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Simulation engine for Heta-based models

Home Page: https://hetalang.github.io/HetaSimulator.jl/stable/

License: MIT License

Julia 100.00%

qsp-modeling modeling heta differential-equations identification

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stjordanis mlubin

hetasimulator.jl's Issues

excel files support in `read_parameters`

Allow Int parameters values in Scenario

Currently parameters arg in Scenario object supports only pairs with {Symbol, Float64}

Merge parameters in strict mode

Current setup allows adding new parameters at Scenario level with @warn warning the user, that the parameter is missing in the model.
Is that the intended behavior ? Potentially it may cause misprints.

An idea is to set strict=true kwarg and change the default behavior to throwing an error in case the provided parameter is missing in the model. If the user is sure about this new parameter he can change strict=false.

faster show for `Model`

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Allow add new parameters at Scenario/sim level with @warn

Replace @assert in merge_strict to @warn

TagBot trigger issue

This issue is used to trigger TagBot; feel free to unsubscribe.

If you haven't already, you should update your TagBot.yml to include issue comment triggers.
Please see this post on Discourse for instructions and more details.

If you'd like for me to do this for you, comment TagBot fix on this issue.
I'll open a PR within a few hours, please be patient!

Spaces (misprints) in column names in scenarios, measurements and parameters tables

Now we simply ignore columns with misprints.
The case with spaces in column names can be simply addressed. I propose to automatically remove space characters in a column name and inform the user by displaying a warning. We may also think of solving a general misprint.

StackOverflow when simulating large-scale models

StackOverflow warning is printed while running sim on large-scale model, with FBDF() solver (and other sovers except Sundials.CVODE_BDF()). However StackOverflow does't terminate the simulation.
The environment is:

julia> versioninfo()
Julia Version 1.9.2
Commit e4ee485e90 (2023-07-05 09:39 UTC)
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: 4 × Intel(R) Core(TM) i3-6100U CPU @ 2.30GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, skylake)
  Threads: 4 on 4 virtual cores

Stacktrace is :

Internal error: stack overflow in type inference of 

  kwcall(
    NamedTuple{
      (:alg, :reltol, :abstol), 
      Tuple{OrdinaryDiffEq.FBDF{5, 0, true, Nothing, OrdinaryDiffEq.NLNewton{Base.Rational{Int64}, Base.Rational{Int64}, Base.Rational{Int64}, Base.Rational{Int64}}, typeof(OrdinaryDiffEq.DEFAULT_PRECS), Base.Val{:forward}, true, nothing, Nothing, Nothing}, Float64, Float64}
    }, 
    typeof(HetaSimulator.sim), 
    HetaSimulator.Scenario{
      Main.var"#nameless_init_func_#10", 
      SciMLBase.ODEProblem{
        Array{Float64, 1}, Tuple{Float64, Float64}, true, Array{Float64, 1}, 
        SciMLBase.ODEFunction{true, SciMLBase.FullSpecialize, Main.var"#nameless_ode_func_#11", LinearAlgebra.UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing, Nothing}, 
        Base.Pairs{
          Symbol, 
          SciMLBase.CallbackSet{
            Tuple{}, 
            Tuple{
              SciMLBase.DiscreteCallback{HetaSimulator.var"#92#93", HetaSimulator.SavingEvent{Main.var"#saving_#14"{Array{Union{Nothing, Int64}, 1}}, HetaSimulator.SavedValues{Array{LabelledArrays.LArray{Float64, 1, Array{Float64, 1}, (:v1, :v2)}, 1}, Array{Float64, 1}, Array{Symbol, 1}}, DataStructures.BinaryHeap{Float64, Base.Order.ForwardOrdering}, Array{Float64, 1}}, typeof(HetaSimulator.saving_initialize), typeof(SciMLBase.FINALIZE_DEFAULT)}, 
              SciMLBase.DiscreteCallback{HetaSimulator.var"#37#42"{Array{Float64, 1}}, HetaSimulator.var"#38#43"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#15", Main.var"#nameless_affect_func_#27"}, Tuple{Bool, Bool}, Symbol}, HetaSimulator.var"#init_time_event#39"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#15", Main.var"#nameless_affect_func_#27"}, Array{Float64, 1}}, typeof(SciMLBase.FINALIZE_DEFAULT)}, 
              SciMLBase.DiscreteCallback{HetaSimulator.var"#37#42"{Array{Float64, 1}}, HetaSimulator.var"#38#43"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#18", Main.var"#nameless_affect_func_#30"}, Tuple{Bool, Bool}, Symbol}, HetaSimulator.var"#init_time_event#39"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#18", Main.var"#nameless_affect_func_#30"}, Array{Float64, 1}}, typeof(SciMLBase.FINALIZE_DEFAULT)}, 
              SciMLBase.DiscreteCallback{HetaSimulator.var"#37#42"{Array{Float64, 1}}, HetaSimulator.var"#38#43"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#19", Main.var"#nameless_affect_func_#31"}, Tuple{Bool, Bool}, Symbol}, HetaSimulator.var"#init_time_event#39"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#19", Main.var"#nameless_affect_func_#31"}, Array{Float64, 1}}, typeof(SciMLBase.FINALIZE_DEFAULT)}, 
              SciMLBase.DiscreteCallback{HetaSimulator.var"#37#42"{Array{Float64, 1}}, HetaSimulator.var"#38#43"{HetaSimulator.TimeEvent{Main.var"#nameless_on_tstops_func_#20", Main.var"#nameless_on_affect_func_#32"}, Tuple{Bool, Bool}, Symbol}, HetaSimulator.var"#init_time_event#39"{HetaSimulator.TimeEvent{Main.var"#nameless_on_tstops_func_#20", Main.var"#nameless_on_affect_func_#32"}, Array{Float64, 1}}, typeof(SciMLBase.FINALIZE_DEFAULT)}, 
              SciMLBase.DiscreteCallback{HetaSimulator.var"#37#42"{Array{Float64, 1}}, HetaSimulator.var"#38#43"{HetaSimulator.TimeEvent{Main.var"#nameless_off_tstops_func_#21", Main.var"#nameless_off_affect_func_#33"}, Tuple{Bool, Bool}, Symbol}, HetaSimulator.var"#init_time_event#39"{HetaSimulator.TimeEvent{Main.var"#nameless_off_tstops_func_#21", Main.var"#nameless_off_affect_func_#33"}, Array{Float64, 1}}, typeof(SciMLBase.FINALIZE_DEFAULT)}, 
              SciMLBase.DiscreteCallback{Main.var"#nameless_condition_func_#26", HetaSimulator.var"#48#49"{Tuple{Bool, Bool}, Symbol}, typeof(SciMLBase.INITIALIZE_DEFAULT), typeof(SciMLBase.FINALIZE_DEFAULT)}
            }
          },
          Tuple{Symbol}, 
          NamedTuple{
            (:callback,), 
            Tuple{
              SciMLBase.CallbackSet{Tuple{}, Tuple{
                SciMLBase.DiscreteCallback{HetaSimulator.var"#92#93", HetaSimulator.SavingEvent{Main.var"#saving_#14"{Array{Union{Nothing, Int64}, 1}}, HetaSimulator.SavedValues{Array{LabelledArrays.LArray{Float64, 1, Array{Float64, 1}, (:v1, :v2)}, 1}, Array{Float64, 1}, Array{Symbol, 1}}, DataStructures.BinaryHeap{Float64, Base.Order.ForwardOrdering}, Array{Float64, 1}}, typeof(HetaSimulator.saving_initialize), typeof(SciMLBase.FINALIZE_DEFAULT)}, 
                SciMLBase.DiscreteCallback{HetaSimulator.var"#37#42"{Array{Float64, 1}}, HetaSimulator.var"#38#43"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#15", Main.var"#nameless_affect_func_#27"}, Tuple{Bool, Bool}, Symbol}, HetaSimulator.var"#init_time_event#39"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#15", Main.var"#nameless_affect_func_#27"}, Array{Float64, 1}}, typeof(SciMLBase.FINALIZE_DEFAULT)}, 
                SciMLBase.DiscreteCallback{HetaSimulator.var"#37#42"{Array{Float64, 1}}, HetaSimulator.var"#38#43"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#18", Main.var"#nameless_affect_func_#30"}, Tuple{Bool, Bool}, Symbol}, HetaSimulator.var"#init_time_event#39"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#18", Main.var"#nameless_affect_func_#30"}, Array{Float64, 1}}, typeof(SciMLBase.FINALIZE_DEFAULT)}, 
                SciMLBase.DiscreteCallback{HetaSimulator.var"#37#42"{Array{Float64, 1}}, HetaSimulator.var"#38#43"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#19", Main.var"#nameless_affect_func_#31"}, Tuple{Bool, Bool}, Symbol}, HetaSimulator.var"#init_time_event#39"{HetaSimulator.TimeEvent{Main.var"#nameless_tstops_func_#19", Main.var"#nameless_affect_func_#31"}, Array{Float64, 1}}, typeof(SciMLBase.FINALIZE_DEFAULT)}, 
                SciMLBase.DiscreteCallback{HetaSimulator.var"#37#42"{Array{Float64, 1}}, HetaSimulator.var"#38#43"{HetaSimulator.TimeEvent{Main.var"#nameless_on_tstops_func_#20", Main.var"#nameless_on_affect_func_#32"}, Tuple{Bool, Bool}, Symbol}, HetaSimulator.var"#init_time_event#39"{HetaSimulator.TimeEvent{Main.var"#nameless_on_tstops_func_#20", Main.var"#nameless_on_affect_func_#32"}, Array{Float64, 1}}, typeof(SciMLBase.FINALIZE_DEFAULT)}, 
                SciMLBase.DiscreteCallback{HetaSimulator.var"#37#42"{Array{Float64, 1}}, HetaSimulator.var"#38#43"{HetaSimulator.TimeEvent{Main.var"#nameless_off_tstops_func_#21", Main.var"#nameless_off_affect_func_#33"}, Tuple{Bool, Bool}, Symbol}, HetaSimulator.var"#init_time_event#39"{HetaSimulator.TimeEvent{Main.var"#nameless_off_tstops_func_#21", Main.var"#nameless_off_affect_func_#33"}, Array{Float64, 1}}, typeof(SciMLBase.FINALIZE_DEFAULT)}, 
                SciMLBase.DiscreteCallback{Main.var"#nameless_condition_func_#26", HetaSimulator.var"#48#49"{Tuple{Bool, Bool}, Symbol}, typeof(SciMLBase.INITIALIZE_DEFAULT), typeof(SciMLBase.FINALIZE_DEFAULT)}}
              }
            }
          }
        }, 
        SciMLBase.StandardODEProblem
      }, 
      Array{HetaSimulator.AbstractMeasurementPoint, 1}
    }
  ).

This might be caused by recursion over very long tuples or argument lists.

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