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Merge pull request #56 from boydorr/phylo
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Fix phylogenetic diversity handling
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@richardreeve
richardreeve authored Apr 23, 2021
2 parents 1032162 + 2b566b2 commit 2ed9237
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Showing 9 changed files with 12 additions and 8 deletions.
2 changes: 2 additions & 0 deletions NEWS.md
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# NEWS

- v0.1.2
- Fix phylogenetic diversity management
- v0.1.1
- Remove unnecessary Compat dependency
- Fix incompatibility with latest Diversity release
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4 changes: 2 additions & 2 deletions Project.toml
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name = "EcoSISTEM"
uuid = "ed2dc23b-ada4-5fdb-a26f-56368a14ad8f"
authors = ["Claire Harris <claire.harris@bioss.ac.uk>", "Richard Reeve <Richard.Reeve@glasgow.ac.uk>"]
version = "0.1.1"
version = "0.1.2"

[deps]
ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"
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Calculus = "0.4.1, 0.5"
DataFrames = "0.21.8, 0.22, 1.0"
Distributions = "0.24.15"
Diversity = "=0.5.4"
Diversity = "0.5.6"
EcoBase = "0.1.3"
Feather = "0.5.7"
HCubature = "1.5.0"
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4 changes: 2 additions & 2 deletions docs/Manifest.toml
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Expand Up @@ -239,7 +239,7 @@ version = "0.24.18"
deps = ["AxisArrays", "DataFrames", "EcoBase", "InteractiveUtils", "LinearAlgebra", "Missings", "RecipesBase", "Requires", "Statistics"]
git-tree-sha1 = "b0601dcd6efbf6e560c329f5c03bb5294357c598"
uuid = "d3d5718d-52de-57ab-b67a-eca7fd6175a4"
version = "0.5.5"
version = "0.5.6"

[[DocStringExtensions]]
deps = ["LibGit2", "Markdown", "Pkg", "Test"]
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deps = ["ArchGDAL", "AxisArrays", "Calculus", "Compat", "DataFrames", "Dates", "Distributions", "Diversity", "EcoBase", "Feather", "HCubature", "IndexedTables", "Interpolations", "JLD", "JuliaDB", "LibGit2", "Libdl", "LinearAlgebra", "Logging", "MPI", "Markdown", "Measures", "Missings", "NetCDF", "OnlineStats", "Optim", "Phylo", "Plots", "Printf", "RCall", "REPL", "Random", "RecipesBase", "Requires", "SHA", "SpatialEcology", "Statistics", "StatsBase", "UUIDs", "Unitful"]
git-tree-sha1 = "55bcaf9fe1e595691a58c2c6d9a6f1b08a7e7ffb"
uuid = "ed2dc23b-ada4-5fdb-a26f-56368a14ad8f"
version = "0.1.0"
version = "0.1.2"

[[EllipsisNotation]]
deps = ["ArrayInterface"]
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4 changes: 2 additions & 2 deletions examples/Manifest.toml
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Expand Up @@ -245,7 +245,7 @@ version = "0.24.18"
deps = ["AxisArrays", "DataFrames", "EcoBase", "InteractiveUtils", "LinearAlgebra", "Missings", "RecipesBase", "Requires", "Statistics"]
git-tree-sha1 = "b0601dcd6efbf6e560c329f5c03bb5294357c598"
uuid = "d3d5718d-52de-57ab-b67a-eca7fd6175a4"
version = "0.5.5"
version = "0.5.6"

[[DocStringExtensions]]
deps = ["LibGit2", "Markdown", "Pkg", "Test"]
Expand Down Expand Up @@ -273,7 +273,7 @@ version = "0.1.3"
deps = ["ArchGDAL", "AxisArrays", "Calculus", "Compat", "DataFrames", "Dates", "Distributions", "Diversity", "EcoBase", "Feather", "HCubature", "IndexedTables", "Interpolations", "JLD", "JuliaDB", "LibGit2", "Libdl", "LinearAlgebra", "Logging", "MPI", "Markdown", "Measures", "Missings", "NetCDF", "OnlineStats", "Optim", "Phylo", "Plots", "Printf", "RCall", "REPL", "Random", "RecipesBase", "Requires", "SHA", "SpatialEcology", "Statistics", "StatsBase", "UUIDs", "Unitful"]
git-tree-sha1 = "55bcaf9fe1e595691a58c2c6d9a6f1b08a7e7ffb"
uuid = "ed2dc23b-ada4-5fdb-a26f-56368a14ad8f"
version = "0.1.0"
version = "0.1.2"

[[EllipsisNotation]]
deps = ["ArrayInterface"]
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1 change: 0 additions & 1 deletion src/AdditionalDiversity.jl
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using Diversity
using Phylo

"""
makeunique(eco::Ecosystem)
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1 change: 1 addition & 0 deletions src/Generate.jl
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using StatsBase
using LinearAlgebra

"""
get_neighbours(mat::Matrix, x_coord::Int64, y_coord::Int64, chess::Int64=4)
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1 change: 1 addition & 0 deletions src/MPIGenerate.jl
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using MPI
using LinearAlgebra

"""
update!(eco::MPIEcosystem, timestep::Unitful.Time) where N
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2 changes: 1 addition & 1 deletion src/SpeciesList.jl
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Expand Up @@ -210,7 +210,7 @@ end
# return eye(ut.num)
#end

#function _calcsimilarity(ph::PhyloTypes)
#function _calcsimilarity(ph::PhyloBranches)
# return ph.Zmatrix
#end
import Diversity.API: _gettypenames
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1 change: 1 addition & 0 deletions test/test_AdditionalDiversity.jl
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Expand Up @@ -3,6 +3,7 @@ using Diversity
using Phylo
using Statistics
using Test

@testset "diversity" begin
include("TestCases.jl")
eco = TestEcosystem()
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Registration pull request created: JuliaRegistries/General/35169

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.1.2 -m "<description of version>" 2ed9237e831d08ea1abcdee21e6ce1c9ed892940
git push origin v0.1.2

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