JuliaRobotics · dehann · Feb 2, 2023 · Dec 16, 2022 · Dec 16, 2022 · Dec 26, 2022
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -44,8 +44,8 @@ jobs:
           fail_ci_if_error: false
         if: ${{ matrix.version != 'nightly' }}
 
-  upstream-dev:
-    name: Upstream Dev
+  upstream-dev-functional:
+    name: Upstr Dev Functional
     runs-on: ubuntu-latest
     env: 
       JULIA_PKG_SERVER: ""
@@ -55,10 +55,50 @@ jobs:
         arch: 
           - x64
         version:
-          - '1.8'
           - '~1.9.0-0'
         group:
           - 'basic_functional_group'
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - run: |
+          git config --global user.name Tester
+          git config --global user.email [email protected]
+      - name: Upst Dev Functional
+        env:
+          IIF_TEST_GROUP: ${{ matrix.group }}
+        run: |
+          julia --project=@. --check-bounds=yes -e 'using Pkg; Pkg.add(PackageSpec(name="ApproxManifoldProducts",rev="master"));'
+          julia --project=@. --check-bounds=yes -e 'using Pkg; Pkg.add(PackageSpec(name="DistributedFactorGraphs",rev="master"));' 
+          julia --project=@. --check-bounds=yes -e 'using Pkg; Pkg.test("IncrementalInference"; coverage=false)'
+        shell: bash
+
+  upstream-dev-cases:
+    name: Upstr Dev Test Cases
+    runs-on: ubuntu-latest
+    env: 
+      JULIA_PKG_SERVER: ""
+    strategy:
+      fail-fast: false
+      matrix:
+        arch: 
+          - x64
+        version:
+          - '1.8'
+        group:
           - 'test_cases_group'
     steps:
       - uses: actions/checkout@v2
@@ -79,7 +119,7 @@ jobs:
       - run: |
           git config --global user.name Tester
           git config --global user.email [email protected]
-      - name: Upstream Dev
+      - name: Upstr Dev Cases
         env:
           IIF_TEST_GROUP: ${{ matrix.group }}
         run: |
@@ -89,7 +129,7 @@ jobs:
         shell: bash
 
   test-debug-group:
-    needs: [ upstream-dev ]
+    needs: [ upstream-dev-functional ]
     name: JL${{ matrix.version }} - ${{ matrix.group }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     env:

diff --git a/NEWS.md b/NEWS.md
@@ -11,13 +11,26 @@ 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 v0.32
+
+- Major internal refactoring of `CommonConvWrapper` to avoid abstract field types, and better standardization; towards cleanup of internal multihypo handling and naming conventions.
+- Internal refactoring removing several legacy fields from `CalcFactor`.
+- All factors now require a `getManifold` definition.
+- Now have `CalcFactor.manifold` to reduce new allocation load inside hot-loop for solving.
+- Fixed tesing issues in `testSpecialEuclidean2Mani.jl`.
+- Refactored, consolidated, and added more in-place operations in surrounding `ccw.measurement`.
+- Refactor `CommonConvWrapper` to a not non-mutable struct, with several cleanups and some updated compat requirements.
+- Refactor interal hard type `HypoRecipe`.
+- Add `MetaPrior` for adding meta data but not influencing the numerical solution.
+
 # Changes in v0.31
 - `FactorMetaData` is deprecated and replaced by `CalcFactor`.
 - Updated `Base.deepcopy_internal` fix for use with Julia 1.8.1, see #1629.
 - Added a few missing exports incl. `getTags`, `_update!, see #1626 #1628.
 - Refactoring to remove `FactorMetadata` (#1611) and `ConvPerThread` (#1615, #1625) objects, which is consolidated into `CalcFactor` and `CommonConvWrapper`.
 - Added JuliaFormatter, see #1620.
 - Add `SnoopPrecompile.jl` on a few basic solve features to start, see #1631.
+- Support n-ary parametric solving such as OAS factors.
 
 # Changes in v0.30
 

diff --git a/Project.toml b/Project.toml
@@ -2,7 +2,7 @@ name = "IncrementalInference"
 uuid = "904591bb-b899-562f-9e6f-b8df64c7d480"
 keywords = ["MM-iSAMv2", "Bayes tree", "junction tree", "Bayes network", "variable elimination", "graphical models", "SLAM", "inference", "sum-product", "belief-propagation"]
 desc = "Implements the Multimodal-iSAMv2 algorithm."
-version = "0.31.0"
+version = "0.32.2"
 
 [deps]
 ApproxManifoldProducts = "9bbbb610-88a1-53cd-9763-118ce10c1f89"
@@ -46,11 +46,11 @@ TimeZones = "f269a46b-ccf7-5d73-abea-4c690281aa53"
 UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [compat]
-ApproxManifoldProducts = "0.6"
+ApproxManifoldProducts = "0.6.3"
 BSON = "0.2, 0.3"
 Combinatorics = "1.0"
 DataStructures = "0.16, 0.17, 0.18"
-DistributedFactorGraphs = "0.18.4"
+DistributedFactorGraphs = "0.19"
 Distributions = "0.24, 0.25"
 DocStringExtensions = "0.8, 0.9"
 FileIO = "1"

diff --git a/README.md b/README.md
@@ -9,8 +9,8 @@
 
 [iif-deps-img]: https://juliahub.com/docs/IncrementalInference/deps.svg
 [iif-deps-jlh]: https://juliahub.com/ui/Packages/IncrementalInference/NrVw2??page=2
-[doi-img]: https://zenodo.org/badge/55802838.svg
-[doi-url]: https://zenodo.org/badge/latestdoi/55802838
+[doi-img]: https://zenodo.org/badge/DOI/10.5281/zenodo.7498643.svg
+[doi-url]: https://doi.org/10.5281/zenodo.7498643
 
 <!-- replicated in Caesar.jl README -->
 [iif-ci-dev-img]: https://github.com/JuliaRobotics/IncrementalInference.jl/actions/workflows/ci.yml/badge.svg

diff --git a/attic/CliqueStateMachine_fetch.jl b/attic/CliqueStateMachine_fetch.jl
@@ -104,7 +104,7 @@ function blockUntilChildrenHaveStatus_StateMachine(csmc::CliqStateMachineContain
 
       if st in [:null;]
         infocsm(csmc, "4e, blockUntilChildrenHaveStatus_StateMachine, waiting cliq=$(cid), child status=$(st).")
-        wait(getSolveCondition(csmc.tree.cliques[cid]))
+        wait(getSolveCondition(getClique(csmc.tree,cid)))
         notsolved = true
         break
       end

diff --git a/attic/examples/BayesTreeIllustration.jl b/attic/examples/BayesTreeIllustration.jl
@@ -46,7 +46,7 @@ tree = emptyBayesTree()
 buildTree!(tree, fge, p)
 
 # Find potential functions for each clique
-cliq = tree.cliques[1] # start at the root
+cliq = getClique(tree,1) # start at the root
 buildCliquePotentials(fg, tree, cliq);
 
 drawTree(tree, show=true)
@@ -60,7 +60,7 @@ drawTree(tree, show=true)
 
 ## can also show the Clique Association matrix by first importing Cairo, Fontconfig, Gadfly
 
-cliq = tree.cliques[1]
+cliq = getClique(tree,1)
 cliq = getClique(tree, :x0) # where is :x0 a frontal variable
 spyCliqMat(cliq)
 

diff --git a/attic/examples/MultiHypo2Door.jl b/attic/examples/MultiHypo2Door.jl
@@ -113,8 +113,8 @@ plotKDE([upmsgs[:x0]; upmsgs[:l1]; upmsgs[:x1]], c=["red";"green";"blue"])
 
 ## swap iteration order
 #TODO guess order from bellow
-# getCliqueData(tree.cliques[2]).itervarIDs = [5;7;3;1]
-getCliqueData(tree.cliques[2]).itervarIDs = [:x0, :x1, :l0, :l1]
+# getCliqueData(getClique(tree,2)).itervarIDs = [5;7;3;1]
+getCliqueData(getClique(tree,2)).itervarIDs = [:x0, :x1, :l0, :l1]
 
 solveTree!(fg, tree)
 

diff --git a/attic/examples/MultiHypo3Door.jl b/attic/examples/MultiHypo3Door.jl
@@ -104,8 +104,8 @@ spyCliqMat(tree, :x2)
 ## swap iteration order
 
 #TODO
-# getCliqueData(tree.cliques[2]).itervarIDs = [9;7;1;3;5]
-getCliqueData(tree.cliques[1]).itervarIDs = [:x1, :x0, :l2, :l1, :l0]
+# getCliqueData(getClique(tree,2)).itervarIDs = [9;7;1;3;5]
+getCliqueData(getClique(tree,1)).itervarIDs = [:x1, :x0, :l2, :l1, :l0]
 
 solveTree!(fg, tree)
 
@@ -245,7 +245,7 @@ tree = buildTreeReset!(fg, drawpdf=true, show=true)
 spyCliqMat(tree, :l0)
 spyCliqMat(tree, :x2)
 
-cliq = tree.cliques[2]
+cliq = getClique(tree,2)
 
 ## quick debug
 

diff --git a/src/AnalysisTools.jl b/src/AnalysisTools.jl
@@ -147,7 +147,7 @@ function getTreeCost_02(tree::AbstractBayesTree; alpha::Float64 = 1.0)
   # Frontal and number of children.
   ARR = Tuple{Symbol, Int}[]
   for (cliqid, vex) in tree.cliques
-    afrtl = getCliqFrontalVarIds(tree.cliques[cliqid])[1]
+    afrtl = getCliqFrontalVarIds(getClique(tree, cliqid))[1]
     numch = length(getChildren(tree, afrtl))
     push!(ARR, (afrtl, numch))
   end

diff --git a/src/Deprecated.jl b/src/Deprecated.jl
@@ -27,79 +27,47 @@ function convert(::Type{<:Prior}, prior::Dict{String, Any})
   return Prior(z)
 end
 
-##==============================================================================
-## Deprecate code below before v0.32
-##==============================================================================
-
-# NOTE Temporary fix? Overwrite deepcopy on MetaBayesTree to strip out copying the channels. 
-# see https://github.com/JuliaRobotics/IncrementalInference.jl/issues/1530
-# possible fix in https://github.com/JuliaLang/julia/pull/46406
-import Base.deepcopy_internal
-VERSION < v"1.8.1" && function Base.deepcopy_internal(bt::MetaBayesTree, stackdict::IdDict)
-  if haskey(stackdict, bt)
-    return stackdict[bt]
+# more legacy, dont delete yet
+function Base.getproperty(ccw::CommonConvWrapper, f::Symbol)
+  if f == :threadmodel
+    @warn "CommonConvWrapper.threadmodel is obsolete" maxlog=3
+    return SingleThreaded
+  elseif f == :params
+    @warn "CommonConvWrapper.params is deprecated, use .varValsAll instead" maxlog=3
+    return ccw.varValsAll
+  elseif f == :vartypes
+    @warn "CommonConvWrapper.vartypes is deprecated, use typeof.(getVariableType.(ccw.fullvariables) instead" maxlog=3
+    return typeof.(getVariableType.(ccw.fullvariables))
+  else
+    return getfield(ccw, f)
   end
-
-  mg = bt.bt
-
-  graph = deepcopy_internal(mg.graph, stackdict)
-  vprops = deepcopy_internal(mg.vprops, stackdict)
-  T = eltype(mg)
-  # dropping all edge data
-  eprops = Dict{MetaGraphs.SimpleEdge{T}, MetaGraphs.PropDict}()
-  gprops = deepcopy_internal(mg.gprops, stackdict)
-  weightfield = deepcopy_internal(mg.weightfield, stackdict)
-  defaultweight = deepcopy_internal(mg.defaultweight, stackdict)
-  metaindex = deepcopy_internal(mg.metaindex, stackdict)
-  indices = deepcopy_internal(mg.indices, stackdict)
-
-  mg_cpy = MetaDiGraph(
-    graph,
-    vprops,
-    eprops,
-    gprops,
-    weightfield,
-    defaultweight,
-    metaindex,
-    indices,
-  )
-
-  bt_cpy = MetaBayesTree(
-    mg_cpy,
-    bt.btid,
-    deepcopy_internal(bt.frontals, stackdict),
-    deepcopy_internal(bt.eliminationOrder, stackdict),
-    bt.buildTime,
-  )
-
-  stackdict[bt] = bt_cpy
-  return bt_cpy
 end
 
 
-# """
-#     $SIGNATURES
-# Get `.factormetadata` for each CPT in CCW for a specific factor in `fg`. 
-# """
-# _getFMdThread(ccw::CommonConvWrapper, 
-#               thrid::Int=Threads.threadid()) = ccw.cpt[thrid].factormetadata
-# #
-# _getFMdThread(fc::Union{GenericFunctionNodeData,DFGFactor}, 
-#               thrid::Int=Threads.threadid()) = _getFMdThread(_getCCW(fc), thrid)
-# #
-# _getFMdThread(dfg::AbstractDFG,
-#               lbl::Symbol,
-#               thrid::Int=Threads.threadid()) = _getFMdThread(_getCCW(dfg, lbl), thrid)
-# #
-
 ##==============================================================================
-## Deprecate code below before v0.31
+## Deprecate code below before v0.33
 ##==============================================================================
 
+# export setThreadModel!
+  # introduced for approximate convolution operations
+export SingleThreaded, MultiThreaded
+
+function setThreadModel!(fgl::AbstractDFG; model = IIF.SingleThreaded)
+  #
+  @error("Obsolete, ThreadModel types are no longer in use.")
+  # for (key, id) in fgl.fIDs
+  #   _getCCW(fgl, key).threadmodel = model
+  # end
+  return nothing
+end
+
+# should have been deleted in v0.31 but no harm in keeping this one a bit longer
 @deprecate initManual!(w...; kw...) initVariable!(w...; kw...)
 
+
+
 ##==============================================================================
-## Old parametric kept for comparason until code stabilize
+## Old parametric kept for comparason until code is stabilized
 ##==============================================================================
 
 """

diff --git a/src/ExportAPI.jl b/src/ExportAPI.jl
@@ -239,11 +239,6 @@ export CSMHistory,
   getCliqVarInitOrderUp,
   getCliqNumAssocFactorsPerVar,
 
-  # introduced for approximate convolution operations
-  setThreadModel!,
-  SingleThreaded,
-  MultiThreaded,
-
   # user functions
   predictbelief,
   propagateBelief,
@@ -361,4 +356,6 @@ export appendSeparatorToClique!
 export buildTreeFromOrdering! # TODO make internal and deprecate external use to only `buildTreeReset!``
 export makeSolverData!
 
+export MetaPrior
+
 #
diff --git a/src/Factors/Circular.jl b/src/Factors/Circular.jl
@@ -23,7 +23,7 @@ DFG.getManifold(::CircularCircular) = RealCircleGroup()
 
 function (cf::CalcFactor{<:CircularCircular})(X, p, q)
   #
-  M = getManifold(cf.factor)
+  M = cf.manifold # getManifold(cf.factor)
   return distanceTangent2Point(M, X, p, q)
 end
 
@@ -58,11 +58,11 @@ function getSample(cf::CalcFactor{<:PriorCircular})
   # FIXME workaround for issue #TBD with manifolds CircularGroup, 
   # JuliaManifolds/Manifolds.jl#415
   # no method similar(::Float64, ::Type{Float64})
-  return samplePoint(getManifold(cf.factor), cf.factor.Z, [0.0])
+  return samplePoint(cf.manifold, cf.factor.Z, [0.0])
 end
 
 function (cf::CalcFactor{<:PriorCircular})(m, p)
-  M = getManifold(cf.factor)
+  M = cf.manifold # getManifold(cf.factor)
   Xc = vee(M, p, log(M, p, m))
   return Xc
 end

diff --git a/src/Factors/GenericFunctions.jl b/src/Factors/GenericFunctions.jl
@@ -92,7 +92,7 @@ end
 # function (cf::CalcFactor{<:ManifoldFactor{<:AbstractDecoratorManifold}})(Xc, p, q)
 function (cf::CalcFactor{<:ManifoldFactor})(Xc, p, q)
   # function (cf::ManifoldFactor)(X, p, q)
-  M = cf.factor.M
+  M = cf.manifold # .factor.M
   # M = cf.M
   X = hat(M, p, Xc)
   return distanceTangent2Point(M, X, p, q)
@@ -132,7 +132,7 @@ DFG.getManifold(f::ManifoldPrior) = f.M
 function getSample(cf::CalcFactor{<:ManifoldPrior})
   Z = cf.factor.Z
   p = cf.factor.p
-  M = cf.factor.M
+  M = cf.manifold # .factor.M
   basis = cf.factor.basis
   retract_method = cf.factor.retract_method
   point = samplePoint(M, Z, p, basis, retract_method)
@@ -145,7 +145,7 @@ end
 # Xc = [SVector{dim}(rand(Z)) for _ in 1:N]
 
 function (cf::CalcFactor{<:ManifoldPrior})(m, p)
-  M = cf.factor.M
+  M = cf.manifold # .factor.M
   # return log(M, p, m)
   return vee(M, p, log(M, p, m))
   # return distancePrior(M, m, p)
@@ -234,7 +234,7 @@ DFG.getManifold(f::ManifoldPriorPartial) = f.M
 
 function getSample(cf::CalcFactor{<:ManifoldPriorPartial})
   Z = cf.factor.Z
-  M = getManifold(cf.factor)
+  M = cf.manifold # getManifold(cf.factor)
   partial = collect(cf.factor.partial)
 
   return (samplePointPartial(M, Z, partial),)