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Move code depending on CausalInference.jl into extension#523

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pat-alt wants to merge 5 commits intomainfrom
causal-inference-broken
Open

Move code depending on CausalInference.jl into extension#523
pat-alt wants to merge 5 commits intomainfrom
causal-inference-broken

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@pat-alt pat-alt commented Mar 15, 2026

This moves all code depending on CausalInference.jl into an extension to avoid the strong dependency (closes #465). I've noticed that the package is no longer precompiling due to an issue with CausalInference.jl (full stack trace below).

@mschauer @JorgeLuizFranco

(@v1.12) pkg> add CounterfactualExplanations
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [2f13d31b] + CounterfactualExplanations v1.5.0
    Updating `~/.julia/environments/v1.12/Manifest.toml`
  [47edcb42] + ADTypes v1.21.0
  [621f4979] + AbstractFFTs v1.5.0
  [7d9f7c33] + Accessors v0.1.43
  [79e6a3ab] + Adapt v4.5.0
  [dce04be8] + ArgCheck v2.5.0
  [ec485272] + ArnoldiMethod v0.4.0
  [7d9fca2a] + Arpack v0.5.4
  [a9b6321e] + Atomix v1.1.2
  [198e06fe] + BangBang v0.4.8
  [9718e550] + Baselet v0.1.1
  [324d7699] + CategoricalArrays v1.0.2
  [af321ab8] + CategoricalDistributions v0.2.1
  [8e462317] + CausalInference v0.19.2
  [082447d4] + ChainRules v1.73.0
  [d360d2e6] + ChainRulesCore v1.26.0
  [0b6fb165] + ChunkCodecCore v1.0.1
  [4c0bbee4] + ChunkCodecLibZlib v1.0.0
  [55437552] + ChunkCodecLibZstd v1.0.0
  [60701a23] + CliqueTrees v1.17.1
  [08986516] + Collects v1.1.0
  [861a8166] + Combinatorics v1.1.0
  [bbf7d656] + CommonSubexpressions v0.3.1
  [a33af91c] + CompositionsBase v0.1.2
  [ed09eef8] + ComputationalResources v0.3.2
  [187b0558] + ConstructionBase v1.6.0
  [6add18c4] + ContextVariablesX v0.1.3
  [2f13d31b] + CounterfactualExplanations v1.5.0
  [a93c6f00] + DataFrames v1.8.1
  [7806a523] + DecisionTree v0.12.4
  [244e2a9f] + DefineSingletons v0.1.2
  [163ba53b] + DiffResults v1.1.0
  [b552c78f] + DiffRules v1.15.1
  [a0c0ee7d] + DifferentiationInterface v0.7.16
  [b4f34e82] + Distances v0.10.12
  [31c24e10] + Distributions v0.25.123
  [f446124b] + EnergySamplers v1.0.4
  [f151be2c] + EnzymeCore v0.8.18
  [cc61a311] + FLoops v0.2.2
  [b9860ae5] + FLoopsBase v0.1.1
  [1a297f60] + FillArrays v1.16.0
  [3821ddf9] + FixedSizeArrays v1.3.0
  [587475ba] + Flux v0.16.9
  [f6369f11] + ForwardDiff v1.3.2
  [d9f16b24] + Functors v0.5.2
  [46192b85] + GPUArraysCore v0.2.0
  [86223c79] + Graphs v1.14.0
  [076d061b] + HashArrayMappedTries v0.2.0
  [34004b35] + HypergeometricFunctions v0.3.28
  [7869d1d1] + IRTools v0.4.15
  [d25df0c9] + Inflate v0.1.5
  [22cec73e] + InitialValues v0.3.1
  [842dd82b] + InlineStrings v1.4.5
  [3587e190] + InverseFunctions v0.1.17
  [41ab1584] + InvertedIndices v1.3.1
  [033835bb] + JLD2 v0.6.3
  [b14d175d] + JuliaVariables v0.2.4
  [63c18a36] + KernelAbstractions v0.9.40
⌅ [ec8451be] + KernelFunctions v0.10.67
  [8ac3fa9e] + LRUCache v1.6.2
  [92ad9a40] + LearnAPI v2.0.1
  [aa2f6b4e] + LogarithmicNumbers v1.4.1
  [c2834f40] + MLCore v1.0.0
  [7e8f7934] + MLDataDevices v1.17.4
  [a7f614a8] + MLJBase v1.12.1
  [c6f25543] + MLJDecisionTreeInterface v0.4.4
  [e80e1ace] + MLJModelInterface v1.12.1
  [d8e11817] + MLStyle v0.4.17
  [f1d291b0] + MLUtils v0.4.8
  [6fafb56a] + Memoization v0.2.2
⌅ [626554b9] + MetaGraphs v0.8.1
  [128add7d] + MicroCollections v0.2.0
  [6f286f6a] + MultivariateStats v0.10.4
  [872c559c] + NNlib v0.9.33
  [71a1bf82] + NameResolution v0.1.5
  [b8a86587] + NearestNeighbors v0.4.27
  [6fe1bfb0] + OffsetArrays v1.17.0
  [0b1bfda6] + OneHotArrays v0.2.10
  [3bd65402] + Optimisers v0.4.7
  [90014a1f] + PDMats v0.11.37
  [65ce6f38] + PackageExtensionCompat v1.0.2
  [2dfb63ee] + PooledArrays v1.4.3
  [8162dcfd] + PrettyPrint v0.2.0
  [08abe8d2] + PrettyTables v3.2.3
  [92933f4c] + ProgressMeter v1.11.0
  [1fd47b50] + QuadGK v2.11.2
  [c1ae055f] + RealDot v0.1.0
  [42d2dcc6] + Referenceables v0.1.3
  [79098fc4] + Rmath v0.9.0
  [431bcebd] + SciMLPublic v1.0.1
  [321657f4] + ScientificTypes v3.2.0
  [30f210dd] + ScientificTypesBase v3.1.0
  [6e75b9c4] + ScikitLearnBase v0.5.0
  [7e506255] + ScopedValues v1.6.0
  [91c51154] + SentinelArrays v1.4.9
  [efcf1570] + Setfield v1.1.2
  [605ecd9f] + ShowCases v0.1.0
  [699a6c99] + SimpleTraits v0.9.5
  [dc90abb0] + SparseInverseSubset v0.1.2
  [276daf66] + SpecialFunctions v2.7.1
  [171d559e] + SplittablesBase v0.1.15
  [90137ffa] + StaticArrays v1.9.18
  [1e83bf80] + StaticArraysCore v1.4.4
  [c062fc1d] + StatisticalMeasuresBase v0.1.3
  [64bff920] + StatisticalTraits v3.5.0
  [4c63d2b9] + StatsFuns v1.5.2
  [892a3eda] + StringManipulation v0.4.4
  [09ab397b] + StructArrays v0.7.2
  [3eeacb1d] + TabularDisplay v1.3.0
  [10284c91] + TaijaBase v1.2.3
  [ac1d9e8a] + ThreadsX v0.1.12
  [28d57a85] + Transducers v0.4.85
  [013be700] + UnsafeAtomics v0.3.0
  [e88e6eb3] + Zygote v0.7.10
  [700de1a5] + ZygoteRules v0.2.7
⌅ [68821587] + Arpack_jll v3.5.2+0
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [f50d1b31] + Rmath_jll v0.5.1+0
  [8ba89e20] + Distributed v1.11.0
  [9fa8497b] + Future v1.11.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [4607b0f0] + SuiteSparse
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
  ✗ CausalInference
  ✗ CounterfactualExplanations
  ✗ CounterfactualExplanations → DecisionTreeExt
Precompiling packages finished.
  0 dependencies successfully precompiled in 36 seconds. 476 already precompiled.
  3 dependencies errored.
  For a report of the errors see `julia> err`. To retry use `pkg> precompile`

julia> err
PkgPrecompileError: The following 2 direct dependencies failed to precompile:

CounterfactualExplanations → DecisionTreeExt

Failed to precompile DecisionTreeExt [5370ada7-daca-5ee7-9ed3-cddd3c2cf6f4] to "/Users/paltmeyer/.julia/compiled/v1.12/DecisionTreeExt/jl_0pLbxZ".
ERROR: LoadError: MethodError: no method matching sorted_intersect_(::Graphs.FrozenVector{Int64}, ::Graphs.FrozenVector{Int64})
The function `sorted_intersect_` exists, but no method is defined for this combination of argument types.

Closest candidates are:
  sorted_intersect_(::Vector{T}, ::Vector{T}) where T
   @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/pdag.jl:171

Stacktrace:
  [1] neighbors_undirected(g::Graphs.SimpleGraphs.SimpleDiGraph{Int64}, x::Int64)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/pdag.jl:128
  [2] tails_and_adj_neighbors(g::Graphs.SimpleGraphs.SimpleDiGraph{Int64}, x::Int64, y::Int64)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:204
  [3] score_edge_inserts(score::Float64, dataParsed::CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, g::Graphs.SimpleGraphs.SimpleDiGraph{Int64}, x::Int64, y::Int64)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:217
  [4] (::CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}})(::Tuple{Int64, Int64})
    @ CausalInference ./none:-1
  [5] MappingRF
    @ ./reduce.jl:92 [inlined]
  [6] FilteringRF
    @ ./reduce.jl:104 [inlined]
  [7] _foldl_impl
    @ ./reduce.jl:54 [inlined]
  [8] foldl_impl(op::Base.FilteringRF{CausalInference.var"#find_best_insert##6#find_best_insert##7"{Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.MappingRF{CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.BottomRF{typeof(CausalInference.best)}}}, nt::Base._InitialValue, itr::Base.Iterators.ProductIterator{Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}})
    @ Base ./reduce.jl:40
  [9] mapfoldl_impl(f::typeof(identity), op::typeof(CausalInference.best), nt::Base._InitialValue, itr::Base.Generator{Base.Iterators.Filter{CausalInference.var"#find_best_insert##6#find_best_insert##7"{Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.Iterators.ProductIterator{Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}}}, CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}}})
    @ Base ./reduce.jl:36
 [10] mapfoldl(f::Function, op::Function, itr::Base.Generator{Base.Iterators.Filter{CausalInference.var"#find_best_insert##6#find_best_insert##7"{Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.Iterators.ProductIterator{Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}}}, CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}}}; init::Base._InitialValue)
    @ Base ./reduce.jl:167
 [11] mapreduce(f::Function, op::Function, itr::Base.Generator{Base.Iterators.Filter{CausalInference.var"#find_best_insert##6#find_best_insert##7"{Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.Iterators.ProductIterator{Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}}}, CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}}}; kw::@Kwargs{})
    @ Base ./reduce.jl:299
 [12] reduce(op::Function, itr::Base.Generator{Base.Iterators.Filter{CausalInference.var"#find_best_insert##6#find_best_insert##7"{Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.Iterators.ProductIterator{Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}}}, CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}}}; kw::@Kwargs{})
    @ Base ./reduce.jl:479
 [13] find_best_insert(score::Float64, data::CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, g::Graphs.SimpleGraphs.SimpleDiGraph{Int64}, parallel::Bool, verbose::Bool)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:182
 [14] ges_forward_search!(g::Graphs.SimpleGraphs.SimpleDiGraph{Int64}, score::Float64, data::CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, parallel::Bool, verbose::Bool)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:124
 [15] macro expansion
    @ ./timing.jl:461 [inlined]
 [16] ges(n::Int64, data::CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}; score::Float64, parallel::Bool, verbose::Bool)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:54
 [17] ges
    @ ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:49 [inlined]
 [18] #ges#72
    @ ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:34 [inlined]
 [19] ges
    @ ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:28 [inlined]
 [20] #ges#73
    @ ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:41 [inlined]
 [21] macro expansion
    @ ~/.julia/packages/CausalInference/c2bzn/src/workloads.jl:14 [inlined]
 [22] macro expansion
    @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:73 [inlined]
 [23] macro expansion
    @ ~/.julia/packages/CausalInference/c2bzn/src/workloads.jl:13 [inlined]
 [24] macro expansion
    @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:121 [inlined]
 [25] top-level scope
    @ ~/.julia/packages/CausalInference/c2bzn/src/workloads.jl:118
 [26] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:307
 [27] top-level scope
    @ ~/.julia/packages/CausalInference/c2bzn/src/CausalInference.jl:54
 [28] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [29] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
    @ Base ./loading.jl:3024
 [30] top-level scope
    @ stdin:5
 [31] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [32] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2870
 [33] include_string
    @ ./loading.jl:2880 [inlined]
 [34] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [35] _start()
    @ Base ./client.jl:550
in expression starting at /Users/paltmeyer/.julia/packages/CausalInference/c2bzn/src/workloads.jl:3
in expression starting at /Users/paltmeyer/.julia/packages/CausalInference/c2bzn/src/CausalInference.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile CausalInference [8e462317-f959-576b-b3c1-403f26cec956] to "/Users/paltmeyer/.julia/compiled/v1.12/CausalInference/jl_MkiTKs".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3311
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
    @ Base ./loading.jl:2679
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.5+0.aarch64.apple.darwin14/Julia-1.12.app/Contents/Resources/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ ~/.julia/juliaup/julia-1.12.5+0.aarch64.apple.darwin14/Julia-1.12.app/Contents/Resources/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.5+0.aarch64.apple.darwin14/Julia-1.12.app/Contents/Resources/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1297 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1289 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3882
 [10] maybe_cachefile_lock
    @ ./loading.jl:3879 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2665
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2493
 [13] macro expansion
    @ ./loading.jl:2421 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2386
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2362
 [17] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:307
 [18] top-level scope
    @ ~/.julia/packages/CounterfactualExplanations/178eM/src/data_preprocessing/DataPreprocessing.jl:13
 [19] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:307
 [20] top-level scope
    @ ~/.julia/packages/CounterfactualExplanations/178eM/src/CounterfactualExplanations.jl:47
 [21] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [22] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
    @ Base ./loading.jl:3024
 [23] top-level scope
    @ stdin:5
 [24] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2870
 [26] include_string
    @ ./loading.jl:2880 [inlined]
 [27] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [28] _start()
    @ Base ./client.jl:550
in expression starting at /Users/paltmeyer/.julia/packages/CounterfactualExplanations/178eM/src/data_preprocessing/counterfactual_data.jl:7
in expression starting at /Users/paltmeyer/.julia/packages/CounterfactualExplanations/178eM/src/data_preprocessing/DataPreprocessing.jl:1
in expression starting at /Users/paltmeyer/.julia/packages/CounterfactualExplanations/178eM/src/CounterfactualExplanations.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile CounterfactualExplanations [2f13d31b-18db-44c1-bc43-ebaf2cff0be0] to "/Users/paltmeyer/.julia/compiled/v1.12/CounterfactualExplanations/jl_vhBBSZ".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3311
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
    @ Base ./loading.jl:2679
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.5+0.aarch64.apple.darwin14/Julia-1.12.app/Contents/Resources/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ ~/.julia/juliaup/julia-1.12.5+0.aarch64.apple.darwin14/Julia-1.12.app/Contents/Resources/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.5+0.aarch64.apple.darwin14/Julia-1.12.app/Contents/Resources/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1297 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1289 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3882
 [10] maybe_cachefile_lock
    @ ./loading.jl:3879 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2665
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2493
 [13] macro expansion
    @ ./loading.jl:2421 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2386
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2362
 [17] top-level scope
    @ ~/.julia/packages/CounterfactualExplanations/178eM/ext/DecisionTreeExt/DecisionTreeExt.jl:3
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [19] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:3024
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2870
 [23] include_string
    @ ./loading.jl:2880 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [25] _start()
    @ Base ./client.jl:550
in expression starting at /Users/paltmeyer/.julia/packages/CounterfactualExplanations/178eM/ext/DecisionTreeExt/DecisionTreeExt.jl:1
in expression starting at stdin:5
CounterfactualExplanations

Failed to precompile CounterfactualExplanations [2f13d31b-18db-44c1-bc43-ebaf2cff0be0] to "/Users/paltmeyer/.julia/compiled/v1.12/CounterfactualExplanations/jl_cgITIE".
ERROR: LoadError: MethodError: no method matching sorted_intersect_(::Graphs.FrozenVector{Int64}, ::Graphs.FrozenVector{Int64})
The function `sorted_intersect_` exists, but no method is defined for this combination of argument types.

Closest candidates are:
  sorted_intersect_(::Vector{T}, ::Vector{T}) where T
   @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/pdag.jl:171

Stacktrace:
  [1] neighbors_undirected(g::Graphs.SimpleGraphs.SimpleDiGraph{Int64}, x::Int64)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/pdag.jl:128
  [2] tails_and_adj_neighbors(g::Graphs.SimpleGraphs.SimpleDiGraph{Int64}, x::Int64, y::Int64)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:204
  [3] score_edge_inserts(score::Float64, dataParsed::CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, g::Graphs.SimpleGraphs.SimpleDiGraph{Int64}, x::Int64, y::Int64)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:217
  [4] (::CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}})(::Tuple{Int64, Int64})
    @ CausalInference ./none:-1
  [5] MappingRF
    @ ./reduce.jl:92 [inlined]
  [6] FilteringRF
    @ ./reduce.jl:104 [inlined]
  [7] _foldl_impl
    @ ./reduce.jl:54 [inlined]
  [8] foldl_impl(op::Base.FilteringRF{CausalInference.var"#find_best_insert##6#find_best_insert##7"{Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.MappingRF{CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.BottomRF{typeof(CausalInference.best)}}}, nt::Base._InitialValue, itr::Base.Iterators.ProductIterator{Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}})
    @ Base ./reduce.jl:40
  [9] mapfoldl_impl(f::typeof(identity), op::typeof(CausalInference.best), nt::Base._InitialValue, itr::Base.Generator{Base.Iterators.Filter{CausalInference.var"#find_best_insert##6#find_best_insert##7"{Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.Iterators.ProductIterator{Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}}}, CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}}})
    @ Base ./reduce.jl:36
 [10] mapfoldl(f::Function, op::Function, itr::Base.Generator{Base.Iterators.Filter{CausalInference.var"#find_best_insert##6#find_best_insert##7"{Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.Iterators.ProductIterator{Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}}}, CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}}}; init::Base._InitialValue)
    @ Base ./reduce.jl:167
 [11] mapreduce(f::Function, op::Function, itr::Base.Generator{Base.Iterators.Filter{CausalInference.var"#find_best_insert##6#find_best_insert##7"{Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.Iterators.ProductIterator{Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}}}, CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}}}; kw::@Kwargs{})
    @ Base ./reduce.jl:299
 [12] reduce(op::Function, itr::Base.Generator{Base.Iterators.Filter{CausalInference.var"#find_best_insert##6#find_best_insert##7"{Graphs.SimpleGraphs.SimpleDiGraph{Int64}}, Base.Iterators.ProductIterator{Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}}}, CausalInference.var"#find_best_insert##4#find_best_insert##5"{Float64, CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, Graphs.SimpleGraphs.SimpleDiGraph{Int64}}}; kw::@Kwargs{})
    @ Base ./reduce.jl:479
 [13] find_best_insert(score::Float64, data::CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, g::Graphs.SimpleGraphs.SimpleDiGraph{Int64}, parallel::Bool, verbose::Bool)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:182
 [14] ges_forward_search!(g::Graphs.SimpleGraphs.SimpleDiGraph{Int64}, score::Float64, data::CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}, parallel::Bool, verbose::Bool)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:124
 [15] macro expansion
    @ ./timing.jl:461 [inlined]
 [16] ges(n::Int64, data::CausalInference.GaussianScore{Float64, LinearAlgebra.Symmetric{Float64, Matrix{Float64}}}; score::Float64, parallel::Bool, verbose::Bool)
    @ CausalInference ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:54
 [17] ges
    @ ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:49 [inlined]
 [18] #ges#72
    @ ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:34 [inlined]
 [19] ges
    @ ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:28 [inlined]
 [20] #ges#73
    @ ~/.julia/packages/CausalInference/c2bzn/src/ges.jl:41 [inlined]
 [21] macro expansion
    @ ~/.julia/packages/CausalInference/c2bzn/src/workloads.jl:14 [inlined]
 [22] macro expansion
    @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:73 [inlined]
 [23] macro expansion
    @ ~/.julia/packages/CausalInference/c2bzn/src/workloads.jl:13 [inlined]
 [24] macro expansion
    @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:121 [inlined]
 [25] top-level scope
    @ ~/.julia/packages/CausalInference/c2bzn/src/workloads.jl:118
 [26] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:307
 [27] top-level scope
    @ ~/.julia/packages/CausalInference/c2bzn/src/CausalInference.jl:54
 [28] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [29] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
    @ Base ./loading.jl:3024
 [30] top-level scope
    @ stdin:5
 [31] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [32] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2870
 [33] include_string
    @ ./loading.jl:2880 [inlined]
 [34] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [35] _start()
    @ Base ./client.jl:550
in expression starting at /Users/paltmeyer/.julia/packages/CausalInference/c2bzn/src/workloads.jl:3
in expression starting at /Users/paltmeyer/.julia/packages/CausalInference/c2bzn/src/CausalInference.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile CausalInference [8e462317-f959-576b-b3c1-403f26cec956] to "/Users/paltmeyer/.julia/compiled/v1.12/CausalInference/jl_SAfWRf".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3311
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
    @ Base ./loading.jl:2679
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.5+0.aarch64.apple.darwin14/Julia-1.12.app/Contents/Resources/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ ~/.julia/juliaup/julia-1.12.5+0.aarch64.apple.darwin14/Julia-1.12.app/Contents/Resources/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.5+0.aarch64.apple.darwin14/Julia-1.12.app/Contents/Resources/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1297 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1289 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3882
 [10] maybe_cachefile_lock
    @ ./loading.jl:3879 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2665
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2493
 [13] macro expansion
    @ ./loading.jl:2421 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2386
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2362
 [17] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:307
 [18] top-level scope
    @ ~/.julia/packages/CounterfactualExplanations/178eM/src/data_preprocessing/DataPreprocessing.jl:13
 [19] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:307
 [20] top-level scope
    @ ~/.julia/packages/CounterfactualExplanations/178eM/src/CounterfactualExplanations.jl:47
 [21] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [22] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:3024
 [23] top-level scope
    @ stdin:5
 [24] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2870
 [26] include_string
    @ ./loading.jl:2880 [inlined]
 [27] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [28] _start()
    @ Base ./client.jl:550
in expression starting at /Users/paltmeyer/.julia/packages/CounterfactualExplanations/178eM/src/data_preprocessing/counterfactual_data.jl:7
in expression starting at /Users/paltmeyer/.julia/packages/CounterfactualExplanations/178eM/src/data_preprocessing/DataPreprocessing.jl:1
in expression starting at /Users/paltmeyer/.julia/packages/CounterfactualExplanations/178eM/src/CounterfactualExplanations.jl:1
in expression starting at stdin:5

@pat-alt
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pat-alt commented Mar 15, 2026

Extension not yet tested since I can't precompile CI.jl

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codecov bot commented Mar 15, 2026 •
edited
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Codecov Report

❌ Patch coverage is 15.00000% with 17 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.29%. Comparing base (c634199) to head (1fe7d51).

Files with missing lines Patch % Lines
ext/CausalInferenceExt/CausalInferenceExt.jl 0.00% 17 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #523      +/-   ##
==========================================
- Coverage   91.08%   90.29%   -0.79%     
==========================================
  Files          92       93       +1     
  Lines        2265     2267       +2     
==========================================
- Hits         2063     2047      -16     
- Misses        202      220      +18

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@JorgeLuizFranco
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JorgeLuizFranco commented Mar 23, 2026

Extension not yet tested since I can't precompile CI.jl

Hello, Patrick. Yes, I checked here. Lets wait for Moritz answer, maybe we can fix this and open a PR also in CausalInference.jl . Thank you for noticing!

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Move MINT functionality into extensions to avoid depending on CausalInference

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@pat-alt @JorgeLuizFranco