MetaGraphs to attic, starting cleanup

Author: GearsAD

Project.toml

@@ -13,7 +13,6 @@ Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 JSON2 = "2535ab7d-5cd8-5a07-80ac-9b1792aadce3"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 Neo4j = "d2adbeaf-5838-5367-8a2f-e46d570981db"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
@@ -27,7 +26,6 @@ GraphPlot = "0.3.1, 0.4"
 Graphs = "0.10.2, 0.11, 1"
 JSON2 = "0.3.1"
 LightGraphs = "1.2, 1.3"
-MetaGraphs = "^0.6.3"
 Neo4j = "2"
 Reexport = "0.2, 0.3, 0.4, 0.5, 1"
 Requires = "0.5, 0.6, 0.7, 0.8, 0.9, 0.10, 1"

src/DFGPlots/DFGPlots.jl

@@ -2,7 +2,6 @@ module DFGPlots
 
 using Colors
 using LightGraphs
-using MetaGraphs
 using GraphPlot
 using DocStringExtensions
 import GraphPlot: gplot
@@ -84,39 +83,6 @@ using Compose
 draw(PDF("/tmp/graph.pdf", 16cm, 16cm), dfgplot(fg))
 ```
 
-More information at [GraphPlot.jl](https://github.com/JuliaGraphs/GraphPlot.jl)
-"""
-function dfgplot(dfg::DistributedFactorGraphs.MetaGraphsDFG, p::DFGPlotProps = DFGPlotProps())
-    @info "Deprecated, please use GraphsDFG or LightDFG."
-    nodesize = [has_prop(dfg.g,i,:factor) ?  p.nodesize.fac : p.nodesize.var for i=vertices(dfg.g)]
-    if p.drawlabels
-        nodelabel = [has_prop(dfg.g,i,:factor) ? "" : string(get_prop(dfg.g,i,:label)) for i=vertices(dfg.g)]
-    else
-        nodelabel = nothing
-    end
-    nodefillc = [has_prop(dfg.g,i,:factor) ? p.nodefillc.fac : p.nodefillc.var for i=vertices(dfg.g)]
-
-    gplot(dfg.g, nodelabel=nodelabel, nodesize=nodesize, nodefillc=nodefillc, layout=p.layout)
-
-end
-
-"""
-    $(SIGNATURES)
-Plots the structure of the factor graph. GraphPlot must be imported before DistributedFactoGraphs for these functions to be available.
-Returns the plot context.
-
-E.g.
-```
-using GraphPlot
-using DistributedFactorGraphs, DistributedFactorGraphs.DFGPlots
-# ... Make graph...
-# Using GraphViz plotting
-dfgplot(fg)
-# Save to PDFG
-using Compose
-draw(PDF("/tmp/graph.pdf", 16cm, 16cm), dfgplot(fg))
-```
-
 More information at [GraphPlot.jl](https://github.com/JuliaGraphs/GraphPlot.jl)
 """
 function dfgplot(dfg::AbstractDFG, p::DFGPlotProps = DFGPlotProps())
@@ -128,11 +94,6 @@ function dfgplot(dfg::AbstractDFG, p::DFGPlotProps = DFGPlotProps())
     dfgplot(ldfg, p)
 end
 
-function gplot(dfg::DistributedFactorGraphs.MetaGraphsDFG; keyargs...)
-    @info "Deprecated, please use GraphsDFG or LightDFG."
-    gplot(dfg.g; keyargs...)
-end
-
 function gplot(dfg::LightDFG; keyargs...)
     gplot(dfg.g; keyargs...)
 end

src/DistributedFactorGraphs.jl

@@ -9,6 +9,8 @@ using Reexport
 using JSON2
 using LinearAlgebra
 using SparseArrays
+# This is used in the definition of getAdjacencyMatrixSparse
+using LightGraphs
 
 # Entities
 include("entities/AbstractDFG.jl")
@@ -86,9 +88,6 @@ include("GraphsDFG/GraphsDFG.jl")
 # Include the FilesDFG API.
 include("FileDFG/FileDFG.jl")
 
-# Include the LightGraphs.jl (MetaGraphs.jl) API.
-include("MetaGraphsDFG/MetaGraphsDFG.jl")
-
 include("SymbolDFG/SymbolDFG.jl")
 using .SymbolDFGs
 

src/SymbolDFG/services/SymbolDFG.jl

@@ -485,38 +485,6 @@ function getAdjacencyMatrixSparse(dfg::SymbolDFG)::Tuple{LightGraphs.SparseMatri
 	end
 	return adjMat, varLabels, factLabels
 end
-#=
-"""
-    $(SIGNATURES)
-Produces a dot-format of the graph for visualization.
-"""
-function toDot(dfg::SymbolDFG)::String
-	@error "toDot(dfg::SymbolDFG) is not sopported yet, see https://github.com/JuliaGraphs/MetaGraphs.jl/issues/86"
-    m = PipeBuffer()
-    MetaGraphs.savedot(m, dfg.g)
-    data = take!(m)
-    close(m)
-    return String(data)
-end
-
-"""
-    $(SIGNATURES)
-Produces a dot file of the graph for visualization.
-Download XDot to see the data
-
-Note
-- Default location "/tmp/dfg.dot" -- MIGHT BE REMOVED
-- Can be viewed with the `xdot` system application.
-- Based on graphviz.org
-"""
-function toDotFile(dfg::SymbolDFG, fileName::String="/tmp/dfg.dot")::Nothing
-	@error "toDotFile(dfg::SymbolDFG,filename) is not sopported yet, see https://github.com/JuliaGraphs/MetaGraphs.jl/issues/86"
-    open(fileName, "w") do fid
-        MetaGraphs.savedot(fid, dfg.g)
-    end
-    return nothing
-end
-=#
 
 """
     $(SIGNATURES)

src/attic/MetaGraphsDFG/DFGPlots.jl

@@ -0,0 +1,37 @@
+"""
+    $(SIGNATURES)
+Plots the structure of the factor graph. GraphPlot must be imported before DistributedFactoGraphs for these functions to be available.
+Returns the plot context.
+
+E.g.
+```
+using GraphPlot
+using DistributedFactorGraphs, DistributedFactorGraphs.DFGPlots
+# ... Make graph...
+# Using GraphViz plotting
+dfgplot(fg)
+# Save to PDFG
+using Compose
+draw(PDF("/tmp/graph.pdf", 16cm, 16cm), dfgplot(fg))
+```
+
+More information at [GraphPlot.jl](https://github.com/JuliaGraphs/GraphPlot.jl)
+"""
+function dfgplot(dfg::DistributedFactorGraphs.MetaGraphsDFG, p::DFGPlotProps = DFGPlotProps())
+    @info "Deprecated, please use GraphsDFG or LightDFG."
+    nodesize = [has_prop(dfg.g,i,:factor) ?  p.nodesize.fac : p.nodesize.var for i=vertices(dfg.g)]
+    if p.drawlabels
+        nodelabel = [has_prop(dfg.g,i,:factor) ? "" : string(get_prop(dfg.g,i,:label)) for i=vertices(dfg.g)]
+    else
+        nodelabel = nothing
+    end
+    nodefillc = [has_prop(dfg.g,i,:factor) ? p.nodefillc.fac : p.nodefillc.var for i=vertices(dfg.g)]
+
+    gplot(dfg.g, nodelabel=nodelabel, nodesize=nodesize, nodefillc=nodefillc, layout=p.layout)
+
+end
+
+function gplot(dfg::DistributedFactorGraphs.MetaGraphsDFG; keyargs...)
+    @info "Deprecated, please use GraphsDFG or LightDFG."
+    gplot(dfg.g; keyargs...)
+end

src/MetaGraphsDFG/MetaGraphsDFG.jl renamed to src/attic/MetaGraphsDFG/MetaGraphsDFG.jl

@@ -4,6 +4,7 @@ using MetaGraphs
 # Imports
 include("entities/MetaGraphsDFG.jl")
 include("services/MetaGraphsDFG.jl")
+include("DFGPlots.jl")
 
 # Exports
 # Deprecated -

src/MetaGraphsDFG/entities/MetaGraphsDFG.jl renamed to src/attic/MetaGraphsDFG/entities/MetaGraphsDFG.jl

@@ -25,7 +25,18 @@ mutable struct VariableNodeData{T<:InferenceVariable}
 
 end
 
-VariableNodeData(val::Array{Float64,2},bw::Array{Float64,2},BayesNetOutVertIDs::Array{Symbol,1},dimIDs::Array{Int,1},dims::Int,eliminated::Bool,BayesNetVertID::Symbol,separator::Array{Symbol,1},softtype::T,initialized::Bool,inferdim::Float64,ismargin::Bool,dontmargin::Bool) where T <: InferenceVariable = VariableNodeData{T}(val,bw,BayesNetOutVertIDs,dimIDs,dims,eliminated,BayesNetVertID,separator,softtype::T,initialized,inferdim,ismargin,dontmargin)
+VariableNodeData(val::Array{Float64,2},
+				 bw::Array{Float64,2},
+				 BayesNetOutVertIDs::Array{Symbol,1},
+				 dimIDs::Array{Int,1},
+				 dims::Int,eliminated::Bool,
+				 BayesNetVertID::Symbol,
+				 separator::Array{Symbol,1},
+				 softtype::T,
+				 initialized::Bool,
+				 inferdim::Float64,
+				 ismargin::Bool,
+				 dontmargin::Bool) where T <: InferenceVariable = VariableNodeData{T}(val,bw,BayesNetOutVertIDs,dimIDs,dims,eliminated,BayesNetVertID,separator,softtype::T,initialized,inferdim,ismargin,dontmargin)
 
 function VariableNodeData()
     st = stacktrace()

src/MetaGraphsDFG/services/MetaGraphsDFG.jl renamed to src/attic/MetaGraphsDFG/services/MetaGraphsDFG.jl

@@ -15,10 +15,8 @@ using Pkg
 # global_logger(logger)
 
 # Test each interface
-# Still test LightDFG and MetaGraphsDFG for the moment until we remove in 0.4.2
 apis = [
     GraphsDFG,
-    DistributedFactorGraphs.MetaGraphsDFG,
     DistributedFactorGraphs.SymbolDFG,
     LightDFG]
 for api in apis
@@ -29,10 +27,8 @@ for api in apis
     end
 end
 
-# Test that we don't export LightDFG and MetaGraphsDFG
 @testset "Deprecated Drivers Test" begin
     @test_throws UndefVarError SymbolDFG{NoSolverParams}()
-    @test_throws UndefVarError MetaGraphsDFG{NoSolverParams}()
 end
 
 # Test special cases
@@ -66,7 +62,6 @@ if get(ENV, "IIF_TEST", "") == "true"
     apis = [
         GraphsDFG{NoSolverParams}(),
         LightDFG{NoSolverParams}(),
-        # # DistributedFactorGraphs.MetaGraphsDFG{NoSolverParams}(),
         # # DistributedFactorGraphs.SymbolDFG{NoSolverParams}(),
         CloudGraphsDFG{SolverParams}("localhost", 7474, "neo4j", "test",
                                     "testUser", "testRobot", "testSession",