Series of fixes to CI, documentation workflow, and small bug fixes.

- Update CI.yml to point to correct branch (main instead of master)
- Run CI on julia 1.9, 1.10 AND 1.11
- Fix compat in Project.toml, add entries to improve compat for julia
  1.9
- Initialize all caches vectors/matrices to zero instead of undef.
- Separate out ros example from ROS.jl
- Update documentation github workflow to work with GLMakie
- Link to docs from readme

Author: Larbino1

.github/workflows/CI.yml

@@ -2,11 +2,11 @@ name: CI
 on:
   push:
     branches:
-      - master
+      - main
     tags: ['*']
   pull_request:
     branches:
-      - master
+      - main
 concurrency:
   # Skip intermediate builds: always.
   # Cancel intermediate builds: only if it is a pull request build.
@@ -20,8 +20,9 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          # - '1.0'
           - '1.9'
+          - '1.10'
+          - '1.11'
           - 'nightly'
         os:
           - ubuntu-latest

.github/workflows/documentation.yml

@@ -9,22 +9,27 @@ on:
 
 jobs:
   build:
+    env:
+      MODERNGL_DEBUGGING: "true" # turn on errors when running OpenGL tests
     permissions:
       actions: write
       contents: write
       pull-requests: read
       statuses: write
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
         with:
           version: '1'
       - uses: julia-actions/cache@v2
-      - name: Install dependencies
+      - name: Install GLMakie dependencies for headless server # From https://github.com/MakieOrg/Makie.jl/tree/master/GLMakie#troubleshooting-opengl.
+        run: sudo apt-get update && sudo apt-get install -y xorg-dev mesa-utils xvfb libgl1 freeglut3-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev xsettingsd x11-xserver-utils
+      - name: Precompile
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
+      - name: Build and Deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
-        run: julia --project=docs/ docs/make.jl
+        run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs/ docs/make.jl
+

Project.toml

@@ -45,30 +45,30 @@ VMRobotControlMakieExt = "Makie"
 
 [compat]
 BenchmarkTools = "1"
-ColorTypes = ">= 0.11"
-Colors = ">= 0.12"
-DataStructures = ">= 0.18"
-DifferentialEquations = "7"
+ColorTypes = "0.11, 0.12"
+Colors = "0.12, 0.13"
+DataStructures = "0.18"
 DiffResults = "1"
-DigitalAssetExchangeFormatIO = ">= 1.1.2" # This is required, previous versions broken
+DifferentialEquations = "7"
+DigitalAssetExchangeFormatIO = "1.1.2"
 EzXML = "1"
 FileIO = "1"
-ForwardDiff = ">= 0.10"
+ForwardDiff = "0.10"
 FunctionWrappers = "1"
-GeometryBasics = ">= 0.4"
+GeometryBasics = "0.4"
 Graphs = "1"
-JSON = ">= 0.21"
-LoopVectorization = ">= 0.12"
-Makie = ">= 0.21"     
-MeshIO = ">= 0.4"
-Observables = ">= 0.5"
+JSON = "0.21"
+LoopVectorization = "0.12"
+Makie = "0.21"
+MeshIO = "0.4"
+Observables = "0.5"
 OrderedCollections = "1"
-PreallocationTools = ">= 0.4"
-ResultTypes = "4"
-StaticArrays = ">= 1.8.1" # Manual
-StatsBase = ">= 0.34"
 Pkg = "1"
+PreallocationTools = "0.4"
+ResultTypes = "3, 4"
 SparseArrays = "1"
+StaticArrays = "1.8.1"
+StatsBase = "0.34"
 
 [extras]
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"

README.md

@@ -1,6 +1,13 @@
 # VMRobotControl.jl
 
-![VMRobotControl.jl logo](docs/src/assets/Logo.svg)
+<div align="center">
+    <picture>
+      <source srcset="docs/src/assets/Logo.svg" >
+      <img alt="VMRobotControl.jl logo" src="docs/src/assets/Logo.svg" width="350">
+    </picture>
+</div>
+
+[![][docs-dev-img]][docs-dev-url]
 
 VMRobotControl allows you to build dynamic controllers for your robot as intuitive
 virtual mechanisms.
@@ -17,6 +24,9 @@ properties.
 This provides a simple way to program complex robot behaviour incrementally, from mechanical 
 primitives.
 
+[docs-dev-img]: https://img.shields.io/badge/Docs-dev-blue.svg
+[docs-dev-url]: https://cambridge-control-lab.github.io/VMRobotControl.jl/dev
+
 # Installation
 
 Julia must be installed, I recommend using [juliaup](https://github.com/JuliaLang/juliaup). `VMRobotControl.jl` is only tested on the latest julia version. 
@@ -56,7 +66,9 @@ test
 
 # Manually building documentation
 
-Activate the docs environment, from the VMRobotControl.jl folder:
+We recommend [reading the docs online](docs-dev-url), but you can also build 
+them locally. To do so, activate the docs environment, from the
+`VMRobotControl.jl` folder:
 ```
 activate docs
 add DifferentialEquations, Documenter, FileIO, ForwardDiff, GLMakie, Literate, LiveServer, MeshIO, StaticArrays
@@ -67,5 +79,5 @@ include("./docs/make.jl")
 ```
 and host them using `LiveServer.jl`:
 ```julia
-include("./docs/make.jl")
+include("./docs/host.jl")
 ```

docs/Project.toml

@@ -4,6 +4,7 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589"
 MeshIO = "7269a6da-0436-5bbc-96c2-40638cbb6118"

docs/make.jl

@@ -1,4 +1,13 @@
-using Revise
+module_dir = joinpath(splitpath(Base.source_dir())[1:end-1])
+if pwd() != module_dir
+    @info "Changing directory to folder $(module_dir)"
+    cd(module_dir)
+end
+
+# Ensure that VMRobotControl is devved.
+using Pkg
+Pkg.develop(PackageSpec(path=pwd()))
+Pkg.instantiate()
 
 using 
     DifferentialEquations,

ros/ROS.jl

@@ -1,5 +1,3 @@
-using Pkg; Pkg.activate("VMRobotControlEnv"; shared=true)
-
 using Printf
 using Sockets
 using StaticArrays
@@ -397,78 +395,3 @@ function ros_vm_controller(
     (E = stored_energy(control_cache)) > E_max && error("Initial stored energy exceeds $(E_max)J, was $(E)J")
     warmup_and_activate(connection, control_func!; )
 end
-
-#=
-# Enable debug logging
-using Logging
-debuglogger = ConsoleLogger(stderr, Logging.Debug)
-global_logger(debuglogger)
-=#
-
-#=
-# Test connection with python only
-with_rospy_connection(Sockets.localhost, ROSPY_LISTEN_PORT+1, 7, 14) do connection
-    warmup_and_activate(connection, test_control_func; )
-end
-=#
-
-#=
-# Test on franka
-module_path = joinpath(splitpath(splitdir(pathof(VMRobotControl))[1])[1:end-1])
-using FileIO, UUIDs
-try
-    FileIO.add_format(format"DAE", (), ".dae", [:DigitalAssetExchangeFormatIO => UUID("43182933-f65b-495a-9e05-4d939cea427d")])
-catch
-end
-robot = parseRSON(joinpath(module_path, "RSONs/rsons/franka_panda/pandaSurgicalV2.rson"))
-add_gravity_compensation!(robot, 1.1*DEFAULT_GRAVITY)
-
-vms = compile(VirtualMechanismSystem("franka", robot))
-qᵛ = Float64[]
-
-with_rospy_connection(Sockets.localhost, ROSPY_LISTEN_PORT, 7, 14) do connection
-    ros_vm_controller(connection, vms, qᵛ)
-end
-=#
-
-# Test on sciurus
-# Test on franka
-module_path = joinpath(splitpath(splitdir(pathof(VMRobotControl))[1])[1:end-1])
-robot = parseURDF(joinpath(module_path, "URDFs/sciurus17_description/urdf/sciurus17.urdf"))
-add_gravity_compensation!(robot, DEFAULT_GRAVITY)
-
-vms = VirtualMechanismSystem("sciurus", robot)
-# add_gravity_compensation!(vms, -0.2*DEFAULT_GRAVITY)
-add_coordinate!(vms, ReferenceCoord(Ref(SVector(.3, 0.1, 0.2))); id="l_tgt")
-add_coordinate!(vms, FramePoint(".robot.l_link7", SVector(0., 0., 0.)); id="l_hand")
-add_coordinate!(vms, CoordDifference("l_tgt", "l_hand"), id="l_err")
-add_component!(vms, TanhSpring("l_err"; stiffness=200.0, max_force=5.0); id="l_spring")
-add_component!(vms, LinearDamper(5., "l_err"); id="l_damper")
-
-add_coordinate!(vms, ReferenceCoord(Ref(SVector(.3, 0.1, 0.2))); id="r_tgt")
-add_coordinate!(vms, FramePoint(".robot.r_link7", SVector(0., 0., 0.)); id="r_hand")
-add_coordinate!(vms, CoordDifference("r_tgt", "r_hand"), id="r_err")
-add_component!(vms, TanhSpring("r_err"; stiffness=200.0, max_force=5.0); id="r_spring")
-add_component!(vms, LinearDamper(5., "r_err"); id="r_damper")
-
-
-
-function f_setup(cache)
-    l_ref_coord_id = get_compiled_coordID(cache, "l_tgt")
-    r_ref_coord_id = get_compiled_coordID(cache, "r_tgt")
-    return (l_ref_coord_id, r_ref_coord_id)
-end
-
-function f_control(cache, t, setup_ret, extra)
-    l_ref_coord_id, r_ref_coord_id = setup_ret
-    coord = cache[l_ref_coord_id].coord_data.val[] = SVector(0.3, .1 + 0.1*sin(t), 0.2)
-    coord = cache[r_ref_coord_id].coord_data.val[] = SVector(0.3 + 0.1*cos(t), -.1, 0.2 + 0.1*sin(t))
-    nothing 
-end
-
-cvms = compile(vms)
-
-qᵛ = Float64[]
-with_rospy_connection(Sockets.localhost, ROSPY_LISTEN_PORT, 21, 42) do connection
-    ros_vm_controller(connection, cvms, qᵛ; f_control, f_setup, E_max=2.0)
-end

ros/ros_example.jl

@@ -0,0 +1,43 @@
+# Load ROS communication code
+include("ROS.jl")
+
+# Load robot model
+module_path = joinpath(splitpath(splitdir(pathof(VMRobotControl))[1])[1:end-1])
+robot = parseURDF(joinpath(module_path, "URDFs/sciurus17_description/urdf/sciurus17.urdf"))
+# Include gravity compensation done by robot software (not done by our controller)
+add_gravity_compensation!(robot, DEFAULT_GRAVITY) 
+
+# Build our virtual mechanism controller
+vms = VirtualMechanismSystem("sciurus", robot)
+add_coordinate!(vms, ReferenceCoord(Ref(SVector(.3, 0.1, 0.2))); id="l_tgt")
+add_coordinate!(vms, FramePoint(".robot.l_link7", SVector(0., 0., 0.)); id="l_hand")
+add_coordinate!(vms, CoordDifference("l_tgt", "l_hand"), id="l_err")
+add_component!(vms, TanhSpring("l_err"; stiffness=200.0, max_force=5.0); id="l_spring")
+add_component!(vms, LinearDamper(5., "l_err"); id="l_damper")
+
+add_coordinate!(vms, ReferenceCoord(Ref(SVector(.3, 0.1, 0.2))); id="r_tgt")
+add_coordinate!(vms, FramePoint(".robot.r_link7", SVector(0., 0., 0.)); id="r_hand")
+add_coordinate!(vms, CoordDifference("r_tgt", "r_hand"), id="r_err")
+add_component!(vms, TanhSpring("r_err"; stiffness=200.0, max_force=5.0); id="r_spring")
+add_component!(vms, LinearDamper(5., "r_err"); id="r_damper")
+
+function f_setup(cache)
+    l_ref_coord_id = get_compiled_coordID(cache, "l_tgt")
+    r_ref_coord_id = get_compiled_coordID(cache, "r_tgt")
+    return (l_ref_coord_id, r_ref_coord_id)
+end
+
+function f_control(cache, t, setup_ret, extra)
+    l_ref_coord_id, r_ref_coord_id = setup_ret
+    coord = cache[l_ref_coord_id].coord_data.val[] = SVector(0.3, .1 + 0.1*sin(t), 0.2)
+    coord = cache[r_ref_coord_id].coord_data.val[] = SVector(0.3 + 0.1*cos(t), -.1, 0.2 + 0.1*sin(t))
+    nothing 
+end
+
+# Compile the virtual mechanism system, and run the controller via ROS
+# Make sure rospy_client.py is running first.
+cvms = compile(vms)
+qᵛ = Float64[]
+with_rospy_connection(Sockets.localhost, ROSPY_LISTEN_PORT, 21, 42) do connection
+    ros_vm_controller(connection, cvms, qᵛ; f_control, f_setup, E_max=2.0)
+end

src/coordinates/coordinate_cache.jl

@@ -3,7 +3,7 @@ abstract type AbstractCoordinateCache{T} end
 struct CoordKinematicsCache{T} <: AbstractCoordinateCache{T}
     z::Vector{T}
     function CoordKinematicsCache{T}(Nc) where T
-        new{T}(Vector{T}(undef, Nc))
+        new{T}(zeros(T, Nc))
     end
 end
 
@@ -12,8 +12,8 @@ struct CoordJacobiansCache{T} <: AbstractCoordinateCache{T}
     J::Matrix{T}
     function CoordJacobiansCache{T}(Nc, NDOF) where T
         new{T}(
-            Vector{T}(undef, Nc),
-            Matrix{T}(undef, Nc, NDOF)
+            zeros(T, Nc),
+            zeros(T, Nc, NDOF)
         )
     end
 end
@@ -24,9 +24,9 @@ struct CoordRBStatesCache{T} <: AbstractCoordinateCache{T}
     z̈::Vector{T}
     function CoordRBStatesCache{T}(Nc) where T
         new{T}(
-            Vector{T}(undef, Nc),
-            Vector{T}(undef, Nc),
-            Vector{T}(undef, Nc)
+            zeros(T, Nc),
+            zeros(T, Nc),
+            zeros(T, Nc)
         )
     end
 end
@@ -38,10 +38,10 @@ struct CoordRBStatesJacobianCache{T} <: AbstractCoordinateCache{T}
     J::Matrix{T}
     function CoordRBStatesJacobianCache{T}(Nc, NDOF) where T
         new{T}(
-            Vector{T}(undef, Nc),
-            Vector{T}(undef, Nc),
-            Vector{T}(undef, Nc),
-            Matrix{T}(undef, Nc, NDOF)
+            zeros(T, Nc),
+            zeros(T, Nc),
+            zeros(T, Nc),
+            zeros(T, Nc, NDOF)
         )
     end
 end
@@ -53,10 +53,10 @@ struct CoordRBStatesWrenchesCache{T} <: AbstractCoordinateCache{T}
     f::Vector{T}
     function CoordRBStatesWrenchesCache{T}(Nc) where T
         new{T}(
-            Vector{T}(undef, Nc),
-            Vector{T}(undef, Nc),
-            Vector{T}(undef, Nc),
-            Vector{T}(undef, Nc)
+            zeros(T, Nc),
+            zeros(T, Nc),
+            zeros(T, Nc),
+            zeros(T, Nc)
         )
     end
 end

src/coordinates/coordinate_implementations.jl

@@ -283,11 +283,15 @@ end
 
 function __jacobian!(cache::CacheBundle, mc::CMC{<:FramePoint})
     c = mc.coord_data
-    Jz = _vms_jacobian_result_view(cache, J_cache_view(cache, mc), c.frameID)
+    J_view = J_cache_view(cache, mc)
+
+    fill!(J_view, zero(eltype(J_view))) # TODO do this once rather than every time
+    Jz = _vms_jacobian_result_view(cache, J_view, c.frameID)
     Jᵥ⁰ᵃ = get_linear_jacobian(cache, c.frameID)
     Jω⁰ᵃ = get_angular_jacobian(cache, c.frameID)
     T⁰ᵃ = get_transform(cache, c.frameID)
 
+
     pᵃ = c.point
     R⁰ᵃ = rotor(T⁰ᵃ)
     δᵒ = rotate(R⁰ᵃ, pᵃ)
@@ -305,6 +309,7 @@ function __jacobian!(cache::CacheBundle, mc::CMC{<:FramePoint})
     for i in axes(Jz, 1), j in axes(Jz, 2)
         Jz[i, j] = Jᵥ⁰ᵃ[i, j] - skew_p[i, :]' * Jω⁰ᵃ[SVector(1, 2, 3), j]
     end
+
     nothing
 end