Add unit tests for alignPlots() and the getTIS/getRIC/plotTIS/plotRIC family - #50
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… family - alignPlots(): tests the three returned ggplot objects (rt/dt correction plots and the dt_kcorr plot) for labels and expected data, using the align() fixture already in this file. - getTIS()/getRIC(): tests the extracted TIS/RIC matrices' shape and SampleID-keyed dimnames. - plotTIS()/plotRIC(): tests labels, data, and the dt_range/rt_range and sample= filtering, following the same "inspect the returned ggplot object, don't render it" strategy used for the other plot functions. Registering BiocParallel::SerialParam() locally in two tests (instead of the default forking MulticoreParam) runs the per-sample delayed operation in the same process, letting covr instrument .align_fun_extract()'s dt_kcorr fallback and .extract_RIC_and_TIS_fun_extract() -- both already exercised by existing/new tests, just invisible to covr inside a forked worker until now. Brings getTIS_getRIC-GCIMSDataset.R to 100% line coverage, and align-GCIMSDataset.R to 97.5% (116/119) -- the remaining 3 lines are the "pow" package's optional reference-selection call (needs that package installed) and two eval_poly() branches inside alignPlots() that are dead code given its only caller always passes a 2-column matrix. Overall package coverage: 86.83% -> 90.21%. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019V3CHRGSzcEu3k6tpUFv56
Registers BiocParallel::SerialParam() locally in tests that exercise realize_one_sample_disk()/realize_one_sample_ram(), which normally run inside forked bpmapply() workers invisible to covr. Adds direct unit tests of realize_one_sample_disk() for the file.copy fallback path (unreachable via the public API), mocked file.copy()/unlink() failures in updateScratchDir()/subset(), and R6-private-access tests for the directory-vanished and no-pending-ops edge cases. Also covers DelayedDatasetRAM's unnamed-samples-list guard, sampleNames<- length-mismatch guard, and the wrong-return-class abort, plus DelayedDatasetBase's realize() reentrancy guard.
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Summary
alignPlots(): tests the three returned ggplot objects (rt/dt correction plots and the dt_kcorr plot) for labels and expected data, reusing the existingalign()fixture intest-align-GCIMSDataset.R.getTIS()/getRIC(): tests the extracted TIS/RIC matrices' shape and SampleID-keyed dimnames.plotTIS()/plotRIC(): tests labels, data, and thedt_range/rt_rangeandsample=filtering — same "inspect the returned ggplot object, don't render it" strategy used for the other plot functions in Add unit tests for the plotting functions; fix scales >= 1.3.0 compatibility #49.A useful technique for BiocParallel-forked code
Registering
BiocParallel::SerialParam()locally in a test (instead of the default forkingMulticoreParam) runs a delayed operation's per-sample step in the same process, lettingcovrinstrument code that would otherwise run invisibly inside a forked worker. Used this for two tests here to unlock coverage on.align_fun_extract()'sdt_kcorrfallback and.extract_RIC_and_TIS_fun_extract()— both were already being exercised by existing/new tests, just invisible tocovruntil now. This is likely reusable for the similar BiocParallel-fork gaps noted in earlier coverage PRs (e.g. inaaa-class-DelayedDatasetDisk.R).Brings
getTIS_getRIC-GCIMSDataset.Rto 100% line coverage, andalign-GCIMSDataset.Rto 97.5% (116/119) — the remaining 3 lines are thepowpackage's optional reference-selection call (needs that package installed) and twoeval_poly()branches insidealignPlots()that are dead code given its only caller always passes a 2-column matrix.Overall package coverage: 86.83% → 90.21%.
Test plan
testthat::test_local(".")— 701 passing, 1 pre-existing skip, 0 failurescovr::package_coverage()confirms the reported numbersGenerated by Claude Code