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imspy-simulation: depend on mzprov; fix the flaky GMM test that stopped CI - #487
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test_fit started its means at unseeded N(0, 1) draws. In about 4% of runs (8 of 200 measured) all three components collapsed into one cluster and 'assert 1 > 1' failed, which is what stopped the Python 3.12 job on main after #486 and skipped the imspy-simulation suite. Start the means at data points under a fixed seed: 0 of 200 runs collapse.
emit_provenance is on by default, but mzprov was not installable from PyPI, so a normal install silently skipped signing with a warning. mzprov 0.1.1 is now on PyPI: declare it, drop the ImportError fallbacks, and keep signing non-fatal. The .raw docstring's claim that mzprov cannot sign vendor .raw is out of date and goes. test_mzprov_signing runs each vendor path's signer (.d and mzML, sidecar and embedded; .raw) against mzprov's fixtures and checks the result with mzprov's verifier.
mzprov 0.1.2 keeps new keys under ~/.config/mzprov/keys/ and uses an existing ~/.config/timsim/keys/ key in place, so TimSim users keep their signing identity. Require 0.1.2 and describe the default accordingly.
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Why CI on main didn't finish
After #486 merged, the Python 3.12 job failed in
imspy-predictorsontest_mixture.py::TestGaussianMixtureModel::test_fit(assert 1 > 1). Because that step failed, theimspy-simulationstep never ran.The test data was seeded, but the model's initial means were unseeded
N(0, 1)draws. In about 4% of runs all three components collapsed into one cluster. I measured 8 of 200 with the current test, and 0 of 200 after this change. The fixture now starts the means at data points under a fixed seed.mzprov is now a dependency
emit_provenanceis on by default, butmzprovwasn't on PyPI, so a normal install silently skipped signing with a warning. mzprov 0.1.1 is published now:imspy-simulationdeclaresmzprov>=0.1.1. It needs onlycryptography.ImportErrorfallbacks are gone. Signing stays non-fatal: any error is logged and the run continues..rawis removed.CONFIGURATION.mdsays how to check an output:mzprov verify <output>.Test
tests/test_mzprov_signing.pyruns each vendor path's signer against mzprov's own fixture files and checks the result with mzprov's verifier:.dand mzML, both as a sidecar file and embedded in the file.rawLocally, the GMM tests passed three times in a row. The new signing tests pass against these exact helper functions, but I loaded them in isolation, because the local
imspy_connectorbuild is older thanmain's. The full import runs in CI here.