Add unit tests for align-GCIMSSample.R#31
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align-GCIMSSample.R had 0% test coverage despite implementing the retention-time and drift-time alignment logic (the pipeline step right after peak-independent preprocessing, and the file touched by the earlier pow-dependency CI fix). Covers: - alignDt(): exact multiplicative drift-time correction from the RIP (reactant ion peak) position - alignRt_ip(): exact index-based slicing to a common injection-point aligned retention time grid - prealign(): combined dt+injection-point alignment, the pass-through branch when both are disabled, and the guard against aligning an already all-missing sample - align(method_rt = "ptw"): a shifted synthetic RIC is correctly warped onto a reference (peak position and correlation checked), including the branch where the reference RIC lives on a different rt grid and the branch where an already-aligned sample needs no polynomial correction - align(method_rt = "pow") fails with a clear message when the optional pow package isn't installed (skipped if it is) - align() aborts instead of silently returning empty/all-NA data when given an incompatible reference retention time Brings align-GCIMSSample.R from 0% to 82% coverage (the rest is pow's actual warping math, untestable without the optional pow package). Package-wide: 30.8% -> 35.9%.
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Summary
align-GCIMSSample.R— retention-time and drift-time alignment logic — had 0% test coverage.tests/testthat/test-align-GCIMSSample.R, covering:alignDt(): exact multiplicative drift-time correction from the RIP (reactant ion peak) positionalignRt_ip(): exact index-based slicing to a common injection-point-aligned retention time gridprealign(): combined dt + injection-point alignment, the pass-through branch when both are disabled, and the guard against aligning an already all-missing samplealign(method_rt = "ptw"): a shifted synthetic RIC is correctly warped onto a reference (peak position and correlation checked), including the branch where the reference RIC lives on a different rt grid and the branch where an already-aligned sample needs no polynomial correctionalign(method_rt = "pow")fails with a clear message when the optionalpowpackage isn't installed (test skips itself ifpowis installed)align()aborts instead of silently returning empty/all-NA data when given an incompatible reference retention timealign-GCIMSSample.Rcoverage: 0% → 82% (the remaining gap isalignRt_pow()'s actual warping math, untestable without the optionalpowpackage). Package-wide coverage: 30.8% → 35.9%.Test plan
testthat::test_local(".")— full existing suite passes, including the new file (21 assertions)covr::package_coverage()confirmsalign-GCIMSSample.Rat 82% and no regressions elsewhereGenerated by Claude Code