switch to Graphs.jl

bramtayl · bramtayl · commit 307fe682eff2 · 2021-10-29T11:58:23.000-04:00
diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
@@ -0,0 +1,30 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml
@@ -0,0 +1,14 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/daily.yml b/.github/workflows/daily.yml
diff --git a/.github/workflows/permanent.yml b/.github/workflows/permanent.yml
@@ -9,11 +9,6 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
-        with:
-          version: '1.3'
       - uses: julia-actions/julia-docdeploy@releases/v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - uses: JuliaRegistries/TagBot@v1
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -10,7 +10,7 @@ jobs:
       matrix:
         version:
           - '1.0'
-          - '1.4'
+          - '1'
           - 'nightly'
     steps:
       - uses: actions/checkout@v2
@@ -25,7 +25,3 @@ jobs:
       - uses: codecov/codecov-action@v1
         with:
           file: ./lcov.info
-      - uses: domluna/JuliaFormatter-action@master
-        with:
-          args: -v .
-        continue-on-error: true
diff --git a/Project.toml b/Project.toml
@@ -1,14 +1,14 @@
 name = "MetaGraphsNext"
 uuid = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
-version = "0.1.2"
+version = "0.2"
 
 [deps]
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 
 [compat]
 JLD2 = "0.1.11, 0.2, 0.3, 0.4"
-LightGraphs = "1.2"
+Graphs = "1.4.1"
 julia = "1"
 
 [extras]
diff --git a/README.md b/README.md
@@ -7,4 +7,4 @@ Welcome to `MetaGraphsNext.jl`, an experimental, type-stable replacement for [Me
 
 ## Getting started
 
-To see how the package works, take a look at the tutorial in the [documentation](https://juliagraphs.org/MetaGraphsNext.jl/dev/). We first explain [the basics](tutorial_basics.md) of the `MetaGraph` structure, before moving on to its [integration](tutorial_lightgraphs.md) with `LightGraphs.jl`.
+To see how the package works, take a look at the tutorial in the [documentation](https://juliagraphs.org/MetaGraphsNext.jl/dev/). We first explain [the basics](tutorial_basics.md) of the `MetaGraph` structure, before moving on to its [integration](tutorial_graphs.md) with `Graphs.jl`.
diff --git a/docs/make.jl b/docs/make.jl
@@ -14,7 +14,7 @@ makedocs(
         "Home" => "index.md",
         "Tutorial" => [
             "Basics" => "tutorial_basics.md",
-            "LightGraphs.jl interface" => "tutorial_lightgraphs.md",
+            "Graphs.jl interface" => "tutorial_graphs.md",
             "Reading / writing" => "tutorial_files.md",
         ],
         "API reference" => "api.md",
diff --git a/docs/src/api.md b/docs/src/api.md
@@ -22,11 +22,11 @@ Modules = [MetaGraphsNext]
 Pages = ["weights.jl"]
 ```
 
-## LightGraphs.jl interface
+## Graphs.jl interface
 
 ```@autodocs
 Modules = [MetaGraphsNext]
-Pages = ["lightgraphs.jl"]
+Pages = ["graphs.jl"]
 ```
 
 ```@autodocs
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -4,7 +4,7 @@ Welcome to `MetaGraphsNext.jl`, an experimental, type-stable replacement for [Me
 
 ## Getting started
 
-To see how the package works, take a look at the tutorial. We first explain [the basics](tutorial_basics.md) of the `MetaGraph` structure, before moving on to its [integration](tutorial_lightgraphs.md) with `LightGraphs.jl`.
+To see how the package works, take a look at the tutorial. We first explain [the basics](tutorial_basics.md) of the `MetaGraph` structure, before moving on to its [integration](tutorial_graphs.md) with `Graphs.jl`.
 
 ## Index
 
diff --git a/docs/src/tutorial_basics.md b/docs/src/tutorial_basics.md
@@ -1,7 +1,7 @@
 # Working with metagraphs
 
 ```jldoctest example
-julia> using LightGraphs
+julia> using Graphs
 
 julia> using MetaGraphsNext
 ```
@@ -120,7 +120,7 @@ julia> weighted[:red] = nothing; weighted[:blue] = nothing; weighted[:yellow] =
 
 julia> weighted[:red, :blue] = 1.0; weighted[:blue, :yellow] = 2.0;
 
-julia> the_weights = LightGraphs.weights(weighted)
+julia> the_weights = Graphs.weights(weighted)
 metaweights
 
 julia> size(the_weights)
diff --git a/docs/src/tutorial_files.md b/docs/src/tutorial_files.md
@@ -1,7 +1,7 @@
 # Read / write
 
 ```jldoctest readwrite
-julia> using LightGraphs
+julia> using Graphs
 
 julia> using MetaGraphsNext
 ```
diff --git a/docs/src/tutorial_graphs.md b/docs/src/tutorial_graphs.md
@@ -1,16 +1,16 @@
-# LightGraphs.jl  interface
+# Graphs.jl  interface
 
-```jldoctest lightgraphs
-julia> using LightGraphs
+```jldoctest graphs
+julia> using Graphs
 
 julia> using MetaGraphsNext
 ```
 
-`MetaGraph`s inherit many methods from LightGraphs.jl. In general, inherited methods refer to vertices by codes, not labels, for compatibility with AbstractGraph. Vertex codes get reassigned after `rem_vertex!` to remain contiguous, so we recommend using labels if possible.
+`MetaGraph`s inherit many methods from Graphs.jl. In general, inherited methods refer to vertices by codes, not labels, for compatibility with AbstractGraph. Vertex codes get reassigned after `rem_vertex!` to remain contiguous, so we recommend using labels if possible.
 
 ## Undirected graphs
 
-```jldoctest lightgraphs
+```jldoctest graphs
 julia> colors = MetaGraph(Graph(), VertexMeta = String, EdgeMeta = Symbol, gprops = "special");
 
 julia> colors[:red] = "warm";
@@ -56,10 +56,10 @@ false
 julia> has_vertex(colors, 1)
 true
 
-julia> LightGraphs.SimpleGraphs.fadj(colors, 1) == Int[]
+julia> Graphs.SimpleGraphs.fadj(colors, 1) == Int[]
 true
 
-julia> LightGraphs.SimpleGraphs.badj(colors, 1) == Int[]
+julia> Graphs.SimpleGraphs.badj(colors, 1) == Int[]
 true
 
 julia> colors == colors
@@ -76,7 +76,7 @@ julia> SimpleGraph(colors)
 
 You can seemlessly make MetaGraphs based on DiGraphs as well.
 
-```jldoctest lightgraphs
+```jldoctest graphs
 julia> rock_paper_scissors = MetaGraph(DiGraph(), Label = Symbol, EdgeMeta = Symbol);
 
 julia> rock_paper_scissors[:rock] = nothing; rock_paper_scissors[:paper] = nothing; rock_paper_scissors[:scissors] = nothing;
diff --git a/src/MetaGraphsNext.jl b/src/MetaGraphsNext.jl
@@ -1,7 +1,7 @@
 module MetaGraphsNext
 
 using JLD2
-using LightGraphs
+using Graphs
 
 import Base:
     Tuple,
@@ -18,7 +18,7 @@ import Base:
     size,
     zero
 
-import LightGraphs:
+import Graphs:
     AbstractGraph,
     AbstractGraphFormat,
     add_edge!,
@@ -41,7 +41,7 @@ import LightGraphs:
     vertices,
     weights
 
-import LightGraphs.SimpleGraphs: SimpleGraph, SimpleDiGraph, fadj, badj
+import Graphs.SimpleGraphs: SimpleGraph, SimpleDiGraph, fadj, badj
 
 export MetaGraph, weighttype, defaultweight, weightfunction
 export MGFormat, DOTFormat
@@ -51,7 +51,7 @@ export label_for, code_for
 include("metagraph.jl")
 include("metaundigraph.jl")
 include("metadigraph.jl")
-include("lightgraphs.jl")
+include("graphs.jl")
 include("weights.jl")
 include("dict_utils.jl")
 include("overrides.jl")
diff --git a/src/dict_utils.jl b/src/dict_utils.jl
@@ -93,7 +93,7 @@ end
 """
     code_for(meta::MetaGraph, vertex_label)
 
-Find the code associated with a `vertex_label`. This can be useful to pass to methods inherited from `LightGraphs`. Note, however, that vertex codes could be
+Find the code associated with a `vertex_label`. This can be useful to pass to methods inherited from `Graphs`. Note, however, that vertex codes could be
 reassigned after vertex deletion.
 """
 function code_for(meta::MetaGraph, vertex_label)
@@ -104,7 +104,7 @@ end
 """
     label_for(meta::MetaGraph, vertex_code)
 
-Find the label associated with a `vertex_code`. This can be useful to interpret the results of methods inherited from `LightGraphs`. Note, however, that vertex codes could be reassigned after vertex deletion.
+Find the label associated with a `vertex_code`. This can be useful to interpret the results of methods inherited from `Graphs`. Note, however, that vertex codes could be reassigned after vertex deletion.
 """
 function label_for(meta::MetaGraph, vertex_code)
     meta.metaindex[vertex_code]
diff --git a/src/graphs.jl b/src/graphs.jl

Original file line number	Diff line number	Diff line change
@@ -7,4 +7,4 @@ Welcome to `MetaGraphsNext.jl`, an experimental, type-stable replacement for [Me
`7`	`7`
`8`	`8`	`## Getting started`
`9`	`9`
`10`		-To see how the package works, take a look at the tutorial in the [documentation](https://juliagraphs.org/MetaGraphsNext.jl/dev/). We first explain [the basics](tutorial_basics.md) of the `MetaGraph` structure, before moving on to its [integration](tutorial_lightgraphs.md) with `LightGraphs.jl`.
	`10`	+To see how the package works, take a look at the tutorial in the [documentation](https://juliagraphs.org/MetaGraphsNext.jl/dev/). We first explain [the basics](tutorial_basics.md) of the `MetaGraph` structure, before moving on to its [integration](tutorial_graphs.md) with `Graphs.jl`.