Fix numpy v1.24 compatibility #574
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Numpy v1.24 deprecated ragged arrays unless dtype=object is passed (numpy/numpy#22004). The SimulationResult class needs to support different length entries in tout in the case that these differ across simulations. PySB shouldn't convert these to a numpy array, instead preferring to keep them as a list/iterable.
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@@ Coverage Diff @@
## master #574 +/- ##
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- Coverage 80.33% 80.22% -0.12%
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Files 101 101
Lines 10832 10832
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- Hits 8702 8690 -12
- Misses 2130 2142 +12
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JamesPino
reviewed
Mar 29, 2023
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Seems like an easy fix. At first I was curious what prevented tout and trajectories from being lists of different sizes, but found the checks later on. I don't see the check for observables_and_expressions. Would/could that ever occur? It's independent of this fix, but was just looking at how self.tout is used later and noticed.
jmuhlich
approved these changes
Apr 11, 2023
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Numpy v1.24 deprecated ragged arrays unless dtype=object is passed (numpy/numpy#22004). The SimulationResult class needs to support different length entries in tout in the case these differ across simulations. PySB shouldn't convert these to a numpy array, instead preferring to keep them as a list/iterable, which avoids causing an error with Numpy v1.24 when running the PySB test suite.