rename LightGraphs => Graphs (mostly automatic)

- A few manually selected occurrences of LightGraphs are retained
- Some README verbiage is edited to explain and match the rename
- Also replaces the LightGraphs UUID with the Graphs UUID

If you want to generate the automatic rename from the previous commit
you can run the command

    git ls-files | xargs perl -i -ple 's/LightGraphs/Graphs/g'

Author: StefanKarpinski

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,6 +1,6 @@
 ---
 name: Bug report
-about: Report a bug with LightGraphs
+about: Report a bug with Graphs
 title: "[BUG]"
 labels: bug
 assignees: ''
@@ -29,7 +29,7 @@ If applicable, provide a minimal working example of the bug.
 
 **Version information**
  - output from `versioninfo()` surrounded by backticks (``)
- - output from `] status LightGraphs` surrounded by backticks (``)
+ - output from `] status Graphs` surrounded by backticks (``)
 
 
 **Additional context**

.zenodo.json

@@ -1,7 +1,7 @@
 {
     "description": "LightGraphs: An Optimized Graphs Package for the Julia Programming Language",
     "license": "BSD-2-Clause",
-    "title": "JuliaGraphs/LightGraphs.jl",
+    "title": "JuliaGraphs/Graphs.jl",
     "upload_type": "software",
     "publication_date": "2017-09-16",
     "creators": [
@@ -15,7 +15,7 @@
     "related_identifiers": [
         {
             "scheme": "url",
-            "identifier": "https://github.com/JuliaGraphs/LightGraphs.jl/tree/v0.10.5",
+            "identifier": "https://github.com/JuliaGraphs/Graphs.jl/tree/lg-v0.10.5",
             "relation": "isSupplementTo"
         },
         {

CONTRIBUTING.md

@@ -53,34 +53,34 @@ end
 This gives users the option of reusing memory and improving performance.
 
 ### Minimizing use of internal struct fields
-Since LightGraphs supports multiple implementations of the graph datastructure using the `AbstractGraph` [type](https://juliagraphs.github.io/LightGraphs.jl/latest/types.html#AbstractGraph-Type-1), you should refrain from using the internal fields of structs such as `fadjlist`. Instead, you should use the functions provided in the api. Code that is instrumental to defining a concrete graph type can use the internal structure of that type for example graph generators in `/src/StaticGraphs/generators/staticgraphs.jl` use the `fadjlist` field in order to construct graphs efficiently.
+Since Graphs supports multiple implementations of the graph datastructure using the `AbstractGraph` [type](https://juliagraphs.github.io/Graphs.jl/latest/types.html#AbstractGraph-Type-1), you should refrain from using the internal fields of structs such as `fadjlist`. Instead, you should use the functions provided in the api. Code that is instrumental to defining a concrete graph type can use the internal structure of that type for example graph generators in `/src/StaticGraphs/generators/staticgraphs.jl` use the `fadjlist` field in order to construct graphs efficiently.
 
 ## Git usage
 
-In order to make it easier for you to review Pull Requests (PRs), you can add this to your git config file, which should be located at `$HOME/.julia/dev/LightGraphs/.git/config`. Follow the instructions [here](https://gist.github.com/piscisaureus/3342247).
+In order to make it easier for you to review Pull Requests (PRs), you can add this to your git config file, which should be located at `$HOME/.julia/dev/Graphs/.git/config`. Follow the instructions [here](https://gist.github.com/piscisaureus/3342247).
 
 Locate the section for your github remote in the `.git/config` file. It looks like this:
 
 ```
 [remote "origin"]
     fetch = +refs/heads/*:refs/remotes/origin/*
-    url = git@github.com:JuliaGraphs/LightGraphs.jl.git
+    url = git@github.com:JuliaGraphs/Graphs.jl.git
 ```
 
 Now add the line `fetch = +refs/pull/*/head:refs/remotes/origin/pr/*` to this section. Obviously, change the github url to match your project's URL. It ends up looking like this:
 
 ```
 [remote "origin"]
     fetch = +refs/heads/*:refs/remotes/origin/*
-    url = git@github.com:JuliaGraphs/LightGraphs.jl.git
+    url = git@github.com:JuliaGraphs/Graphs.jl.git
     fetch = +refs/pull/*/head:refs/remotes/origin/pr/*
 ```
 
 Now fetch all the pull requests:
 
 ```
 $ git fetch origin
-From github.com:JuliaGraphs/LightGraphs.jl
+From github.com:JuliaGraphs/Graphs.jl
  * [new ref]         refs/pull/1000/head -> origin/pr/1000
  * [new ref]         refs/pull/1002/head -> origin/pr/1002
  * [new ref]         refs/pull/1004/head -> origin/pr/1004
@@ -96,4 +96,4 @@ Branch pr/999 set up to track remote branch pr/999 from origin.
 Switched to a new branch 'pr/999'
 ```
 
-Now you can test a PR by running `git fetch && git checkout pr/PRNUMBER && julia -e 'Pkg.test("LightGraphs")'`
+Now you can test a PR by running `git fetch && git checkout pr/PRNUMBER && julia -e 'Pkg.test("Graphs")'`

LICENSE.md

@@ -1,4 +1,4 @@
-The LightGraphs.jl package is licensed under the Simplified "2-clause" BSD
+The Graphs.jl (formerly called LightGraphs.jl) package is licensed under the Simplified "2-clause" BSD
 License:
 > Copyright (c) 2015: Seth Bromberger and other contributors.
 >
@@ -24,7 +24,7 @@ License:
 > (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 > OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-LightGraphs uses code derived from and/or inspired by the following packages:
+Graphs uses code derived from and/or inspired by the following packages:
 
 NetworkX:
 > Copyright (C) 2004-2012, NetworkX Developers

Project.toml

@@ -1,6 +1,6 @@
-name = "LightGraphs"
-uuid = "093fc24a-ae57-5d10-9952-331d41423f4d"
-version = "1.3.5"
+name = "Graphs"
+uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
+version = "1.4.0"
 
 [deps]
 ArnoldiMethod = "ec485272-7323-5ecc-a04f-4719b315124d"

README.md

@@ -1,13 +1,21 @@
-# LightGraphs
+# Graphs
 
-[![Build Status](https://github.com/JuliaGraphs/LightGraphs.jl/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/JuliaGraphs/LightGraphs.jl/actions/workflows/ci.yml?query=branch%3Amaster)
-[![codecov.io](http://codecov.io/github/JuliaGraphs/LightGraphs.jl/coverage.svg?branch=master)](http://codecov.io/github/JuliaGraphs/LightGraphs.jl?branch=master)
-[![](https://img.shields.io/badge/docs-latest-blue.svg)](https://juliagraphs.github.io/LightGraphs.jl/latest)
+[![Build Status](https://github.com/JuliaGraphs/Graphs.jl/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/JuliaGraphs/Graphs.jl/actions/workflows/ci.yml?query=branch%3Amaster)
+[![codecov.io](http://codecov.io/github/JuliaGraphs/Graphs.jl/coverage.svg?branch=master)](http://codecov.io/github/JuliaGraphs/Graphs.jl?branch=master)
+[![](https://img.shields.io/badge/docs-latest-blue.svg)](https://juliagraphs.github.io/Graphs.jl/latest)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.889971.svg)](https://doi.org/10.5281/zenodo.889971)
 
-**Project Status:** As of 8 October 2021 LightGraphs is no longer under active development. It will remain available on Github at [sbromberger/LightGraphs.jl](https://github.com/sbromberger/LightGraphs.jl). The JuliaGraphs organization will continue to maintain packages that use LightGraphs and transition development over the long term.
+**Project Status:** The Graphs project is a fork of the now-archived LightGraphs
+package, which remains available on GitHub at
+[sbromberger/LightGraphs.jl](https://github.com/sbromberger/LightGraphs.jl). If
+you don't need any new features developed since the fork, you can continue to
+use older versions of LightGraphs indefinitely. New versions will be released
+here using the name Graphs instead of LightGraphs. There was an older package
+also called Graphs, whose source history and versions are still available in
+this repository, but the current code base is unrelated to the old Graphs code
+and is derived purely from LightGraphs.
 
-LightGraphs offers both (a) a set of simple, concrete graph implementations -- `Graph`
+Graphs offers both (a) a set of simple, concrete graph implementations -- `Graph`
 (for undirected graphs) and `DiGraph` (for directed graphs), and (b) an API for
 the development of more sophisticated graph implementations under the `AbstractGraph`
 type.
@@ -33,27 +41,30 @@ Additional functionality may be found in a number of companion packages, includi
   Pajek NET, and more.
 
 ## Documentation
-Full documentation is available at [GitHub Pages](https://juliagraphs.github.io/LightGraphs.jl/latest).
+Full documentation is available at [GitHub Pages](https://juliagraphs.github.io/Graphs.jl/latest).
 Documentation for methods is also available via the Julia REPL help system.
 Additional tutorials can be found at [JuliaGraphsTutorials](https://github.com/JuliaGraphs/JuliaGraphsTutorials).
 
 ## Installation
 Installation is straightforward: enter Pkg mode by hitting `]`, and then
 ```julia-repl
-(v1.0) pkg> add LightGraphs
+(v1.0) pkg> add Graphs
 ```
 
 ## Supported Versions
-* LightGraphs master is generally designed to work with the latest stable version of Julia (except during Julia version increments as we transition to the new version).
-* Julia 0.3: LightGraphs v0.3.7 is the last version guaranteed to work with Julia 0.3.
-* Julia 0.4: LightGraphs versions in the 0.6 series are designed to work with Julia 0.4.
-* Julia 0.5: LightGraphs versions in the 0.7 series are designed to work with Julia 0.5.
-* Julia 0.6: LightGraphs versions in the 0.8 through 0.12 series are designed to work with Julia 0.6.
-* Julia 0.7 / 1.0: LightGraphs versions in the 1.x series are designed to work with Julia 0.7 and Julia 1.0.
+* Graphs master is generally designed to work with the latest stable version of Julia (except during Julia version increments as we transition to the new version).
+* The project was previously developed under the name LightGraphs and older versions of LightGraphs (≤ v1.3.5) must still be used with that name.
+* There was also an older package also called Graphs (git tags `v0.2.5` through `v0.10.3`), but the current code base here is a fork of LightGraphs v1.3.5.
+* All older LightGraphs versions are tagged using the naming scheme `lg-vX.Y.Z` rather than plain `vX.Y.Z` which is used for old Graphs versions (≤ v0.10) and newer versions derived from LightGraphs but released with the Graphs name (≥ v1.4).
+* Julia 0.3: LightGraphs v0.3.7 (`lg-v0.3.7`) is the last version guaranteed to work with Julia 0.3.
+* Julia 0.4: LightGraphs versions in the 0.6 series (`lg-v0.6.*`) are designed to work with Julia 0.4.
+* Julia 0.5: LightGraphs versions in the 0.7 series (`lg-v0.7.*`) are designed to work with Julia 0.5.
+* Julia 0.6: LightGraphs versions in the 0.8 through 0.12 (`lg-v0.{8-12}.*`) series are designed to work with Julia 0.6.
+* Julia 0.7 / 1.0: LightGraphs versions in the 1.x series (`lg-v1.*`) are designed to work with Julia 0.7 and Julia 1.0.
 * Later versions: Some functionality might not work with prerelease / unstable / nightly versions of Julia. If you run into a problem, please file an issue.
 
 # Contributing and Reporting Bugs
-We welcome contributions and bug reports! Please see [CONTRIBUTING.md](https://github.com/JuliaGraphs/LightGraphs.jl/blob/master/CONTRIBUTING.md)
+We welcome contributions and bug reports! Please see [CONTRIBUTING.md](https://github.com/JuliaGraphs/Graphs.jl/blob/master/CONTRIBUTING.md)
 for guidance on development and bug reporting.
 
 # Citing

benchmark/benchmarks.jl

@@ -1,5 +1,5 @@
 using BenchmarkTools
-using LightGraphs
+using Graphs
 
 
 DIGRAPHS = Dict{String,DiGraph}(

benchmark/centrality.jl

@@ -2,24 +2,24 @@
 @benchgroup "centrality" begin
   @benchgroup "graphs" begin
     for (name, g) in GRAPHS
-      @bench "$(name): degree" LightGraphs.degree_centrality($g)
-      @bench "$(name): closeness" LightGraphs.closeness_centrality($g)
+      @bench "$(name): degree" Graphs.degree_centrality($g)
+      @bench "$(name): closeness" Graphs.closeness_centrality($g)
       if nv(g) < 1000
-        @bench "$(name): betweenness" LightGraphs.betweenness_centrality($g)
-        @bench "$(name): katz" LightGraphs.katz_centrality($g)
+        @bench "$(name): betweenness" Graphs.betweenness_centrality($g)
+        @bench "$(name): katz" Graphs.katz_centrality($g)
       end
     end
   end #graphs
   @benchgroup "digraphs" begin
     for (name, g) in DIGRAPHS
-      @bench "$(name): degree" LightGraphs.degree_centrality($g)
-      @bench "$(name): closeness" LightGraphs.closeness_centrality($g)
+      @bench "$(name): degree" Graphs.degree_centrality($g)
+      @bench "$(name): closeness" Graphs.closeness_centrality($g)
       if nv(g) < 1000
-        @bench "$(name): betweenness" LightGraphs.betweenness_centrality($g)
-        @bench "$(name): katz" LightGraphs.katz_centrality($g)
+        @bench "$(name): betweenness" Graphs.betweenness_centrality($g)
+        @bench "$(name): katz" Graphs.katz_centrality($g)
       end
       if nv(g) < 500
-        @bench "$(name): pagerank"  LightGraphs.pagerank($g)
+        @bench "$(name): pagerank"  Graphs.pagerank($g)
       end
     end
   end # digraphs

benchmark/connectivity.jl

@@ -1,12 +1,12 @@
 @benchgroup "connectivity" begin
   @benchgroup "digraphs" begin
     for (name, g) in DIGRAPHS
-      @bench "$(name): strongly_connected_components" LightGraphs.strongly_connected_components($g)
+      @bench "$(name): strongly_connected_components" Graphs.strongly_connected_components($g)
     end
   end # digraphs
   @benchgroup "graphs" begin
     for (name, g) in GRAPHS
-        @bench "$(name): connected_components" LightGraphs.connected_components($g)
+        @bench "$(name): connected_components" Graphs.connected_components($g)
     end
   end # graphs
 end # connectivity

benchmark/edges.jl

@@ -5,9 +5,9 @@ const P = Pair{Int,Int}
 convert(::Type{Tuple}, e::Pair) = (e.first, e.second)
 
 function fille(n)
-    t = Array{LightGraphs.Edge,1}(n)
+    t = Array{Graphs.Edge,1}(n)
     for i in 1:n
-        t[i] = LightGraphs.Edge(i, i + 1)
+        t[i] = Graphs.Edge(i, i + 1)
     end
     return t
 end

benchmark/parallel/egonets.jl

@@ -1,4 +1,4 @@
-using LightGraphs
+using Graphs
 using BenchmarkTools
 @show Threads.nthreads()
 

benchmark/traversals.jl

@@ -1,14 +1,14 @@
 @benchgroup "traversals" begin
   @benchgroup "graphs" begin
     for (name, g) in GRAPHS
-        @bench "$(name): bfs_tree" LightGraphs.bfs_tree($g, 1)
-        @bench "$(name): dfs_tree" LightGraphs.dfs_tree($g, 1)
+        @bench "$(name): bfs_tree" Graphs.bfs_tree($g, 1)
+        @bench "$(name): dfs_tree" Graphs.dfs_tree($g, 1)
     end
   end # graphs
   @benchgroup "digraphs" begin
     for (name, g) in DIGRAPHS
-        @bench "$(name): bfs_tree" LightGraphs.bfs_tree($g, 1)
-        @bench "$(name): dfs_tree" LightGraphs.dfs_tree($g, 1)
+        @bench "$(name): bfs_tree" Graphs.bfs_tree($g, 1)
+        @bench "$(name): dfs_tree" Graphs.dfs_tree($g, 1)
     end
   end # digraphs
 end # traversals

docs/make.jl

@@ -1,20 +1,20 @@
 using Documenter
-#include("../src/LightGraphs.jl")
-using LightGraphs
+#include("../src/Graphs.jl")
+using Graphs
 
 # same for contributing and license
 cp(normpath(@__FILE__, "../../CONTRIBUTING.md"), normpath(@__FILE__, "../src/contributing.md"); force=true)
 cp(normpath(@__FILE__, "../../LICENSE.md"), normpath(@__FILE__, "../src/license.md"); force=true)
 
 makedocs(
-    modules     = [LightGraphs],
+    modules     = [Graphs],
     format      = Documenter.HTML(), 
-    sitename    = "LightGraphs",
+    sitename    = "Graphs",
     doctest     = false,
     pages       = Any[
         "Getting Started"                   => "index.md",
         "Choosing A Graph Type"             => "graphtypes.md",
-        "LightGraphs Types"                 => "types.md",
+        "Graphs Types"                      => "types.md",
         "Accessing Properties"              => "basicproperties.md",
         "Making and Modifying Graphs"       => "generators.md",
         "Reading / Writing Graphs"          => "persistence.md",
@@ -35,12 +35,12 @@ makedocs(
         "Contributing"                      => "contributing.md",
         "Developer Notes"                   => "developing.md",
         "License Information"               => "license.md",
-        "Citing LightGraphs"                => "citing.md"
+        "Citing Graphs"                     => "citing.md"
     ]
 )
 
 deploydocs(
-    repo        = "github.com/JuliaGraphs/LightGraphs.jl.git",
+    repo        = "github.com/JuliaGraphs/Graphs.jl.git",
     target      = "build",
 )
 

docs/notebooks/triangles.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Improving Triangle counting in LightGraphs\n",
+    "# Improving Triangle counting in Graphs\n",
     "We want to make triangle counting faster by improving the algorithm.\n",
     "BenchmarkTools is used to make sure that we are measuring times with sufficient accuracy."
    ]
@@ -17,7 +17,7 @@
    },
    "outputs": [],
    "source": [
-    "using LightGraphs\n",
+    "using Graphs\n",
     "using BenchmarkTools"
    ]
   },

docs/src/centrality.md

@@ -2,7 +2,7 @@
 
 [Centrality measures](https://en.wikipedia.org/wiki/Centrality) describe the
 importance of a vertex to the rest of the graph using some set of criteria.
-Centrality measures implemented in *LightGraphs.jl* include the following:
+Centrality measures implemented in *Graphs.jl* include the following:
 
 
 ```@index
@@ -12,7 +12,7 @@ Pages   = ["centrality.md"]
 ## Full docs
 
 ```@autodocs
-Modules = [LightGraphs]
+Modules = [Graphs]
 Pages   = [
     "centrality/betweenness.jl",
     "centrality/closeness.jl",

docs/src/citing.md

@@ -1,6 +1,6 @@
 We encourage you to cite our work if you have used our libraries, tools or datasets. Starring the repository on GitHub is also appreciated.
 
-The latest citation information may be found in the [CITATION.bib](https://raw.githubusercontent.com/JuliaGraphs/LightGraphs.jl/master/CITATION.bib) file
-within the LightGraphs repository.
+The latest citation information may be found in the [CITATION.bib](https://raw.githubusercontent.com/JuliaGraphs/Graphs.jl/master/CITATION.bib) file
+within the Graphs repository.
 
 For previous versions, [please reference the zenodo site](https://zenodo.org/record/889971).

docs/src/coloring.md

@@ -1,6 +1,6 @@
 # Coloring
 
-*LightGraphs.jl* defines a structure and basic interface for coloring algorithms.
+*Graphs.jl* defines a structure and basic interface for coloring algorithms.
 Since coloring is a hard problem in the general case, users can extend the behavior
 and define their own function taking a graph as input and returning the `Coloring` structure.
 
@@ -10,7 +10,7 @@ Pages = ["coloring.md"]
 ```
 
 ```@autodocs
-Modules = [LightGraphs]
+Modules = [Graphs]
 Pages   = [
     "traversals/greedy_color.jl",
 ]

docs/src/community.md

@@ -1,6 +1,6 @@
 # Community Structures
 
-*LightGraphs.jl* contains many algorithm to detect and analyze community structures
+*Graphs.jl* contains many algorithm to detect and analyze community structures
 in graphs. These include:
 
 ```@index
@@ -11,7 +11,7 @@ Pages   = ["community.md"]
 ## Full Docs
 
 ```@autodocs
-Modules = [LightGraphs]
+Modules = [Graphs]
 Pages   = [
     "community/cliques.jl",
     "community/clustering.jl",