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Raise meaningful test coverage toward portfolio target (≥90%) - #76
bbuchsbaum merged 8 commits into
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Raise the coverage-target gate by exercising bids_datatype_spec, tabular validators/summary, file_pairs edge branches, real bids_project subject graphs, report/index helpers, infer_tr fallbacks, and mock query/confound error paths. Co-authored-by: bbuchsbaum <bbuchsbaum@users.noreply.github.com>
Exercise mock validation, plot modes, metadata/query edges, example-zip extraction, and dataset_description print paths. Fix plot_bids heatmap mode discarding its plot object, and stabilize create_virtual_bids_project rbind column schemas. Co-authored-by: bbuchsbaum <bbuchsbaum@users.noreply.github.com>
Cover list_files_github mocking, formula rescue in search/query, metadata provenance, compliance/session edges, nested confound cleaning/plot views, infer_tr stem sidecars, and pack listing. Co-authored-by: bbuchsbaum <bbuchsbaum@users.noreply.github.com>
Add tests for downsample stub fallback, BIDS URI resolution (including DatasetLinks schemes), schema filename validation, inheritance-aware read_sidecar/n_volumes, print crayon fallback, and remaining summary/query edges. Co-authored-by: bbuchsbaum <bbuchsbaum@users.noreply.github.com>
Accept either fallback or normal print output so the coverage gate run does not fail when trace injection is ineffective. Co-authored-by: bbuchsbaum <bbuchsbaum@users.noreply.github.com>
Cover bids_uri/resolve validation, entity-filter formula errors, schema empty helpers, sidecar empty/corrupt JSON, event input checks, and unsupported pack_bids downsample methods. Co-authored-by: bbuchsbaum <bbuchsbaum@users.noreply.github.com>
Remove a missing-argument style lint introduced by a trailing comma in expect_warning(). Co-authored-by: bbuchsbaum <bbuchsbaum@users.noreply.github.com>
Move switch() default stop() out of the switch expression in .bidser_event_path_entity so lintr no longer treats later code as unreachable. Behavior unchanged. Co-authored-by: bbuchsbaum <bbuchsbaum@users.noreply.github.com>
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Cursor Bugbot has reviewed your changes using high effort and found 1 potential issue.
Bugbot Autofix prepared a fix for the issue found in the latest run.
- ✅ Fixed: Unprotected setwd in zip test
- Registered on.exit(setwd(old_wd)) immediately after setwd(staging) so a utils::zip failure restores the working directory before later tests run.
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diff --git a/tests/testthat/test_coverage_target2.R b/tests/testthat/test_coverage_target2.R
--- a/tests/testthat/test_coverage_target2.R
+++ b/tests/testthat/test_coverage_target2.R
@@ -190,6 +190,7 @@
))
old_wd <- getwd()
setwd(staging)
+ on.exit(setwd(old_wd), add = TRUE)
utils::zip(
zipfile = zip_file,
files = "bids-examples-master",You can send follow-ups to the cloud agent here.
Reviewed by Cursor Bugbot for commit 1af20a2. Configure here.
| files = "bids-examples-master", | ||
| flags = "-rq" | ||
| ) | ||
| setwd(old_wd) |
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Unprotected setwd in zip test
Medium Severity
setwd(staging) is restored only after utils::zip(...) succeeds. If zip fails, the process stays in the staging temp directory and the later on.exit(unlink(staging)) never registers, so later tests inherit a leftover or vanished working directory.
Reviewed by Cursor Bugbot for commit 1af20a2. Configure here.
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| pre <- file.path(tempdir(), "bids_example_ds_preexist") | ||
| dir.create(pre, showWarnings = FALSE) | ||
| on.exit(unlink(pre, recursive = TRUE, force = TRUE), add = TRUE) | ||
| got <- get_example_bids_dataset("ds_preexist") |
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In offline R CMD check environments, this call fails before reaching the supposedly pre-existing cache path: get_example_bids_dataset() performs httr::HEAD("https://github.com", ...) and raises “Internet connection required” before it checks whether tempdir()/bids_example_ds_preexist exists. Mock the HEAD request here (and guard for the suggested httr dependency) so this offline-safe test can actually exercise the disk-cache branch without requiring network access.
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Summary
Addresses portfolio gate
coverage-targetfor #75.Coverage
432ca6b)Hosted
test-coverageon this PR: success. Codecov project/patch: pass.Changes
Meaningful tests only (plus small bugfixes exposed by those tests):
Tests added
test_coverage_target.R–test_coverage_target5.Rcovering uncovered exports, boundary cases, and error paths (bids_datatype_spec, tabulars,file_pairs, realbuild_subject_graph, report/index helpers, URI resolution, schema validation, confound/plot edges, and more).Bugfixes
plot_bids(..., visualization_mode = "heatmap")discarded its plot (never assignedcombined_plot)create_virtual_bids_project(derivatives = TRUE)rbindcolumn mismatchunreachable_code_linterfalse positive in.bidser_event_path_entity(switchdefaultstop())Checks
covr::package_coverage()= 90.19%;lintr::lint_package()cleanNotes
# nocov