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Make everything dimensional #82

Make everything dimensional

Make everything dimensional #82

Triggered via pull request January 3, 2025 16:10
Status Failure
Total duration 13m 45s
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Matrix: test
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2 errors and 10 warnings
Julia 1.10 - ubuntu-latest - x64 - pull_request
Process completed with exit code 1.
Julia 1 - ubuntu-latest - x64 - pull_request
Process completed with exit code 1.
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L46
failed to run `@example` block in src/eucalyptus_regnans.md:88-91 ```@example test pred = SDM.predict(ensemble, bio_aus; reducer = mean) plot(pred; colorrange = (0,1)) ``` exception = MethodError: no method matching predict(::SDMensemble{2, Tuple{DimensionalData.Dimensions.Dim{:model, DimensionalData.Dimensions.Lookups.Categorical{Symbol, Vector{Symbol}, DimensionalData.Dimensions.Lookups.Unordered, DimensionalData.Dimensions.Lookups.NoMetadata}}, DimensionalData.Dimensions.Dim{:fold, DimensionalData.Dimensions.Lookups.Sampled{Int64, UnitRange{Int64}, DimensionalData.Dimensions.Lookups.ForwardOrdered, DimensionalData.Dimensions.Lookups.Regular{Int64}, DimensionalData.Dimensions.Lookups.Points, DimensionalData.Dimensions.Lookups.NoMetadata}}}, Tuple{}, OffsetArrays.OffsetMatrix{SpeciesDistributionModels.SDMmachine, Matrix{SpeciesDistributionModels.SDMmachine}}}, ::Rasters.RasterStack{(:bio1, :bio12), @NamedTuple{bio1::Float32, bio12::Float32}, 2, @NamedTuple{bio1::SubArray{Float32, 2, Matrix{Float32}, Tuple{UnitRange{Int64}, UnitRange{Int64}}, false}, bio12::SubArray{Float32, 2, Matrix{Float32}, Tuple{UnitRange{Int64}, UnitRange{Int64}}, false}}, Tuple{DimensionalData.Dimensions.X{Rasters.Projected{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, DimensionalData.Dimensions.Lookups.ForwardOrdered, DimensionalData.Dimensions.Lookups.Regular{Float64}, DimensionalData.Dimensions.Lookups.Intervals{DimensionalData.Dimensions.Lookups.Start}, DimensionalData.Dimensions.Lookups.NoMetadata, GeoFormatTypes.WellKnownText{GeoFormatTypes.CRS}, Nothing, DimensionalData.Dimensions.X{Colon}}}, DimensionalData.Dimensions.Y{Rasters.Projected{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, DimensionalData.Dimensions.Lookups.ReverseOrdered, DimensionalData.Dimensions.Lookups.Regular{Float64}, DimensionalData.Dimensions.Lookups.Intervals{DimensionalData.Dimensions.Lookups.Start}, DimensionalData.Dimensions.Lookups.NoMetadata, GeoFormatTypes.WellKnownText{GeoFormatTypes.CRS}, Nothing, DimensionalData.Dimensions.Y{Colon}}}}, Tuple{}, @NamedTuple{bio1::Tuple{DimensionalData.Dimensions.X{Colon}, DimensionalData.Dimensions.Y{Colon}}, bio12::Tuple{DimensionalData.Dimensions.X{Colon}, DimensionalData.Dimensions.Y{Colon}}}, DimensionalData.Dimensions.Lookups.NoMetadata, @NamedTuple{bio1::DimensionalData.Dimensions.Lookups.Metadata{Rasters.GDALsource, Dict{String, Any}}, bio12::DimensionalData.Dimensions.Lookups.Metadata{Rasters.GDALsource, Dict{String, Any}}}, Float32}; reducer::typeof(Statistics.mean)) This error has been manually thrown, explicitly, so the method may exist but be intentionally marked as unimplemented. Closest candidates are: predict(::SDMensemble, ::Any; clamp, threaded) got unsupported keyword argument "reducer" @ SpeciesDistributionModels ~/work/SpeciesDistributionModels.jl/SpeciesDistributionModels.jl/src/interface.jl:152 predict(!Matched::SpeciesDistributionModels.SDMmachine, ::Any; clamp) got unsupported keyword argument "reducer" @ SpeciesDistributionModels ~/work/SpeciesDistributionModels.jl/SpeciesDistributionModels.jl/src/interface.jl:149 Stacktrace: [1] kwerr(::@NamedTuple{reducer::typeof(Statistics.mean)}, ::Function, ::SDMensemble{2, Tuple{DimensionalData.Dimensions.Dim{:model, DimensionalData.Dimensions.Lookups.Categorical{Symbol, Vector{Symbol}, DimensionalData.Dimensions.Lookups.Unordered, DimensionalData.Dimensions.Lookups.NoMetadata}}, DimensionalData.Dimensions.Dim{:fold, DimensionalData.Dimensions.Lookups.Sampled{Int64, UnitRange{Int64}, DimensionalData.Dimensions.Lookups.ForwardOrdered, DimensionalData.Dimensions.Lookups.Regular{Int64}, DimensionalData.Dimensions.Lookups.Points, DimensionalData.Dimensions.Lookups.NoMetadata}}}, Tuple{}, OffsetArrays.OffsetMatrix{SpeciesDistributionModels.SDMmachine, Matrix{SpeciesDistributionModels.SDMmachine}}}, ::Rasters.RasterStack{(:bio1, :bio12), @NamedTuple{bio1::Float32, bio12::Float32}, 2, @NamedTuple{bio1::SubA
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L46
failed to run `@example` block in src/eucalyptus_regnans.md:96-99 ```@example test expl = SDM.explain(ensemble; method = ShapleyValues(8)) variable_importance(expl) ``` exception = UndefVarError: `ShapleyValues` not defined in `Main.__atexample__named__test` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ eucalyptus_regnans.md:97 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [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/Bs999/src/expander_pipeline.jl:802 [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::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}}, 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"#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/Bs999/src/expander_pipeline.jl:801
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L46
failed to run `@example` block in src/eucalyptus_regnans.md:102-104 ```@example test interactive_response_curves(expl) ``` exception = UndefVarError: `interactive_response_curves` not defined in `Main.__atexample__named__test` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ eucalyptus_regnans.md:103 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [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/Bs999/src/expander_pipeline.jl:802 [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::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}}, 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"#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/Bs999/src/expander_pipeline.jl:801
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L46
invalid local link/image: file does not exist in src/eucalyptus_regnans.md link = @ast MarkdownAST.Link("www.github.com/rafaqz/Rasters.jl", "") do MarkdownAST.Text("Rasters") end
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L46
invalid local link/image: file does not exist in src/eucalyptus_regnans.md link = @ast MarkdownAST.Link("www.github.com/rafaqz/GBIF2.jl", "") do MarkdownAST.Text("GBIF2.jl") end
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L46
Cannot resolve @ref for md"[SDM.explain](@ref)" in src/eucalyptus_regnans.md. - Exception trying to find docref for `SDM.explain`: unable to get the binding for `SDM.explain` in module Main
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L46
invalid local link/image: file does not exist in src/eucalyptus_regnans.md link = @ast MarkdownAST.Link("www.gitlab.com/ExpandingMan/Shapley.jl", "") do MarkdownAST.Text("Shapley.jl") end
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L46
Cannot resolve @ref for md"[SDMmachine](@ref)" in src/getting_started.md. - No docstring found in doc for binding `Main.SDMmachine`.
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L46
Cannot resolve @ref for md"[SDMgroup](@ref)" in src/getting_started.md. - No docstring found in doc for binding `Main.SDMgroup`.
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L46
Cannot resolve @ref for md"[SDMensemble](@ref)" in src/getting_started.md. - No docstring found in doc for binding `SpeciesDistributionModels.SDMensemble`.