Merge branch 'master' into 23Q2/test/restore3alttests

Author: dehann

.github/workflows/ci.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - master
-      - develop
       - release**
   workflow_dispatch:
 jobs:
@@ -55,7 +54,7 @@ jobs:
         arch: 
           - x64
         version:
-          - '1.9'
+          - '~1.10.0-0'
         group:
           - 'basic_functional_group'
     steps:
@@ -97,7 +96,7 @@ jobs:
         arch: 
           - x64
         version:
-          - '1.9'
+          - '~1.10.0-0'
         group:
           - 'test_cases_group'
     steps:

NEWS.md

@@ -11,6 +11,14 @@ Alternatively, either use the Github Blame, or the Github `/compare/v0.18.0...v0
 
 The list below highlights breaking changes according to normal semver workflow -- i.e. breaking changes go through at least one deprecatation (via warnings) on the dominant number in the version number.  E.g. v0.18 -> v0.19 (warnings) -> v0.20 (breaking).  Note that ongoing efforts are made to properly deprecate old code/APIs
 
+# Changes in v0.34
+
+- Start transition to Manopt.jl via Riemannian Levenberg Marquart.
+- Deprecate `AbstractRelativeRoots`.
+
+# Changes in v0.33
+
+- Upgrades for DFG using StructTypes.jl (serialization).
 # Changes in v0.32
 
 - Major internal refactoring of `CommonConvWrapper` to avoid abstract field types, and better standardization; towards cleanup of internal multihypo handling and naming conventions.

Project.toml

@@ -8,6 +8,7 @@ version = "0.34.0"
 ApproxManifoldProducts = "9bbbb610-88a1-53cd-9763-118ce10c1f89"
 BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -17,6 +18,7 @@ DistributedFactorGraphs = "b5cc3c7e-6572-11e9-2517-99fb8daf2f04"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41"
 FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000"
 FunctionalStateMachine = "3e9e306e-7e3c-11e9-12d2-8f8f67a2f951"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
@@ -26,9 +28,8 @@ Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 ManifoldDiff = "af67fdf4-a580-4b9f-bbec-742ef357defd"
 Manifolds = "1cead3c2-87b3-11e9-0ccd-23c62b72b94e"
 ManifoldsBase = "3362f125-f0bb-47a3-aa74-596ffd7ef2fb"
+Manopt = "0fc0a36d-df90-57f3-8f93-d78a9fc72bb5"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
-NLSolversBase = "d41bc354-129a-5804-8e4c-c37616107c6c"
-NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
@@ -38,6 +39,7 @@ RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+SparseDiffTools = "47a9eef4-7e08-11e9-0b38-333d64bd3804"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
@@ -47,32 +49,47 @@ TensorCast = "02d47bb6-7ce6-556a-be16-bb1710789e2b"
 TimeZones = "f269a46b-ccf7-5d73-abea-4c690281aa53"
 UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
+[weakdeps]
+DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
+Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004"
+InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
+
+[extensions]
+DiffEqFactorExt = "DifferentialEquations"
+GadflyExt = "Gadfly"
+InteractiveUtilsExt = "InteractiveUtils"
+InterpolationsExt = "Interpolations"
+
 [compat]
 ApproxManifoldProducts = "0.7"
 BSON = "0.2, 0.3"
+BlockArrays = "0.16"
 Combinatorics = "1.0"
 DataStructures = "0.16, 0.17, 0.18"
-DistributedFactorGraphs = "0.21"
+DelimitedFiles = "1"
+DistributedFactorGraphs = "0.21, 0.22"
 Distributions = "0.24, 0.25"
 DocStringExtensions = "0.8, 0.9"
 FileIO = "1"
+FiniteDiff = "2"
 FiniteDifferences = "0.12"
 FunctionalStateMachine = "0.2.9"
 JSON3 = "1"
 KernelDensityEstimate = "0.5.6"
 ManifoldDiff = "0.3"
 Manifolds = "0.8.15"
 ManifoldsBase = "0.13.12, 0.14"
+Manopt = "0.4.27"
 MetaGraphs = "0.7"
-NLSolversBase = "7.6"
-NLsolve = "3, 4"
 Optim = "1"
 OrderedCollections = "1"
 PrecompileTools = "1"
 ProgressMeter = "1"
 RecursiveArrayTools = "2.31.1"
 Reexport = "1"
 Requires = "1"
+SparseDiffTools = "2"
 StaticArrays = "1"
 StatsBase = "0.32, 0.33, 0.34"
 StructTypes = "1"
@@ -81,15 +98,14 @@ TimeZones = "1.3.1"
 julia = "1.8"
 
 [extras]
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
-InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
-Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
+LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
 Manopt = "0fc0a36d-df90-57f3-8f93-d78a9fc72bb5"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Rotations = "6038ab10-8711-5258-84ad-4b1120ba62dc"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = ["DifferentialEquations", "Flux", "Graphs", "Manopt", "InteractiveUtils", "Interpolations", "Pkg", "Rotations", "Test"]
+test = ["DifferentialEquations", "Flux", "Graphs", "Manopt", "InteractiveUtils", "Interpolations", "LineSearches", "Pkg", "Rotations", "Test", "Zygote"]

src/ODE/DERelative.jl ext/DiffEqFactorExt.jlsrc/ODE/DERelative.jl renamed to ext/DiffEqFactorExt.jl

@@ -1,41 +1,20 @@
+module DiffEqFactorExt
 
-@info "IncrementalInference.jl is loading tools related to DifferentialEquations.jl"
+@info "IncrementalInference.jl is loading extensions related to DifferentialEquations.jl"
 
-using .DifferentialEquations
+using DifferentialEquations
+import DifferentialEquations: solve
 
-import .DifferentialEquations: solve
+using Dates
 
-import IncrementalInference: getSample, getManifold
+using IncrementalInference
+import IncrementalInference: getSample, getManifold, DERelative
 
-export DERelative
+using DocStringExtensions
 
-"""
-    $TYPEDEF
+export DERelative
 
-Build a full ODE solution into a relative factor to condense possible sensor data into a relative transformation,
-but keeping the parameter estimation process fluid.  Assumes first and second variable in order 
-are of same dimension and compatible manifolds, such that ODE runs from Xi to Xi+1 on all
-dimensions.  Internal state vector can be decoupled onto different domain as needed.
 
-Notes
-- Based on DifferentialEquations.jl
-- `getSample` step does the `solve(ODEProblem)` step.
-- `tspan` is taken from variables only once at object construction -- i.e. won't detect changed timestamps.
-- Regular factor evaluation is done as full dimension `AbstractRelativeRoots`, and is basic linear difference.
-
-DevNotes
-- FIXME see 1025, `multihypo=` will not yet work. 
-- FIXME Lots of consolidation and standardization to do, see RoME.jl #244 regarding Manifolds.jl.
-- TODO does not yet handle case where a factor spans across two timezones.
-"""
-struct DERelative{T <: InferenceVariable, P, D} <: AbstractRelativeRoots
-  domain::Type{T}
-  forwardProblem::P
-  backwardProblem::P
-  # second element of this data tuple is additional variables that will be passed down as a parameter
-  data::D
-  specialSampler::Function
-end
 
 getManifold(de::DERelative{T}) where {T} = getManifold(de.domain)
 
@@ -132,6 +111,8 @@ function _solveFactorODE!(measArr, prob, u0pts, Xtra...)
   return sol
 end
 
+getSample(cf::CalcFactor{<:DERelative}) = error("getSample(::CalcFactor{<:DERelative}) not implemented yet")
+
 # FIXME see #1025, `multihypo=` will not work properly yet
 function sampleFactor(cf::CalcFactor{<:DERelative}, N::Int = 1)
   #
@@ -220,3 +201,5 @@ end
 # ode.problem.f.f
 
 #
+
+end # module

src/EmbeddedPlottingUtils.jl ext/GadflyExt.jlsrc/EmbeddedPlottingUtils.jl renamed to ext/GadflyExt.jl

@@ -1,9 +1,15 @@
+module GadflyExt
 
-@info "Defining spyCliqMat(..) for visualizing association matrix of a clique in the Bayes (Junction) tree"
+@info "IncrementalInference.jl is loading plotting extensions relating to Gadfly.jl"
 
-exportimg(pl) = Gadfly.PNG(pl)
+using Gadfly
+using DocStringExtensions
+using IncrementalInference: AbstractBayesTree, TreeClique, getCliqueData, getCliqAssocMat, getCliqMat, getLabel, getCliqMsgMat, getClique
+import IncrementalInference: exportimg, spyCliqMat
+
+export exportimg, spyCliqMat
 
-export spyCliqMat
+exportimg(pl) = Gadfly.PNG(pl)
 
 """
     $SIGNATURES
@@ -59,3 +65,6 @@ function spyCliqMat(
 )
   return spyCliqMat(getClique(bt, lbl); showmsg = showmsg, suppressprint = suppressprint)
 end
+
+
+end

src/services/HeatmapSampler.jl ext/HeatmapSampler.jlsrc/services/HeatmapSampler.jl renamed to ext/HeatmapSampler.jl

@@ -1,15 +1,5 @@
 # heatmap sampler (experimental)
 
-@info "IncrementalInference.jl is loading tools related to Interpolations.jl."
-
-using .Interpolations
-
-# only export on Requires.jl
-export HeatmapGridDensity, PackedHeatmapGridDensity
-export LevelSetGridNormal, PackedLevelSetGridNormal
-
-export sampleHeatmap
-
 ##
 
 getManifold(hgd::HeatmapGridDensity) = getManifold(hgd.densityFnc)

src/RequireInteractiveUtils.jl ext/InteractiveUtilsExt.jlsrc/RequireInteractiveUtils.jl renamed to ext/InteractiveUtilsExt.jl

@@ -1,7 +1,12 @@
+module InteractiveUtilsExt
 
-@info "IncrementalInference.jl is loading tools related to InteractiveUtils.jl."
+@info "IncrementalInference.jl is loading extension related to InteractiveUtils.jl."
 
-# this requires InteractiveUtils
+using InteractiveUtils
+using DocStringExtensions
+using IncrementalInference: InferenceVariable, AbstractPrior, AbstractRelativeMinimize, AbstractManifoldMinimize
+# using IncrementalInference: getCurrentWorkspaceFactors, getCurrentWorkspaceVariables, listTypeTree
+import IncrementalInference: getCurrentWorkspaceFactors, getCurrentWorkspaceVariables, listTypeTree
 
 export getCurrentWorkspaceFactors, getCurrentWorkspaceVariables
 export listTypeTree
@@ -14,7 +19,7 @@ Return all factors currently registered in the workspace.
 function getCurrentWorkspaceFactors()
   return [
     InteractiveUtils.subtypes(AbstractPrior)...,
-    InteractiveUtils.subtypes(AbstractRelativeRoots)...,
+    # InteractiveUtils.subtypes(AbstractRelativeRoots)...,
     InteractiveUtils.subtypes(AbstractRelativeMinimize)...,
   ]
 end
@@ -25,7 +30,7 @@ end
 Return all variables currently registered in the workspace.
 """
 function getCurrentWorkspaceVariables()
-  return InteractiveUtils.subtypes(IIF.InferenceVariable)
+  return InteractiveUtils.subtypes(InferenceVariable)
 end
 
 function _listTypeTree(mytype, printlevel::Int)
@@ -50,3 +55,5 @@ function listTypeTree(T)
   println(T)
   return _listTypeTree(T, 0)
 end
+
+end #module

ext/InterpolationsExt.jl

@@ -0,0 +1,25 @@
+module InterpolationsExt
+
+@info "IncrementalInference.jl is loading extensions related to Interpolations.jl."
+
+using Interpolations
+using Statistics
+using DocStringExtensions
+using TensorCast
+using Manifolds
+using ApproxManifoldProducts
+import ApproxManifoldProducts: sample
+const AMP = ApproxManifoldProducts
+
+import IncrementalInference: getManifold
+import IncrementalInference: HeatmapGridDensity, PackedHeatmapGridDensity
+import IncrementalInference: LevelSetGridNormal, PackedLevelSetGridNormal
+
+export HeatmapGridDensity, PackedHeatmapGridDensity
+export LevelSetGridNormal, PackedLevelSetGridNormal
+export sampleHeatmap
+
+
+include("HeatmapSampler.jl")
+
+end # module

ext/WeakDepsPrototypes.jl

@@ -0,0 +1,37 @@
+
+"""
+    $TYPEDEF
+
+Build a full ODE solution into a relative factor to condense possible sensor data into a relative transformation,
+but keeping the parameter estimation process fluid.  Assumes first and second variable in order 
+are of same dimension and compatible manifolds, such that ODE runs from Xi to Xi+1 on all
+dimensions.  Internal state vector can be decoupled onto different domain as needed.
+
+Notes
+- Based on DifferentialEquations.jl
+- `getSample` step does the `solve(ODEProblem)` step.
+- `tspan` is taken from variables only once at object construction -- i.e. won't detect changed timestamps.
+- Regular factor evaluation is done as full dimension `AbstractRelativeRoots`, and is basic linear difference.
+
+DevNotes
+- FIXME see 1025, `multihypo=` will not yet work. 
+- FIXME Lots of consolidation and standardization to do, see RoME.jl #244 regarding Manifolds.jl.
+- TODO does not yet handle case where a factor spans across two timezones.
+"""
+struct DERelative{T <: InferenceVariable, P, D} <: AbstractRelativeMinimize
+  domain::Type{T}
+  forwardProblem::P
+  backwardProblem::P
+  # second element of this data tuple is additional variables that will be passed down as a parameter
+  data::D
+  specialSampler::Function
+end
+
+# InteractiveUtils.jl
+function getCurrentWorkspaceFactors end
+function getCurrentWorkspaceVariables end
+function listTypeTree end
+
+# Gadfly.jl
+function exportimg end 
+function spyCliqMat end