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bump makie and rasters compat #23

Merged
merged 2 commits into from
Jan 21, 2025
Merged

bump makie and rasters compat #23

merged 2 commits into from
Jan 21, 2025

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tiemvanderdeure
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@tiemvanderdeure
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Do you know why the docs are segfaulting @lazarusA? I guess it might have nothing to do with the compats?

@lazarusA
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well, testing locally, it already looks like you need to do some other updates:

 Warning: failed to run `@example` block in src/eucalyptus_regnans.md:64-75
│ ```@example test
│ using Maxnet: MaxnetBinaryClassifier
│ using EvoTrees: EvoTreeClassifier
│ using MLJGLMInterface: LinearBinaryClassifier
│ models = (
│   maxnet = MaxnetBinaryClassifier(),
│   brt = EvoTreeClassifier(),
│   glm = LinearBinaryClassifier()
│ )
│ 
│ ensemble = sdm(data, models)
│ ```
│   exception =
│    ArgumentError: reducing over an empty collection is not allowed; consider supplying `init` to the reducer
│    Stacktrace:
│      [1] _empty_reduce_error()
│        @ Base ./reduce.jl:319
│      [2] mapreduce_empty(f::Function, op::Base.BottomRF{typeof(Base._rf_findmax)}, T::Type)
│        @ Base ./reduce.jl:321
│      [3] reduce_empty(op::Base.MappingRF{Base.var"#353#354"{typeof(identity)}, Base.BottomRF{typeof(Base._rf_findmax)}}, ::Type{Pair{Int64, Float64}})
│        @ Base ./reduce.jl:358
│      [4] reduce_empty_iter
│        @ ./reduce.jl:381 [inlined]
│      [5] reduce_empty_iter
│        @ ./reduce.jl:380 [inlined]
│      [6] foldl_impl
│        @ ./reduce.jl:49 [inlined]
│      [7] mapfoldl_impl
│        @ ./reduce.jl:44 [inlined]
│      [8] mapfoldl
│        @ ./reduce.jl:175 [inlined]
│      [9] _findmax
│        @ ./reduce.jl:906 [inlined]
│     [10] findmax
│        @ ./reducedim.jl:1198 [inlined]
│     [11] _findmax
│        @ ./reduce.jl:935 [inlined]
│     [12] findmax
│        @ ./reducedim.jl:1175 [inlined]
│     [13] _broadcast_getindex_evalf
│        @ ./broadcast.jl:673 [inlined]
│     [14] _broadcast_getindex
│        @ ./broadcast.jl:646 [inlined]
│     [15] getindex
│        @ ./broadcast.jl:605 [inlined]
│     [16] macro expansion
│        @ ./broadcast.jl:968 [inlined]
│     [17] macro expansion
│        @ ./simdloop.jl:77 [inlined]
│     [18] copyto!
│        @ ./broadcast.jl:967 [inlined]
│     [19] copyto!
│        @ ./broadcast.jl:920 [inlined]
│     [20] copy
│        @ ./broadcast.jl:892 [inlined]
│     [21] materialize
│        @ ./broadcast.jl:867 [inlined]
│     [22] grow_tree!(tree::EvoTrees.Tree{EvoTrees.MLogLoss, 2}, nodes::Vector{EvoTrees.TrainNode{SubArray{UInt32, 1, Vector{UInt32}, Tuple{UnitRange{Int64}}, true}, Vector{Float64}, Matrix{Float64}}}, params::EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, ∇::Matrix{Float32}, edges::Vector{Any}, js::Vector{UInt32}, out::Vector{UInt32}, left::Vector{UInt32}, right::Vector{UInt32}, x_bin::Matrix{UInt8}, feattypes::Vector{Bool}, monotone_constraints::Vector{Int32})
│        @ EvoTrees ~/.julia/packages/EvoTrees/9X6ti/src/fit.jl:103
│     [23] grow_evotree!(m::EvoTrees.EvoTree{EvoTrees.MLogLoss, 2}, cache::@NamedTuple{info::Dict{Symbol, Int64}, x_bin::Matrix{UInt8}, y::Vector{UInt32}, w::Vector{Float32}, pred::Matrix{Float32}, K::Int64, nodes::Vector{EvoTrees.TrainNode{SubArray{UInt32, 1, Vector{UInt32}, Tuple{UnitRange{Int64}}, true}, Vector{Float64}, Matrix{Float64}}}, is_in::Vector{UInt32}, is_out::Vector{UInt32}, mask::Vector{UInt8}, js_::Vector{UInt32}, js::Vector{UInt32}, out::Vector{UInt32}, left::Vector{UInt32}, right::Vector{UInt32}, ∇::Matrix{Float32}, edges::Vector{Any}, fnames::Tuple{Symbol, Symbol}, featbins::Vector{UInt8}, feattypes::Vector{Bool}, monotone_constraints::Vector{Int32}}, params::EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, ::Type{EvoTrees.CPU})
│        @ EvoTrees ~/.julia/packages/EvoTrees/9X6ti/src/fit.jl:18
│     [24] grow_evotree!(m::EvoTrees.EvoTree{EvoTrees.MLogLoss, 2}, cache::@NamedTuple{info::Dict{Symbol, Int64}, x_bin::Matrix{UInt8}, y::Vector{UInt32}, w::Vector{Float32}, pred::Matrix{Float32}, K::Int64, nodes::Vector{EvoTrees.TrainNode{SubArray{UInt32, 1, Vector{UInt32}, Tuple{UnitRange{Int64}}, true}, Vector{Float64}, Matrix{Float64}}}, is_in::Vector{UInt32}, is_out::Vector{UInt32}, mask::Vector{UInt8}, js_::Vector{UInt32}, js::Vector{UInt32}, out::Vector{UInt32}, left::Vector{UInt32}, right::Vector{UInt32}, ∇::Matrix{Float32}, edges::Vector{Any}, fnames::Tuple{Symbol, Symbol}, featbins::Vector{UInt8}, feattypes::Vector{Bool}, monotone_constraints::Vector{Int32}}, params::EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss})
│        @ EvoTrees ~/.julia/packages/EvoTrees/9X6ti/src/fit.jl:9
│     [25] fit(model::EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, verbosity::Int64, A::@NamedTuple{bio1::Vector{Union{Missing, Float32}}, bio12::Vector{Union{Missing, Float32}}}, y::CategoricalArrays.CategoricalVector{Bool, UInt8, Bool, CategoricalArrays.CategoricalValue{Bool, UInt8}, Union{}}, w::Nothing)
│        @ EvoTrees ~/.julia/packages/EvoTrees/9X6ti/src/MLJ.jl:10
│     [26] fit(model::EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, verbosity::Int64, A::@NamedTuple{bio1::Vector{Union{Missing, Float32}}, bio12::Vector{Union{Missing, Float32}}}, y::CategoricalArrays.CategoricalVector{Bool, UInt8, Bool, CategoricalArrays.CategoricalValue{Bool, UInt8}, Union{}})
│        @ EvoTrees ~/.julia/packages/EvoTrees/9X6ti/src/MLJ.jl:3
│     [27] fit_only!(mach::MLJBase.Machine{EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, true}; rows::Vector{Int64}, verbosity::Int64, force::Bool, composite::Nothing)
│        @ MLJBase ~/.julia/packages/MLJBase/7nGJF/src/machines.jl:692
│     [28] fit_only!
│        @ ~/.julia/packages/MLJBase/7nGJF/src/machines.jl:617 [inlined]
│     [29] #fit!#63
│        @ ~/.julia/packages/MLJBase/7nGJF/src/machines.jl:789 [inlined]
│     [30] _fit_sdm_model(data::SpeciesDistributionModels.SDMdata{(:bio1, :bio12)}, model::EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, fold::Int64, train::Vector{Int64}, test::Vector{Int64}, verbosity::Int64, cache::Bool, scitype_check_level::Int64)
│        @ SpeciesDistributionModels ~/Desktop/tmp/SpeciesDistributionModels.jl/src/ensemble.jl:182
│     [31] #32
│        @ ~/Desktop/tmp/SpeciesDistributionModels.jl/src/ensemble.jl:197 [inlined]
│     [32] iterate
│        @ ./generator.jl:48 [inlined]
│     [33] collect(itr::Base.Generator{Base.Iterators.Enumerate{Vector{Tuple{Vector{Int64}, Vector{Int64}}}}, SpeciesDistributionModels.var"#32#33"{SpeciesDistributionModels.SDMdata{(:bio1, :bio12)}, EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, Int64, Bool, Int64}})
│        @ Base ./array.jl:791
│     [34] map(f::Function, A::Base.Iterators.Enumerate{Vector{Tuple{Vector{Int64}, Vector{Int64}}}})
│        @ Base ./abstractarray.jl:3399
│     [35] _fit_sdm_group(data::SpeciesDistributionModels.SDMdata{(:bio1, :bio12)}, model::EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, model_key::Symbol, verbosity::Int64, cache::Bool, scitype_check_level::Int64, cpu_backend::ComputationalResources.CPU1{Nothing})
│        @ SpeciesDistributionModels ~/Desktop/tmp/SpeciesDistributionModels.jl/src/ensemble.jl:196
│     [36] #34
│        @ ~/Desktop/tmp/SpeciesDistributionModels.jl/src/ensemble.jl:215 [inlined]
│     [37] map(f::SpeciesDistributionModels.var"#34#35"{SpeciesDistributionModels.SDMdata{(:bio1, :bio12)}, @NamedTuple{maxnet::Maxnet.MaxnetBinaryClassifier, brt::EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, glm::MLJGLMInterface.LinearBinaryClassifier}, Int64, Bool, Int64, ComputationalResources.CPU1{Nothing}}, t::Tuple{Symbol, Symbol, Symbol})
│        @ Base ./tuple.jl:357
│     [38] _sdm(data::SpeciesDistributionModels.SDMdata{(:bio1, :bio12)}, models::@NamedTuple{maxnet::Maxnet.MaxnetBinaryClassifier, brt::EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, glm::MLJGLMInterface.LinearBinaryClassifier}, verbosity::Int64, cache::Bool, scitype_check_level::Int64, threaded::Bool)
│        @ SpeciesDistributionModels ~/Desktop/tmp/SpeciesDistributionModels.jl/src/ensemble.jl:213
│     [39] #sdm#130
│        @ ~/Desktop/tmp/SpeciesDistributionModels.jl/src/interface.jl:75 [inlined]
│     [40] sdm(data::SpeciesDistributionModels.SDMdata{(:bio1, :bio12)}, models::@NamedTuple{maxnet::Maxnet.MaxnetBinaryClassifier, brt::EvoTrees.EvoTreeClassifier{EvoTrees.MLogLoss}, glm::MLJGLMInterface.LinearBinaryClassifier})
│        @ SpeciesDistributionModels ~/Desktop/tmp/SpeciesDistributionModels.jl/src/interface.jl:68
│     [41] top-level scope
│        @ eucalyptus_regnans.md:74
│     [42] eval
│        @ ./boot.jl:430 [inlined]
│     [43] #60
│        @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined]
│     [44] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
│        @ Base.Filesystem ./file.jl:112
│     [45] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
│        @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802
│     [46] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, Base.TTY, Base.TTY})()
│        @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
│     [47] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, Base.TTY, Base.TTY}, logstate::Base.CoreLogging.LogState)
│        @ Base.CoreLogging ./logging/logging.jl:522
│     [48] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger)
│        @ Base.CoreLogging ./logging/logging.jl:632
│     [49] 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
│     [50] 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
└ @ Documenter ~/.julia/packages/Documenter/Bs999/src/utilities/utilities.jl:46
┌ Warning: failed to run `@example` block in src/eucalyptus_regnans.md:80-83
│ ```@example test
│ import SpeciesDistributionModels as SDM
│ ev = SDM.evaluate(ensemble; measures = (; auc, accuracy))
│ ```
│   exception =
│    UndefVarError: `ensemble` not defined in `Main.__atexample__named__test`
│    Suggestion: check for spelling errors or missing imports.
│    Stacktrace:
│      [1] top-level scope
│        @ eucalyptus_regnans.md:82
│      [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}, Base.TTY, Base.TTY})()
│        @ 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}, Base.TTY, Base.TTY}, 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
└ @ Documenter ~/.julia/packages/Documenter/Bs999/src/utilities/utilities.jl:46
┌ Warning: 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 =
│    UndefVarError: `ensemble` not defined in `Main.__atexample__named__test`
│    Suggestion: check for spelling errors or missing imports.
│    Stacktrace:
│      [1] top-level scope
│        @ eucalyptus_regnans.md:89
│      [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}, Base.TTY, Base.TTY})()
│        @ 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}, Base.TTY, Base.TTY}, 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
└ @ Documenter ~/.julia/packages/Documenter/Bs999/src/utilities/utilities.jl:46
┌ Warning: 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: `ensemble` 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}, Base.TTY, Base.TTY})()
│        @ 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}, Base.TTY, Base.TTY}, 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
└ @ Documenter ~/.julia/packages/Documenter/Bs999/src/utilities/utilities.jl:46
┌ Warning: failed to run `@example` block in src/eucalyptus_regnans.md:102-104
│ ```@example test
│ interactive_response_curves(expl)
│ ```
│   exception =
│    UndefVarError: `expl` 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}, Base.TTY, Base.TTY})()
│        @ 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}, Base.TTY, Base.TTY}, 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
└ @ Documenter ~/.julia/packages/Documenter/Bs999/src/utilities/utilities.jl:46

@tiemvanderdeure
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Turns out that (I think due to the commondatamodel implementation in Rasters) stack[indices] returned a Union{Missing, Float} eltype, and this (very annoyingly) made the EvoTrees model segfault (rather than just throw an error). Sorry for bothering you with that one.

@tiemvanderdeure tiemvanderdeure merged commit b0cb48f into main Jan 21, 2025
4 checks passed
@tiemvanderdeure tiemvanderdeure deleted the rasters_014 branch January 21, 2025 19:51
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