Store transposed transition matrix to speed up forward #133
Triggered via pull request
September 28, 2024 07:11
Status
Failure
Total duration
12m 34s
Artifacts
–
Annotations
3 errors, 2 warnings, and 1 notice
Documentation:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/examples/interfaces.md:229-232
```@example interfaces
prior_hmm_est, prior_logl_evolution = baum_welch(prior_hmm_guess, obs_seq)
first(prior_logl_evolution), last(prior_logl_evolution)
```
exception =
TaskFailedException
nested task error: MethodError: no method matching transpose_transition_matrix(::Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}})
Closest candidates are:
transpose_transition_matrix(::AbstractHMM, !Matched::Nothing)
@ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/types/abstract_hmm.jl:115
transpose_transition_matrix(::AbstractHMM, !Matched::Any)
@ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/types/abstract_hmm.jl:78
transpose_transition_matrix(!Matched::HMM)
@ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/types/hmm.jl:67
Stacktrace:
[1] transpose_transition_matrix(hmm::Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}, ::Nothing)
@ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/types/abstract_hmm.jl:115
[2] forward!(storage::HiddenMarkovModels.ForwardBackwardStorage{Float64, Matrix{Float64}}, hmm::Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}, obs_seq::Vector{Main.__atexample__named__interfaces.Stuff{Float64}}, control_seq::FillArrays.Fill{Nothing, 1, Tuple{Base.OneTo{Int64}}}, t1::Int64, t2::Int64)
@ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/inference/forward.jl:73
[3] forward_backward!(storage::HiddenMarkovModels.ForwardBackwardStorage{Float64, Matrix{Float64}}, hmm::Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}, obs_seq::Vector{Main.__atexample__named__interfaces.Stuff{Float64}}, control_seq::FillArrays.Fill{Nothing, 1, Tuple{Base.OneTo{Int64}}}, t1::Int64, t2::Int64; transition_marginals::Bool)
@ HiddenMarkovModels ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/inference/forward_backward.jl:72
[4] forward_backward!
@ ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/inference/forward_backward.jl:60 [inlined]
[5] macro expansion
@ ~/work/HiddenMarkovModels.jl/HiddenMarkovModels.jl/src/inference/forward_backward.jl:113 [inlined]
[6] (::HiddenMarkovModels.var"#131#threadsfor_fun#17"{HiddenMarkovModels.var"#131#threadsfor_fun#16#18"{FillArrays.Fill{Int64, 1, Tuple{Base.OneTo{Int64}}}, Bool, HiddenMarkovModels.ForwardBackwardStorage{Float64, Matrix{Float64}}, Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}, Vector{Main.__atexample__named__interfaces.Stuff{Float64}}, FillArrays.Fill{Nothing, 1, Tuple{Base.OneTo{Int64}}}, Vector{Float64}, Base.OneTo{Int64}}})(tid::Int64; onethread::Bool)
@ HiddenMarkovModels ./threadingconstructs.jl:215
[7] #131#threadsfor_fun
@ ./threadingconstructs.jl:182 [inlined]
[8] (::Base.Threads.var"#1#2"{HiddenMarkovModels.var"#131#threadsfor_fun#17"{HiddenMarkovModels.var"#131#threadsfor_fun#16#18"{FillArrays.Fill{Int64, 1, Tuple{Base.OneTo{Int64}}}, Bool, HiddenMarkovModels.ForwardBackwardStorage{Float64, Matrix{Float64}}, Main.__atexample__named__interfaces.PriorHMM{Float64, Main.__atexample__named__interfaces.StuffDist{Float64}}, Vector{Main.__atexample__named__interfaces.Stuff{Float64}}, FillArrays.Fill{Nothing, 1, Tuple{Base.OneTo{Int64}}}, Vector{Float64}, Base.OneTo{Int64}}}, Int64})()
@ Base.Threads ./threadingconstructs.jl:154
Stacktrace:
[1] threading_run(fun::HiddenMarkovModels.var"#131#threadsfor_fun#17"{HiddenMarkovModels.var"#131#threadsfor_fun#16#18"{FillArrays.Fill{Int64, 1, Tuple{Base
|
Documentation:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/examples/interfaces.md:236-238
```@example interfaces
cat(transition_matrix(hmm_est), transition_matrix(prior_hmm_est); dims=3)
```
exception =
UndefVarError: `prior_hmm_est` not defined
Stacktrace:
[1] top-level scope
@ interfaces.md:237
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
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Documentation
Process completed with exit code 1.
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Documentation
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Documentation
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v2, julia-actions/setup-julia@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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[julia-buildpkg] Caching of the julia depot was not detected
Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`
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