Fix indexing deprecation warning

[isaacsas]

Hopefully this fixes the timeout for the prerelease hybrid tests.

@ChrisRackauckas should doing stuff like some_vector .+= sol(times; idxs = :X) causing the following message:

┌ Warning: `Base.getindex(A::AbstractDiffEqArray, i::Int)` is deprecated, use `Base.getindex(A, :, i)` instead.
│   caller = _broadcast_getindex at broadcast.jl:652 [inlined]

It seems like this is something that should work?

[isaacsas]

(And here by work I mean not cause issues due to the deprecation warning.)

[ChrisRackauckas]

Yes, it's just lowering to something that is deprecated. It should lower to sol.u[i], it sounds like it's lowering to sol[i]. To figure out where it's doing this, make the depwarn an error (can just Revise https://github.com/SciML/RecursiveArrayTools.jl/blob/master/src/vector_of_array.jl#L405) and then we can probably find the spot in SII to patch.

[isaacsas]

Turning depwarns into errors I just get:

ERROR: `Base.getindex(A::AbstractDiffEqArray, i::Int)` is deprecated, use `Base.getindex(A, :, i)` instead.
Stacktrace:
  [1] _depwarn(msg::Any, funcsym::Any, force::Bool)
    @ Base ./deprecated.jl:152
  [2] #invokelatest#2
    @ ./essentials.jl:1055 [inlined]
  [3] invokelatest
    @ ./essentials.jl:1052 [inlined]
  [4] #depwarn#1188
    @ ./deprecated.jl:146 [inlined]
  [5] depwarn
    @ ./deprecated.jl:141 [inlined]
  [6] getindex(A::RecursiveArrayTools.DiffEqArray{…}, i::Int64)
    @ RecursiveArrayTools ./deprecated.jl:104
  [7] _broadcast_getindex
    @ ./broadcast.jl:631 [inlined]
  [8] _getindex
    @ ./broadcast.jl:675 [inlined]
  [9] _getindex
    @ ./broadcast.jl:674 [inlined]
 [10] _broadcast_getindex
    @ ./broadcast.jl:650 [inlined]
 [11] getindex
    @ ./broadcast.jl:610 [inlined]
 [12] macro expansion
    @ ./broadcast.jl:973 [inlined]
 [13] macro expansion
    @ ./simdloop.jl:77 [inlined]
 [14] copyto!
    @ ./broadcast.jl:972 [inlined]
 [15] copyto!
    @ ./broadcast.jl:925 [inlined]
 [16] materialize!
    @ ./broadcast.jl:883 [inlined]
 [17] materialize!(dest::Vector{…}, bc::Base.Broadcast.Broadcasted{…})
    @ Base.Broadcast ./broadcast.jl:880
 [18] top-level scope
    @ REPL[28]:1
Some type information was truncated. Use `show(err)` to see complete types.

which doesn't seem helpful. I guess because the issue is really in sol(times; idxs = :X) generating the wrong object. But I'd note that the same issue arises even without symbolic indexing, i.e. I get the same error and stacktrace doing:

Xv .+= sol(times; idxs = 1)

(Note that wrapping with an Array fixes this.)

[ChrisRackauckas]

I think to get a useful stacktrace you may just need to set that to actually error().

[ChrisRackauckas]

What's your reproducer?

using RecursiveArrayTools
Base.getindex(A::RecursiveArrayTools.AbstractVectorOfArray, I::Int) = error()

using OrdinaryDiffEq
function lorenz!(du, u, p, t)
    du[1] = 10.0(u[2] - u[1])
    du[2] = u[1] * (28.0 - u[3]) - u[2]
    du[3] = u[1] * u[2] - (8 / 3) * u[3]
end
u0 = [1.0; 0.0; 0.0]
tspan = (0.0, 100.0)
prob = ODEProblem(lorenz!, u0, tspan)
sol = solve(prob, Tsit5())
sol([1,2,3], idxs = 1)

seems to work fine.

[isaacsas]

I'll try to reduce the test that is giving the warning down to a MWE when I have a chance. Have some deadlines currently so don't really have time to explore this currently.

[isaacsas]

Start Julia with depwarn=error,

using Catalyst, OrdinaryDiffEqTsit5
rn = @reaction_network begin
      β, X --> 0
      β, Y --> 0  
      α, 0 --> Y
      (α * (1 + Y)), 0 --> X
  end    
p = (α = 6.0, β = 2.0, X₀ = 2.0, Y₀ = 1.0)
u0map = [:X => p.X₀, :Y => p.Y₀]
pmap = [:α => p.α, :β => p.β]
tspan = (0.0, 20.0)
oprob = ODEProblem(rn, u0map, tspan, pmap)
sol = solve(oprob, Tsit5())
times = range(0.0, tspan[2], length = 100)
Xv = zeros(length(times))
s =  sol(times, idxs = 1)
Xv .+= s

gives

ERROR: `Base.getindex(A::AbstractDiffEqArray, i::Int)` is deprecated, use `Base.getindex(A, :, i)` instead.
Stacktrace:
  [1] _depwarn(msg::Any, funcsym::Any, force::Bool)
    @ Base ./deprecated.jl:152
  [2] #invokelatest#2
    @ ./essentials.jl:1055 [inlined]
  [3] invokelatest
    @ ./essentials.jl:1052 [inlined]
  [4] #depwarn#1188
    @ ./deprecated.jl:146 [inlined]
  [5] depwarn
    @ ./deprecated.jl:141 [inlined]
  [6] getindex(A::RecursiveArrayTools.DiffEqArray{…}, i::Int64)
    @ RecursiveArrayTools ./deprecated.jl:104
  [7] _broadcast_getindex
    @ ./broadcast.jl:631 [inlined]
  [8] _getindex
    @ ./broadcast.jl:675 [inlined]
  [9] _getindex
    @ ./broadcast.jl:674 [inlined]
 [10] _broadcast_getindex
    @ ./broadcast.jl:650 [inlined]
 [11] getindex
    @ ./broadcast.jl:610 [inlined]
 [12] macro expansion
    @ ./broadcast.jl:973 [inlined]
 [13] macro expansion
    @ ./simdloop.jl:77 [inlined]
 [14] copyto!
    @ ./broadcast.jl:972 [inlined]
 [15] copyto!
    @ ./broadcast.jl:925 [inlined]
 [16] materialize!
    @ ./broadcast.jl:883 [inlined]
 [17] materialize!(dest::Vector{…}, bc::Base.Broadcast.Broadcasted{…})
    @ Base.Broadcast ./broadcast.jl:880
 [18] top-level scope
    @ REPL[17]:1
Some type information was truncated. Use `show(err)` to see complete types.

[isaacsas]

The function definition you are changing doesn't seem to get called?

[isaacsas]

This seems to be the right deprecation to redefine:

julia> Base.getindex(A::AbstractDiffEqArray, i::Int) = error()

julia> Xv .+= s
ERROR: 
Stacktrace:
  [1] error()
    @ Base ./error.jl:44
  [2] getindex(A::DiffEqArray{Float64, 1, Vector{…}, StepRangeLen{…}, MTKParameters{…}, ODESolution{…}, Nothing}, i::Int64)
    @ Main ./REPL[34]:1
  [3] _broadcast_getindex
    @ ./broadcast.jl:631 [inlined]
  [4] _getindex
    @ ./broadcast.jl:675 [inlined]
  [5] _getindex
    @ ./broadcast.jl:674 [inlined]
  [6] _broadcast_getindex
    @ ./broadcast.jl:650 [inlined]
  [7] getindex
    @ ./broadcast.jl:610 [inlined]
  [8] macro expansion
    @ ./broadcast.jl:973 [inlined]
  [9] macro expansion
    @ ./simdloop.jl:77 [inlined]
 [10] copyto!
    @ ./broadcast.jl:972 [inlined]
 [11] copyto!
    @ ./broadcast.jl:925 [inlined]
 [12] materialize!
    @ ./broadcast.jl:883 [inlined]
 [13] materialize!(dest::Vector{…}, bc::Base.Broadcast.Broadcasted{…})
    @ Base.Broadcast ./broadcast.jl:880
 [14] top-level scope
    @ REPL[35]:1
Some type information was truncated. Use `show(err)` to see complete types.

[ChrisRackauckas]

Oh yes, that's because the return of the interpolation is a DiffEqArray.

using Catalyst, OrdinaryDiffEqTsit5
using RecursiveArrayTools
Base.getindex(A::AbstractDiffEqArray, i::Int) = error()
rn = @reaction_network begin
      β, X --> 0
      β, Y --> 0
      α, 0 --> Y
      (α * (1 + Y)), 0 --> X
  end
p = (α = 6.0, β = 2.0, X₀ = 2.0, Y₀ = 1.0)
u0map = [:X => p.X₀, :Y => p.Y₀]
pmap = [:α => p.α, :β => p.β]
tspan = (0.0, 20.0)
oprob = ODEProblem(rn, u0map, tspan, pmap)
sol = solve(oprob, Tsit5())
times = range(0.0, tspan[2], length = 100)
Xv = zeros(length(times))
s =  sol(times, idxs = 1)
Xv .+= s.u

Though actually this is the one case that will actually work post deprecation because the linear index is already correct. I'm not sure if we can signal that better somehow.

[isaacsas]

The docs on solution manipulating at https://docs.sciml.ai/DiffEqDocs/stable/basics/solution/#Interpolations-and-Calculating-Derivatives would probably benefit from more fully explaining what is being returned and how to use it in calculations.

[ChrisRackauckas]

Alright, I took a moment to more properly spell out the interface and update some of the old docs on this. Hopefully this clarifies it. Though @AayushSabharwal you should follow up with some additions to the DiffEqArray interface on discretes definitions and symbolic indexing.

• More precise deprecations of linear indexing and add an interface definition page RecursiveArrayTools.jl#439
• Add more details to the indexing interface page DiffEqDocs.jl#776
• SciML/DiffEqDocs.jl@ac56adc

[isaacsas]

Thanks, that should be helpful to users (and me!).