Add DRAGON cross-language parity test#406
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Add a parity test asserting that netZooR's dragon() reproduces a fixed snapshot of lambdas, shrunken covariance, precision matrix, and partial correlation matrix. The same shared inputs (X1.csv, X2.csv) and gold values are byte-identical to netZooPy's tests/dragon_parity/ -- if both tests pass, the two implementations agree to 1e-5 (atol). The fixtures are generated by netZooPy's tests/dragon_parity/regenerate.py from simulate_dragon_data with seed=20250510. Kappa / p-values are not covered, since estimate_kappa_dragon and estimate_p_values_dragon are unimplemented stubs in netZooR. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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The DRAGON parity test runs alongside the rest of testthat, so it shares the same test-coverage and bioc-check jobs as everything else. Both have pre-existing problems on devel that this PR was hitting: - test-coverage was installing the reticulate R package but not Python itself, so reticulate::source_python() in pandaPy failed and broke the whole testthat run. Mirror bioc-check's Python setup (install numpy/scipy/pandas and export RETICULATE_PYTHON), Linux only since test-coverage runs on ubuntu-latest. - bioc-check on R devel couldn't resolve GOstats via pak, taking down the dependency install. Use pak directly for the devel matrix entry and pass "GOstats=?ignore" so the rest of the deps still resolve. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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@taraeicher if you accept this, we can rebase and fix #404 for free |
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Summary
Add a parity test that pins netZooR's
dragon()outputs to a fixed numeric snapshot. The same shared inputs and gold values are committed byte-identical in netZooPy (companion PR: netZoo/netZooPy#389). If both tests pass, the two implementations agree to 1e-5 absolute tolerance.What's covered
lambdas(penalty parameters)cov— shrunken covarianceprec— precision matrixggm— partial correlation matrixWhat's not covered
estimate_kappa_dragonandestimate_p_values_dragonin R/DRAGON.R have empty function bodies; the publicdragon()prints "not yet implemented in R; to estimate p-values, use netZooPy"). When R gains a κ/p-value implementation, this parity test should be extended to cover it.Fixtures
X1.csv(50×20),X2.csv(50×15) — generated deterministically in netZooPy viatests/dragon_parity/regenerate.pyfromsimulate_dragon_data(seed=20250510), then column-scaled.lambdas.txt,cov.csv,prec.csv,ggm.csv. Snapshot of netZooPy's pipeline at the time of generation.tests/dragon_parity/.Local results
R and Python agree two orders of magnitude tighter than the 1e-5 tolerance.
Companion PR
Test plan
Rscript -e 'library(testthat); library(netZooR); setwd("tests/testthat"); test_file("test-dragon-parity.R")'— 4 PASS / 0 FAIL locallytests/testthat/test-dragon.R🤖 Generated with Claude Code