Merge 5a9952f into 8576861

src/LightGraphs.jl

@@ -54,6 +54,9 @@ difference, symmetric_difference,
 join, tensor_product, cartesian_product, crosspath,
 induced_subgraph, egonet, merge_vertices!, merge_vertices,
 
+# allsimplepaths
+all_simple_paths,
+
 # bfs
 gdistances, gdistances!, bfs_tree, bfs_parents, has_path,
 
@@ -219,6 +222,7 @@ include("cycles/hawick-james.jl")
 include("cycles/karp.jl")
 include("cycles/basis.jl")
 include("cycles/limited_length.jl")
+include("traversals/allsimplepaths.jl")
 include("traversals/bfs.jl")
 include("traversals/bipartition.jl")
 include("traversals/greedy_color.jl")

src/traversals/allsimplepaths.jl

@@ -0,0 +1,185 @@
+using DataStructures
+
+"""
+    all_simple_paths(g, source, targets, cutoff=nothing)
+
+Returns an iterator that generates all simple paths in the graph `g` from `source` to `targets`.
+If `cutoff` is given, the paths' lengths are limited to equal or less than `cutoff`.
+Note that the length of a path is defined as the number of edges, not the number of elements.
+ex. the path length of `[1, 2, 3]` is two.
+Internally, a DFS algorithm is used to search paths.
+
+# Examples
+
+```jldoctest
+julia> using LightGraphs
+julia> g = complete_graph(4)
+julia> collect(all_simple_paths(g, 1, [4]))
+5-element Array{Array{Int64,1},1}:
+ [1, 4]
+ [1, 3, 4]
+ [1, 3, 2, 4]
+ [1, 2, 4]
+ [1, 2, 3, 4]
+ ```
+"""
+function all_simple_paths(g::AbstractGraph, source::T, targets::Vector{T}; cutoff::Union{Int,Nothing}=nothing) where T <: Integer
+    return SimplePathIterator(g, source, targets, cutoff=cutoff)
+end
+
+
+"""
+    all_simple_paths(g, source, target, cutoff=nothing)
+
+This function is equivalent to `all_simple_paths(g, source, [target], cutoff)`.
+This is provided for convenience.
+
+See also `all_simple_paths(g, source, targets, cutoff)`.
+"""
+function all_simple_paths(g::AbstractGraph, source::T, target::T; cutoff::Union{Int,Nothing}=nothing) where T <: Integer
+    return SimplePathIterator(g, source, [target], cutoff=cutoff)
+end
+
+
+"""
+    SimplePathIterator{T <: Integer}
+
+Iterator that generates all simple paths.
+The iterator holds the condition specified in `all_simple_path` function.
+"""
+struct SimplePathIterator{T <: Integer}
+    g::AbstractGraph
+    source::T  # Starting node
+    targets::Set{T}  # Target nodes
+    cutoff::Union{Int,Nothing}  # Max length of resulting paths
+
+    function SimplePathIterator(g::AbstractGraph, source::T, targets::Vector{T}; cutoff::Union{Int,Nothing}=nothing) where T <: Integer
+        new{T}(g, source, Set(targets), cutoff)
+    end
+end
+
+
+"""
+    SimplePathIteratorState{T <: Integer}
+
+SimplePathIterator's state.
+"""
+mutable struct SimplePathIteratorState{T <: Integer}
+    stack::Stack{Vector{T}}  # Store child nodes
+    visited::Stack{T}  # Store current path candidate
+    queued_targets::Vector{T}  # Store rest targets if path length reached cutoff.
+    function SimplePathIteratorState(spi::SimplePathIterator{T}) where T <: Integer
+        stack = Stack{Vector{T}}()
+        visited = Stack{T}()
+        queued_targets = Vector{T}()
+        push!(visited, spi.source)  # Add a starting node to the path candidate
+        push!(stack, copy(outneighbors(spi.g, spi.source)))  # Add child nodes from the start
+        new{T}(stack, visited, queued_targets)
+    end
+end
+
+"""
+    function stepback!(state)
+
+A helper function that updates iterator state.
+For internal use only.
+"""
+function stepback!(state::SimplePathIteratorState)
+    pop!(state.stack)
+    pop!(state.visited)
+end
+
+
+"""
+    Base.iterate(spi::SimplePathIterator{T}, state=nothing)
+
+Returns a next simple path based on DFS.
+If `cutoff` is specified in `SimplePathIterator`, the path length is limited up to `cutoff`
+"""
+function Base.iterate(spi::SimplePathIterator{T}, state::Union{SimplePathIteratorState,Nothing}=nothing) where T <: Integer
+
+    state = isnothing(state) ? SimplePathIteratorState(spi) : state
+
+    while !isempty(state.stack)
+
+        if !isempty(state.queued_targets)
+            # Consumes queueed targets
+            target = pop!(state.queued_targets)
+            result = vcat(reverse(collect(state.visited)), target)
+            if isempty(state.queued_targets)
+                stepback!(state)
+            end
+            return result, state
+        end
+
+        children = first(state.stack)
+
+        if isempty(children)
+            # Now leaf node, step back.
+            stepback!(state)
+            continue
+        end
+
+        child = pop!(children)
+        if child in state.visited
+            # Avoid loop
+            continue
+        end
+
+        if isnothing(spi.cutoff) || length(state.visited) < spi.cutoff
+            result = (child in spi.targets) ? vcat(reverse(collect(state.visited)), [child]) : nothing
+
+            # Update state variables
+            push!(state.visited, child)  # Move to child node
+            if !isempty(setdiff(spi.targets, state.visited))  # Expand stack until find all targets
+                push!(state.stack, copy(outneighbors(spi.g, child)))  # Add child nodes and step forward
+            else
+                pop!(state.visited)  # Step back and explore the remaining child nodes
+            end
+
+            # If found a new path, returns it.
+            if !isnothing(result)
+                return result, state
+            end
+        else
+            # Now length(visited) == cutoff
+            # Collect adjacent targets if exist and add them to queue.
+            rest_children = union(Set(children), Set(child))
+            state.queued_targets = collect(setdiff(intersect(spi.targets, rest_children), Set(state.visited)))
+
+            if isempty(state.queued_targets)
+                stepback!(state)
+            end
+        end
+    end
+end
+
+
+"""
+    Base.collect(spi::SimplePathIterator{T})
+
+Makes an array of paths from iterator.
+Note that this can take much memory space and cpu time when the graph is dense.
+"""
+function Base.collect(spi::SimplePathIterator{T}) where T <: Integer
+    res = Vector{Vector{T}}()
+    for x in spi
+        push!(res, x)
+    end
+    return res
+end
+
+
+"""
+    Base.length(spi::SimplePathIterator{T})
+
+Returns searched paths count.
+Note that this can take much cpu time when the graph is dense.
+"""
+function Base.length(spi::SimplePathIterator{T}) where T <: Integer
+    c = 0
+    for x in spi
+        c += 1
+    end
+    return c
+end

test/runtests.jl

@@ -11,13 +11,13 @@ using Statistics: mean
 
 const testdir = dirname(@__FILE__)
 
-testgraphs(g) = is_directed(g) ? [g, DiGraph{UInt8}(g), DiGraph{Int16}(g)] : [g, Graph{UInt8}(g), Graph{Int16}(g)] 
+testgraphs(g) = is_directed(g) ? [g, DiGraph{UInt8}(g), DiGraph{Int16}(g)] : [g, Graph{UInt8}(g), Graph{Int16}(g)]
 testgraphs(gs...) = vcat((testgraphs(g) for g in gs)...)
 testdigraphs = testgraphs
 
 # some operations will create a large graph from two smaller graphs. We
 # might error out on very small eltypes.
-testlargegraphs(g) = is_directed(g) ? [g, DiGraph{UInt16}(g), DiGraph{Int32}(g)] : [g, Graph{UInt16}(g), Graph{Int32}(g)] 
+testlargegraphs(g) = is_directed(g) ? [g, DiGraph{UInt16}(g), DiGraph{Int32}(g)] : [g, Graph{UInt16}(g), Graph{Int32}(g)]
 testlargegraphs(gs...) = vcat((testlargegraphs(g) for g in gs)...)
 
 tests = [
@@ -46,6 +46,7 @@ tests = [
     "shortestpaths/floyd-warshall",
     "shortestpaths/yen",
     "shortestpaths/spfa",
+    "traversals/allsimplepaths",
     "traversals/bfs",
     "traversals/bipartition",
     "traversals/greedy_color",

test/traversals/allsimplepaths.jl

@@ -0,0 +1,124 @@
+@testset "All Simple Paths" begin
+
+    # single path
+    g = path_graph(4)
+    paths = all_simple_paths(g, 1, 4)
+    @test Set(p for p in paths) == Set([[1, 2, 3, 4]])
+    @test Set(collect(paths)) == Set([[1, 2, 3, 4]])
+    @test 1 == length(paths)
+
+    # two paths
+    g = path_graph(4)
+    add_vertex!(g)
+    add_edge!(g, 3, 5)
+    paths = all_simple_paths(g, 1, [4, 5])
+    @test Set(p for p in paths) == Set([[1, 2, 3, 4], [1, 2, 3, 5]])
+    @test Set(collect(paths)) == Set([[1, 2, 3, 4], [1, 2, 3, 5]])
+    @test 2 == length(paths)
+
+    # two paths with cutoff
+    g = path_graph(4)
+    add_vertex!(g)
+    add_edge!(g, 3, 5)
+    paths = all_simple_paths(g, 1, [4, 5], cutoff=3)
+    @test Set(p for p in paths) == Set([[1, 2, 3, 4], [1, 2, 3, 5]])
+
+    # two targets in line emits two paths
+    g = path_graph(4)
+    add_vertex!(g)
+    paths = all_simple_paths(g, 1, [3, 4])
+    @test Set(p for p in paths) == Set([[1, 2, 3], [1, 2, 3, 4]])
+
+    # two paths digraph
+    g = SimpleDiGraph(5)
+    add_edge!(g, 1, 2)
+    add_edge!(g, 2, 3)
+    add_edge!(g, 3, 4)
+    add_edge!(g, 3, 5)    
+    paths = all_simple_paths(g, 1, [4, 5])
+    @test Set(p for p in paths) == Set([[1, 2, 3, 4], [1, 2, 3, 5]])
+
+    # two paths digraph with cutoff
+    g = SimpleDiGraph(5)
+    add_edge!(g, 1, 2)
+    add_edge!(g, 2, 3)
+    add_edge!(g, 3, 4)
+    add_edge!(g, 3, 5)    
+    paths = all_simple_paths(g, 1, [4, 5], cutoff=3)
+    @test Set(p for p in paths) == Set([[1, 2, 3, 4], [1, 2, 3, 5]])
+
+    # digraph with a cycle
+    g = SimpleDiGraph(4)
+    add_edge!(g, 1, 2)
+    add_edge!(g, 2, 3)
+    add_edge!(g, 3, 1)
+    add_edge!(g, 2, 4)
+    paths = all_simple_paths(g, 1, 4)
+    @test Set(p for p in paths) == Set([[1, 2, 4]])
+
+    # digraph with a cycle. paths with two targets share a node in the cycle.
+    g = SimpleDiGraph(4)
+    add_edge!(g, 1, 2)
+    add_edge!(g, 2, 3)
+    add_edge!(g, 3, 1)
+    add_edge!(g, 2, 4)
+    paths = all_simple_paths(g, 1, [3, 4])
+    @test Set(p for p in paths) == Set([[1, 2, 3], [1, 2, 4]])
+
+    # source equals targets
+    g = SimpleGraph(4)
+    paths = all_simple_paths(g, 1, 1)
+    @test Set(p for p in paths) == Set([])
+
+    # cutoff prones paths
+    # Note, a path lenght is node - 1
+    g = complete_graph(4)
+    paths = all_simple_paths(g, 1, 2; cutoff=1)
+    @test Set(p for p in paths) == Set([[1, 2]])
+
+    paths = all_simple_paths(g, 1, 2; cutoff=2)
+    @test Set(p for p in paths) == Set([[1, 2], [1, 3, 2], [1, 4, 2]])
+
+    # non trivial graph
+    g = SimpleDiGraph(6)
+    add_edge!(g, 1, 2)
+    add_edge!(g, 2, 3)
+    add_edge!(g, 3, 4)
+    add_edge!(g, 4, 5)
+
+    add_edge!(g, 1, 6)
+    add_edge!(g, 2, 6)
+    add_edge!(g, 2, 4)
+    add_edge!(g, 6, 5)
+    add_edge!(g, 5, 3)
+    add_edge!(g, 5, 4)
+
+    paths = all_simple_paths(g, 2, [3, 4])
+    @test Set(p for p in paths) == Set([
+         [2, 3],
+         [2, 4, 5, 3],
+         [2, 6, 5, 3],
+         [2, 4],
+         [2, 3, 4],
+         [2, 6, 5, 4],
+         [2, 6, 5, 3, 4],
+    ])
+
+    paths = all_simple_paths(g, 2, [3, 4], cutoff=3)
+    @test Set(p for p in paths) == Set([
+         [2, 3],
+         [2, 4, 5, 3],
+         [2, 6, 5, 3],
+         [2, 4],
+         [2, 3, 4],
+         [2, 6, 5, 4],
+    ])
+
+    paths = all_simple_paths(g, 2, [3, 4], cutoff=2)
+    @test Set(p for p in paths) == Set([
+         [2, 3],
+         [2, 4],
+         [2, 3, 4],
+    ])
+
+end