More Actions (#3)

* More actions

* Format files

.github/Dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+ - package-ecosystem: "github-actions"
+ directory: "/" # Location of package manifests
+ schedule:
+ interval: "weekly"

.github/workflows/CompatHelper.yml

@@ -0,0 +1,18 @@
+
+name: CompatHelper
+on:
+ schedule:
+ - cron: '00 00 * * *'
+ workflow_dispatch:
+jobs:
+ CompatHelper:
+ runs-on: ubuntu-latest
+ steps:
+ - 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(; subdirs = ["", "docs"])'

.github/workflows/FormatCheck.yml

@@ -0,0 +1,42 @@
+name: format-check
+
+on:
+ push:
+ branches:
+ - 'master'
+ - 'release-'
+ tags: '*'
+ pull_request:
+
+jobs:
+ build:
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ julia-version: [1]
+ julia-arch: [x86]
+ os: [ubuntu-latest]
+ steps:
+ - uses: julia-actions/setup-julia@latest
+ with:
+ version: ${{ matrix.julia-version }}
+
+ - uses: actions/checkout@v4
+ - name: Install JuliaFormatter and format
+ # This will use the latest version by default but you can set the version like so:
+ #
+ # julia -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+ run: |
+ julia -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+ julia -e 'using JuliaFormatter; format(".", verbose=true)'
+ - name: Format check
+ run: |
+ julia -e '
+ out = Cmd(`git diff --name-only`) |> read |> String
+ if out == ""
+ exit(0)
+ else
+ @error "Some files have not been formatted !!!"
+ write(stdout, out)
+ exit(1)
+ end'

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+ issue_comment:
+ types:
+ - created
+ workflow_dispatch:
+jobs:
+ TagBot:
+ if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+ runs-on: ubuntu-latest
+ steps:
+ - uses: JuliaRegistries/TagBot@v1
+ with:
+ token: ${{ secrets.GITHUB_TOKEN }}
+ ssh: ${{ secrets.DOCUMENTER_KEY }}

docs/make.jl

@@ -4,8 +4,7 @@ push!(LOAD_PATH, joinpath(@__DIR__, ".."))
 
 using DynamicOED
 
-makedocs(
- modules = [DynamicOED],
+makedocs(modules = [DynamicOED],
  sitename = "DynamicOED.jl",
  remotes = nothing,
  draft = false,
@@ -16,6 +15,5 @@ makedocs(
  "Lotka-Volterra" => "examples/lotka.md",
  ],
  "Theory" => "theory.md",
- "API" => "api.md"
- ]
-)
+ "API" => "api.md",
+ ])

src/problem.jl

@@ -92,14 +92,12 @@ function get_initial_variables(prob::OEDProblem)
  generate_initial_variables(prob.system, prob.timegrid)
 end
 
-
 function Optimization.OptimizationProblem(prob::OEDProblem,
- AD::Optimization.ADTypes.AbstractADType,
- u0::ComponentVector = get_initial_variables(prob), p = SciMLBase.NullParameters();
- integer_constraints::Bool = false,
- constraints = nothing, variable_type::Type{T} = Float64,
- kwargs...) where {T}
-
+ AD::Optimization.ADTypes.AbstractADType,
+ u0::ComponentVector = get_initial_variables(prob), p = SciMLBase.NullParameters();
+ integer_constraints::Bool = false,
+ constraints = nothing, variable_type::Type{T} = Float64,
+ kwargs...) where {T}
  u0 = T.(u0)
  p = !isa(p, SciMLBase.NullParameters) ? T.(p) : p
 

src/utilities.jl

@@ -48,7 +48,7 @@ function compute_local_information_gain(Qs::AbstractVector)
  n_h = size(first(Qs), 1)
  map(1:n_h) do i
  map(Qs) do Qi
- (Qi[i:i,:]'Qi[i:i,:])
+ (Qi[i:i, :]'Qi[i:i, :])
  end
  end
 end

test/references/1D.jl

@@ -54,7 +54,7 @@ oed = structural_simplify(oed)
  integer_constraints = false)
  res = solve(opt_prob, optimizer)
 
- @test isapprox(res.u[1:end-1],
+ @test isapprox(res.u[1:(end - 1)],
  [0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],
  atol = 1e-5,
  rtol = 1e-1)
@@ -95,8 +95,7 @@ end
  integer_constraints = true)
  res = solve(opt_prob, optimizer)
 
-
- @test isapprox(res.u[1:end-1],
+ @test isapprox(res.u[1:(end - 1)],
  [0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0],
  atol = 1e-5,
  rtol = 1e-1)