From 96bb8fff86659be4de85f904f429abfe17b8c7c4 Mon Sep 17 00:00:00 2001
From: damianodegaspari <144324904+damianodegaspari@users.noreply.github.com>
Date: Fri, 28 Feb 2025 11:03:09 +0100
Subject: [PATCH 1/4] Update core.jl

Fixed the documentation of the functions indegree, outdegree and degree and removed the TODO comment in the source code that was asking for it.
---
 src/core.jl | 51 ++++++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 40 insertions(+), 11 deletions(-)

diff --git a/src/core.jl b/src/core.jl
index cb8abd175..f7276f245 100644
--- a/src/core.jl
+++ b/src/core.jl
@@ -44,15 +44,15 @@ julia> add_vertices!(g, 2)
 """
 add_vertices!(g::AbstractGraph, n::Integer) = sum([add_vertex!(g) for i in 1:n])
 
-# TODO the behaviour of indegree (and as well outdegree and degree) is very
-# badly documented for the case indegree(g, vs) where vs is not a single vertex
-# but rather a collection of vertices
 
 """
     indegree(g[, v])
 
-Return a vector corresponding to the number of edges which end at each vertex in
-graph `g`. If `v` is specified, only return degrees for vertices in `v`.
+Return a vector containing the indegrees of every vertex of the graph `g`, where
+the indegree of a vertex is defined as the number of edges which end at that 
+vertex. If `v` is specified and is a single vertex, only return the indegree of
+`v`. If `v` is specified and is a vector of vertices, only return the indegrees
+of the vertices in `v`.
 
 # Examples
 ```jldoctest
@@ -69,6 +69,14 @@ julia> indegree(g)
  1
  0
  1
+
+julia> indegree(g,[2,3])
+2-element Vector{Int64}:
+ 0
+ 1
+
+julia> indegree(g,2)
+0
 ```
 """
 indegree(g::AbstractGraph, v::Integer) = length(inneighbors(g, v))
@@ -77,8 +85,11 @@ indegree(g::AbstractGraph, vs=vertices(g)) = [indegree(g, x) for x in vs]
 """
     outdegree(g[, v])
 
-Return a vector corresponding to the number of edges which start at each vertex in
-graph `g`. If `v` is specified, only return degrees for vertices in `v`.
+Return a vector containing the outdegrees of every vertex of the graph `g`, where
+the outdegree of a vertex is defined as the number of edges which start at that 
+vertex. If `v` is specified and is a single vertex, only return the outdegree of
+`v`. If `v` is specified and is a vector of vertices, only return the outdegrees
+of the vertices in `v`.
 
 # Examples
 ```jldoctest
@@ -95,6 +106,14 @@ julia> outdegree(g)
  0
  1
  1
+
+julia> outdegree(g,[1,2])
+2-element Vector{Int64}:
+ 0
+ 1
+
+julia> outdegree(g,2)
+1
 ```
 """
 outdegree(g::AbstractGraph, v::Integer) = length(outneighbors(g, v))
@@ -103,10 +122,12 @@ outdegree(g::AbstractGraph, vs=vertices(g)) = [outdegree(g, x) for x in vs]
 """
     degree(g[, v])
 
-Return a vector corresponding to the number of edges which start or end at each
-vertex in graph `g`. If `v` is specified, only return degrees for vertices in `v`.
-For directed graphs, this value equals the incoming plus outgoing edges.
-For undirected graphs, it equals the connected edges.
+Return a vector containing the degrees of every vertex of the graph `g`, where
+the degree of a vertex is defined as the number of edges which start or end at
+that vertex. For directed graphs, the degree of a vertex is equal to the sum of
+its indegree and outdegree. If `v` is specified and is a single vertex, only 
+return the degree of `v`. If `v` is specified and is a vector of vertices, only
+return the degrees of the vertices in `v`.
 
 # Examples
 ```jldoctest
@@ -123,6 +144,14 @@ julia> degree(g)
  1
  1
  2
+
+julia> degree(g,[1,3])
+2-element Vector{Int64}:
+ 1
+ 2
+
+julia> degree(g,3)
+2
 ```
 """
 function degree end

From 7b05f219af1b9a5ed70631c3c57ab97d153a46ba Mon Sep 17 00:00:00 2001
From: damianodegaspari <144324904+damianodegaspari@users.noreply.github.com>
Date: Tue, 11 Mar 2025 23:26:11 +0100
Subject: [PATCH 2/4] update to the previous doc changes, this time formatting
 according to BlueStyle() using JuliaFormatter

---
 src/core.jl | 45 ++++++++++++++++++++++-----------------------
 1 file changed, 22 insertions(+), 23 deletions(-)

diff --git a/src/core.jl b/src/core.jl
index f7276f245..5780dcbe2 100644
--- a/src/core.jl
+++ b/src/core.jl
@@ -1,12 +1,12 @@
 """
-    AbstractPathState
+	AbstractPathState
 
 An abstract type that provides information from shortest paths calculations.
 """
 abstract type AbstractPathState end
 
 """
-    is_ordered(e)
+	is_ordered(e)
 
 Return true if the source vertex of edge `e` is less than or equal to
 the destination vertex.
@@ -26,7 +26,7 @@ false
 is_ordered(e::AbstractEdge) = src(e) <= dst(e)
 
 """
-    add_vertices!(g, n)
+	add_vertices!(g, n)
 
 Add `n` new vertices to the graph `g`.
 Return the number of vertices that were added successfully.
@@ -44,9 +44,8 @@ julia> add_vertices!(g, 2)
 """
 add_vertices!(g::AbstractGraph, n::Integer) = sum([add_vertex!(g) for i in 1:n])
 
-
 """
-    indegree(g[, v])
+	indegree(g[, v])
 
 Return a vector containing the indegrees of every vertex of the graph `g`, where
 the indegree of a vertex is defined as the number of edges which end at that 
@@ -83,7 +82,7 @@ indegree(g::AbstractGraph, v::Integer) = length(inneighbors(g, v))
 indegree(g::AbstractGraph, vs=vertices(g)) = [indegree(g, x) for x in vs]
 
 """
-    outdegree(g[, v])
+	outdegree(g[, v])
 
 Return a vector containing the outdegrees of every vertex of the graph `g`, where
 the outdegree of a vertex is defined as the number of edges which start at that 
@@ -120,7 +119,7 @@ outdegree(g::AbstractGraph, v::Integer) = length(outneighbors(g, v))
 outdegree(g::AbstractGraph, vs=vertices(g)) = [outdegree(g, x) for x in vs]
 
 """
-    degree(g[, v])
+	degree(g[, v])
 
 Return a vector containing the degrees of every vertex of the graph `g`, where
 the degree of a vertex is defined as the number of edges which start or end at
@@ -166,48 +165,48 @@ end
 degree(g::AbstractGraph, vs=vertices(g)) = [degree(g, x) for x in vs]
 
 """
-    Δout(g)
+	Δout(g)
 
 Return the maximum [`outdegree`](@ref) of vertices in `g`.
 """
 Δout(g) = noallocextreme(outdegree, (>), typemin(Int), g)
 """
-    δout(g)
+	δout(g)
 
 Return the minimum [`outdegree`](@ref) of vertices in `g`.
 """
 δout(g) = noallocextreme(outdegree, (<), typemax(Int), g)
 
 """
-    Δin(g)
+	Δin(g)
 
 Return the maximum [`indegree`](@ref) of vertices in `g`.
 """
 Δin(g) = noallocextreme(indegree, (>), typemin(Int), g)
 
 """
-    δin(g)
+	δin(g)
 
 Return the minimum [`indegree`](@ref) of vertices in `g`.
 """
 δin(g) = noallocextreme(indegree, (<), typemax(Int), g)
 
 """
-    Δ(g)
+	Δ(g)
 
 Return the maximum [`degree`](@ref) of vertices in `g`.
 """
 Δ(g) = noallocextreme(degree, (>), typemin(Int), g)
 
 """
-    δ(g)
+	δ(g)
 
 Return the minimum [`degree`](@ref) of vertices in `g`.
 """
 δ(g) = noallocextreme(degree, (<), typemax(Int), g)
 
 """
-    noallocextreme(f, comparison, initial, g)
+	noallocextreme(f, comparison, initial, g)
 
 Compute the extreme value of `[f(g,i) for i=i:nv(g)]` without gathering them all
 """
@@ -223,7 +222,7 @@ function noallocextreme(f, comparison, initial, g)
 end
 
 """
-    degree_histogram(g, degfn=degree)
+	degree_histogram(g, degfn=degree)
 
 Return a `Dict` with values representing the number of vertices that have degree
 represented by the key.
@@ -242,7 +241,7 @@ function degree_histogram(g::AbstractGraph{T}, degfn=degree) where {T}
 end
 
 """
-    neighbors(g, v)
+	neighbors(g, v)
 
 Return a list of all neighbors reachable from vertex `v` in `g`.
 For directed graphs, the default is equivalent to [`outneighbors`](@ref);
@@ -278,7 +277,7 @@ julia> neighbors(g, 3)
 neighbors(g::AbstractGraph, v::Integer) = outneighbors(g, v)
 
 """
-    all_neighbors(g, v)
+	all_neighbors(g, v)
 
 Return a list of all inbound and outbound neighbors of `v` in `g`.
 For undirected graphs, this is equivalent to both [`outneighbors`](@ref)
@@ -320,7 +319,7 @@ end
 @traitfn all_neighbors(g::::(!IsDirected), v::Integer) = neighbors(g, v)
 
 """
-    common_neighbors(g, u, v)
+	common_neighbors(g, u, v)
 
 Return the neighbors common to vertices `u` and `v` in `g`.
 
@@ -360,7 +359,7 @@ function common_neighbors(g::AbstractGraph, u::Integer, v::Integer)
 end
 
 """
-    has_self_loops(g)
+	has_self_loops(g)
 
 Return true if `g` has any self loops.
 
@@ -386,7 +385,7 @@ function has_self_loops(g::AbstractGraph)
 end
 
 """
-    num_self_loops(g)
+	num_self_loops(g)
 
 Return the number of self loops in `g`.
 
@@ -410,7 +409,7 @@ julia> num_self_loops(g)
 num_self_loops(g::AbstractGraph) = nv(g) == 0 ? 0 : sum(v -> has_edge(g, v, v), vertices(g))
 
 """
-    density(g)
+	density(g)
 
 Return the density of `g`.
 Density is defined as the ratio of the number of actual edges to the
@@ -422,7 +421,7 @@ function density end
 @traitfn density(g::::(!IsDirected)) = (2 * ne(g)) / (nv(g) * (nv(g) - 1))
 
 """
-    squash(g)
+	squash(g)
 
 Return a copy of a graph with the smallest practical eltype that
 can accommodate all vertices.
@@ -448,7 +447,7 @@ function squash(g::AbstractGraph)
 end
 
 """
-    weights(g)
+	weights(g)
 
 Return the weights of the edges of a graph `g` as a matrix. Defaults
 to [`Graphs.DefaultDistance`](@ref).

From a36b8bd0e428929fbd44a3f0d10206ba0281a431 Mon Sep 17 00:00:00 2001
From: damianodegaspari <damiano.degas@gmail.com>
Date: Sun, 16 Mar 2025 22:58:49 +0100
Subject: [PATCH 3/4] Another try at getting formatting right.

---
 src/core.jl | 56 ++++++++++++++++++++++++++---------------------------
 1 file changed, 28 insertions(+), 28 deletions(-)

diff --git a/src/core.jl b/src/core.jl
index 5780dcbe2..ef354bbe6 100644
--- a/src/core.jl
+++ b/src/core.jl
@@ -1,12 +1,12 @@
 """
-	AbstractPathState
+    AbstractPathState
 
 An abstract type that provides information from shortest paths calculations.
 """
 abstract type AbstractPathState end
 
 """
-	is_ordered(e)
+    is_ordered(e)
 
 Return true if the source vertex of edge `e` is less than or equal to
 the destination vertex.
@@ -26,7 +26,7 @@ false
 is_ordered(e::AbstractEdge) = src(e) <= dst(e)
 
 """
-	add_vertices!(g, n)
+    add_vertices!(g, n)
 
 Add `n` new vertices to the graph `g`.
 Return the number of vertices that were added successfully.
@@ -45,7 +45,7 @@ julia> add_vertices!(g, 2)
 add_vertices!(g::AbstractGraph, n::Integer) = sum([add_vertex!(g) for i in 1:n])
 
 """
-	indegree(g[, v])
+    indegree(g[, v])
 
 Return a vector containing the indegrees of every vertex of the graph `g`, where
 the indegree of a vertex is defined as the number of edges which end at that 
@@ -79,10 +79,10 @@ julia> indegree(g,2)
 ```
 """
 indegree(g::AbstractGraph, v::Integer) = length(inneighbors(g, v))
-indegree(g::AbstractGraph, vs=vertices(g)) = [indegree(g, x) for x in vs]
+indegree(g::AbstractGraph, vs = vertices(g)) = [indegree(g, x) for x in vs]
 
 """
-	outdegree(g[, v])
+    outdegree(g[, v])
 
 Return a vector containing the outdegrees of every vertex of the graph `g`, where
 the outdegree of a vertex is defined as the number of edges which start at that 
@@ -116,10 +116,10 @@ julia> outdegree(g,2)
 ```
 """
 outdegree(g::AbstractGraph, v::Integer) = length(outneighbors(g, v))
-outdegree(g::AbstractGraph, vs=vertices(g)) = [outdegree(g, x) for x in vs]
+outdegree(g::AbstractGraph, vs = vertices(g)) = [outdegree(g, x) for x in vs]
 
 """
-	degree(g[, v])
+    degree(g[, v])
 
 Return a vector containing the degrees of every vertex of the graph `g`, where
 the degree of a vertex is defined as the number of edges which start or end at
@@ -162,51 +162,51 @@ function degree(g::AbstractGraph, v::Integer)
     return indegree(g, v) + outdegree(g, v)
 end
 
-degree(g::AbstractGraph, vs=vertices(g)) = [degree(g, x) for x in vs]
+degree(g::AbstractGraph, vs = vertices(g)) = [degree(g, x) for x in vs]
 
 """
-	Δout(g)
+    Δout(g)
 
 Return the maximum [`outdegree`](@ref) of vertices in `g`.
 """
 Δout(g) = noallocextreme(outdegree, (>), typemin(Int), g)
 """
-	δout(g)
+    δout(g)
 
 Return the minimum [`outdegree`](@ref) of vertices in `g`.
 """
 δout(g) = noallocextreme(outdegree, (<), typemax(Int), g)
 
 """
-	Δin(g)
+    Δin(g)
 
 Return the maximum [`indegree`](@ref) of vertices in `g`.
 """
 Δin(g) = noallocextreme(indegree, (>), typemin(Int), g)
 
 """
-	δin(g)
+    δin(g)
 
 Return the minimum [`indegree`](@ref) of vertices in `g`.
 """
 δin(g) = noallocextreme(indegree, (<), typemax(Int), g)
 
 """
-	Δ(g)
+    Δ(g)
 
 Return the maximum [`degree`](@ref) of vertices in `g`.
 """
 Δ(g) = noallocextreme(degree, (>), typemin(Int), g)
 
 """
-	δ(g)
+    δ(g)
 
 Return the minimum [`degree`](@ref) of vertices in `g`.
 """
 δ(g) = noallocextreme(degree, (<), typemax(Int), g)
 
 """
-	noallocextreme(f, comparison, initial, g)
+    noallocextreme(f, comparison, initial, g)
 
 Compute the extreme value of `[f(g,i) for i=i:nv(g)]` without gathering them all
 """
@@ -222,7 +222,7 @@ function noallocextreme(f, comparison, initial, g)
 end
 
 """
-	degree_histogram(g, degfn=degree)
+    degree_histogram(g, degfn=degree)
 
 Return a `Dict` with values representing the number of vertices that have degree
 represented by the key.
@@ -230,8 +230,8 @@ represented by the key.
 Degree function (for example, [`indegree`](@ref) or [`outdegree`](@ref)) may be specified by
 overriding `degfn`.
 """
-function degree_histogram(g::AbstractGraph{T}, degfn=degree) where {T}
-    hist = Dict{T,Int}()
+function degree_histogram(g::AbstractGraph{T}, degfn = degree) where {T}
+    hist = Dict{T, Int}()
     for v in vertices(g)        # minimize allocations by
         for d in degfn(g, v)    # iterating over vertices
             hist[d] = get(hist, d, 0) + 1
@@ -241,7 +241,7 @@ function degree_histogram(g::AbstractGraph{T}, degfn=degree) where {T}
 end
 
 """
-	neighbors(g, v)
+    neighbors(g, v)
 
 Return a list of all neighbors reachable from vertex `v` in `g`.
 For directed graphs, the default is equivalent to [`outneighbors`](@ref);
@@ -277,7 +277,7 @@ julia> neighbors(g, 3)
 neighbors(g::AbstractGraph, v::Integer) = outneighbors(g, v)
 
 """
-	all_neighbors(g, v)
+    all_neighbors(g, v)
 
 Return a list of all inbound and outbound neighbors of `v` in `g`.
 For undirected graphs, this is equivalent to both [`outneighbors`](@ref)
@@ -319,7 +319,7 @@ end
 @traitfn all_neighbors(g::::(!IsDirected), v::Integer) = neighbors(g, v)
 
 """
-	common_neighbors(g, u, v)
+    common_neighbors(g, u, v)
 
 Return the neighbors common to vertices `u` and `v` in `g`.
 
@@ -359,7 +359,7 @@ function common_neighbors(g::AbstractGraph, u::Integer, v::Integer)
 end
 
 """
-	has_self_loops(g)
+    has_self_loops(g)
 
 Return true if `g` has any self loops.
 
@@ -385,7 +385,7 @@ function has_self_loops(g::AbstractGraph)
 end
 
 """
-	num_self_loops(g)
+    num_self_loops(g)
 
 Return the number of self loops in `g`.
 
@@ -409,7 +409,7 @@ julia> num_self_loops(g)
 num_self_loops(g::AbstractGraph) = nv(g) == 0 ? 0 : sum(v -> has_edge(g, v, v), vertices(g))
 
 """
-	density(g)
+    density(g)
 
 Return the density of `g`.
 Density is defined as the ratio of the number of actual edges to the
@@ -421,7 +421,7 @@ function density end
 @traitfn density(g::::(!IsDirected)) = (2 * ne(g)) / (nv(g) * (nv(g) - 1))
 
 """
-	squash(g)
+    squash(g)
 
 Return a copy of a graph with the smallest practical eltype that
 can accommodate all vertices.
@@ -433,7 +433,7 @@ function squash(g::AbstractGraph)
     # TODO this version check can be removed when we increase the required Julia version
     deprecation_msg = "squash(::AbstractGraph) is deprecated in favor of methods that specialize on the graph type."
     if VERSION >= v"1.5.2"
-        Base.depwarn(deprecation_msg, :squash; force=true)
+        Base.depwarn(deprecation_msg, :squash; force = true)
     else
         Base.depwarn(deprecation_msg, :squash)
     end
@@ -447,7 +447,7 @@ function squash(g::AbstractGraph)
 end
 
 """
-	weights(g)
+    weights(g)
 
 Return the weights of the edges of a graph `g` as a matrix. Defaults
 to [`Graphs.DefaultDistance`](@ref).

From de43b2eb9921a47a7c5121cda4f4df3309aad307 Mon Sep 17 00:00:00 2001
From: damianodegaspari <damiano.degas@gmail.com>
Date: Sun, 16 Mar 2025 22:59:07 +0100
Subject: [PATCH 4/4] Another try at getting formatting right

---
 src/core.jl | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/core.jl b/src/core.jl
index ef354bbe6..3c6659faa 100644
--- a/src/core.jl
+++ b/src/core.jl
@@ -79,7 +79,7 @@ julia> indegree(g,2)
 ```
 """
 indegree(g::AbstractGraph, v::Integer) = length(inneighbors(g, v))
-indegree(g::AbstractGraph, vs = vertices(g)) = [indegree(g, x) for x in vs]
+indegree(g::AbstractGraph, vs=vertices(g)) = [indegree(g, x) for x in vs]
 
 """
     outdegree(g[, v])
@@ -116,7 +116,7 @@ julia> outdegree(g,2)
 ```
 """
 outdegree(g::AbstractGraph, v::Integer) = length(outneighbors(g, v))
-outdegree(g::AbstractGraph, vs = vertices(g)) = [outdegree(g, x) for x in vs]
+outdegree(g::AbstractGraph, vs=vertices(g)) = [outdegree(g, x) for x in vs]
 
 """
     degree(g[, v])
@@ -162,7 +162,7 @@ function degree(g::AbstractGraph, v::Integer)
     return indegree(g, v) + outdegree(g, v)
 end
 
-degree(g::AbstractGraph, vs = vertices(g)) = [degree(g, x) for x in vs]
+degree(g::AbstractGraph, vs=vertices(g)) = [degree(g, x) for x in vs]
 
 """
     Δout(g)
@@ -230,8 +230,8 @@ represented by the key.
 Degree function (for example, [`indegree`](@ref) or [`outdegree`](@ref)) may be specified by
 overriding `degfn`.
 """
-function degree_histogram(g::AbstractGraph{T}, degfn = degree) where {T}
-    hist = Dict{T, Int}()
+function degree_histogram(g::AbstractGraph{T}, degfn=degree) where {T}
+    hist = Dict{T,Int}()
     for v in vertices(g)        # minimize allocations by
         for d in degfn(g, v)    # iterating over vertices
             hist[d] = get(hist, d, 0) + 1
@@ -433,7 +433,7 @@ function squash(g::AbstractGraph)
     # TODO this version check can be removed when we increase the required Julia version
     deprecation_msg = "squash(::AbstractGraph) is deprecated in favor of methods that specialize on the graph type."
     if VERSION >= v"1.5.2"
-        Base.depwarn(deprecation_msg, :squash; force = true)
+        Base.depwarn(deprecation_msg, :squash; force=true)
     else
         Base.depwarn(deprecation_msg, :squash)
     end