Fix most failing doctests (#305)

Author: gdalle

docs/Manifest.toml

@@ -76,7 +76,7 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
 
 [[deps.Graphs]]
 deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
-path = "/home/hyrodium/.julia/dev/Graphs"
+path = ".."
 uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
 version = "1.8.0"
 
@@ -227,9 +227,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "Random", "StaticArraysCore"]
-git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881"
+git-tree-sha1 = "51621cca8651d9e334a659443a74ce50a3b6dfab"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.6.2"
+version = "1.6.3"
 weakdeps = ["Statistics"]
 
     [deps.StaticArrays.extensions]

src/Experimental/ShortestPaths/ShortestPaths.jl

@@ -181,8 +181,8 @@ algorithm `alg` (one of [`BellmanFord`](@ref) or [`SPFA`](@ref)), return
 `true` if any cycle detected in the graph has a negative weight.
 # Examples
 
-```
-julia> using Graphs
+```jldoctest
+julia> using Graphs, Graphs.Experimental.ShortestPaths
 
 julia> g = complete_graph(3);
 

src/community/modularity.jl

@@ -53,23 +53,21 @@ julia> modularity(barbell, [1, 1, 1, 2, 2, 2])
 julia> modularity(barbell, [1, 1, 1, 2, 2, 2], γ=0.5)
 0.6071428571428571  
 ```
-```
-julia> using SimpleWeightedGraphs
-
-julia> triangle = SimpleWeightedGraph(3);
+```jldoctest
+julia> using Graphs
 
-julia> add_edge!(triangle, 1, 2, 1);
+julia> triangle = cycle_graph(3);
 
-julia> add_edge!(triangle, 2, 3, 1);
+julia> barbell = blockdiag(triangle, triangle);
 
-julia> add_edge!(triangle, 3, 1, 1);
+julia> add_edge!(barbell, 1, 4);
 
-julia> barbell = blockdiag(triangle, triangle);
+julia> distmx = Matrix(weights(barbell));
 
-julia> add_edge!(barbell, 1, 4, 5); # this edge has a weight of 5
+julia> distmx[1, 4] = distmx[4, 1] = 5;  # additional edge has a weight of 5
 
-julia> modularity(barbell, [1, 1, 1, 2, 2, 2])
-0.045454545454545456
+julia> round(modularity(barbell, [1, 1, 1, 2, 2, 2]; distmx), digits=6)
+0.045455
 ```
 """
 function modularity(

src/digraph/transitivity.jl

@@ -54,52 +54,18 @@ is `true`, add self loops to the graph.
 Time complexity is ``\\mathcal{O}(|E||V|)``.
 
 # Examples
-```
+```jldoctest
 julia> using Graphs
 
 julia> barbell = blockdiag(complete_digraph(3), complete_digraph(3));
 
 julia> add_edge!(barbell, 1, 4);
 
-julia> collect(edges(barbell))
-13-element Vector{Graphs.SimpleGraphs.SimpleEdge{Int64}}:
- Edge 1 => 2
- Edge 1 => 3
- Edge 1 => 4
- Edge 2 => 1
- Edge 2 => 3
- Edge 3 => 1
- Edge 3 => 2
- Edge 4 => 5
- Edge 4 => 6
- Edge 5 => 4
- Edge 5 => 6
- Edge 6 => 4
- Edge 6 => 5
+julia> ne(barbell)
+13
 
-julia> collect(edges(transitiveclosure(barbell)))
-21-element Vector{Graphs.SimpleGraphs.SimpleEdge{Int64}}:
- Edge 1 => 2
- Edge 1 => 3
- Edge 1 => 4
- Edge 1 => 5
- Edge 1 => 6
- Edge 2 => 1
- Edge 2 => 3
- Edge 2 => 4
- Edge 2 => 5
- Edge 2 => 6
- Edge 3 => 1
- Edge 3 => 2
- Edge 3 => 4
- Edge 3 => 5
- Edge 3 => 6
- Edge 4 => 5
- Edge 4 => 6
- Edge 5 => 4
- Edge 5 => 6
- Edge 6 => 4
- Edge 6 => 5
+julia> ne(transitiveclosure(barbell))
+21
 ```
 """
 function transitiveclosure(g::DiGraph, selflooped=false)

src/shortestpaths/spfa.jl

@@ -34,15 +34,16 @@ julia> spfa_shortest_paths(g, 1, d)
   0
 ```
 
-```
+```jldoctest
+julia> using Graphs
 
 julia> g = complete_graph(3);
 
 julia> d = [1 -3 1; -3 1 1; 1 1 1];
 
 julia> spfa_shortest_paths(g, 1, d)
-
 ERROR: Graphs.NegativeCycleError()
+[...]
 ```
 """
 function spfa_shortest_paths(