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SciML / SBMLToolkit.jl

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
https://docs.sciml.ai/SBMLToolkit/stable/
MIT License
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typos + Aqua CI #138

Closed ArnoStrouwen closed 10 months ago

codecov[bot] commented 10 months ago

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (f85fdd2) 94.24% compared to head (4078785) 0.27%. Report is 2 commits behind head on main.

Files Patch % Lines
src/reactions.jl 0.00% 1 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #138 +/- ## ========================================== - Coverage 94.24% 0.27% -93.98% ========================================== Files 7 7 Lines 365 362 -3 ========================================== - Hits 344 1 -343 - Misses 21 361 +340 ```

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paulflang commented 10 months ago

That's a shocking amount of typos detected by spell check.😅🙈

ChrisRackauckas commented 10 months ago

@paulflang can you look into getting tests fixed here? All I did was update the retcode check https://github.com/SciML/SBMLToolkitTestSuite.jl/pull/20 and it's failing. It would be good to keep master passing, even if it's just marking a test as broken. But here, I'm a bit confused on why anything would break: the numbers shouldn't change due to that.

paulflang commented 10 months ago

@ChrisRackauckas this probably has to do with an update in the dependencies. Here is a MWE that reproduces the error:

using DataFrames, ModelingToolkit, OrdinaryDiffEq

@variables t x(t)=1
D = Differential(t)
eqs = [D(x) ~ -x]
@named sys = ODESystem(eqs)
prob = ODEProblem(sys)
sol = solve(prob, Tsit5(), tspan=(0.0, 1.0))
df = DataFrame(sol)  # worked before, doesn't work now
ERROR: MethodError: no method matching SciMLBase.AbstractTimeseriesSolutionRows(::Vector{Any}, ::Vector{Type}, ::Dict{Any, Int64}, ::Vector{Float64}, ::Vector{Vector{Float64}})

Is this known? Do you know if/when it will be fixed?

ChrisRackauckas commented 10 months ago

That is not known. @AayushSabharwal did you test the dataframe generation? I can see an SII change in there. https://github.com/SciML/SciMLBase.jl/blob/master/src/tabletraits.jl#L28

AayushSabharwal commented 10 months ago

Table traits test passes. I'll look into the issue

AayushSabharwal commented 10 months ago

https://github.com/SciML/SciMLBase.jl/pull/570