support Julia 1.7 #1382

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#1438

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support Julia 1.7#1382

#1438

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breaking changesbugjulia versionmaintenanceupstream

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v0.26.1

dehann

opened

on Sep 9, 2021

Member

Likely issue on complex numbers and log.

dehann

added this to the v0.25.1 milestone

added

modified the milestones: v0.25.2, v0.25.3

on Oct 14, 2021

Affie

Member

I just had a quick look at the CI log and the first failure is from the log of a negative number called from KDE.
Stacktrace:

DomainError with -2.3542838229142713e306:
log will only return a complex result if called with a complex argument. Try log(Complex(x)).
Stacktrace:
  [1] throw_complex_domainerror(f::Symbol, x::Float64)
    @ Base.Math ./math.jl:33
  [2] _log(x::Float64, base::Val{:ℯ}, func::Symbol)
    @ Base.Math ./special/log.jl:304
  [3] log
    @ ./special/log.jl:269 [inlined]
  [4] _broadcast_getindex_evalf
    @ ./broadcast.jl:670 [inlined]
  [5] _broadcast_getindex
    @ ./broadcast.jl:643 [inlined]
  [6] getindex
    @ ./broadcast.jl:597 [inlined]
  [7] macro expansion
    @ ./broadcast.jl:1005 [inlined]
  [8] macro expansion
    @ ./simdloop.jl:77 [inlined]
  [9] copyto!
    @ ./broadcast.jl:1004 [inlined]
 [10] copyto!
    @ ./broadcast.jl:957 [inlined]
 [11] copy
    @ ./broadcast.jl:929 [inlined]
 [12] materialize
    @ ./broadcast.jl:904 [inlined]
 [13] evalAvgLogL(bd1::BallTreeDensity, bd2::BallTreeDensity, addop::Tuple{typeof(+)}, diffop::Tuple{typeof(-)})
    @ KernelDensityEstimate ~/.julia/dev/KernelDensityEstimate/src/DualTree01.jl:468
 [14] entropy
    @ ~/.julia/dev/KernelDensityEstimate/src/DualTree01.jl:507 [inlined]
 [15] nLOO_LL(alpha::Float64, bd::BallTreeDensity, addop::Tuple{typeof(+)}, diffop::Tuple{typeof(-)})
    @ KernelDensityEstimate ~/.julia/dev/KernelDensityEstimate/src/CrossValidation.jl:20
 [16] golden(bd::BallTreeDensity, ax::Float64, bx::Float64, cx::Float64, tol::Float64, addop::Tuple{typeof(+)}, diffop::Tuple{typeof(-)})
    @ KernelDensityEstimate ~/.julia/dev/KernelDensityEstimate/src/CrossValidation.jl:83
 [17] ksize(bd::BallTreeDensity, addop::Tuple{typeof(+)}, diffop::Tuple{typeof(-)})
    @ KernelDensityEstimate ~/.julia/dev/KernelDensityEstimate/src/CrossValidation.jl:116
 [18] kde!(points::Matrix{Float64}, addop::Tuple{typeof(+)}, diffop::Tuple{typeof(-)})
    @ KernelDensityEstimate ~/.julia/dev/KernelDensityEstimate/src/KDE01.jl:19
 [19] kde! (repeats 2 times)
    @ ~/.julia/dev/KernelDensityEstimate/src/KDE01.jl:31 [inlined]
 [20] getKDEManifoldBandwidths(pts::Matrix{Float64}, manif::Tuple{Symbol, Symbol, Symbol})
    @ ApproxManifoldProducts ~/.julia/packages/ApproxManifoldProducts/oopxJ/src/Legacy.jl:83
 [21] ManifoldKernelDensity(M::GroupManifold{ℝ, ProductManifold{ℝ, Tuple{TranslationGroup{Tuple{2}, ℝ}, SpecialOrthogonal{2}}}, Manifolds.SemidirectProductOperation{RotationAction{TranslationGroup{Tuple{2}, ℝ}, SpecialOrthogonal{2}, LeftAction}}}, vecP::Vector{ProductRepr{Tuple{Vector{Float64}, Matrix{Float64}}}}, u0::ProductRepr{Tuple{Vector{Float64}, Matrix{Float64}}}; partial::Nothing, infoPerCoord::Vector{Float64}, dims::Int64, bw::Nothing)
    @ ApproxManifoldProducts ~/.julia/packages/ApproxManifoldProducts/oopxJ/src/services/ManifoldKernelDensity.jl:64
 [22] #manikde!#37
    @ ~/.julia/packages/ApproxManifoldProducts/oopxJ/src/services/ManifoldKernelDensity.jl:81 [inlined]
 [23] approxConvBelief(dfg::LightDFG{SolverParams, DFGVariable, DFGFactor}, fc::DFGFactor{CommonConvWrapper{ManifoldPrior{GroupManifold{ℝ, ProductManifold{ℝ, Tuple{TranslationGroup{Tuple{2}, ℝ}, SpecialOrthogonal{2}}}, Manifolds.SemidirectProductOperation{RotationAction{TranslationGroup{Tuple{2}, ℝ}, SpecialOrthogonal{2}, LeftAction}}}, ZeroMeanDiagNormal{Tuple{Base.OneTo{Int64}}}, ProductRepr{Tuple{MVector{2, Float64}, MMatrix{2, 2, Float64, 4}}}, ManifoldsBase.VeeOrthogonalBasis{ℝ}}, Nothing, Vector{Int64}, NamedTuple{(:x0,), Tuple{Vector{Any}}}, Nothing, ProductRepr{Tuple{MVector{2, Float64}, MMatrix{2, 2, Float64, 4}}}}, 1}, target::Symbol, measurement::Vector{Tuple}; solveKey::Symbol, N::Int64, skipSolve::Bool)
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/services/ApproxConv.jl:26
 [24] #calcProposalBelief#320
    @ ~/.julia/dev/IncrementalInference/src/services/ApproxConv.jl:161 [inlined]
 [25] proposalbeliefs!(dfg::LightDFG{SolverParams, DFGVariable, DFGFactor}, destlbl::Symbol, factors::Vector{DFGFactor}, dens::Vector{ManifoldKernelDensity}, measurement::Vector{Tuple}; solveKey::Symbol, N::Int64, dbg::Bool)
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/services/ApproxConv.jl:229
 [26] propagateBelief(dfg::LightDFG{SolverParams, DFGVariable, DFGFactor}, destvar::DFGVariable{SpecialEuclidean2}, factors::Vector{DFGFactor}; solveKey::Symbol, dens::Vector{ManifoldKernelDensity}, N::Int64, needFreshMeasurements::Bool, dbg::Bool, logger::Base.CoreLogging.SimpleLogger)
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/GraphProductOperations.jl:30
 [27] predictbelief(dfg::LightDFG{SolverParams, DFGVariable, DFGFactor}, destvert::DFGVariable{SpecialEuclidean2}, factors::Vector{DFGFactor}; asPartial::Bool, kw::Base.Pairs{Symbol, Any, NTuple{4, Symbol}, NamedTuple{(:needFreshMeasurements, :N, :dbg, :logger), Tuple{Bool, Int64, Bool, Base.CoreLogging.SimpleLogger}}})
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/GraphProductOperations.jl:67
 [28] predictbelief(dfg::LightDFG{SolverParams, DFGVariable, DFGFactor}, destlbl::Symbol, fctlbls::Vector{Symbol}; kw::Base.Pairs{Symbol, Any, NTuple{4, Symbol}, NamedTuple{(:needFreshMeasurements, :N, :dbg, :logger), Tuple{Bool, Int64, Bool, Base.CoreLogging.SimpleLogger}}})
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/GraphProductOperations.jl:76
 [29] #predictbelief#332
    @ ~/.julia/dev/IncrementalInference/src/GraphProductOperations.jl:82 [inlined]
 [30] doFMCIteration(fgl::LightDFG{SolverParams, DFGVariable, DFGFactor}, vsym::Symbol, solveKey::Symbol, cliq::IncrementalInference.TreeClique, fmsgs::Vector{LikelihoodMessage}, N::Int64, dbg::Bool, needFreshMeasurements::Bool, logger::Base.CoreLogging.SimpleLogger)
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/SolveTree.jl:65
 [31] fmcmc!(fgl::LightDFG{SolverParams, DFGVariable, DFGFactor}, cliq::IncrementalInference.TreeClique, fmsgs::Vector{LikelihoodMessage}, lbls::Vector{Symbol}, solveKey::Symbol, N::Int64, MCMCIter::Int64, dbg::Bool, logger::Base.CoreLogging.SimpleLogger, multithreaded::Bool)
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/SolveTree.jl:116
 [32] upGibbsCliqueDensity(dfg::LightDFG{SolverParams, DFGVariable, DFGFactor}, cliq::IncrementalInference.TreeClique, solveKey::Symbol, inmsgs::Vector{LikelihoodMessage}, N::Int64, dbg::Bool, iters::Int64, logger::Base.CoreLogging.SimpleLogger)
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/SolveTree.jl:186
 [33] approxCliqMarginalUp!(csmc::CliqStateMachineContainer{BayesTreeNodeData, LightDFG{SolverParams, DFGVariable, DFGFactor}, LightDFG{SolverParams, DFGVariable, DFGFactor}, MetaBayesTree}, childmsgs::Vector{LikelihoodMessage}; N::Int64, dbg::Bool, multiproc::Bool, logger::Base.CoreLogging.SimpleLogger, iters::Int64, drawpdf::Bool)
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/CliqStateMachineUtils.jl:387
 [34] __doCliqUpSolveInitialized!(csmc::CliqStateMachineContainer{BayesTreeNodeData, LightDFG{SolverParams, DFGVariable, DFGFactor}, LightDFG{SolverParams, DFGVariable, DFGFactor}, MetaBayesTree})
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/CliqStateMachineUtils.jl:32
 [35] solveUp_StateMachine(csmc::CliqStateMachineContainer{BayesTreeNodeData, LightDFG{SolverParams, DFGVariable, DFGFactor}, LightDFG{SolverParams, DFGVariable, DFGFactor}, MetaBayesTree})
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/CliqueStateMachine.jl:367
 [36] (::StateMachine{CliqStateMachineContainer})(userdata::CliqStateMachineContainer{BayesTreeNodeData, LightDFG{SolverParams, DFGVariable, DFGFactor}, LightDFG{SolverParams, DFGVariable, DFGFactor}, MetaBayesTree}, timeout::Nothing; pollinterval::Float64, breakafter::Function, verbose::Bool, verbosefid::Base.TTY, verboseXtra::IncrementalInference.CliqStatus, iterlimit::Int64, injectDelayBefore::Nothing, recordhistory::Bool, housekeeping_cb::IncrementalInference.var"#445#447"{IncrementalInference.TreeClique, CliqStateMachineContainer{BayesTreeNodeData, LightDFG{SolverParams, DFGVariable, DFGFactor}, LightDFG{SolverParams, DFGVariable, DFGFactor}, MetaBayesTree}})
    @ FunctionalStateMachine ~/.julia/packages/FunctionalStateMachine/2JZFG/src/StateMachine.jl:82
 [37] initStartCliqStateMachine!(dfg::LightDFG{SolverParams, DFGVariable, DFGFactor}, tree::MetaBayesTree, cliq::IncrementalInference.TreeClique, timeout::Nothing; oldcliqdata::BayesTreeNodeData, verbose::Bool, verbosefid::Base.TTY, drawtree::Bool, show::Bool, incremental::Bool, limititers::Int64, upsolve::Bool, downsolve::Bool, recordhistory::Bool, delay::Bool, logger::Base.CoreLogging.SimpleLogger, solve_progressbar::Nothing, algorithm::Symbol, solveKey::Symbol)
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/CliqueStateMachine.jl:64
 [38] tryCliqStateMachineSolve!(dfg::LightDFG{SolverParams, DFGVariable, DFGFactor}, treel::MetaBayesTree, cliqKey::Int64, timeout::Nothing; oldtree::MetaBayesTree, verbose::Bool, verbosefid::Base.TTY, drawtree::Bool, limititers::Int64, downsolve::Bool, incremental::Bool, delaycliqs::Vector{Symbol}, recordcliqs::Vector{Symbol}, solve_progressbar::Nothing, algorithm::Symbol, solveKey::Symbol)
    @ IncrementalInference ~/.julia/dev/IncrementalInference/src/SolverAPI.jl:112
 [39] (::IncrementalInference.var"#496#499"{MetaBayesTree, Bool, Bool, Base.TTY, Bool, Bool, Vector{Symbol}, Vector{Symbol}, Symbol, Symbol, LightDFG{SolverParams, DFGVariable, DFGFactor}, MetaBayesTree, Nothing, Nothing, Int64, Int64})()
    @ IncrementalInference ./task.jl:411

dehann

modified the milestones: v0.25.3, v0.25.4

assigned

modified the milestones: v0.25.4, v0.25.5

on Oct 19, 2021

Affie

Member

see discourse: https://discourse.julialang.org/t/whats-going-on-with-exp-and-math-mode-fast/64619/27

Function causing issues is called here:
https://github.com/JuliaRobotics/KernelDensityEstimate.jl/blob/fda7f5d54447cbdabbccb8828971c2ad83d960e9/src/DualTree01.jl#L44

dehann

MemberAuthor

xref JuliaLang/julia#42747

1 remaining item

Affie

Member

The issue above is now fixed in the julia nightly build. It will be included in v1.7.0/v1.7.0-RC3.

Affie

Member

The nightly tests now shows a different upstream issue:

Test loading and saving of Bayes (Junction) tree: Error During Test at /home/runner/work/IncrementalInference.jl/IncrementalInference.jl/test/testTreeSaveLoad.jl:6
  Got exception outside of a @test
  type DataType has no field mutable
  Stacktrace:
    [1] getproperty
      @ ./Base.jl:33 [inlined]
    [2] hasfielddata(T::Any, encounteredtypes::Vector{DataType})
      @ JLD2 ~/.julia/packages/JLD2/qncOK/src/data/writing_datatypes.jl:24
    [3] hasdata(T::DataType, encounteredtypes::Vector{DataType})
      @ JLD2 ~/.julia/packages/JLD2/qncOK/src/data/writing_datatypes.jl:32
    [4] hasdata
      @ ~/.julia/packages/JLD2/qncOK/src/data/writing_datatypes.jl:30 [inlined]
    [5] odr(#unused#::Type{MetaBayesTree})
      @ JLD2 ~/.julia/packages/JLD2/qncOK/src/data/writing_datatypes.jl:563
    [6] objodr
      @ ~/.julia/packages/JLD2/qncOK/src/data/writing_datatypes.jl:109 [inlined]
    [7] write_dataset
      @ ~/.julia/packages/JLD2/qncOK/src/datasets.jl:541 [inlined]
    [8] write(g::JLD2.Group{JLD2.JLDFile{JLD2.MmapIO}}, name::String, obj::MetaBayesTree, wsession::JLD2.JLDWriteSession{Dict{UInt64, JLD2.RelOffset}})
      @ JLD2 ~/.julia/packages/JLD2/qncOK/src/groups.jl:119
    [9] write(f::JLD2.JLDFile{JLD2.MmapIO}, name::String, obj::MetaBayesTree, wsession::JLD2.JLDWriteSession{Dict{UInt64, JLD2.RelOffset}})
      @ JLD2 ~/.julia/packages/JLD2/qncOK/src/JLD2.jl:347
   [10] macro expansion
      @ ~/.julia/packages/JLD2/qncOK/src/loadsave.jl:66 [inlined]
   [11] saveTree(treel::MetaBayesTree, filepath::String)
      @ IncrementalInference ~/work/IncrementalInference.jl/IncrementalInference.jl/src/JunctionTree.jl:1636
   [12] saveTree(treel::MetaBayesTree)
      @ IncrementalInference ~/work/IncrementalInference.jl/IncrementalInference.jl/src/JunctionTree.jl:1629
   [13] macro expansion
      @ ~/work/IncrementalInference.jl/IncrementalInference.jl/test/testTreeSaveLoad.jl:12 [inlined]
   [14] macro expansion
      @ /opt/hostedtoolcache/julia/nightly/x64/share/julia/stdlib/v1.8/Test/src/Test.jl:1321 [inlined]
   [15] top-level scope
      @ ~/work/IncrementalInference.jl/IncrementalInference.jl/test/testTreeSaveLoad.jl:8
   [16] include(fname::String)
      @ Base.MainInclude ./client.jl:451
   [17] top-level scope
      @ ~/work/IncrementalInference.jl/IncrementalInference.jl/test/runtests.jl:30
   [18] include(fname::String)
      @ Base.MainInclude ./client.jl:451
   [19] top-level scope
      @ none:6
   [20] eval
      @ ./boot.jl:368 [inlined]
   [21] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:271
   [22] _start()
      @ Base ./client.jl:497

dehann

MemberAuthor

Looks like it's the test for saveTree. How far do the tests get if you suppress just that JLD2 save/load tree test?

Affie

Member

Lets see: #1438

Affie

Member

Yes, It's the only issue on the nightly build.
I'm leaning towards fixing together with the change of LightGraphs (MetaGraphs) to Graphs and when the next julia rc or stable version is released.

dehann

modified the milestones: v0.25.5, v0.25.6

on Oct 23, 2021

dehann

linked a pull request that will close this issueBson testTreeSaveLoad for julia 1.7 #1438

on Oct 23, 2021

dehann

modified the milestones: v0.25.6, v0.26.0

on Nov 8, 2021

dehann

modified the milestones: v0.26.0, v0.0.x

on Nov 15, 2021