ci: fix CI and standardize things

.github/workflows/CI.yml

@@ -3,72 +3,34 @@ on:
   push:
     branches:
       - main
-    tags: ['*']
+    paths-ignore:
+      - 'docs/**'
   pull_request:
-  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/') }}
+    paths-ignore:
+      - 'docs/**'
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
-    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'
+          - '1'
         os:
           - ubuntu-latest
-        arch:
-          - x64
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
       - uses: julia-actions/cache@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+        with:
+          depwarn: error
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v3
         with:
           files: lcov.info
-  docs:
-    name: Documentation
-    runs-on: ubuntu-latest
-    permissions:
-      actions: write # needed to allow julia-actions/cache to proactively delete old caches that it has created
-      contents: write
-      statuses: write
-    steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v2
-        with:
-          version: '1'
-      - uses: julia-actions/cache@v1
-      - name: Configure doc environment
-        shell: julia --project=docs --color=yes {0}
-        run: |
-          using Pkg
-          Pkg.develop(PackageSpec(path=pwd()))
-          Pkg.instantiate()
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-docdeploy@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Run doctests
-        shell: julia --project=docs --color=yes {0}
-        run: |
-          using Documenter: DocMeta, doctest
-          using UDEComponents
-          DocMeta.setdocmeta!(UDEComponents, :DocTestSetup, :(using UDEComponents); recursive=true)
-          doctest(UDEComponents)

.github/workflows/CompatHelper.yml

@@ -1,16 +1,24 @@
 name: CompatHelper
+
 on:
   schedule:
-    - cron: 0 0 * * *
+    - cron: '00 00 * * *'
   workflow_dispatch:
+
+permissions:
+  contents: write
+  pull-requests: write
+
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: 1.3
       - name: Pkg.add("CompatHelper")
         run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
       - name: CompatHelper.main()
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
+        run: julia -e 'using CompatHelper; CompatHelper.main(;subdirs=["", "docs"])'

.github/workflows/Documentation.yml

@@ -0,0 +1,28 @@
+name: Documentation
+on:
+  push:
+    branches:
+      - main
+    tags: '*'
+  pull_request:
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --project=docs/ docs/make.jl
+      - uses: julia-actions/julia-processcoverage@v1
+        with:
+          directories: src
+      - uses: codecov/codecov-action@v3
+        with:
+          files: lcov.info

.github/workflows/Downgrade.yml

@@ -1,8 +1,6 @@
 name: Downgrade
 on:
   pull_request:
-    branches:
-      - main
     paths-ignore:
       - 'docs/**'
   push:
@@ -12,20 +10,24 @@ on:
       - 'docs/**'
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        version: ['1']
-        group:
-          - Core
+        version:
+          - '1'
+        os:
+          - ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
       - uses: julia-actions/julia-downgrade-compat@v1
-#        if: ${{ matrix.version == '1.6' }}
         with:
           skip: Pkg,TOML
+      - uses: julia-actions/cache@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1

Project.toml

@@ -14,23 +14,23 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
 Aqua = "0.8"
-ComponentArrays = "0.15"
+ComponentArrays = "0.15.11"
 ForwardDiff = "0.10.36"
 JET = "0.8"
 Lux = "0.5.32"
 LuxCore = "0.1.14"
-ModelingToolkit = "9.9.0"
+ModelingToolkit = "9.9"
 ModelingToolkitStandardLibrary = "2.6"
-Optimization = "3.22"
-OptimizationOptimisers = "0.2"
+Optimization = "3.24"
+OptimizationOptimisers = "0.2.1"
 OrdinaryDiffEq = "6.74"
-Random = "1"
+Random = "1.10"
 SafeTestsets = "0.1"
 SciMLStructures = "1.1.0"
 StableRNGs = "1"
 SymbolicIndexingInterface = "0.3.15"
 Symbolics = "5.27"
-Test = "1"
+Test = "1.10"
 julia = "1.10"
 
 [extras]

README.md

@@ -4,7 +4,7 @@
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://SciML.github.io/UDEComponents.jl/dev/)
 [![Build Status](https://github.com/SciML/UDEComponents.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/SciML/UDEComponents.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/SciML/UDEComponents.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/SciML/UDEComponents.jl)
-[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
+[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
 [![Aqua](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 
 ## Build UDEs with ModelingToolkit

src/UDEComponents.jl

@@ -15,14 +15,14 @@ include("utils.jl")
 """
     NeuralNetworkBlock(n_input = 1, n_output = 1;
         chain = multi_layer_feed_forward(n_input, n_output),
-        rng = Xoshiro(0))
+        rng = Xoshiro(0), eltype = Float64)
 
 Create an `ODESystem` with a neural network inside.
 """
 function NeuralNetworkBlock(n_input = 1,
         n_output = 1;
         chain = multi_layer_feed_forward(n_input, n_output),
-        rng = Xoshiro(0), eltype=Float64)
+        rng = Xoshiro(0), eltype = Float64)
     lux_p = Lux.initialparameters(rng, chain)
     ca = ComponentArray{eltype}(lux_p)
 

test/lotka_volterra.jl

@@ -14,7 +14,7 @@ using StableRNGs
 
 function lotka_ude()
     @variables t x(t)=3.1 y(t)=1.5
-    @parameters α=1.3 [tunable=false] δ=1.8 [tunable=false]
+    @parameters α=1.3 [tunable = false] δ=1.8 [tunable = false]
     Dt = ModelingToolkit.D_nounits
     @named nn_in = RealInput(nin = 2)
     @named nn_out = RealOutput(nout = 2)
@@ -115,7 +115,7 @@ res = solve(op, Adam(), maxiters = 5000)#, callback = plot_cb)
 
 res_p = SciMLStructures.replace(Tunable(), prob.p, res)
 res_prob = remake(prob, p = res_p)
-res_sol = solve(res_prob, Rodas4(), saveat=sol_ref.t)
+res_sol = solve(res_prob, Rodas4(), saveat = sol_ref.t)
 
 # using Plots
 # plot(sol_ref, idxs = [model_true.x, model_true.y])