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SciML / JumpProcesses.jl

Build and simulate jump equations like Gillespie simulations and jump diffusions with constant and state-dependent rates and mix with differential equations and scientific machine learning (SciML)
https://docs.sciml.ai/JumpProcesses/stable/
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Indexing fixes #408

Closed isaacsas closed 3 months ago

isaacsas commented 3 months ago

@AayushSabharwal can you check I've got the correct dispatches now for mutating parameters within JumpProblems ensuring update_parameters!(...) is called to update the associated MassActionJump?

isaacsas commented 3 months ago

If this looks ok I'll add some more symbolic tests for integrators and for remake.

coveralls commented 3 months ago

Pull Request Test Coverage Report for Build 8363146682

Details

Changes Missing Coverage Covered Lines Changed/Added Lines %
src/problem.jl 5 7 71.43%
<!-- Total: 5 7 71.43% -->
Files with Coverage Reduction New Missed Lines %
src/spatial/utils.jl 1 91.67%
src/spatial/topology.jl 1 93.44%
src/spatial/bracketing.jl 2 72.0%
src/spatial/reaction_rates.jl 2 94.29%
src/extended_jump_array.jl 2 78.21%
src/spatial/hop_rates.jl 2 98.88%
src/problem.jl 2 66.84%
src/spatial/spatial_massaction_jump.jl 3 85.45%
src/aggregators/frm.jl 3 95.38%
src/aggregators/bracketing.jl 3 90.0%
<!-- Total: 103 -->
Totals Coverage Status
Change from base Build 8038301646: -2.6%
Covered Lines: 2209
Relevant Lines: 2568
💛 - Coveralls
isaacsas commented 3 months ago

@ChrisRackauckas this hadn't yet been updated for https://github.com/SciML/SymbolicIndexingInterface.jl/pull/58, which is the interface we are supposed to use (and was only merged/released today).

I'll open another PR to update this to the correct interface, hopefully later today or tomorrow.