Merge pull request #451 from JuliaRobotics/tk/julia-0.7

Fixes for 0.7

Author: tkoolen

.travis.yml

@@ -1,9 +1,9 @@
 language: julia
 os:
   - linux
-#  - osx
+  - osx
 julia:
-  - 0.6
+  - nightly
 branches:
   only:
     - master
@@ -13,9 +13,8 @@ notifications:
 before_install:
   - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
 script:
-  - julia -e 'ENV["PYTHON"]=""; Pkg.clone(pwd()); Pkg.build("RigidBodyDynamics"); Pkg.test("RigidBodyDynamics"; coverage=true)'
+  # - julia -e 'ENV["PYTHON"]=""; Pkg.clone(pwd()); Pkg.build("RigidBodyDynamics"); Pkg.test("RigidBodyDynamics"; coverage=true)'
   # Note: PYTHON env is to ensure that PyCall uses the Conda.jl package's Miniconda distribution within Julia. Otherwise the sympy Python module won't be installed/imported properly.
 after_success:
-  - julia -e 'cd(Pkg.dir("RigidBodyDynamics")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
-  - julia -e 'Pkg.add("Documenter")'
-  - julia -e 'cd(Pkg.dir("RigidBodyDynamics")); include(joinpath("docs", "make.jl"))'
+  - julia -e 'import Pkg; Pkg.add("Documenter"); include("docs/make.jl")'
+  - julia -e 'import Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'

REQUIRE

@@ -1,10 +1,8 @@
-julia 0.6
-StaticArrays 0.6.2
-Rotations 0.6.0
-TypeSortedCollections 0.4.0
+julia 0.7
+StaticArrays 0.8.2
+Rotations 0.7.1
+TypeSortedCollections 0.5.0
 LightXML 0.4.0
 DocStringExtensions 0.4.1
-Compat 0.59 # for undef
 Reexport 0.0.3
 LoopThrottle 0.0.1
-Nullables 0.0.5 # TODO: remove after dropping 0.6 support

docs/src/benchmarks.md

@@ -17,16 +17,14 @@ Note that results on Travis builds are **not at all** representative because of
 Output of `versioninfo()`:
 
 ```
-Julia Version 0.6.2
-Commit d386e40c17 (2017-12-13 18:08 UTC)
+Julia Version 0.7.0-beta.133
+Commit 60174a9 (2018-07-03 20:03 UTC)
 Platform Info:
-  OS: Linux (x86_64-pc-linux-gnu)
+  OS: Linux (x86_64-linux-gnu)
   CPU: Intel(R) Core(TM) i7-6950X CPU @ 3.00GHz
   WORD_SIZE: 64
-  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Haswell)
-  LAPACK: libopenblas64_
   LIBM: libopenlibm
-  LLVM: libLLVM-3.9.1 (ORCJIT, broadwell)
+  LLVM: libLLVM-6.0.0 (ORCJIT, broadwell)
 ```
 
 Mass matrix:
@@ -35,10 +33,10 @@ Mass matrix:
   memory estimate:  0 bytes
   allocs estimate:  0
   --------------
-  minimum time:     9.697 μs (0.00% GC)
-  median time:      10.003 μs (0.00% GC)
-  mean time:        10.076 μs (0.00% GC)
-  maximum time:     47.473 μs (0.00% GC)
+  minimum time:     7.577 μs (0.00% GC)
+  median time:      8.250 μs (0.00% GC)
+  mean time:        8.295 μs (0.00% GC)
+  maximum time:     45.776 μs (0.00% GC)
 ```
 
 Mass matrix and Jacobian from left hand to right foot:
@@ -47,10 +45,10 @@ Mass matrix and Jacobian from left hand to right foot:
   memory estimate:  0 bytes
   allocs estimate:  0
   --------------
-  minimum time:     10.426 μs (0.00% GC)
-  median time:      10.737 μs (0.00% GC)
-  mean time:        10.754 μs (0.00% GC)
-  maximum time:     49.830 μs (0.00% GC)
+  minimum time:     8.070 μs (0.00% GC)
+  median time:      8.461 μs (0.00% GC)
+  mean time:        8.801 μs (0.00% GC)
+  maximum time:     45.001 μs (0.00% GC)
 ```
 
 Note the low additional cost of computing a Jacobian when the mass matrix is already computed. This is because RigidBodyDynamics.jl caches intermediate computation results.
@@ -61,20 +59,20 @@ Inverse dynamics:
   memory estimate:  0 bytes
   allocs estimate:  0
   --------------
-  minimum time:     10.988 μs (0.00% GC)
-  median time:      11.294 μs (0.00% GC)
-  mean time:        11.383 μs (0.00% GC)
-  maximum time:     33.164 μs (0.00% GC)
+  minimum time:     8.907 μs (0.00% GC)
+  median time:      9.341 μs (0.00% GC)
+  mean time:        9.633 μs (0.00% GC)
+  maximum time:     40.387 μs (0.00% GC)
 ```
 
 Forward dynamics:
 
 ```
-  memory estimate:  64 bytes
-  allocs estimate:  3
+  memory estimate:  0 bytes
+  allocs estimate:  0
   --------------
-  minimum time:     39.481 μs (0.00% GC)
-  median time:      54.874 μs (0.00% GC)
-  mean time:        55.230 μs (0.00% GC)
-  maximum time:     594.235 μs (0.00% GC)
+  minimum time:     32.671 μs (0.00% GC)
+  median time:      38.204 μs (0.00% GC)
+  mean time:        38.177 μs (0.00% GC)
+  maximum time:     188.785 μs (0.00% GC)
 ```

docs/src/index.md

@@ -39,16 +39,16 @@ Download links and more detailed instructions are available on the [Julia](http:
     Do **not** use `apt-get` or `brew` to install Julia, as the versions provided by these package managers tend to be out of date.
 
 ### Installing RigidBodyDynamics
-To install the latest tagged release of RigidBodyDynamics, simply run
+To install the latest tagged release of RigidBodyDynamics, start Julia and enter `Pkg` mode by pressing `]`, and then simply run
 
 ```julia
-Pkg.add("RigidBodyDynamics") 
+add RigidBodyDynamics
 ```
 
 To check out the master branch and work on the bleeding edge (generally, not recommended), additionally run
 
 ```julia
-Pkg.checkout("RigidBodyDynamics")
+develop RigidBodyDynamics
 ```
 
 ## About

notebooks/Derivatives and gradients using ForwardDiff.ipynb

@@ -15,7 +15,8 @@
    "source": [
     "using RigidBodyDynamics\n",
     "using ForwardDiff\n",
-    "using Compat.Test\n",
+    "using Test\n",
+    "using Random\n",
     "srand(1);"
    ]
   },
@@ -418,7 +419,7 @@
     "    \n",
     "    # compute momentum and store it in `out`\n",
     "    m = momentum(state)\n",
-    "    copy!(out, [angular(m); linear(m)])\n",
+    "    copyto!(out, [angular(m); linear(m)])\n",
     "end"
    ]
   },

notebooks/Four-bar linkage - simulation and visualization.ipynb

@@ -25,7 +25,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We'll be using `RigidBodyDynamics` and `StaticArrays` for the simulation part."
+    "We'll be using `LinearAlgebra`, `RigidBodyDynamics`, and `StaticArrays` for the simulation part."
    ]
   },
   {
@@ -34,6 +34,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "using LinearAlgebra\n",
     "using RigidBodyDynamics\n",
     "using StaticArrays"
    ]
@@ -160,23 +161,23 @@
    "source": [
     "# link1 and joint1\n",
     "joint1 = Joint(\"joint1\", Revolute(axis))\n",
-    "inertia1 = SpatialInertia(CartesianFrame3D(\"inertia1_centroidal\"), I_1*axis*axis', zeros(SVector{3, T}), m_1)\n",
+    "inertia1 = SpatialInertia(CartesianFrame3D(\"inertia1_centroidal\"), I_1*axis*axis', zero(SVector{3, T}), m_1)\n",
     "link1 = RigidBody(inertia1)\n",
     "before_joint1_to_world = eye(Transform3D, frame_before(joint1), default_frame(world))\n",
     "c1_to_joint = Transform3D(inertia1.frame, frame_after(joint1), SVector(c_1, 0, 0))\n",
     "attach!(fourbar, world, link1, joint1, joint_pose = before_joint1_to_world, successor_pose = c1_to_joint)\n",
     "\n",
     "# link2 and joint2\n",
     "joint2 = Joint(\"joint2\", Revolute(axis))\n",
-    "inertia2 = SpatialInertia(CartesianFrame3D(\"inertia2_centroidal\"), I_2*axis*axis', zeros(SVector{3, T}), m_2)\n",
+    "inertia2 = SpatialInertia(CartesianFrame3D(\"inertia2_centroidal\"), I_2*axis*axis', zero(SVector{3, T}), m_2)\n",
     "link2 = RigidBody(inertia2)\n",
     "before_joint2_to_after_joint1 = Transform3D(frame_before(joint2), frame_after(joint1), SVector(l_1, 0., 0.))\n",
     "c2_to_joint = Transform3D(inertia2.frame, frame_after(joint2), SVector(c_2, 0, 0))\n",
     "attach!(fourbar, link1, link2, joint2, joint_pose = before_joint2_to_after_joint1, successor_pose = c2_to_joint)\n",
     "\n",
     "# link3 and joint3\n",
     "joint3 = Joint(\"joint3\", Revolute(axis))\n",
-    "inertia3 = SpatialInertia(CartesianFrame3D(\"inertia3_centroidal\"), I_3*axis*axis', zeros(SVector{3, T}), m_3)\n",
+    "inertia3 = SpatialInertia(CartesianFrame3D(\"inertia3_centroidal\"), I_3*axis*axis', zero(SVector{3, T}), m_3)\n",
     "link3 = RigidBody(inertia3)\n",
     "before_joint3_to_world = Transform3D(frame_before(joint3), default_frame(world), SVector(l_0, 0., 0.))\n",
     "c3_to_joint = Transform3D(inertia3.frame, frame_after(joint3), SVector(c_3, 0, 0))\n",

notebooks/Jacobian_IK_and_Control.ipynb renamed to notebooks/Jacobian IK and Control.ipynb

@@ -32,6 +32,7 @@
     "using StaticArrays\n",
     "\n",
     "# Fix the random seed, so we get repeatable results\n",
+    "using Random\n",
     "srand(42)"
    ]
   },
@@ -337,9 +338,9 @@
    "source": [
     "# Choose a desired location. We'll move the tip of the arm to\n",
     "# [0.5, 0, 2]\n",
-    "desired = Point3D(root_frame(mechanism), 0.5, 0, 2)\n",
+    "desired_tip_location = Point3D(root_frame(mechanism), 0.5, 0, 2)\n",
     "# Run the IK, updating `state` in place\n",
-    "jacobian_transpose_ik!(state, body, point, desired)"
+    "jacobian_transpose_ik!(state, body, point, desired_tip_location)"
    ]
   },
   {
@@ -391,7 +392,7 @@
     "qs = typeof(configuration(state))[]\n",
     "\n",
     "# Vary the desired x position from -1 to 1\n",
-    "for x in linspace(-1, 1, 100)\n",
+    "for x in range(-1, stop=1, length=100)\n",
     "    desired = Point3D(root_frame(mechanism), x, 0, 2)\n",
     "    jacobian_transpose_ik!(state, body, point, desired)\n",
     "    push!(qs, copy(configuration(state)))\n",
@@ -416,7 +417,7 @@
    ],
    "source": [
     "#NBSKIP\n",
-    "ts = collect(linspace(0, 1, length(qs)))\n",
+    "ts = collect(range(0, stop=1, length=length(qs)))\n",
     "setanimation!(vis, ts, qs)"
    ]
   },
@@ -482,7 +483,7 @@
     "#NBSKIP\n",
     "\n",
     "# Draw the circle in the viewer\n",
-    "θ = repeat(linspace(0, 2π, 100), inner=(2,))[2:end]\n",
+    "θ = repeat(linspace(0, stop=2π, length=100), inner=(2,))[2:end]\n",
     "cx, cy, cz = circle_origin\n",
     "geometry = PointCloud(Point.(cx .+ radius .* sin.(θ), cy, cz .+ 0.5 .* cos.(θ)))\n",
     "setobject!(vis[:circle], LineSegments(geometry, LineBasicMaterial()))"

notebooks/Quickstart - double pendulum.ipynb

@@ -21,6 +21,7 @@
    "outputs": [],
    "source": [
     "using RigidBodyDynamics\n",
+    "using LinearAlgebra\n",
     "using StaticArrays"
    ]
   },
@@ -94,7 +95,7 @@
     "c_1 = -0.5 # center of mass location with respect to joint axis\n",
     "m_1 = 1. # mass\n",
     "frame1 = CartesianFrame3D(\"upper_link\") # the reference frame in which the spatial inertia will be expressed\n",
-    "inertia1 = SpatialInertia(frame1, I_1 * axis * axis.', m_1 * SVector(0, 0, c_1), m_1)"
+    "inertia1 = SpatialInertia(frame1, I_1 * axis * axis', m_1 * SVector(0, 0, c_1), m_1)"
    ]
   },
   {
@@ -255,7 +256,7 @@
     "I_2 = 0.333 # moment of inertia about joint axis\n",
     "c_2 = -0.5 # center of mass location with respect to joint axis\n",
     "m_2 = 1. # mass\n",
-    "inertia2 = SpatialInertia(CartesianFrame3D(\"lower_link\"), I_2 * axis * axis.', m_2 * SVector(0, 0, c_2), m_2)\n",
+    "inertia2 = SpatialInertia(CartesianFrame3D(\"lower_link\"), I_2 * axis * axis', m_2 * SVector(0, 0, c_2), m_2)\n",
     "lowerlink = RigidBody(inertia2)\n",
     "elbow = Joint(\"elbow\", Revolute(axis))\n",
     "before_elbow_to_after_shoulder = Transform3D(frame_before(elbow), frame_after(shoulder), SVector(0, 0, l_1))\n",
@@ -464,7 +465,7 @@
     }
    ],
    "source": [
-    "transform(state, Point3D(frame_after(elbow), zeros(SVector{3})), default_frame(world))"
+    "transform(state, Point3D(frame_after(elbow), zero(SVector{3})), default_frame(world))"
    ]
   },
   {
@@ -627,8 +628,8 @@
    ],
    "source": [
     "v̇ = similar(velocity(state)) # the joint acceleration vector, i.e., the time derivative of the joint velocity vector v\n",
-    "v̇[shoulder][:] = 1\n",
-    "v̇[elbow][:] = 2\n",
+    "v̇[shoulder][1] = 1\n",
+    "v̇[elbow][1] = 2\n",
     "inverse_dynamics(state, v̇)"
    ]
   },

notebooks/Rigorous error bounds using IntervalArithmetic.ipynb

@@ -252,7 +252,7 @@
     }
    ],
    "source": [
-    "using Compat.Test\n",
+    "using Test\n",
     "@test (2.6 - 0.7 - 1.9) ∈ i"
    ]
   },

notebooks/Symbolic double pendulum.ipynb

@@ -94,14 +94,14 @@
     "world = root_body(double_pendulum) # the fixed 'world' rigid body\n",
     "\n",
     "# Attach the first (upper) link to the world via a revolute joint named 'shoulder'\n",
-    "inertia1 = SpatialInertia(CartesianFrame3D(\"upper_link\"), I_1 * axis * axis.', m_1 * SVector(zero(T), zero(T), c_1), m_1)\n",
+    "inertia1 = SpatialInertia(CartesianFrame3D(\"upper_link\"), I_1 * axis * axis', m_1 * SVector(zero(T), zero(T), c_1), m_1)\n",
     "body1 = RigidBody(inertia1)\n",
     "joint1 = Joint(\"shoulder\", Revolute(axis))\n",
     "joint1_to_world = eye(Transform3D{T}, frame_before(joint1), default_frame(world))\n",
     "attach!(double_pendulum, world, body1, joint1, joint_pose = joint1_to_world)\n",
     "\n",
     "# Attach the second (lower) link to the world via a revolute joint named 'elbow'\n",
-    "inertia2 = SpatialInertia(CartesianFrame3D(\"lower_link\"), I_2 * axis * axis.', m_2 * SVector(zero(T), zero(T), c_2), m_2)\n",
+    "inertia2 = SpatialInertia(CartesianFrame3D(\"lower_link\"), I_2 * axis * axis', m_2 * SVector(zero(T), zero(T), c_2), m_2)\n",
     "body2 = RigidBody(inertia2)\n",
     "joint2 = Joint(\"elbow\", Revolute(axis))\n",
     "joint2_to_body1 = Transform3D(frame_before(joint2), default_frame(body1), SVector(zero(T), zero(T), l_1))\n",