Can't get overview example working following repo's Project.toml Julia version

[DavidRobertsSBL]

I'm trying to recreate the first part of the overview file (up to the first call of solve using Tsit()).

I started from a clean setup, and even ran extra clean-up in my IJulia notebook running in VSCode to be sure, restarted language server etc. (I can't attach notebooks, so I will put the code at the bottom as raw Julia).

The Project.toml file in Decapodes.jl specifies Julia 1.9, so I'm using that today. Last night I started with Julia 1.11 and got all the way to just before the line soln = solve(prob, Tsit5()) when it failed. It was a version incompatibility problem, so I decided to start with the version of Julia the Project.toml in the GitHub repo was pinned to. And now I can't even get Decapodes to be added without things failing!

---

So here's what I have as a MWE to make this problem happen (### indicates cell boundaries in the notebook)

rm(joinpath(first(DEPOT_PATH), "compiled"),
  recursive=true, force=true)
  println("Cleared precompiled cache")

###
if isfile("Project.toml")
    rm("Project.toml")
    println("Deleted Project.toml")
end
if isfile("Manifest.toml")
    rm("Manifest.toml")
    println("Deleted Manifest.toml")
end

###
import Pkg
Pkg.activate(".")

###
Pkg.add("Decapodes")
Pkg.status()

# output:
# Resolving package versions...
#    Updating `~/Documents/Sirius-Beta/CEM-experiments/julia/CEMProject/src/Project.toml`
# ⌃ [679ab3ea] + Decapodes v0.5.2
# [updating Manifest.toml stuff]
# 212 dependencies successfully precompiled in 221 seconds. 7 already precompiled. 2 skipped during auto due to previous errors.
# Status `~/Documents/Sirius-Beta/CEM-experiments/julia/CEMProject/src/Project.toml`
# ⌃ [679ab3ea] Decapodes v0.5.2
# Info Packages marked with ⌃ have new versions available and may be upgradable.

### 
# restarted the language server for clean session

###
import Pkg
Pkg.activate(".")

# output:
# Activating project at `~/Documents/Sirius-Beta/CEM-experiments/julia/CEMProject/src`

### 
using Decapodes

###

and here I get the big error: [sorry for any possible junk characters]

�[91m�[1mERROR: �[22m�[39mLoadError: UndefVarError: `UntypedUnnamedRelationDiagram` not defined
Stacktrace:
 [1] �[0m�[1mgetproperty�[22m�[0m�[1m(�[22m�[90mx�[39m::�[0mModule, �[90mf�[39m::�[0mSymbol�[0m�[1m)�[22m
�[90m   @�[39m �[90mBase�[39m �[90m./�[39m�[90m�[4mBase.jl:31�[24m�[39m
 [2] top-level scope
�[90m   @�[39m �[90m~/.julia/packages/DiagrammaticEquations/7dmXn/src/�[39m�[90m�[4mcollages.jl:1�[24m�[39m
 [3] �[0m�[1minclude�[22m�[0m�[1m(�[22m�[90mmod�[39m::�[0mModule, �[90m_path�[39m::�[0mString�[0m�[1m)�[22m
�[90m   @�[39m �[90mBase�[39m �[90m./�[39m�[90m�[4mBase.jl:457�[24m�[39m
 [4] �[0m�[1minclude�[22m�[0m�[1m(�[22m�[90mx�[39m::�[0mString�[0m�[1m)�[22m
�[90m   @�[39m �[35mDiagrammaticEquations�[39m �[90m~/.julia/packages/DiagrammaticEquations/7dmXn/src/�[39m�[90m�[4mDiagrammaticEquations.jl:3�[24m�[39m
 [5] top-level scope
�[90m   @�[39m �[90m~/.julia/packages/DiagrammaticEquations/7dmXn/src/�[39m�[90m�[4mDiagrammaticEquations.jl:56�[24m�[39m
 [6] �[0m�[1minclude�[22m
�[90m   @�[39m �[90m./�[39m�[90m�[4mBase.jl:457�[24m�[39m�[90m [inlined]�[39m
 [7] �[0m�[1minclude_package_for_output�[22m�[0m�[1m(�[22m�[90mpkg�[39m::�[0mBase.PkgId, �[90minput�[39m::�[0mString, �[90mdepot_path�[39m::�[0mVector�[90m{String}�[39m, �[90mdl_load_path�[39m::�[0mVector�[90m{String}�[39m, �[90mload_path�[39m::�[0mVector�[90m{String}�[39m, �[90mconcrete_deps�[39m::�[0mVector�[90m{Pair{Base.PkgId, UInt128}}�[39m, �[90msource�[39m::�[0mString�[0m�[1m)�[22m
�[90m   @�[39m �[90mBase�[39m �[90m./�[39m�[90m�[4mloading.jl:2049�[24m�[39m
 [8] top-level scope
�[90m   @�[39m �[90m�[4mstdin:3�[24m�[39m
in expression starting at /Users/test/.julia/packages/DiagrammaticEquations/7dmXn/src/collages.jl:1
in expression starting at /Users/test/.julia/packages/DiagrammaticEquations/7dmXn/src/DiagrammaticEquations.jl:1
in expression starting at stdin:3
�[91m�[1mERROR: �[22m�[39mLoadError: Failed to precompile DiagrammaticEquations [6f00c28b-6bed-4403-80fa-30e0dc12f317] to "/Users/test/.julia/compiled/v1.9/DiagrammaticEquations/jl_Xl8csn".
Stacktrace:
  [1] �[0m�[1merror�[22m�[0m�[1m(�[22m�[90ms�[39m::�[0mString�[0m�[1m)�[22m
�[90m    @�[39m �[90mBase�[39m �[90m./�[39m�[90m�[4merror.jl:35�[24m�[39m
  [2] �[0m�[1mcompilecache�[22m�[0m�[1m(�[22m�[90mpkg�[39m::�[0mBase.PkgId, �[90mpath�[39m::�[0mString, �[90minternal_stderr�[39m::�[0mIO, �[90minternal_stdout�[39m::�[0mIO, �[90mkeep_loaded_modules�[39m::�[0mBool�[0m�[1m)�[22m
�[90m    @�[39m �[90mBase�[39m �[90m./�[39m�[90m�[4mloading.jl:2294�[24m�[39m
  [3] �[0m�[1mcompilecache�[22m
�[90m    @�[39m �[90m./�[39m�[90m�[4mloading.jl:2167�[24m�[39m�[90m [inlined]�[39m
  [4] �[0m�[1m_require�[22m�[0m�[1m(�[22m�[90mpkg�[39m::�[0mBase.PkgId, �[90menv�[39m::�[0mString�[0m�[1m)�[22m
�[90m    @�[39m �[90mBase�[39m �[90m./�[39m�[90m�[4mloading.jl:1805�[24m�[39m
  [5] �[0m�[1m_require_prelocked�[22m�[0m�[1m(�[22m�[90muuidkey�[39m::�[0mBase.PkgId, �[90menv�[39m::�[0mString�[0m�[1m)�[22m
�[90m    @�[39m �[90mBase�[39m �[90m./�[39m�[90m�[4mloading.jl:1660�[24m�[39m
  [6] �[0m�[1mmacro expansion�[22m
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  [7] �[0m�[1mmacro expansion�[22m
�[90m    @�[39m �[90m./�[39m�[90m�[4mlock.jl:267�[24m�[39m�[90m [inlined]�[39m
  [8] �[0m�[1mrequire�[22m�[0m�[1m(�[22m�[90minto�[39m::�[0mModule, �[90mmod�[39m::�[0mSymbol�[0m�[1m)�[22m
�[90m    @�[39m �[90mBase�[39m �[90m./�[39m�[90m�[4mloading.jl:1611�[24m�[39m
  [9] �[0m�[1minclude�[22m
�[90m    @�[39m �[90m./�[39m�[90m�[4mBase.jl:457�[24m�[39m�[90m [inlined]�[39m
 [10] �[0m�[1minclude_package_for_output�[22m�[0m�[1m(�[22m�[90mpkg�[39m::�[0mBase.PkgId, �[90minput�[39m::�[0mString, �[90mdepot_path�[39m::�[0mVector�[90m{String}�[39m, �[90mdl_load_path�[39m::�[0mVector�[90m{String}�[39m, �[90mload_path�[39m::�[0mVector�[90m{String}�[39m, �[90mconcrete_deps�[39m::�[0mVector�[90m{Pair{Base.PkgId, UInt128}}�[39m, �[90msource�[39m::�[0mString�[0m�[1m)�[22m
�[90m    @�[39m �[90mBase�[39m �[90m./�[39m�[90m�[4mloading.jl:2049�[24m�[39m
 [11] top-level scope
�[90m    @�[39m �[90m�[4mstdin:3�[24m�[39m
in expression starting at /Users/test/.julia/packages/Decapodes/ZgTfi/src/Decapodes.jl:1
in expression starting at stdin:3

[lukem12345]

That minimum bound on Julia 1.9 in the Project.toml was added some time ago. Code in the Decapodes.jl repo does not require any features of 1.10 or 1.11, but certain dependencies might. This sounds like what you are describing with the version incompatibility. The particular error message quoted here seems to be due to a broken update of Catlab.jl, encountered by this issue in DiagrammaticEquations.jl Using the latest release of Julia is recommended; our github actions test on Julia 1.10 and Julia 1.11.6.

You can post the original error message from version 1.11 to this issue and I can take a look at it as well.

[DavidRobertsSBL]

OK, so perhaps the Project.toml's need updating? :-)

In any case, thanks for clarifying, it looked like my setup wasn't treating the version as a minimum, but an exact requirement. That's probably on me for not being familiar with Julia!

Regarding the 1.11 issue, now it is working! There may have been left-over crud from fiddling around trying to set stuff up that polluted the project. I did get another error in the very last code block from the overview example, possibly due to type piracy/collision involving ComponentArrays but that's a separate issue, and I seem to have solved it by re-using the modules in a specific order.