Harden pkgcheck and CI paths

.github/workflows/test-coverage.yaml

@@ -9,7 +9,9 @@ on:
 
 name: test-coverage.yaml
 
-permissions: read-all
+permissions:
+  contents: read
+  id-token: write
 
 jobs:
   test-coverage:
@@ -39,10 +41,9 @@ jobs:
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
+          use_oidc: true
           fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
-          file: ./cobertura.xml
-          plugin: noop
+          files: ./cobertura.xml
           disable_search: true
-          token: ${{ secrets.CODECOV_TOKEN }} 

.gitignore

@@ -2,6 +2,7 @@
 .Rhistory
 .RData
 .Ruserdata
+.DS_Store
 old
 repomix.*
 Rplots.pdf

NEWS.md

@@ -1,5 +1,10 @@
 # bidser 0.5.0
 
+* Allow `create_mock_bids()` to construct an empty project when
+  `file_structure` has the required columns but zero rows.
+* Make the quickstart vignette exit cleanly when its example dataset cannot be
+  downloaded, instead of passing a missing path to `bids_project()`.
+
 * `read_sidecar(inherit = TRUE)` now anchors on the imaging scans matching the
   query and resolves each scan's effective metadata via BIDS inheritance,
   returning one row per scan. Previously it anchored on JSON sidecar *files*, so

R/all_generic.R

@@ -968,6 +968,17 @@ read_dataset_description <- function(x, ...) {
 #' @param ... Additional arguments passed to methods.
 #' @return A character scalar.
 #' @export
+#' @examples
+#' desc_dir <- tempfile("bids-description-")
+#' dir.create(desc_dir)
+#' writeLines(
+#'   '{"Name":"Example Dataset","BIDSVersion":"1.9.0","DatasetType":"raw"}',
+#'   file.path(desc_dir, "dataset_description.json")
+#' )
+#' desc <- read_dataset_description(desc_dir)
+#' dataset_name(desc)
+#' dataset_type(desc)
+#' unlink(desc_dir, recursive = TRUE)
 dataset_name <- function(x, ...) UseMethod("dataset_name")
 #' @rdname dataset_name
 #' @export

R/mock_bids.R

@@ -522,7 +522,7 @@ create_mock_bids <- function(project_name,
   generated_event_paths <- character() # Keep track of event files defined
   generated_confound_paths <- character() # Keep track of confound files defined
 
-  for (i in 1:nrow(file_structure)) {
+  for (i in seq_len(nrow(file_structure))) {
     row <- file_structure[i, ]
 
     # Extract all potential BIDS entities from the row
@@ -689,9 +689,11 @@ create_mock_bids <- function(project_name,
     if (row$fmriprep) {
         prep_dir_parts <- strsplit(prep_dir,"/")[[1]]
         # Check if path_parts start with prep_dir_parts and remove them
-        if (length(path_parts) >= length(prep_dir_parts) &&
-            all(path_parts[1:length(prep_dir_parts)] == prep_dir_parts)) {
-            path_parts <- path_parts[-(1:length(prep_dir_parts))]
+        prep_dir_index <- seq_along(prep_dir_parts)
+        if (length(prep_dir_parts) > 0L &&
+            length(path_parts) >= length(prep_dir_parts) &&
+            all(path_parts[prep_dir_index] == prep_dir_parts)) {
+            path_parts <- path_parts[-prep_dir_index]
         }
     }
 

R/pack_bids.R

@@ -915,7 +915,7 @@ list_pack_bids <- function(archive_path, verbose = TRUE) {
     # We need to extract to temp dir to get file sizes
     temp_extract <- tempfile("bids_list_")
     dir.create(temp_extract)
-    on.exit(unlink(temp_extract, recursive = TRUE))
+    on.exit(unlink(temp_extract, recursive = TRUE), add = TRUE)
 
     untar(archive_path, exdir = temp_extract)
 

tests/testthat/test_mock_bids.R

@@ -88,6 +88,28 @@ test_that("Mock BIDS project can be created", {
   expect_equal(mock_proj$prep_dir, "derivatives/mockprep")
 })
 
+test_that("create_mock_bids supports an empty file structure", {
+  empty_structure <- tibble::tibble(
+    subid = character(),
+    datatype = character(),
+    suffix = character(),
+    fmriprep = logical()
+  )
+
+  mock_proj <- create_mock_bids(
+    project_name = "EmptyMock",
+    participants = "01",
+    file_structure = empty_structure
+  )
+
+  expect_s3_class(mock_proj, "mock_bids_project")
+  expect_equal(mock_proj$name, "EmptyMock")
+  expect_equal(nrow(mock_proj$tbl), 0L)
+  expect_identical(mock_proj$subjects, character())
+  expect_false(mock_proj$has_sessions)
+  expect_false(mock_proj$has_fmriprep)
+})
+
 test_that("create_mock_bids accepts shorthand suffixes for stub datasets", {
   td <- tempfile("mock-bids-shorthand-")
   dir.create(td, recursive = TRUE)

tests/testthat/test_vignette_resilience.R

@@ -0,0 +1,31 @@
+test_that("quickstart exits cleanly when the example dataset is unavailable", {
+  skip_if_not_installed("knitr")
+
+  vignette_path <- testthat::test_path(
+    "..", "..", "vignettes", "quickstart.Rmd"
+  )
+  if (!file.exists(vignette_path)) {
+    vignette_path <- system.file(
+      "doc", "quickstart.Rmd", package = "bidser"
+    )
+  }
+  skip_if(!nzchar(vignette_path) || !file.exists(vignette_path))
+
+  knit_env <- new.env(parent = globalenv())
+  knit_env$params <- list(family = "red", preset = "homage")
+  knit_env$get_example_bids_dataset <- function(...) {
+    stop("simulated offline failure")
+  }
+  output_path <- tempfile(fileext = ".md")
+
+  expect_no_error(
+    knitr::knit(
+      vignette_path,
+      output = output_path,
+      envir = knit_env,
+      quiet = TRUE
+    )
+  )
+  output <- paste(readLines(output_path, warn = FALSE), collapse = "\n")
+  expect_match(output, "Example dataset not available.", fixed = TRUE)
+})

vignettes/quickstart.Rmd

@@ -95,8 +95,9 @@ ds001_path <- tryCatch(
 )
 if (is.null(ds001_path)) {
   knitr::knit_exit("Example dataset not available.")
+} else {
+  proj <- bids_project(ds001_path)
 }
-proj <- bids_project(ds001_path)
 ```
 
 ```{r}