API Redesign

PoisotLab · Dec 20, 2024 · 78f006b · 78f006b
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diff --git a/Project.toml b/Project.toml
@@ -4,36 +4,47 @@ authors = ["michael catchen <michael.catchen@colorado.edu>"]
 version = "0.2.1"
 
 [deps]
-CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
+DelaunayTriangulation = "927a84f5-c5f4-47a5-9785-b46e178433df"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
+GeometryOps = "3251bfac-6a57-4b6d-aa61-ac1fef2975ab"
 HaltonSequences = "13907d55-377f-55d6-a9d6-25ac19e11b95"
 HiGHS = "87dc4568-4c63-4d18-b0c0-bb2238e4078b"
 JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SimpleSDMLayers = "2c645270-77db-11e9-22c3-0f302a89c64c"
 SliceMap = "82cb661a-3f19-5665-9e27-df437c7e54c8"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+SpeciesDistributionToolkit = "72b53823-5c0b-4575-ad0e-8e97227ad13b"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Term = "22787eb5-b846-44ae-b979-8e399b8463ab"
 TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
 
 [weakdeps]
 NeutralLandscapes = "71847384-8354-4223-ac08-659a5128069f"
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 
 [extensions]
+BONsMakieExt = "Makie"
 
 [compat]
+Clustering = "0.15.7"
+DelaunayTriangulation = "1.6.3"
 Distributions = "0.25"
+GeoInterface = "1.4.0"
+GeometryOps = "0.1.13"
 HaltonSequences = "0.2"
 HiGHS = "1.5"
 JuMP = "1.11"
+MultivariateStats = "0.10.3"
 ProgressMeter = "1.7.2"
-Requires = "1.3"
 SliceMap = "0.2.7"
 SpecialFunctions = "2.1"
+SpeciesDistributionToolkit = "1.2.0"
 StatsBase = "0.34"
 julia = "1.9"
diff --git a/_OLD/src/BiodiversityObservationNetworks.jl b/_OLD/src/BiodiversityObservationNetworks.jl
@@ -0,0 +1,68 @@
+module BiodiversityObservationNetworks
+
+using SimpleSDMLayers
+using Distributions
+using Random
+using HaltonSequences
+using StatsBase
+using SpecialFunctions
+using ProgressMeter
+using SliceMap
+using JuMP
+using HiGHS
+using LinearAlgebra
+using Term
+using TestItems
+
+include("types.jl")
+export BONSampler
+export Sites, numsites, pool
+export LayerType, DataLayer, InclusionProbability
+export Layer, Stack
+
+include("sample.jl")
+export sample
+
+include("exceptions.jl")
+export BONException, TooFewSites, TooManySites
+
+include("simplerandom.jl")
+export SimpleRandom
+
+include("spatialstratified.jl")
+export SpatiallyStratified
+
+include("balancedacceptance.jl")
+export BalancedAcceptance
+
+include("weightedbas.jl")
+export WeightedBalancedAcceptance
+
+include("adaptivehotspot.jl")
+export AdaptiveHotspot
+
+include("cubesampling.jl")
+export CubeSampling
+
+include("fractaltriad.jl")
+export FractalTriad
+
+include("grts.jl")
+export GeneralizedRandomTessellatedStratified
+
+include("uniqueness.jl")
+export Uniqueness
+
+#include("seed.jl")
+#export seed, seed!
+
+#include("refine.jl")
+#export refine, refine!
+
+include("entropize.jl")
+export entropize, entropize!
+
+include("utils.jl")
+export stack
+
+end
diff --git a/src/adaptivehotspot.jl → _OLD/src/adaptivehotspot.jl b/src/adaptivehotspot.jl → _OLD/src/adaptivehotspot.jl
diff --git a/src/balancedacceptance.jl → _OLD/src/balancedacceptance.jl b/src/balancedacceptance.jl → _OLD/src/balancedacceptance.jl
diff --git a/src/cubesampling.jl → _OLD/src/cubesampling.jl b/src/cubesampling.jl → _OLD/src/cubesampling.jl
diff --git a/src/entropize.jl → _OLD/src/entropize.jl b/src/entropize.jl → _OLD/src/entropize.jl
diff --git a/src/exceptions.jl → _OLD/src/exceptions.jl b/src/exceptions.jl → _OLD/src/exceptions.jl
diff --git a/src/fractaltriad.jl → _OLD/src/fractaltriad.jl b/src/fractaltriad.jl → _OLD/src/fractaltriad.jl
diff --git a/src/grts.jl → _OLD/src/grts.jl b/src/grts.jl → _OLD/src/grts.jl
diff --git a/_OLD/src/new_api.md b/_OLD/src/new_api.md
@@ -0,0 +1,32 @@
+
+
+
+
+
+SDMLayer
+Matrix
+
+struct Layer{T}
+    layer::T
+end
+
+struct Stack{T}
+    stack::Vector{Layer{T}}
+end
+
+
+
+abstract type InclusionType end 
+struct CategoricalInclusion <: InclusionType
+    layer::Layer
+    inclusion_probability::Dict
+end
+struct ContinuousInclusion <: InclusionType
+    layer::Layer
+end
+
+
+
+struct InclusionProbability{<:InclusionType}
+
+end 
diff --git a/src/refine.jl → _OLD/src/refine.jl b/src/refine.jl → _OLD/src/refine.jl
diff --git a/_OLD/src/sample.jl b/_OLD/src/sample.jl
@@ -0,0 +1,26 @@
+
+function sample(alg::BONSampler) 
+    _sample!(
+        _allocate_sites(numsites(alg)), 
+        _default_pool(alg),
+        alg
+    )
+end
+
+
+function sample(alg::BONSampler, l::L) where L<:Layer
+    _sample!(
+        _allocate_sites(numsites(alg)), 
+        l,
+        alg
+    )
+end
+
+
+function sample(alg::BONSampler, candidates::C) where C<:Sites
+    _sample!(
+        _allocate_sites(numsites(alg)), 
+        candidates,
+        alg
+    )
+end
diff --git a/src/simplerandom.jl → _OLD/src/simplerandom.jl b/src/simplerandom.jl → _OLD/src/simplerandom.jl
diff --git a/src/spatialstratified.jl → _OLD/src/spatialstratified.jl b/src/spatialstratified.jl → _OLD/src/spatialstratified.jl
@@ -88,7 +88,6 @@ function _default_strata(sz)
     mat[begin:x, :] .= 1
     mat[(x + 1):end, begin:y] .= 2
     mat[(x + 1):end, (y + 1):end] .= 3
-
     return Layer(mat)
 end
 

diff --git a/src/types.jl → _OLD/src/types.jl b/src/types.jl → _OLD/src/types.jl
diff --git a/src/uniqueness.jl → _OLD/src/uniqueness.jl b/src/uniqueness.jl → _OLD/src/uniqueness.jl
diff --git a/src/utils.jl → _OLD/src/utils.jl b/src/utils.jl → _OLD/src/utils.jl
diff --git a/src/weightedbas.jl → _OLD/src/weightedbas.jl b/src/weightedbas.jl → _OLD/src/weightedbas.jl
diff --git a/docs/make.jl b/docs/make.jl
@@ -8,7 +8,7 @@ using BiodiversityObservationNetworks
 bib = CitationBibliography(joinpath(@__DIR__, "BONs.bib"))
 
 makedocs(
-    sitename = "BiodiversityObservationNetwork.jl",
+    sitename = "BiodiversityObservationNetworks.jl",
     authors = "Michael D. Catchen, Timothée Poisot, Kari Norman, Hana Mayall, Tom Malpas",
     modules = [BiodiversityObservationNetworks],
     format = DocumenterVitepress.MarkdownVitepress(

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -4,49 +4,7 @@ The purpose of this package is to provide a high-level, extensible, modular
 interface to the selection of sampling point for biodiversity processes in
 space. It is based around a collection of types representing point selection
 algorithms, used to select the most informative sampling points based on raster
-data. Specifically, many algorithms work from a layer indicating *entropy* of a
-model based prediction at each location.
+data. 
 
 !!! warning "This package is in development"
     The `BiodiversityObservationNetworks.jl` package is currently under development. The API is not expected to change a lot, but it may change in order to facilitate the integration of new features.
-
-## High-level types
-
-```@docs
-BONSampler
-BONSeeder
-BONRefiner
-```
-
-## Seeder and refiner functions
-
-```@docs
-seed
-seed!
-```
-
-```@docs
-refine
-refine!
-```
-
-## Seeder algorithms
-
-```@docs
-BalancedAcceptance
-```
-
-## Refiner algorithms
-
-```@docs
-AdaptiveSpatial
-Uniqueness
-```
-
-## Helper functions
-
-```@docs
-squish
-entropize!
-entropize
-```
diff --git a/ext/BONsMakieExt/BONsMakieExt.jl b/ext/BONsMakieExt/BONsMakieExt.jl
@@ -0,0 +1,11 @@
+module BONsMakieExt
+
+@info "Loading Makie Extension for BiodiversityObservationNetworks.jl..."
+
+@static if isdefined(Base, :get_extension)
+    using Makie, BiodiversityObservationNetworks
+else    
+    using ..Makie, ..BiodiversityObservationNetworks
+end
+
+end
diff --git a/ext/SDTExt.jl b/ext/SDTExt.jl
diff --git a/src/BiodiversityObservationNetworks.jl b/src/BiodiversityObservationNetworks.jl
@@ -1,68 +1,41 @@
 module BiodiversityObservationNetworks
-
-using SimpleSDMLayers
-using Distributions
-using Random
-using HaltonSequences
-using StatsBase
-using SpecialFunctions
-using ProgressMeter
-using SliceMap
-using JuMP
-using HiGHS
-using LinearAlgebra
-using Term
-using TestItems
-
-include("types.jl")
-export BONSampler
-export Sites, numsites, pool
-export LayerType, DataLayer, InclusionProbability
-export Layer, Stack
-
-include("sample.jl")
-export sample
-
-include("exceptions.jl")
-export BONException, TooFewSites, TooManySites
-
-include("simplerandom.jl")
-export SimpleRandom
-
-include("spatialstratified.jl")
-export SpatiallyStratified
-
-include("balancedacceptance.jl")
-export BalancedAcceptance
-
-include("weightedbas.jl")
-export WeightedBalancedAcceptance
-
-include("adaptivehotspot.jl")
-export AdaptiveHotspot
-
-include("cubesampling.jl")
-export CubeSampling
-
-include("fractaltriad.jl")
-export FractalTriad
-
-include("grts.jl")
-export GeneralizedRandomTessellatedStratified
-
-include("uniqueness.jl")
-export Uniqueness
-
-#include("seed.jl")
-#export seed, seed!
-
-#include("refine.jl")
-#export refine, refine!
-
-include("entropize.jl")
-export entropize, entropize!
-
-include("utils.jl")
-export stack
-
-end
+    using Clustering
+    using DelaunayTriangulation
+    using Distributions
+    using GeometryOps
+    using GeoInterface
+    using MultivariateStats
+    using SpeciesDistributionToolkit
+    using Random
+
+    import GeoInterface as GI
+    import GeometryOps as GO
+    import SpeciesDistributionToolkit as SDT
+    import SpeciesDistributionToolkit.GeoJSON as GJSON
+
+    export BiodiversityObservationNetwork
+    export Node
+    export Polygon
+    export Raster
+    export RasterStack
+
+    export BONSampler
+    export SimpleRandom, Grid, KMeans, SpatiallyStratified
+    export sample
+    export datatype
+    export nonempty
+    export is_polygonizable, is_rasterizable, is_bonifyable
+
+    include(joinpath("geometry", "bon.jl"))
+    include(joinpath("geometry", "polygon.jl"))
+    include(joinpath("geometry", "raster.jl"))
+    include(joinpath("geometry", "stack.jl"))
+
+    include("sample.jl")
+    include(joinpath("samplers", "simplerandom.jl"))
+    include(joinpath("samplers", "grid.jl"))
+    include(joinpath("samplers", "kmeans.jl"))
+    include(joinpath("samplers", "spatiallystratified.jl"))
+
+
+end