Prepare for integration with SpeciesInteractionNetworks

.github/workflows/CI.yml

@@ -17,6 +17,9 @@ jobs:
         version:
           - '1.5'
           - '1.6'
+          - '1.7'
+          - '1.8'
+          - '1.9'
         os:
           - ubuntu-latest
           - macOS-latest

.github/workflows/CompatHelper.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: [1.4.0]
+        julia-version: [1.9.0]
         julia-arch: [x86]
         os: [ubuntu-latest]
     steps:

.github/workflows/Documentation.yml

@@ -15,7 +15,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
         with:
-          version: '1.5'
+          version: '1.9'
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

Project.toml

@@ -2,18 +2,17 @@ name = "Mangal"
 uuid = "b8b640a6-63d9-51e6-b784-5033db27bef2"
 authors = ["Timothée Poisot <timothee.poisot@umontreal.ca>"]
 repo-url = "https://github.com/PoisotLab/Mangal.jl.git"
-version = "0.4.3"
+version = "0.5.0"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
-EcologicalNetworks = "f03a62fe-f8ab-5b77-a061-bb599b765229"
 GeoInterface = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
 
 [compat]
-EcologicalNetworks = "0.4, 0.5"
 GeoInterface = "1.3"
 HTTP = "0.8, 0.9, 1.8"
 JSON = "0.21"
-julia = "1.5"
+julia = "1.5, 1.6, 1.7, 1.8, 1.9"

docs/Project.toml

@@ -2,4 +2,3 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Weave = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9"
-

docs/make.jl

@@ -16,7 +16,6 @@ _pkg_doc = [
 _pkg_vig = [
    "Introduction" => "vignettes/introduction.md",
    "Counting & paging" => "vignettes/counting.md",
-   "Network analysis" => "vignettes/ecologicalnetworks.md"
 ]
 
 _list_of_pages = [
@@ -34,6 +33,6 @@ makedocs(
 
 deploydocs(
    deps   = Deps.pip("pygments", "python-markdown-math"),
-   repo   = "github.com/EcoJulia/Mangal.jl.git",
-   devbranch = "master"
+   repo   = "github.com/PoisotLab/Mangal.jl.git",
+   devbranch = "main"
 )

src/Mangal.jl

@@ -3,8 +3,8 @@ module Mangal
 using HTTP
 using JSON
 using GeoInterface
-using EcologicalNetworks
 using Dates
+using TestItems
 
 const web_root = "https://mangal.io/"
 const api_root = web_root * "api/v2/"
@@ -86,9 +86,15 @@ include(joinpath(".", "count.jl"))
 # Show
 include(joinpath(".", "show.jl"))
 
-# EcologicalNetworks wrapper
-using EcologicalNetworks: EcologicalNetworks
-include(joinpath(".", "ecologicalnetworks.jl"))
-export taxonize
+@testitem "We can get data in/out of cache" begin
+    N = nodes()[1]
+    n = node(N.id)
+    @test length(Mangal._MANGAL_CACHES[MangalNode]) != 0
+end
+
+@testitem "We can get attribute data" begin
+    @test typeof(attributes()) <: Vector{MangalAttribute}
+    @test typeof(attribute(6)) <: MangalAttribute
+end
 
 end # module

src/backbone.jl

@@ -7,3 +7,21 @@ function backbone(name::AbstractString)
     q = backbones(Pair("name", name))
     return isequal(1)(length(q)) ? only(q) : nothing
 end
+
+
+@testitem "We can get data from the backbone" begin
+    @test typeof(backbones()) <: Vector{MangalReferenceTaxon}
+end
+
+@testitem "We can get data from the backbone with a search" begin
+    @test typeof(backbones("q" => "Salix")) <: Vector{MangalReferenceTaxon}
+end
+
+@testitem "We can get specific taxa from the backbone" begin
+    @test backbone(1).name == "Abutilon theophrasti"
+    @test backbone("Abutilon theophrasti").id == 1
+end
+
+@testitem "We can get paged data from the backbone" begin
+    @test length(backbones(Pair("count", 10))) == 10
+end

src/dataset.jl

@@ -7,3 +7,20 @@ function dataset(name::AbstractString)
     q = datasets(Pair("name", name))
     return isequal(1)(length(q)) ? only(q) : nothing
 end
+
+@testitem "We can get dataset data" begin
+    @test typeof(datasets()) <: Vector{MangalDataset}
+
+    # Datasets with count
+    count_2 = datasets(Pair("count", 2))
+    @test typeof(count_2) <: Vector{MangalDataset}
+    @test length(count_2) == 2
+
+    # Dataset by id
+    @test typeof(dataset(1)) <: MangalDataset
+
+    # Dataset by name
+    @test typeof(dataset("roberson_1929")) <: MangalDataset
+
+    @test isnothing(dataset("This_DOESNOT_exist"))
+end

src/generators.jl

@@ -20,7 +20,7 @@ for mg_type_pair in types_names
 
         Returns the number of $($mg_type) objects that match a query.
         """
-        function count(::Type{$mg_type}, query::Pair...)
+        function Base.count(::Type{$mg_type}, query::Pair...)
             return Mangal.number_of_objects(Mangal._MANGAL_ENDPOINTS[$mg_type], query...)
         end
     end

src/interaction.jl

@@ -45,3 +45,35 @@ Returns interactions within a network.
 function interactions(n::MangalNetwork, query::Pair...)
     return interactions("network_id" => n.id, query...)
 end
+
+@testitem "We can get all interactions" begin
+    @test typeof(interactions()) <: Vector{MangalInteraction}
+end
+
+@testitem "We can get all interactions by type" begin
+    @test typeof(interactions(Pair("type", "mutualism"))) <: Vector{MangalInteraction}
+end
+
+@testitem "We can get all interactions to a node" begin
+    @test typeof(interactions(:, node(31863))) <: Vector{MangalInteraction}
+end
+
+@testitem "We can get all interactions from a node" begin
+    @test typeof(interactions(node(31904), :)) <: Vector{MangalInteraction}    
+end
+
+@testitem "We can get all interactions to a node by type" begin
+    @test typeof(interactions(:, node(31863), Pair("type", "predation"))) <: Vector{MangalInteraction}
+end
+
+@testitem "We can get all interactions from a node by type" begin
+    @test typeof(interactions(node(31904), :, Pair("type", "predation"))) <: Vector{MangalInteraction}
+end
+
+@testitem "We can get interactions between nodes" begin
+    @test typeof(interactions(node(31904), node(31863))) <: Vector{MangalInteraction}
+end
+
+@testitem "We can get interactions between nodes by type" begin
+    @test typeof(interactions(node(31904), node(31863), Pair("type", "predation"))) <: Vector{MangalInteraction}
+end

src/login.jl

@@ -52,3 +52,7 @@ function login_message()
 
     @info msg
 end
+
+@testitem "We can get user data" begin
+    @test typeof(users()) <: Vector{MangalUser}
+end

src/network.jl

@@ -16,3 +16,41 @@ function network(name::AbstractString)
     q = networks(Pair("name", name))
     return isequal(1)(length(q)) ? only(q) : nothing
 end
+
+@testitem "We can get networks" begin
+    @test typeof(networks()) <: Vector{MangalNetwork} 
+end
+
+@testitem "We can get a network by ID" begin
+    @test typeof(network(19)) <: MangalNetwork
+end
+
+@testitem "We can get a network by name" begin
+    @test typeof(network("howking_1968_19680601_12")) <: MangalNetwork
+end
+
+@testitem "We can get a network by dataset" begin
+    ds = dataset(62)
+    n_ds = networks(ds)
+    @test typeof(n_ds) <: Vector{MangalNetwork}
+end
+
+@testitem "We can get a network by dataset with additional arguments" begin
+    ds = dataset(62)
+    n_ds_q = networks(ds, Pair("count", 2))
+    @test typeof(n_ds_q) <: Vector{MangalNetwork}
+    @test length(n_ds_q) == 2
+end
+
+@testitem "We can page through multiple network queries" begin
+    this_page = 1
+    networks_ponisio = networks(dataset("ponisio_2017"), Pair("count", 10), Pair("page", this_page))
+    keep_querying = true
+    while keep_querying
+        global this_page += 1
+        response = networks(dataset("ponisio_2017"), Pair("count", 10), Pair("page", this_page))
+        append!(networks_ponisio, response)
+        global keep_querying = length(response) > 0
+    end
+    @test length(networks_ponisio) == 131
+end

src/node.jl

@@ -15,3 +15,26 @@ Returns the nodes that are instance of a `MangalReferenceTaxon`, with an additio
 function nodes(taxon::MangalReferenceTaxon, query::Pair...)
     return nodes(Pair("taxonomy_id", taxon.id), query...)
 end
+
+@testitem "We can get node data" begin
+    @test typeof(nodes()) <: Vector{MangalNode}
+end
+
+@testitem "We can get nodes of a network" begin
+    N1 = network(19)
+    nN1 = nodes(N1)
+    @test typeof(nN1) <: Vector{MangalNode}
+end
+
+
+@testitem "We can get taxonomic data in nodes" begin
+    n1 = node(2158)
+    @test typeof(n1) <: MangalNode
+    @test typeof(n1.taxon) <: MangalReferenceTaxon
+end
+
+@testitem "We can get nodes from backbone data" begin
+    b1 = backbone(1)
+    nb1 = nodes(b1)
+    @test first(nb1).taxon == b1
+end

test/Project.toml

@@ -1,3 +1,3 @@
 [deps]
-EcologicalNetworks = "f03a62fe-f8ab-5b77-a061-bb599b765229"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"