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Bugfixes for PGG FPR and Germ Selection #545

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Merged
merged 7 commits into from
Mar 14, 2025
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coreyostrove
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@coreyostrove coreyostrove commented Feb 21, 2025

Three quick bugfixes:

  1. Per-germ global FPR requires the matrix forward simulator for some subroutines, but the default forward simulator for models is now map. We now automatically make a copy of the model with the correct forward simulator as needed. Also for pgg FPR, fix to account for change to previously changed return value format when not passing in a precomputed germ spanning vector set. The same fix was also made to the germ_set_spanning_vectors function.
  2. The change for germ selection line-labels in PR Bugfix Germ Selection and ProcessorSpec Documentation #540 introduced a bug caught by some annoyingly nondeterministic unit test failures. Germ selection returning None is a valid outcome when the initial candidate germ set is not amplificationally complete and we weren't checking for that case when doing the line label conversion. The test that caught this involved making random selections of the candidate set and wasn't seeded which is why it only failed some of the time. It is now seeded.

Corey Ostrove added 2 commits February 21, 2025 14:23
Minor bugfix for per-germ global FPR which uses some germ selection primitives that require the matrix forward simulator.
Fix a bug that was introduced in a recent PR related to the fact that the germ list can in some instances be None (correctly so).
@coreyostrove coreyostrove added this to the 0.9.13.1 milestone Feb 21, 2025
@coreyostrove coreyostrove self-assigned this Feb 21, 2025
@coreyostrove coreyostrove requested review from rileyjmurray and a team as code owners February 21, 2025 21:35
@coreyostrove coreyostrove requested a review from sserita February 21, 2025 21:35
Corey Ostrove added 4 commits February 21, 2025 14:43
Minor pgg FPR bugfix
Same fix as was needed in the pgg fpr function.
Proper fix for the tuple unpacking in pgg fpr.
Add a check for the fastcalc cython module and add fallback for when that isn't present.
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This all looks good. Will merge as soon as I get the tests passing (with a develop merge).

@sserita sserita merged commit 2a7c440 into develop Mar 14, 2025
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@sserita sserita deleted the bugfix-pgg-fpr-forwardsim branch March 14, 2025 04:16
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2 participants