Merge pull request #18 from EcoJulia/next

Prepare compatiblity with EcologicalNetworks 0.4

.github/workflows/CI.yml

@@ -4,6 +4,8 @@ on:
   push:
     branches:
       - master
+    tags:
+      - '*'
   pull_request:
 
 jobs:
@@ -13,8 +15,9 @@ jobs:
     strategy:
       matrix:
         version:
+          - '1.3'
           - '1.4'
-          - 'nightly'
+          - '1.5'
         os:
           - ubuntu-latest
           - macOS-latest

.github/workflows/CompatHelper.yml

@@ -2,7 +2,7 @@ name: CompatHelper
 
 on:
   schedule:
-    - cron: '00 00 * * *'
+    - cron: '0 * * * *'
 
 jobs:
   CompatHelper:

.github/workflows/Documentation.yml

@@ -1,26 +1,24 @@
 name: Documentation
 
 on:
+  release:
   push:
     branches:
       - master
     tags: '*'
   pull_request:
 
 jobs:
-  docs:
-    name: Documentation
+  build:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@latest
         with:
-          version: '1.4'
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-      - run: julia --project=docs docs/make.jl
+          version: '1.5'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
         env:
-          GITHUB_TOKEN: ${{ secrets.TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.TOKEN }} # For authentication with GitHub Actions token
+        run: julia --project=docs/ docs/make.jl

.github/workflows/TagBot.yml

@@ -1,11 +1,11 @@
 name: TagBot
 on:
   schedule:
-    - cron: 0 0 * * *
+    - cron: 0 * * * *
 jobs:
   TagBot:
     runs-on: ubuntu-latest
     steps:
       - uses: JuliaRegistries/TagBot@v1
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ secrets.TOKEN }}

Project.toml

@@ -1,7 +1,7 @@
 name = "Mangal"
 uuid = "b8b640a6-63d9-51e6-b784-5033db27bef2"
 authors = ["Timothée Poisot <[email protected]>"]
-version = "0.3.0"
+version = "0.3.1"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -11,14 +11,8 @@ HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 
 [compat]
-EcologicalNetworks = "0.3"
+EcologicalNetworks = "0.3, 0.4"
 GeoInterface = "0.5"
-HTTP = "0.8"
+HTTP = "0.8, 0.9"
 JSON = "0.21"
 julia = "1.3"
-
-[extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["Test"]

README.md

@@ -1,7 +1,10 @@
 ### Mangal.jl
 
-[![Build Status](https://travis-ci.org/EcoJulia/Mangal.jl.svg?branch=master)](https://travis-ci.org/EcoJulia/Mangal.jl) [![Coverage Status](https://coveralls.io/repos/github/EcoJulia/Mangal.jl/badge.svg?branch=master)](https://coveralls.io/github/EcoJulia/Mangal.jl?branch=master)
-[![Manual](https://img.shields.io/badge/manual-latest-orange.svg)](http://EcoJulia.github.io/Mangal.jl/dev/)
+[![latest doc](https://img.shields.io/badge/documentation-stable-brightgreen)](https://ecojulia.github.io/Mangal.jl/stable/) [![latest doc](https://img.shields.io/badge/documentation-latest-green)](https://ecojulia.github.io/Mangal.jl/latest/)
+
+![CI](https://github.com/EcoJulia/Mangal.jl/workflows/CI/badge.svg?branch=master) [![codecov](https://codecov.io/gh/EcoJulia/Mangal.jl/branch/master/graph/badge.svg?token=HKaubLliPG)](https://codecov.io/gh/EcoJulia/Mangal.jl)
+
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![DOI](https://zenodo.org/badge/144035225.svg)](https://zenodo.org/badge/latestdoi/144035225)
 
 This package is a wrapper around the *new* API for the mangal ecological
 interactions database. It uses [Julia 1.1][jl] to provide a programmatic
@@ -12,3 +15,14 @@ database was funded by the [Canadian Foundation for Innovation][cfi] and
 [cfi]: https://www.innovation.ca/
 [nserc]: http://www.nserc-crsng.gc.ca/index_eng.asp
 [jl]: https://julialang.org/
+
+## Getting started
+
+Enter package mode by pressing `]` from the Julia REPL. Then install:
+
+~~~
+add Mangal
+~~~
+
+That's it. Now head over to the
+[documentation](https://ecojulia.github.io/Mangal.jl/dev/).

docs/make.jl

@@ -34,6 +34,6 @@ makedocs(
 
 deploydocs(
    deps   = Deps.pip("pygments", "python-markdown-math"),
-   repo   = "github.com/PoisotLab/Mangal.jl.git",
+   repo   = "github.com/EcoJulia/Mangal.jl.git",
    devbranch = "master"
 )

src/ecologicalnetworks.jl

@@ -1,5 +1,11 @@
-EcologicalNetworks.check_species_validity(::Type{MangalNode}) = nothing
-EcologicalNetworks.check_species_validity(::Type{MangalReferenceTaxon}) = nothing
+try
+    EcologicalNetworks._check_species_validity(::Type{MangalNode}) = nothing
+    EcologicalNetworks._check_species_validity(::Type{MangalReferenceTaxon}) = nothing
+catch e
+    @info "Compatibility with EcologicalNetworks 0.3 will be removed soon"
+    EcologicalNetworks.check_species_validity(::Type{MangalNode}) = nothing
+    EcologicalNetworks.check_species_validity(::Type{MangalReferenceTaxon}) = nothing
+end
 
 function get_all_interactions(n::MangalNetwork, query::Pair...)
     page_size = 250
@@ -91,7 +97,7 @@ end
 missing are dropped
 """
 function taxonize(N::T) where {T <: EcologicalNetworks.UnipartiteNetwork}
-    @assert last(eltype(N)) == MangalNode
+    @assert eltype(species(N)) == MangalNode
     unique_ref_taxa = unique([s.taxon for s in EcologicalNetworks.species(N)])
     @warn "This function really should inform of dropped nodes"
     filter!(!ismissing, unique_ref_taxa)

test/Project.toml

@@ -0,0 +1,3 @@
+[deps]
+EcologicalNetworks = "f03a62fe-f8ab-5b77-a061-bb599b765229"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/knownbugs.jl

@@ -11,6 +11,8 @@ module MangalTestKnownBugs
         @test typeof(thisnet) <: MangalNetwork
         U = convert(UnipartiteNetwork, thisnet) 
         @test typeof(U) <: UnipartiteNetwork
+        T = taxonize(U)
+        @test eltype(EcologicalNetworks.species(T)) <: MangalReferenceTaxon
     end
 
 end