Use Julia 1.11 for CI tests and docs #648

ferrolho · 2024-11-09T17:00:40Z

This PR is for using Julia 1.11 for CI tests and docs.

I have tested it locally and the pipelines below also seem to be happy. 🎉

Important

There's something missing from this PR that I cannot fix myself because it has to do with the repo settings regarding the secret keys for Documenter.jl (this) and the GitHub action that deploys the documentation after it has been built. You can see the error from the last deploy attempt here (or pasted below) — FYI @tkoolen @rdeits.

Please make sure you have the correct access rights
and the repository exists.
┌ Error: Git failed to fetch [email protected]:JuliaRobotics/RigidBodyDynamics.jl.git
│ This can be caused by a DOCUMENTER_KEY variable that is not correctly set up.
│ Make sure that the environment variable is properly set up as a Base64-encoded string
│ of the SSH private key. You may need to re-generate the keys with DocumenterTools.
└ @ Documenter ~/.julia/packages/Documenter/H5y27/src/Documenter.jl:652

Here's how to build the docs and serve them locally:

cd RigidBodyDynamics.jl
julia --project=docs docs/make.jl
julia -e 'using LiveServer; serve(dir="docs/build")'

I keep forgetting this and have to check it every time I do maintenance on documentation of Julia packages, so I am writing this here mostly for my future reference... 😛

ferrolho · 2024-11-09T17:06:30Z

.github/workflows/CI.yml

-
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1.6'
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()
-            include("docs/make.jl")'
-        env:
-          PYTHON: ""
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}


I have moved this into .github/workflows/Documentation.yml.

ferrolho · 2024-11-09T17:06:52Z

.github/workflows/Documentation.yml

+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1.11'


Docs are now being built using Julia v1.11.

ferrolho · 2024-11-09T17:11:05Z

docs/make.jl

+    if VERSION >= v"1.6"
+        push!(excludefiles, "6. Symbolics.jl")
+        push!(excludefiles, "7. Rigorous error bounds using IntervalArithmetic.jl")


This is a bit annoying... I have already spent a lot of time on this PR, but I haven't been able to fix the issues with these two notebooks.

~~For 6. Symbolics.jl, I am not sure how to fix it and there is an open issue for this (Symbolic Derivatives with SymPy do not work #630).~~ Update: I have managed to get the 6. Symbolics.jl example notebook back up and running in 5155344.

For 7. Rigorous error bounds using IntervalArithmetic.jl I have already applied a few updates to use the new syntax and API of IntervalArithmetic.jl, but not all the cells of the notebook are fixed yet.

ferrolho · 2024-11-09T17:13:13Z

docs/make.jl

-      ],
-    format = Documenter.HTML(prettyurls = parse(Bool, get(ENV, "CI", "false")))
+    ],
+    warnonly = Documenter.except(),


I had to add this line warnonly = Documenter.except() because otherwise the build fails due to :missing_docs errors (which means not all docstrings are being used by the Docs).

ferrolho · 2024-11-09T17:16:28Z

examples/3. Four-bar linkage/Manifest.toml

 [[deps.MeshCatMechanisms]]
 deps = ["ColorTypes", "CoordinateTransformations", "GeometryBasics", "InteractBase", "Interpolations", "LoopThrottle", "MechanismGeometries", "MeshCat", "OrderedCollections", "RigidBodyDynamics"]
-git-tree-sha1 = "b766636d31175340e542c833cff1895c2f3f41cc"
+git-tree-sha1 = "c6ca2052dc571cfe1395a12e970101c9356cf85f"
+repo-rev = "hf/upstream-changes"
+repo-url = "https://github.com/ferrolho/MeshCatMechanisms.jl.git"
 uuid = "6ad125db-dd91-5488-b820-c1df6aab299d"
-version = "0.9.0"
+version = "0.9.1"


The Manifest.toml files of the notebooks need to be generated again after JuliaRobotics/MeshCatMechanisms.jl#71 has been merged. Right now, they are referring to the PR branch from my fork.

ferrolho · 2024-11-09T17:17:34Z

test/runtests.jl

@@ -30,7 +30,7 @@ include("test_simulate.jl")
 include("test_mechanism_modification.jl")
 include("test_pd_control.jl")

-if v"1.9" <= VERSION < v"1.10"
+if v"1.11" <= VERSION < v"1.12"  # Test notebooks on Julia v1.11


This is for running the notebook tests and benchmarks only on Julia v1.11 runners.

ferrolho · 2024-11-09T17:23:16Z

docs/make.jl

-    repo = "github.com/JuliaRobotics/RigidBodyDynamics.jl.git"
+    repo="github.com/JuliaRobotics/RigidBodyDynamics.jl",
+    devbranch="master",
+    push_preview=true,


push_preview = true turned out to be useless for this PR because it only works for PRs originating from the same repo instead of from forked repositories — see this line of the job.

ferrolho · 2024-11-10T12:41:39Z

examples/6. Symbolics/6. Symbolics.jl

+## Type piracy needed in order to make Symbolics.jl types interact well with Quaternions.jl.
+## This should be avoided — see https://docs.julialang.org/en/v1/manual/style-guide/#avoid-type-piracy.
+function Base.:/(q::Quaternions.Quaternion, x::Symbolics.Num)
+    return Quaternions.Quaternion(q.s / x.val, q.v1 / x.val, q.v2 / x.val, q.v3 / x.val)
+end


I took this from https://github.com/dionysos-dev/Dionysos.jl/blob/master/BipedRobot/src/piracy.jl to check if it would fix the issue in #630 and it did! So, we can close that issue when we merge this PR.

ferrolho · 2024-11-10T12:50:08Z

examples/6. Symbolics/6. Symbolics.jl

+try
+    ## This throws `ERROR: TypeError: non-boolean (Num) used in boolean context` because
+    ## of `m > 0 || return zero(cache_eltype(state))` in `gravitational_potential_energy`.
+    ## See https://docs.sciml.ai/Symbolics/stable/manual/faq/ for more details.
+    simplify(gravitational_potential_energy(x), expand=true)
+catch e
+    e
+end


This cell is not working because of the short-circuiting on this line:

RigidBodyDynamics.jl/src/mechanism_state.jl

Line 900 in d6df4eb

m > 0 || return zero(cache_eltype(state))

I tried removing the short-circuiting statement and it seems to fix it, but the repercussions of doing that are not clear to me. I am afraid that not having the early return might affect performance somehow, but on the other hand I could not see it being used as part of other methods...

@tkoolen would be the best person to chip in. 😛

Use Julia 1.11 for CI tests and docs

29e479a

ferrolho commented Nov 9, 2024

View reviewed changes

ferrolho added 2 commits November 9, 2024 17:55

Add repo arg to makedocs

d87e016

Fix example '6. Symbolics'

5155344

ferrolho commented Nov 10, 2024

View reviewed changes

ferrolho mentioned this pull request Nov 10, 2024

Symbolic Derivatives with SymPy do not work #630

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ferrolho commented Nov 10, 2024

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Update version of GitHub actions in CI.yml

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Use Julia 1.11 for CI tests and docs #648

Use Julia 1.11 for CI tests and docs #648

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Use Julia 1.11 for CI tests and docs #648

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