Update CI, fix BE.size default and rm some deprecated code (#1117)

* Fix BE.size default and rm some deprecated code

* update CI

* update stale links

---------

Co-authored-by: Johannes Terblanche <Affie@users.noreply.github.com>

Author: Affie

.github/workflows/ci.yml

@@ -8,67 +8,59 @@ on:
     tags:
       - v**
   workflow_dispatch:
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
     runs-on: ${{ matrix.os }}
-    env:
-      JULIA_PKG_SERVER: ""
+    timeout-minutes: 60
+    permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
+      actions: write
+      contents: read
     strategy:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
-          - 'nightly'
+          - 'lts' # long term support
+          - '1'   # stable
+          # - 'pre' # pre-release
         os:
           - ubuntu-latest
         arch:
           - x64
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Setup Julia
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
 
       - name: Cache Artifacts
-        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/cache@v2
 
       - name: Julia Build Pkg
         uses: julia-actions/julia-buildpkg@latest
-      
-      - name: Git Test Credentials
-        run: |
-          git config --global user.name Tester
-          git config --global user.email te@st.er
-      
+
       - name: Run tests
         env:
           IIF_TEST: true
-          DO_CGDFG_TESTS: false
-          DFG_USE_CGDFG: false
-        uses: julia-actions/julia-runtest@latest
-        continue-on-error: ${{ matrix.version == 'nightly' }}
-      
+        uses: julia-actions/julia-runtest@latest      
       - name: Process Coverage
         uses: julia-actions/julia-processcoverage@v1
 
       - name: Code Coverage
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v4
         with:
-          file: lcov.info
+          files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
 
   docs:
     needs: test
@@ -80,9 +72,9 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Setup julia
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
-          version: '1.10'
+          version: 'lts'
           arch: x64
 
       - name: Build Docs

README.md

@@ -10,8 +10,8 @@ Click on badges to follow links:
 [dfg-ci-dev-url]: https://github.com/JuliaRobotics/DistributedFactorGraphs.jl/actions/workflows/ci.yml
 [dfg-ci-stb-img]: https://github.com/JuliaRobotics/DistributedFactorGraphs.jl/actions/workflows/ci.yml/badge.svg?branch=release%2Fv0.25
 [dfg-ci-stb-url]: https://github.com/JuliaRobotics/DistributedFactorGraphs.jl/actions/workflows/ci.yml
-[dfg-cov-img]: https://codecov.io/github/JuliaRobotics/DistributedFactorGraphs.jl/coverage.svg?branch=master
-[dfg-cov-url]: https://codecov.io/github/JuliaRobotics/DistributedFactorGraphs.jl?branch=master
+[dfg-cov-img]: https://codecov.io/github/JuliaRobotics/DistributedFactorGraphs.jl/coverage.svg?branch=develop
+[dfg-cov-url]: https://codecov.io/github/JuliaRobotics/DistributedFactorGraphs.jl?branch=develop
 [dfg-build-img]: https://github.com/JuliaRobotics/DistributedFactorGraphs.jl/actions/workflows/ci.yml/badge.svg
 [dfg-build-url]: https://github.com/JuliaRobotics/DistributedFactorGraphs.jl/actions/workflows/ci.yml
 
@@ -23,7 +23,7 @@ DistributedFactorGraphs.jl provides a flexible factor graph API for use in the [
 **Note** this package is still under initial development, and will adopt parts of the functionality currently contained in [IncrementalInference.jl](http://www.github.com/JuliaRobotics/IncrementalInference.jl).
 
 # Documentation
-Please see the [documentation](http://juliarobotics.github.io/DistributedFactorGraphs.jl/latest/) and the [unit tests](https://github.com/JuliaRobotics/DistributedFactorGraphs.jl/tree/master/test) for examples on using DistributedFactorGraphs.jl.
+Please see the [documentation](http://juliarobotics.github.io/DistributedFactorGraphs.jl/latest/) and the [unit tests](https://github.com/JuliaRobotics/DistributedFactorGraphs.jl/tree/develop/test) for examples on using DistributedFactorGraphs.jl.
 
 # Installation
 DistributedFactorGraphs can be installed from Julia packages using:

src/DataBlobs/entities/BlobEntry.jl

@@ -28,7 +28,7 @@ Base.@kwdef struct BlobEntry
     """ Context from which a BlobEntry=>Blob was first created. E.g. agent|graph|varlabel. """
     origin::String = ""
     """ number of bytes in blob as a string"""
-    size::Union{String, Nothing} = "" #TODO remove union, use "" as nothing
+    size::Union{String, Nothing} = "-1" #TODO remove union -> size::String = "-1"
     """ Additional information that can help a different user of the Blob. """
     description::String = ""
     """ MIME description describing the format of binary data in the `Blob`, e.g. 'image/png' or 'application/json; _type=CameraModel'. """

src/GraphsDFG/services/GraphsDFG.jl

@@ -197,7 +197,6 @@ function getVariables(
     tags::Vector{Symbol} = Symbol[],
     solvable::Int = 0,
     solvableFilter::Union{Nothing, Base.Fix2} = nothing,
-    detail = nothing,
 )
 
     # variables = map(v -> v.dfgNode, filter(n -> n.dfgNode isa VariableCompute, vertices(dfg.g)))

src/entities/DFGFactor.jl

@@ -158,7 +158,7 @@ function FactorDFG(
         nstime = string(nstime),
         fnctype,
         solvable,
-        data = base64encode(JSON3.write(factordata)),
+        data = JSON3.write(factordata),
         metadata = base64encode(JSON3.write(metadata)),
     )
 

src/services/AbstractDFG.jl

@@ -429,7 +429,6 @@ function getVariables(
     regexFilter::Union{Nothing, Regex} = nothing;
     tags::Vector{Symbol} = Symbol[],
     solvable::Int = 0,
-    detail = nothing,
 ) where {G <: AbstractDFG}
     return error("getVariables not implemented for $(typeof(dfg))")
 end