add all the compat bounds

.github/workflows/CompatHelper.yml

@@ -3,14 +3,42 @@ on:
   schedule:
     - cron: 0 0 * * *
   workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v2
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main(; subdirs=["", "docs", "test", "benchmark"])
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-        run: julia -e 'using CompatHelper; CompatHelper.main()'

benchmark/Project.toml

@@ -1,7 +1,6 @@
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
-BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Chairmarks = "0ca39b1e-fe0b-4e98-acfc-b1656634c4de"
@@ -22,3 +21,24 @@ UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
 
 [sources]
 NetworkDynamics = {path = ".."}
+
+[compat]
+AbstractTrees = "0.4.5"
+ArgParse = "1.2.0"
+CairoMakie = "0.13.1"
+Chairmarks = "1.3.1"
+Makie = "0.22.1"
+OrderedCollections = "1.7.0"
+PkgBenchmark = "0.2.12"
+PrettyTables = "2.4.0"
+ProgressMeter = "1.10.2"
+StableRNGs = "1.0.2"
+ThreadPinning = "1.0.2"
+UnicodePlots = "3.7.2"
+# the ones below are bound by NetworkDynamics.jl
+CUDA = "≥0.0.1"
+Graphs = "≥0.0.1"
+SciMLBase = "≥0.0.1"
+StaticArrays = "≥0.0.1"
+StyledStrings = "≥0.0.1"
+TimerOutputs = "≥0.0.1"

docs/Project.toml

@@ -15,19 +15,42 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NetworkDynamics = "22e9dc34-2a0d-11e9-0de0-8588d035468b"
 OrdinaryDiffEqNonlinearSolve = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8"
 OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce"
-OrdinaryDiffEqSDIRK = "2d112036-d095-4a1e-ab9a-08536f3ecdbf"
 OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
-StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 StyledStrings = "f489334b-da3d-4c2e-b8f0-e476e12c162b"
 SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 
 [sources]
 NetworkDynamics = {path = ".."}
+
+[compat]
+CairoMakie = "0.13.1"
+DiffEqCallbacks = "4.2.2"
+Distributions = "0.25.117"
+Documenter = "1.8.0"
+DynamicQuantities = "1.4.0"
+GraphMakie = "0.5.13"
+LaTeXStrings = "1.4.0"
+LinearInterpolations = "0.1.4"
+Literate = "2.20.1"
+OrdinaryDiffEqNonlinearSolve = "1.3.0"
+OrdinaryDiffEqRosenbrock = "1.4.0"
+OrdinaryDiffEqTsit5 = "1.1.0"
+Plots = "1.40.9"
+SimpleWeightedGraphs = "1.4.0"
+StableRNGs = "1.0.2"
+# the ones below are bound by NetworkDynamics.jl
+Graphs = "≥0.0.1"
+ModelingToolkit = "≥0.0.1"
+Printf = "≥0.0.1"
+Random = "≥0.0.1"
+SciMLBase = "≥0.0.1"
+StaticArrays = "≥0.0.1"
+StyledStrings = "≥0.0.1"
+SymbolicIndexingInterface = "≥0.0.1"

test/Project.toml

@@ -47,3 +47,48 @@ TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 
 [sources]
 NetworkDynamics = {path = ".."}
+
+[compat]
+Aqua = "0.8.9"
+CairoMakie = "0.13.1"
+Chairmarks = "1.3.1"
+DelimitedFiles = "1.9.1"
+DiffEqCallbacks = "4.1.0"
+DifferentiationInterface = "0.6.32"
+DifferentiationInterfaceTest = "0.9"
+DynamicQuantities = "1.4.0"
+ExplicitImports = "1.10.1"
+FiniteDiff = "2.26.2"
+GraphMakie = "0.5.13"
+LinearInterpolations = "0.1.4"
+Logging = "1"
+OrderedCollections = "1.7.0"
+OrdinaryDiffEqNonlinearSolve = "1.3.0"
+OrdinaryDiffEqRosenbrock = "1.4.0"
+OrdinaryDiffEqSDIRK = "1.2.0"
+OrdinaryDiffEqTsit5 = "1.1.0"
+Pkg = "1"
+Plots = "1.40.9"
+SafeTestsets = "0.1.0"
+SimpleWeightedGraphs = "1.4.0"
+StableRNGs = "1.0.2"
+Test = "1"
+# the ones below are bound by NetworkDynamics.jl
+Adapt = "≥0.0.1"
+CUDA = "≥0.0.1"
+ForwardDiff = "≥0.0.1"
+Graphs = "≥0.0.1"
+InteractiveUtils = "≥0.0.1"
+KernelAbstractions = "≥0.0.1"
+LinearAlgebra = "≥0.0.1"
+ModelingToolkit = "≥0.0.1"
+Printf = "≥0.0.1"
+Random = "≥0.0.1"
+SciMLBase = "≥0.0.1"
+SparseArrays = "≥0.0.1"
+Static = "≥0.0.1"
+StaticArrays = "≥0.0.1"
+SteadyStateDiffEq = "≥0.0.1"
+SymbolicIndexingInterface = "≥0.0.1"
+Symbolics = "≥0.0.1"
+TimerOutputs = "≥0.0.1"