Merge pull request #895 from JuliaRobotics/master

v0.18.5-rc1

Author: dehann

.github/workflows/CompatHelper.yml

@@ -1,24 +1,45 @@
 name: CompatHelper
-
 on:
   schedule:
-    - cron: '00 00 * * *'
-
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        julia-version: [1.2.0]
-        julia-arch: [x86]
-        os: [ubuntu-latest]
+    runs-on: ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
         with:
-          version: ${{ matrix.julia-version }}
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+          version: '1'
+          # arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/ci.yml

@@ -7,7 +7,7 @@ on:
       - release/*
     tags:
       - v**
-
+  workflow_dispatch:
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
@@ -19,7 +19,7 @@ jobs:
       matrix:
         version:
           - '1.6'
-          - '1.7'
+          - '1.8'
           - 'nightly'
         os:
           - ubuntu-latest
@@ -82,7 +82,7 @@ jobs:
       matrix:
         version:
           - '1.6'
-          - '1.7'
+          - '1.8'
         os:
           - ubuntu-latest
         arch:
@@ -125,6 +125,8 @@ jobs:
             ${{ runner.os }}-
 
       - name: Julia Build Pkg
+        env:
+          DFG_USE_CGDFG: true
         uses: julia-actions/julia-buildpkg@latest
 
       - name: Git Test Credentials
@@ -159,7 +161,7 @@ jobs:
       - name: Setup julia
         uses: julia-actions/setup-julia@v1
         with:
-          version: 1.7
+          version: 1.8
           arch: x64
 
       - name: Build Docs

.gitignore

@@ -1,6 +1,7 @@
 *.jl.cov
 *.jl.*.cov
 *.jl.mem
+*.mem
 deps/deps.jl
 docs/build
 Manifest.toml

.travis.yml

@@ -1,13 +1,11 @@
-Copyright (c) 2017-2021 NavAbility
-
-NOTICE: this license will be relaxed to be much more permissive soon.
+Copyright (c) 2017-2022 NavAbility
 
 The source code in this repository is separated into two parts 
 that are licensed separately.  The Neo4jDFG library/driver
 is licensed separately.  For more details see: 
 https://github.com/JuliaRobotics/DistributedFactorGraphs.jl/blob/develop/src/Neo4jDFG/LICENSE
 
-DistributedFactorGraphs.jl, is not licensed for hosted, webservice or cloud 
+DistributedFactorGraphs' Neo4jDFG Driver is not licensed for hosted, webservice or cloud 
 solutions (public or private).  Please contact NavAbility via email at 
 <[email protected]> for clarification or additional licensing options.
 NavAbility reserves all rights regarding, and to deny use of the software 
@@ -18,9 +16,9 @@ Other general use or modification of the software beyond that of
 webservices or clouds (private or public) is permitted 
 according to terms defined by Apache 2.0 or other library specifc licenses.
 
-   Copyright 2017-2021 NavAbility
+   Copyright 2017-2022 NavAbility
 
-   Licensed under a Market Limited version of the Apache License, Version 2.0 (the "License");
+   Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.
 
    Unless required by applicable law or agreed to in writing, software

LICENSE

@@ -1,6 +1,6 @@
 name = "DistributedFactorGraphs"
 uuid = "b5cc3c7e-6572-11e9-2517-99fb8daf2f04"
-version = "0.18.4"
+version = "0.18.5"
 
 [deps]
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -15,7 +15,9 @@ LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 ManifoldsBase = "3362f125-f0bb-47a3-aa74-596ffd7ef2fb"
 Neo4j = "d2adbeaf-5838-5367-8a2f-e46d570981db"
+OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce"
@@ -29,13 +31,14 @@ Unmarshal = "cbff2730-442d-58d7-89d1-8e530c41eb02"
 Colors = "0.10, 0.11, 0.12"
 Distributions = "0.23, 0.24, 0.25"
 DocStringExtensions = "0.8, 0.9"
-Graphs = "1.4"
 GraphPlot = "0.5.0"
+Graphs = "1.4"
 JSON = "0.21"
 JSON2 = "0.3.1"
 LightGraphs = "1.2, 1.3"
 ManifoldsBase = "0.11, 0.12, 0.13"
 Neo4j = "2"
+OrderedCollections = "1.4"
 Pkg = "1.4, 1.5"
 Reexport = "1"
 Requires = "1"

Project.toml

@@ -9,6 +9,25 @@ function Base.convert(::Type{DateTime}, ts::ZonedDateTime)
     return DateTime(ts, Local)
 end
 
+## ================================================================================
+## Deprecate before v0.20 - Kept longer with error
+##=================================================================================
+
+function getTypeFromSerializationModule(dfg::G, moduleType::Symbol) where G <: AbstractDFG
+  error("Deprecating getTypeFromSerializationModule(dfg,symbol), use getTypeFromSerializationModule(string) instead.")
+  st = nothing
+  try
+      st = getfield(Main, Symbol(moduleType))
+  catch ex
+      @error "Unable to deserialize packed variableType $(moduleType)"
+      io = IOBuffer()
+      showerror(io, ex, catch_backtrace())
+      err = String(take!(io))
+      @error(err)
+  end
+  return st
+end
+
 ## ================================================================================
 ## Deprecate before v0.19 - Kept longer with error
 ##=================================================================================

src/Deprecated.jl

@@ -36,6 +36,9 @@ import ManifoldsBase
 import ManifoldsBase: AbstractManifold, manifold_dimension
 export AbstractManifold, manifold_dimension
 
+import RecursiveArrayTools: ArrayPartition
+export ArrayPartition
+
 import Base: getindex
 
 

src/DistributedFactorGraphs.jl

@@ -1,6 +1,8 @@
 module FactorGraphs
 using Graphs
 
+using OrderedCollections
+
 import Base:
     eltype, show, ==, Pair,
     Tuple, copy, length, size,
@@ -42,18 +44,18 @@ include("BiMaps.jl")
 struct FactorGraph{T <: Integer,V <: AbstractVariableType, F <: AbstractFactorType} <: AbstractGraph{T}
     graph::SimpleGraph{T}
     labels::BiDictMap{T}
-    variables::Dict{Symbol,V}
-    factors::Dict{Symbol,F}
+    variables::OrderedDict{Symbol,V}
+    factors::OrderedDict{Symbol,F}
 end
 
 function FactorGraph{T, V, F}(nv::Int=100, nf::Int=100) where {T <: Integer, V <: AbstractVariableType, F <: AbstractFactorType}
     fadjlist = Vector{Vector{T}}()
         sizehint!(fadjlist, nv + nf)
     g = SimpleGraph{T}(0, fadjlist)
     labels = BiDictMap{T}(sizehint=nv+nf)
-    variables = Dict{Symbol,V}()
+    variables = OrderedDict{Symbol,V}()
         sizehint!(variables, nv)
-    factors = Dict{Symbol,F}()
+    factors = OrderedDict{Symbol,F}()
         sizehint!(factors, nf)
     return FactorGraph{T, V, F}(g, labels, variables, factors)
 end

src/GraphsDFG/FactorGraphs/FactorGraphs.jl

@@ -455,3 +455,28 @@ function findShortestPathDijkstra(  dfg::GraphsDFG,
     return dijkpath
 end
 
+export bfs_tree
+export dfs_tree
+export traverseGraphTopologicalSort
+
+function Graphs.bfs_tree(fg::GraphsDFG, s::Symbol)
+    return bfs_tree(fg.g, fg.g.labels[s])
+end
+
+function Graphs.dfs_tree(fg::GraphsDFG, s::Symbol)
+    return dfs_tree(fg.g, fg.g.labels[s])
+end
+
+"""
+    $SIGNATURES
+
+Return a topological sort of a factor graph as a vector of vertex labels in topological order.
+Starting from s::Symbol  
+"""
+function traverseGraphTopologicalSort(fg::GraphsDFG, s::Symbol, fs_tree=bfs_tree)
+    tree = fs_tree(fg, s)
+    list = topological_sort_by_dfs(tree)
+    symlist = map(s->fg.g.labels[s], list)
+    return symlist
+end
+