Merging 0.30 to upstream

.github/workflows/CompatHelper.yml

@@ -1,26 +1,35 @@
 name: CompatHelper
-
 on:
   schedule:
-    - cron: '20 00 * * *'
-  issues:
-    types: [opened]
-
+    - 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
-        with:
-          version: ${{ matrix.julia-version }}
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+      - 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/TagBot.yml

@@ -1,8 +1,6 @@
 name: TagBot
 
 on:
-  schedule:
-    - cron: '20 00 * * *'
   issues:
     types: [closed,]
 

.github/workflows/ci.yml

@@ -6,9 +6,10 @@ on:
       - master
       - develop
       - release**
+  workflow_dispatch:
 jobs:
   test-stable:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    name: JL${{ matrix.version }} - ${{ matrix.arch }} - ${{ matrix.group }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     env:
       JULIA_PKG_SERVER: ""
@@ -17,53 +18,48 @@ jobs:
       matrix:
         version:
           - '1.6'
-          - '1.7'
+          - '1.8'
         os:
           - ubuntu-latest
         arch:
           - x64
+        group:
+          - 'basic_functional_group'
+          - 'test_cases_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 }}-
-      - uses: julia-actions/julia-buildpkg@latest
-      - run: |
-          git config --global user.name Tester
-          git config --global user.email te@st.er
-      - uses: julia-actions/julia-runtest@latest
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
         continue-on-error: ${{ matrix.version == 'nightly' }}
+        env:
+          IIF_TEST_GROUP: ${{ matrix.group }}
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v2
         with:
-          file: lcov.info
+          files: lcov.info
+          fail_ci_if_error: false
+        if: ${{ matrix.version != 'nightly' }}
 
-  # hacky way to remove code coverage from nightly
-  test-nightly-nocov:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
-    runs-on: ${{ matrix.os }}
-    env:
+  upstream-dev:
+    name: Upstream Dev
+    runs-on: ubuntu-latest
+    env: 
       JULIA_PKG_SERVER: ""
     strategy:
       fail-fast: false
       matrix:
-        version:
-          - 'nightly'
-        os:
-          - ubuntu-latest
-        arch:
+        arch: 
           - x64
+        version:
+          - '1.8'
+        group:
+          - 'basic_functional_group'
+          - 'test_cases_group'
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
@@ -80,45 +76,44 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@latest
       - run: |
           git config --global user.name Tester
           git config --global user.email te@st.er
-      - uses: julia-actions/julia-runtest@latest
-        continue-on-error: ${{ matrix.version == 'nightly' }}
+      - name: Upstream Dev
+        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:
-    #if: github.ref != 'refs/heads/release**'
-    name: Upstream Dev
-    runs-on: ubuntu-latest
-    env: 
+  test-debug-group:
+    needs: [ upstream-dev ]
+    name: JL${{ matrix.version }} - ${{ matrix.group }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    env:
       JULIA_PKG_SERVER: ""
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+        version:
+          - '1.8'
+        arch:
+          - x64
+        group:
+          - 'tmp_debug_group'
+    continue-on-error: true
     steps:
       - uses: actions/checkout@v2
-
       - uses: julia-actions/setup-julia@v1
         with:
-          version: 1.7
-          arch: x64
-
-      - uses: actions/cache@v1
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@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 te@st.er
-
-      - name: Upstream Dev
-        run: |
-          julia --project=@. --check-bounds=yes -e 'using Pkg; Pkg.add(PackageSpec(name="DistributedFactorGraphs",rev="master"));' 
-          julia --project=@. --check-bounds=yes -e 'using Pkg; Pkg.add(PackageSpec(name="ApproxManifoldProducts",rev="master"));'
-          julia --project=@. --check-bounds=yes -e 'using Pkg; Pkg.test("IncrementalInference"; coverage=false)'
-        shell: bash
+          IIF_TEST_GROUP: ${{ matrix.group }}

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2019
+Copyright (c) 2019 - 2022
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NEWS.md

@@ -9,28 +9,52 @@ Also see automated TagBot Release note, e.g.:
 Alternatively, either use the Github Blame, or the Github `/compare/v0.18.0...v0.19.0` API, e.g.:
 - https://github.com/JuliaRobotics/IncrementalInference.jl/compare/v0.18.0...v0.19.0
 
-The list below highlights major breaking changes, and please note that significant efforts are made to properly deprecate old code/APIs 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).
+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
 
-# Major Changes in v0.27
+# Changes in v0.30
+
+- `ArrayPartition` should be used instead of `ProductRepr`, see issue #1537.
+- Remove old deprecated option keywords in `addVariable` and `addFactor`.
+- Improve `IIF.solveGraphParametric`.
+- Introduce `IIF.autoinitParametric!`.
+- Upgrade `initAll!(dfg, :parametric)`.
+- Refactor many files to subfolders `src/services` or `src/entities`.
+
+# Changes in v0.29
+
+- Upgrade to Manifolds.jl v0.8
+- Deprecate `initManual!`, instead use `initVariable!`.
+# Changes in v0.28
+
+- `HeatmapGridDensity` now only supports `ManifoldKernelDensity` functions.
+- `PackedHeatmapGridDensity` has an expanded fields to support future stash and cache serialization strategies.
+- Internal `parchDistribution` functions have been added towards future stashed serialization strategies.
+- Internal `_update!` function supports updating of the `HeatmapGridDensity` distribution.
+- Unpacking of `PackedManifoldKernelDensity` is more versatile with improved `.partial` and `.bw` options.
+- Bugfix on `multihypo=` which now includes `nullSurplus` on sibling relative factors to a variable with a `multihypo` factor, #1518.
+
+# Changes in v0.27
 
 - InMemDFGType is deprecated in favor of LocalDFG (exported from DistributedFactorGraphs).
 - Factor serialization is now top level JSON only #1476.
 - Serialization of distributions are now JSON only #1468, #1472, #1473 (removed custom string legacy).
 - Fix chicken and egg problem on unpackFactor, change `convert` to `reconstFactorData`, #1424.
-- Add factor `preambleCache(dfg, vlbls, usrfnc)`, #1462, #1466.  Doesn't work for parametric yet (#1480).
+- Add factor `preambleCache(dfg, vecVars, usrfnc)`, #1462, #1466.  Doesn't work for parametric yet (#1480).
 - Add `CalcFactor.cache` using preamble, #1481.  Not thread safe yet.
 - Standardize local graph naming to `LocalDFG`, #1479.
 - Refactor getDimension and sampling, #1463.
 - Language upgrades on `qr` for Julia 1.7, #1464.
 - Various other fixes and upgrades, https://github.com/JuliaRobotics/IncrementalInference.jl/milestone/111?closed=1
+- Add distribution serialization for Rayleigh.
+- Add `Position{N}` and `Position1`..`Position4` as new standard and aliases for `ContinuousScalar`, `ContinuousEuclid{N}`.
 
-# Major changes in v0.26
+# Changes in v0.26
 
 - Standarding (non-binding) easy factor dipatch cases so measurement field is under `.Z` (#1441).
 - `CalcFactor._allowThreads` can now be used as workaround for `Threads` yield blocking issue during first run (#1451).
 - Canonical graph generator API change to `generateGraph_ABC` (#1454).
 
-# Major changes in v0.25
+# Changes in v0.25
 
 - Changed API to `testFactorResidualBinary(fct, meas::Tuple, (T_i, param_i),...)` to grow beyond binary.
 - PPE methods used keyword `method::AbstractPointParametricType` which is now replaced with the keyword `ppeType`.
@@ -46,23 +70,23 @@ The list below highlights major breaking changes, and please note that significa
 - `solveTree!` / `solveGraph!` now returns just one value `tree<:AbstractBayesTree`.  Previous version returned three values, `tree, smt, hist` (#1379).
 - **Note for v0.25.5** Serialization of newly introduced type `PackedHeatmapGridDensity` changed from v0.25.4, unlikely have yet been used publically, therefore emphasizing fastest possible standardization in this case (even though this particular event does not strictly follow semver).  General usage and operation is effectively unchanged,see #1435.
 
-# Major changes in v0.24
+# Changes in v0.24
 
 - Update compat for ManifoldsBase.jl v0.11 with `AbstractManifold`.
 - Transition to only `getManifold` (instead of `getManifolds`), thereby moving towards exclusively using Manifolds.jl, see #1234.
 - Deprecate use of `getFactorMean`, use `IIF.getParametricMeasurement` instead.
 - Upstreamed `is/set Marginalized` to DFG (#1269).
-# Major changes in v0.23
+# Changes in v0.23
 
 - New `@defVariable` only uses `ManifoldsBase.Manifold` as base abstraction for variable types.
-# Major changes in v0.22
+# Changes in v0.22
 
 - Work in progress toward `ManifoldsBase.Manifold` as base abstraction for variable types.
-# Major changes in v0.21
+# Changes in v0.21
 
 - `CalcResidual` no longer takes a `residual` as input parameter and should return `residual`, see #467 .
 
-# Major changes in v0.20
+# Changes in v0.20
 
 - The user factor API call strategy has been simplified via `CalcResidual`, see #467 for details.
 - User factor API for `getSample` and `.specialsampler` has been standardized via `CalcResidual` (#927) -- for ongoing work please follow #1099 and #1094 and #1069.