdown,
formatR
knitr,
markdown,
testthat (>= 3.2.0),
rmarkdown,
formatR
LinkingTo: Rcpp, BH
URL: https://github.com/project-Gen3sis/R-package
BugReports: https://github.com/project-Gen3sis/R-package/issues
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Config/testthat/edition: 3
21 changes: 14 additions & 7 deletions tests/testthat/test-config_handling.R
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Expand Up @@ -27,7 +27,8 @@ test_that("prepare_directories: Error on non-existing input directory", {
test_that("derive input/output directories from config path", {
skip("skip for now")
new_dirs <- list()
local_mock(dir.create = function(new_dir, ...){ new_dirs <<- append(new_dirs, new_dir)} )
testthat::local_mocked_bindings(dir.create = function(new_dir, ...){ new_dirs <<- append(new_dirs, new_dir)},
.env = baseenv())
config_file <- "data/config/tests_config_handling_0d/tests_run/config_empty.R"
dirs <- evaluate_promise(prepare_directories(config_file = config_file))
expect_true(all(new_dirs %in% dirs$result))
Expand All @@ -37,7 +38,8 @@ test_that("derive input/output directories from config path", {
test_that("prepare_directories: default config, input_directory given, output directory derived", {
skip("skip until config handling settled")
new_dirs <- list()
local_mock(dir.create = function(new_dir, ...){ new_dirs <<- append(new_dirs, new_dir)} )
testthat::local_mocked_bindings(dir.create = function(new_dir, ...){ new_dirs <<- append(new_dirs, new_dir)},
.env = baseenv())
input_directory <- "data/input"
dirs <- evaluate_promise(prepare_directories(input_directory = input_directory))
expect_true(all(new_dirs %in% dirs$result))
Expand All @@ -48,7 +50,8 @@ test_that("prepare_directories: default config, input_directory given, output di
test_that("prepare_directories: config, input-, and output- directory given", {
skip("skip for now")
new_dirs <- list()
local_mock(dir.create = function(new_dir, ...){ new_dirs <<- append(new_dirs, new_dir)} )
testthat::local_mocked_bindings(dir.create = function(new_dir, ...){ new_dirs <<- append(new_dirs, new_dir)},
.env = baseenv())
config_file <- "data/config/tests_config_handling_0d/tests_run/config_empty.R"
input_directory <- "data/input"
output_directory <- "data/output"
Expand All @@ -62,7 +65,8 @@ test_that("prepare_directories: config, input-, and output- directory given", {

test_that("no user config provided, using default config" , {
skip("skip until devtools updated in docker image")
local_mock(dir.create = function(new_dir, ...) { } )
testthat::local_mocked_bindings(dir.create = function(new_dir, ...) { },
.env = baseenv())
empty_config <- "data/config/tests_config_handling_0d/tests_run/config_empty.R"
dirs <- evaluate_promise(prepare_directories(config_file = empty_config))
expect_known_output(create_input_config(empty_config, dirs$result),
Expand All @@ -72,7 +76,8 @@ test_that("no user config provided, using default config" , {

test_that("partial user config provided" , {
skip("skip until devtools updated in docker image")
local_mock(dir.create = function(new_dir, ...) { } )
testthat::local_mocked_bindings(dir.create = function(new_dir, ...) { },
.env = baseenv())
empty_config <- "data/config/tests_config_handling_0d/tests_run/config_partial.R"
dirs <- evaluate_promise(prepare_directories(config_file = empty_config))
expect_known_output(create_input_config(empty_config, dirs$result),
Expand All @@ -82,7 +87,8 @@ test_that("partial user config provided" , {

test_that("full user config provided" , {
skip("skip until devtools updated in docker image")
local_mock(dir.create = function(new_dir, ...) { } )
testthat::local_mocked_bindings(dir.create = function(new_dir, ...) { },
.env = baseenv())
empty_config <- "data/config/tests_config_handling_0d/tests_run/config_complete.R"
dirs <- evaluate_promise(prepare_directories(config_file = empty_config))
expect_known_output(create_input_config(empty_config, dirs$result),
Expand All @@ -92,7 +98,8 @@ test_that("full user config provided" , {

test_that("user config provided with extra values" , {
skip("skip until devtools updated in docker image")
local_mock(dir.create = function(new_dir, ...) { } )
testthat::local_mocked_bindings(dir.create = function(new_dir, ...) { },
.env = baseenv())
empty_config <- "data/config/tests_config_handling_0d/tests_run/config_additional_user_values.R"
dirs <- evaluate_promise(prepare_directories(config_file = empty_config))
expect_known_output(create_input_config(empty_config, dirs$result),
Expand Down
25 changes: 21 additions & 4 deletions tests/testthat/test-input_creation.R
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@@ -1,10 +1,22 @@
test_that("create_directories overwrite protection works", {
skip("can't mock file.exists")
# remove temporary skip added due to mocking issue
# testthat::skip("can't mock file.exists")
# mocking base functions is no longer feasible, overwrite is not tested as it calls "unlink"
new_dirs <- list()
local_mock(dir.create = function(new_dir, ...){ new_dirs <<- append(new_dirs, new_dir)} )
testthat::local_mocked_bindings(
dir.create = function(new_dir, ...) {
new_dirs <<- append(new_dirs, new_dir)
},
.env = base::.BaseNamespaceEnv
)

# test overwrite protection
local_mock(file.exists = function(...){ return(TRUE)} )
testthat::local_mocked_bindings(
file.exists = function(...) {
return(TRUE)
},
.env = base::.BaseNamespaceEnv
)
expect_error(create_directories("test", overwrite = FALSE, full_matrices = FALSE),
"output directory already exists", fixed = TRUE)
})
Expand All @@ -13,7 +25,12 @@ test_that("create_directories overwrite protection works", {
test_that("create_directories works", {
# mocking base functions is no longer feasible, overwrite is not tested as it calls "unlink"
new_dirs <- list()
local_mock(dir.create = function(new_dir, ...){ new_dirs <<- append(new_dirs, new_dir)} )
testthat::local_mocked_bindings(
dir.create = function(new_dir, ...) {
new_dirs <<- append(new_dirs, new_dir)
},
.env = base::.BaseNamespaceEnv
)

create_directories("test", overwrite = FALSE, full_matrices = FALSE)
expect_true("test" %in% new_dirs)
Expand Down