Merge pull request #54 from MurrellGroup/single-node-tree #153
nossleinadAnnotations
10 warnings
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Documentation:
../../../.julia/packages/DocumenterVitepress/WL3xD/src/writer.jl#L877
DocumenterVitepress: un-expanded `@example viz` block encountered on page src/generated/viz.md.
The first few lines of code in this node are:
```
plot_multiple_trees(
trees,
reference,
y_jitter = 0.05,
weight_fn = n::FelNode ->
ifelse(MolecularEvolution.isroot(n) || isleafnode(n), 1.0, 0.0)
```
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Documentation:
../../../.julia/packages/DocumenterVitepress/WL3xD/src/writer.jl#L877
DocumenterVitepress: un-expanded `@example viz` block encountered on page src/generated/viz.md.
The first few lines of code in this node are:
```
plot_multiple_trees(trees, reference)
```
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Documentation:
../../../.julia/packages/DocumenterVitepress/WL3xD/src/writer.jl#L877
DocumenterVitepress: un-expanded `@example viz` block encountered on page src/generated/viz.md.
The first few lines of code in this node are:
```
using MolecularEvolution, Plots
tree = sim_tree(10, 1, 1)
nodelist = getnodelist(tree); mean = sum([n.branchlength for n in nodelist]) / length(nodelist)
rparams(n::Int) = MolecularEvolution.sum2one(rand(n))
model = DiagonalizedCTMC(reversibleQ(ones(6) ./ (6 * mean), rparams(4)))
```
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Documentation:
../../../.julia/packages/DocumenterVitepress/WL3xD/src/vitepress_config.jl#L56
DocumenterVitepress: Did not detect `docs/src/.vitepress/theme/docstrings.css` file. Substituting in the default file.
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Documentation:
../../../.julia/packages/DocumenterVitepress/WL3xD/src/vitepress_config.jl#L52
DocumenterVitepress: Did not detect `docs/src/.vitepress/theme/style.css` file. Substituting in the default file.
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Documentation:
../../../.julia/packages/DocumenterVitepress/WL3xD/src/vitepress_config.jl#L48
DocumenterVitepress: Did not detect `docs/src/.vitepress/theme/index.ts` file. Substituting in the default file.
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Documentation:
../../../.julia/packages/DocumenterVitepress/WL3xD/src/vitepress_config.jl#L40
DocumenterVitepress: Did not detect `docs/src/.vitepress/config.mts` file. Substituting in the default file.
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Documentation:
../../../.julia/packages/Documenter/QLA7E/src/utilities/utilities.jl#L46
failed to run `@example` block in src/generated/viz.md:107-115
```@example viz
plot_multiple_trees(
trees,
reference,
y_jitter = 0.05,
weight_fn = n::FelNode ->
ifelse(MolecularEvolution.isroot(n) || isleafnode(n), 1.0, 0.0)
)
```
exception =
UndefVarError: `trees` not defined in `Main.__atexample__named__viz`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
[1] top-level scope
@ viz.md:108
[2] eval
@ ./boot.jl:430 [inlined]
[3] #61
@ ~/.julia/packages/Documenter/QLA7E/src/expander_pipeline.jl:806 [inlined]
[4] cd(f::Documenter.var"#61#63"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#60#62"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/QLA7E/src/expander_pipeline.jl:805
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#60#62"{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::IOCapture.var"#5#9"{DataType, Documenter.var"#60#62"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState)
@ Base.CoreLogging ./logging/logging.jl:522
[8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger)
@ Base.CoreLogging ./logging/logging.jl:632
[9] capture(f::Documenter.var"#60#62"{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/QLA7E/src/expander_pipeline.jl:804
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Documentation:
../../../.julia/packages/Documenter/QLA7E/src/utilities/utilities.jl#L46
failed to run `@example` block in src/generated/viz.md:99-101
```@example viz
plot_multiple_trees(trees, reference)
```
exception =
UndefVarError: `trees` not defined in `Main.__atexample__named__viz`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
[1] top-level scope
@ viz.md:100
[2] eval
@ ./boot.jl:430 [inlined]
[3] #61
@ ~/.julia/packages/Documenter/QLA7E/src/expander_pipeline.jl:806 [inlined]
[4] cd(f::Documenter.var"#61#63"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#60#62"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/QLA7E/src/expander_pipeline.jl:805
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#60#62"{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::IOCapture.var"#5#9"{DataType, Documenter.var"#60#62"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState)
@ Base.CoreLogging ./logging/logging.jl:522
[8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger)
@ Base.CoreLogging ./logging/logging.jl:632
[9] capture(f::Documenter.var"#60#62"{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/QLA7E/src/expander_pipeline.jl:804
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|
Documentation:
../../../.julia/packages/Documenter/QLA7E/src/utilities/utilities.jl#L46
failed to run `@example` block in src/generated/viz.md:83-95
```@example viz
using MolecularEvolution, Plots
tree = sim_tree(10, 1, 1)
nodelist = getnodelist(tree); mean = sum([n.branchlength for n in nodelist]) / length(nodelist)
rparams(n::Int) = MolecularEvolution.sum2one(rand(n))
model = DiagonalizedCTMC(reversibleQ(ones(6) ./ (6 * mean), rparams(4)))
internal_message_init!(tree, NucleotidePartition(ones(4) ./ 4, 100))
sample_down!(tree, model)
@time trees, LLs = metropolis_sample(tree, [model], 300, collect_LLs=true);
reference = trees[argmax(LLs)];
nothing #hide
```
exception =
InexactError: Float64(-0.1610632714322493 - 1.962615573354719e-17im)
Stacktrace:
[1] Real
@ ./complex.jl:44 [inlined]
[2] convert
@ ./number.jl:7 [inlined]
[3] setindex!
@ ./genericmemory.jl:243 [inlined]
[4] unsafe_copyto!(dest::Memory{Float64}, doffs::Int64, src::Memory{ComplexF64}, soffs::Int64, n::Int64)
@ Base ./genericmemory.jl:153
[5] unsafe_copyto!
@ ./genericmemory.jl:133 [inlined]
[6] _copyto_impl!
@ ./array.jl:308 [inlined]
[7] copyto!
@ ./array.jl:294 [inlined]
[8] copyto!
@ ./array.jl:319 [inlined]
[9] copyto_axcheck!
@ ./abstractarray.jl:1167 [inlined]
[10] Array
@ ./array.jl:626 [inlined]
[11] convert
@ ./array.jl:618 [inlined]
[12] DiagonalizedCTMC(Q::Matrix{Float64})
@ MolecularEvolution ~/work/MolecularEvolution.jl/MolecularEvolution.jl/src/models/discrete_models/pmatrix_models/DiagonalizedCTMC.jl:15
[13] top-level scope
@ viz.md:89
[14] eval
@ ./boot.jl:430 [inlined]
[15] #61
@ ~/.julia/packages/Documenter/QLA7E/src/expander_pipeline.jl:806 [inlined]
[16] cd(f::Documenter.var"#61#63"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[17] (::Documenter.var"#60#62"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/QLA7E/src/expander_pipeline.jl:805
[18] (::IOCapture.var"#5#9"{DataType, Documenter.var"#60#62"{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
[19] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#60#62"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState)
@ Base.CoreLogging ./logging/logging.jl:522
[20] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger)
@ Base.CoreLogging ./logging/logging.jl:632
[21] capture(f::Documenter.var"#60#62"{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
[22] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/QLA7E/src/expander_pipeline.jl:804
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