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tskit-dev / msprime

Simulate genealogical trees and genomic sequence data using population genetic models
GNU General Public License v3.0
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Tests fail with stdpopsim 0.2.0 #2233

Open benjeffery opened 9 months ago

benjeffery commented 9 months ago

Looks like all other dep updates are good, but stdpopsim is failing:

AttributeError: 'DemographicModel' object has no attribute 'population_configurations'

GertjanBisschop commented 9 months ago

The tests that are failing are tests that are marked as temporary: # This test is temporary while we are updating stdpopsim to use the msprime APIs. See the nodes in the _ooa_model() code. I am not familiar with the details here. Is this simply a case of bumping up the dependency version and removing these temporary tests @jeromekelleher ?

jeromekelleher commented 9 months ago

Yeah, let's bump the dependencey and nuke those tests. What do the notes in the _ooa_model code say?

GertjanBisschop commented 9 months ago

Hmm, can't find the notes.

jeromekelleher commented 9 months ago

Definitely delete then

GertjanBisschop commented 9 months ago

Aha found it: thought the notes were in the stdpopsim code but they are in the msprime code instead:

" This version is included here temporarily as a way to get some test coverage on the model compared with stdpopsim. Because we use this model in the documentation, we want make sure that it's doing what we think. We compare the model defined here then with the one presented in the docs, to ensure that no errors creep in. Once the upstream code in stdpopsim is updated to use msprime 1.0 APIs we can remove this model and instead compare directly to the stdpopsim model with .is_equivalent() or whatever. "

jeromekelleher commented 9 months ago

Hmm, this is annoying. The code has changed slightly in stdpopsim, so the tests of the demographic models don't quite line up any more. It will take a bit of fiddling to get these working again...

jeromekelleher commented 9 months ago

Temporary workaround for release would be to pin stdpopsim back to previous version, and register an issue to track updating the tests.