Matt J Owen

BifurcationProblem drops observed variables from ODESystem

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**Describe the bug 🐞** Using observed variables in the RHS of an ODESystem leads to errors when computing bifurcation diagrams. **Expected behavior** A bifurcation diagram should be plotted, instead an...

1 timestep delay in integrator respecting changes in parameters

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**Describe the bug 🐞** When the integrator is stepped following parameter mutation with integrator.p, the old value of params is used for 1 timestep. **Expected behavior** The step after parameters...

Error from empty set_population_size() call in PopulationBasedOptimiser

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### Bug Refusing to set a population size (using the default of `population_size=None`) leads to an error when the optimisation is run but the docstring for [set_population_size](https://github.com/pints-team/pints/blob/9843b6402e4c2f0e8eb58f3f394b6d139212cbab/pints/_optimisers/__init__.py#L273) suggests this is...

precompile fails on Julia v1.12.0

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Looks like to compat for MetaGraphs is still at 0.7.0 which restricts JLD2 to 0.4.54. [email protected] doesn't compile on Julia v1.12.0. If the compat for MetaGraphs can be updated (v0.8.1...

Offending code https://github.com/tlnagy/FCSFiles.jl/blob/2e05efdba37e1cda1a192d56b4917d3f54f66d97/src/type.jl#L16-L33 Still uses f.params I'm happy to make a quick PR for a fix Example: ```julia (base) qr24461@G5QGX0H45W esm % julia --depwarn=error _ _ _ _(_)_ | Documentation:...

Identifying variable indexes after discretization

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**Question❓** Is there a nice way to identify the indexes of the state vector after discretization? Similar to [`variable_index(sys, sym)`](https://docs.sciml.ai/ModelingToolkit/stable/basics/FAQ/#Getting-the-index-for-a-symbol) for ModelingToolkit. I know you can index the final solution...