Bayesian inference updates in manifest.toml and project.toml

[ParamThakkar123]

Checklist

• Appropriate tests were added
• Any code changes were done in a way that does not break public API
• All documentation related to code changes were updated
• The new code follows the
  contributor guidelines, in particular the SciML Style Guide and
  COLPRAC.
• Any new documentation only uses public API

Additional context

Add any other context about the problem here.

[ParamThakkar123]

@ChrisRackauckas I was working on updating the PINN benchmarks but they always show the following error while updating the dependencies.

This occurs while updating almost any dependency. What can be done for this ?? Also I didn't find the repositories for OptimizationOptimJL, OptimizationFlux

[ParamThakkar123]

Also for this PR the manifest.toml file has been bumped with the latest updates

[ParamThakkar123]

@ErikQQY Can you please take a look at this PR as well as the error that is repeatedly occurring here

[ErikQQY]

The compats you bumped have version conflicts, you would have to read the error message carefully and find the appropriate versions, you can refer to https://pkgdocs.julialang.org/dev/managing-packages/#conflicts-1 and https://discourse.julialang.org/t/a-guide-how-to-handle-error-unsatisfiable-requirements-detected/43406

[ParamThakkar123]

The compats you bumped have version conflicts, you would have to read the error message carefully and find the appropriate versions, you can refer to https://pkgdocs.julialang.org/dev/managing-packages/#conflicts-1 and https://discourse.julialang.org/t/a-guide-how-to-handle-error-unsatisfiable-requirements-detected/43406

Got it. I'll go through this and fix things. Thank you.

[ParamThakkar123]

@ChrisRackauckas @ErikQQY Can you please take a look at this ?? I think this is done. All the benchmarks for BayesianInference including the manifest.toml has been updated and bumped.

[ChrisRackauckas]

https://buildkite.com/julialang/scimlbenchmarks-dot-jl/builds/2894#0192c1d7-e872-4975-8ff3-79c0898f56f0/561-678

you need to resolve on v1.10

[ParamThakkar123]

@ChrisRackauckas Can you please review this PR ?? I think this is done all the jmd files run without any errors, also the manifest and project.toml files are bumped to the latest versions on julia version 1.9.1

[ParamThakkar123]

DynamicalODE has been resolved on Julia version 1.10.4

[ChrisRackauckas]

Needs to bump the manifest

and remove the DynamicalODE stuff from this PR

[ParamThakkar123]

@ChrisRackauckas While keeping only the top ones in the compat, the package errors with unsatisfiable requirements error for every package. How that should be dealt with ?? Actually this error occurs when bumping the manifest

[ChrisRackauckas]

find the package that needs to bump

[ParamThakkar123]

@ChrisRackauckas The required changes have been made to the Project.toml file. Manifest.toml has been bumped and DynamicalODE has been removed from this PR

[ChrisRackauckas]

It's not all on the latest majors.

[ParamThakkar123]

@ChrisRackauckas all changes so far have been made. Any more changes needed ??

[ErikQQY]

Seems Stan.jl backend still have error

[ParamThakkar123]

@ErikQQY What does the stan_inference error exactly point to ?? I went through the documentation and test files and made changes, but that didn't solve the error

[ErikQQY]

Are you sure stan_inference(prob, t, data, priors; ......) you are using is the correct syntax?

Quote from the latest DiffEqBayes docs:

stan_inference(prob::DiffEqBase.DEProblem, alg, t, data, priors = nothing;
stanmodel = nothing, likelihood = Normal, vars = (StanODEData(), InverseGamma(3, 3)), sample_u0 = false, solve_kwargs = Dict(), diffeq_string = nothing, sample_kwargs = Dict(), output_format = :mcmcchains, print_summary = true, tmpdir = mktempdir())

[ChrisRackauckas]

What do you get locally?

[ParamThakkar123]

What do you get locally?

Locally it gives an IOError while on the CI it shows some issues with stan_inference. Here's the issue:

Warning: build_function(::Array{<:Equation}...) is deprecated. Use build_function(::AbstractArray...) instead.
└ @ Symbolics [C:\Users\Hp\.julia\packages\Symbolics\5BibL\src\build_function.jl:832](file:///C:/Users/Hp/.julia/packages/Symbolics/5BibL/src/build_function.jl:832)
┌ Info: [C:\Users\Hp\AppData\Local\Temp\jl_mR6Rav\parameter_estimation_model.stan](file:///C:/Users/Hp/AppData/Local/Temp/jl_mR6Rav/parameter_estimation_model.stan) updated.
└ @ StanBase [C:\Users\Hp\.julia\packages\StanBase\IgV1g\src\common\update_model_file.jl:34](file:///C:/Users/Hp/.julia/packages/StanBase/IgV1g/src/common/update_model_file.jl:34)
IOError: cd(""): invalid argument (EINVAL)

Stacktrace:
 [1] uv_error
   @ .\libuv.jl:100 [inlined]
 [2] cd(dir::String)
   @ Base.Filesystem .\file.jl:91
 [3] cd(f::StanSample.var"#1#2"{IOBuffer, String, String}, dir::String)
   @ Base.Filesystem .\file.jl:100
 [4] SampleModel(name::String, model::String, tmpdir::String)
   @ StanSample C:\Users\Hp\.julia\packages\StanSample\mnc5W\src\stanmodel\SampleModel.jl:122
 [5] stan_inference(prob::ODEProblem{Vector{Float64}, Tuple{Float64, Float64}, true, Vector{Float64}, FitzhughNagumo{var"###ParameterizedDiffEqFunction#293", var"###ParameterizedTGradFunction#294", var"###ParameterizedJacobianFunction#295", Nothing, Nothing, ODESystem}, Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}, SciMLBase.StandardODEProblem}, t::Vector{Float64}, data::Matrix{Float64}, priors::Vector{Truncated{Normal{Float64}, Continuous, Float64, Float64, Float64}}, stanmodel::Nothing; likelihood::Type, vars::Tuple{DiffEqBayes.StanODEData, InverseGamma{Float64}}, sample_u0::Bool, save_idxs::Nothing, diffeq_string::Nothing, alg::Symbol, reltol::Float64, abstol::Float64, maxiter::Int64, num_samples::Int64, num_warmups::Int64, num_cpp_chains::Int64, num_chains::Int64, num_threads::Int64, delta::Float64, output_format::Symbol, print_summary::Bool, tmpdir::String)
   @ DiffEqBayes C:\Users\Hp\.julia\packages\DiffEqBayes\gXPkn\src\stan_inference.jl:194
 [6] stan_inference
   @ C:\Users\Hp\.julia\packages\DiffEqBayes\gXPkn\src\stan_inference.jl:54 [inlined]
 [7] top-level scope
   @ .\timing.jl:273 [inlined]
 [8] top-level scope
   @ c:\Users\Hp\Desktop\SciMLBenchmarks.jl\benchmarks\BayesianInference\jl_notebook_cell_df34fa98e69747e1a8f8a730347b8e2f_X20sZmlsZQ==.jl:0

This is the only method that error after bumping updates of packages. rest seem to work fine without making updates to the existing code