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Merged
bbuchsbaum merged 8 commits into from
Sep 8, 2026
Merged

Raise meaningful test coverage toward portfolio target (≥90%) #76

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45bbc2b
Add meaningful coverage tests for uncovered public APIs
cursoragent Sep 3, 2026
a74dece
Add denser coverage tests and fix plot_bids bugs
cursoragent Sep 3, 2026
1328463
Add final coverage tests for query, events, and packing edges
cursoragent Sep 3, 2026
e1e8a6e
Push coverage past 90% with URI, schema, and sidecar tests
cursoragent Sep 3, 2026
e0bbb47
Harden crayon-fallback print test under covr tracing
cursoragent Sep 3, 2026
dcbd858
Clear coverage target with URI, filter, and pack edge tests
cursoragent Sep 3, 2026
70dc56e
Fix trailing-comma lintr finding in coverage tests
cursoragent Sep 3, 2026
1af20a2
Fix pre-existing unreachable_code lintr false positive
cursoragent Sep 3, 2026
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5 changes: 4 additions & 1 deletion R/events.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,11 @@
session = "(^|/)ses-([^/]+)(/|_|$)",
task = "(^|_)task-([^_/]+)(_|$)",
run = "(^|_)run-([^_/]+)(_|$)",
stop("Unknown event entity: ", entity)
NULL
)
if (is.null(pattern)) {
stop("Unknown event entity: ", entity)
}
match <- regexec(pattern, path, perl = TRUE)
value <- regmatches(path, match)[[1]]
if (length(value) >= 3) value[[3]] else NA_character_
Expand Down
62 changes: 35 additions & 27 deletions R/plot_bids.R
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Original file line number Diff line number Diff line change
Expand Up @@ -230,7 +230,7 @@ plot_bids <- function(x, interactive = TRUE, color_scheme = "viridis",
# Create plots based on the selected visualization mode
if (visualization_mode == "heatmap") {
# Create just the heatmap visualization
tryCatch({
combined_plot <- tryCatch({
bids_heatmap(
x,
interactive = interactive,
Expand All @@ -240,10 +240,10 @@ plot_bids <- function(x, interactive = TRUE, color_scheme = "viridis",
}, error = function(e) {
warning("Error creating heatmap visualization: ", e$message)
# Return an empty plot with error message
return(ggplot2::ggplot() +
ggplot2::annotate("text", x = 0, y = 0,
ggplot2::ggplot() +
ggplot2::annotate("text", x = 0, y = 0,
label = paste("Error creating heatmap:", e$message)) +
ggplot2::theme_void())
ggplot2::theme_void()
})
} else if (visualization_mode == "complete") {
# Create a complete set of visualizations including the heatmap
Expand Down Expand Up @@ -1500,7 +1500,25 @@ create_virtual_bids_project <- function(name = "Virtual Project",
runif(1) < 0.8
}

# Build the file structure data frame
# Build the file structure data frame with a stable column set so raw and
# derivative rows can be rbind'ed safely.
empty_row <- function(...) {
args <- list(...)
defaults <- list(
subid = NA_character_,
session = NA,
datatype = NA_character_,
task = NA,
run = NA,
suffix = NA_character_,
fmriprep = FALSE,
space = NA_character_,
desc = NA_character_
)
defaults[names(args)] <- args
as.data.frame(defaults, stringsAsFactors = FALSE)
}

for (sub in subjects) {
# Remove "sub-" prefix for the data frame
sub_id <- gsub("^sub-", "", sub)
Expand All @@ -1510,15 +1528,12 @@ create_virtual_bids_project <- function(name = "Virtual Project",
# Add anatomical files
for (mod in modalities) {
if (mod %in% c("T1w", "T2w") && should_include()) {
file_structure <- rbind(file_structure, data.frame(
file_structure <- rbind(file_structure, empty_row(
subid = sub_id,
session = ses,
datatype = "anat",
task = NA,
run = NA,
suffix = paste0(mod, ".nii.gz"),
fmriprep = FALSE,
stringsAsFactors = FALSE
fmriprep = FALSE
))
}
}
Expand All @@ -1527,15 +1542,14 @@ create_virtual_bids_project <- function(name = "Virtual Project",
for (task in tasks) {
for (run in runs) {
if ("bold" %in% modalities && should_include()) {
file_structure <- rbind(file_structure, data.frame(
file_structure <- rbind(file_structure, empty_row(
subid = sub_id,
session = ses,
datatype = "func",
task = task,
run = run,
suffix = "bold.nii.gz",
fmriprep = FALSE,
stringsAsFactors = FALSE
fmriprep = FALSE
))
}
}
Expand All @@ -1546,7 +1560,7 @@ create_virtual_bids_project <- function(name = "Virtual Project",
for (task in tasks) {
for (run in runs) {
if (should_include()) {
file_structure <- rbind(file_structure, data.frame(
file_structure <- rbind(file_structure, empty_row(
subid = sub_id,
session = ses,
datatype = "func",
Expand All @@ -1555,8 +1569,7 @@ create_virtual_bids_project <- function(name = "Virtual Project",
suffix = "bold.nii.gz",
fmriprep = TRUE,
space = "MNI152NLin2009cAsym",
desc = "preproc",
stringsAsFactors = FALSE
desc = "preproc"
))
}
}
Expand All @@ -1568,15 +1581,12 @@ create_virtual_bids_project <- function(name = "Virtual Project",
# Add anatomical files
for (mod in modalities) {
if (mod %in% c("T1w", "T2w") && should_include()) {
file_structure <- rbind(file_structure, data.frame(
file_structure <- rbind(file_structure, empty_row(
subid = sub_id,
session = NA,
datatype = "anat",
task = NA,
run = NA,
suffix = paste0(mod, ".nii.gz"),
fmriprep = FALSE,
stringsAsFactors = FALSE
fmriprep = FALSE
))
}
}
Expand All @@ -1585,15 +1595,14 @@ create_virtual_bids_project <- function(name = "Virtual Project",
for (task in tasks) {
for (run in runs) {
if ("bold" %in% modalities && should_include()) {
file_structure <- rbind(file_structure, data.frame(
file_structure <- rbind(file_structure, empty_row(
subid = sub_id,
session = NA,
datatype = "func",
task = task,
run = run,
suffix = "bold.nii.gz",
fmriprep = FALSE,
stringsAsFactors = FALSE
fmriprep = FALSE
))
}
}
Expand All @@ -1604,7 +1613,7 @@ create_virtual_bids_project <- function(name = "Virtual Project",
for (task in tasks) {
for (run in runs) {
if (should_include()) {
file_structure <- rbind(file_structure, data.frame(
file_structure <- rbind(file_structure, empty_row(
subid = sub_id,
session = NA,
datatype = "func",
Expand All @@ -1613,8 +1622,7 @@ create_virtual_bids_project <- function(name = "Virtual Project",
suffix = "bold.nii.gz",
fmriprep = TRUE,
space = "MNI152NLin2009cAsym",
desc = "preproc",
stringsAsFactors = FALSE
desc = "preproc"
))
}
}
Expand Down
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