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Process distributions from SBML models #393

Merged
merged 10 commits into from
Oct 29, 2024
Merged

Process distributions from SBML models #393

merged 10 commits into from
Oct 29, 2024

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bgyori
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@bgyori bgyori commented Oct 29, 2024

This PR extends the SBML processor to extract distributions from SBML models. Since distributions are not explicitly encoded in SBML, only as MathML expressions, we first convert MathML to SymPy and then map the name of the function representing the distribution and its arguments to ProbOnto. Generalization to a broader class of distributions can be done on a later PR. Distributions associated both with rate parameters and initial condition parameters are recognized.

The PR also adjusts Python versions for testing from 3.8-3.10 to 3.9-3.12. sbmlmath is nominally Python 3.10+ and works in practice on 3.9+, though not on 3.8 hence the version shift.

Fixes #361

@bgyori bgyori merged commit 094d61f into main Oct 29, 2024
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Supporting probability distributions of initial conditions and parameters specified in SBML
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