Have CI tests depend on formatter passing (#2451)

chriselrod · web-flow · commit 85801be7dcd7 · 2024-02-08T00:53:15.000-05:00
diff --git a/.github/workflows/FormatCheck.yml b/.github/workflows/FormatCheck.yml
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -3,6 +3,7 @@ on:
   pull_request:
     branches:
       - master
+      - 'release-'
     paths-ignore:
       - 'docs/**'
   push:
@@ -18,7 +19,39 @@ concurrency:
   cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}
 
 jobs:
+  formatter:
+    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`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'
   test:
+    needs: formatter
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
diff --git a/docs/src/tutorials/bifurcation_diagram_computation.md b/docs/src/tutorials/bifurcation_diagram_computation.md
@@ -56,7 +56,7 @@ Let us consider the `BifurcationProblem` from the last section. If we wish to co
 ```@example Bif1
 p_span = (-4.0, 6.0)
 opts_br = ContinuationPar(nev = 2,
-    p_min = p_span[1], 
+    p_min = p_span[1],
     p_max = p_span[2])
 ```
 
@@ -111,8 +111,7 @@ bprob = BifurcationProblem(osys,
 
 p_span = (-3.0, 3.0)
 opts_br = ContinuationPar(nev = 2,
-    p_max = p_span[2], p_min = p_span[1],
-    )
+    p_max = p_span[2], p_min = p_span[1])
 
 bf = bifurcationdiagram(bprob, PALC(), 2, (args...) -> opts_br; bothside = true)
 using Plots
@@ -130,21 +129,19 @@ We compute the branch of periodic orbits which is nearby the Hopf Bifurcation. W
 
 ```@example Bif2
 br_po = continuation(bf.γ, 2, opts_br,
-    PeriodicOrbitOCollProblem(20, 5);
-    )
+    PeriodicOrbitOCollProblem(20, 5);)
 
 plot(bf; putspecialptlegend = false,
     markersize = 2,
     plotfold = false,
     xguide = "μ",
     yguide = "x")
-plot!(br_po,  xguide = "μ", yguide = "x", label = "Maximum of periodic orbit")
+plot!(br_po, xguide = "μ", yguide = "x", label = "Maximum of periodic orbit")
 ```
 
 Let's see how to plot the periodic solution we just computed:
 
 ```@example Bif2
 sol = get_periodic_orbit(br_po, 10)
-plot(sol.t, sol[1,:], yguide = "x", xguide = "time", label = "")
+plot(sol.t, sol[1, :], yguide = "x", xguide = "time", label = "")
 ```
-
diff --git a/docs/src/tutorials/optimization.md b/docs/src/tutorials/optimization.md
@@ -71,7 +71,12 @@ cons = [
 @named sys = OptimizationSystem(loss, [x, y], [a, b], constraints = cons)
 u0 = [x => 0.14
     y => 0.14]
-prob = OptimizationProblem(complete(sys), u0, grad = true, hess = true, cons_j = true, cons_h = true)
+prob = OptimizationProblem(complete(sys),
+    u0,
+    grad = true,
+    hess = true,
+    cons_j = true,
+    cons_h = true)
 solve(prob, IPNewton())
 ```
 
diff --git a/src/structural_transformation/symbolics_tearing.jl b/src/structural_transformation/symbolics_tearing.jl
@@ -541,8 +541,8 @@ function tearing_reassemble(state::TearingState, var_eq_matching;
     sys = state.sys
     @set! sys.eqs = neweqs
     @set! sys.unknowns = Any[v
-                           for (i, v) in enumerate(fullvars)
-                               if diff_to_var[i] === nothing && ispresent(i)]
+                             for (i, v) in enumerate(fullvars)
+                                 if diff_to_var[i] === nothing && ispresent(i)]
     @set! sys.substitutions = Substitutions(subeqs, deps)
 
     obs_sub = dummy_sub
diff --git a/src/systems/abstractsystem.jl b/src/systems/abstractsystem.jl
@@ -921,7 +921,9 @@ function toexpr(sys::AbstractSystem)
                 name = $name, checks = false)))
     end
 
-    expr = :(let; $expr; end)
+    expr = :(let
+        $expr
+    end)
     Base.remove_linenums!(expr) # keeping the line numbers is never helpful
 end
 
diff --git a/src/systems/connectors.jl b/src/systems/connectors.jl
@@ -270,7 +270,8 @@ function connection2set!(connectionsets, namespace, ss, isouter)
             orientation_vars = Symbolics.unwrap.(vec(O.R))
             unknown_vars = [unknown_vars; orientation_vars]
         end
-        i != 1 && ((num_unknowns == length(unknown_vars) && all(Base.Fix2(in, sts1), unknown_vars)) ||
+        i != 1 && ((num_unknowns == length(unknown_vars) &&
+          all(Base.Fix2(in, sts1), unknown_vars)) ||
          connection_error(ss))
         io = isouter(s)
         for (j, v) in enumerate(unknown_vars)
@@ -410,7 +411,7 @@ end
 
 function generate_connection_equations_and_stream_connections(csets::AbstractVector{
         <:ConnectionSet,
-    })
+})
     eqs = Equation[]
     stream_connections = ConnectionSet[]
 
@@ -605,7 +606,8 @@ function expand_instream(csets::AbstractVector{<:ConnectionSet}, sys::AbstractSy
         vtype = get_connection_type(sv)
         vtype === Stream || continue
         if n_inners == 1 && n_outers == 1
-            push!(additional_eqs, unknowns(cset[1].sys.sys, sv) ~ unknowns(cset[2].sys.sys, sv))
+            push!(additional_eqs,
+                unknowns(cset[1].sys.sys, sv) ~ unknowns(cset[2].sys.sys, sv))
         elseif n_inners == 0 && n_outers == 2
             # we don't expand `instream` in this case.
             v1 = unknowns(cset[1].sys.sys, sv)
@@ -664,7 +666,8 @@ function expand_instream(csets::AbstractVector{<:ConnectionSet}, sys::AbstractSy
 end
 
 function get_current_var(namespace, cele, sv)
-    unknowns(renamespace(unnamespace(namespace, _getname(cele.sys.namespace)), cele.sys.sys),
+    unknowns(renamespace(unnamespace(namespace, _getname(cele.sys.namespace)),
+            cele.sys.sys),
         sv)
 end
 
diff --git a/src/systems/diffeqs/abstractodesystem.jl b/src/systems/diffeqs/abstractodesystem.jl
@@ -101,7 +101,8 @@ function generate_tgrad(sys::AbstractODESystem, dvs = unknowns(sys), ps = parame
     end
 end
 
-function generate_jacobian(sys::AbstractODESystem, dvs = unknowns(sys), ps = parameters(sys);
+function generate_jacobian(sys::AbstractODESystem, dvs = unknowns(sys),
+        ps = parameters(sys);
         simplify = false, sparse = false, kwargs...)
     jac = calculate_jacobian(sys; simplify = simplify, sparse = sparse)
     pre = get_preprocess_constants(jac)
@@ -139,7 +140,8 @@ function generate_dae_jacobian(sys::AbstractODESystem, dvs = unknowns(sys),
         postprocess_fbody = pre, kwargs...)
 end
 
-function generate_function(sys::AbstractODESystem, dvs = unknowns(sys), ps = parameters(sys);
+function generate_function(sys::AbstractODESystem, dvs = unknowns(sys),
+        ps = parameters(sys);
         implicit_dae = false,
         ddvs = implicit_dae ? map(Differential(get_iv(sys)), dvs) :
                nothing,
@@ -294,7 +296,8 @@ function DiffEqBase.ODEFunction{false}(sys::AbstractODESystem, args...;
     ODEFunction{false, SciMLBase.FullSpecialize}(sys, args...; kwargs...)
 end
 
-function DiffEqBase.ODEFunction{iip, specialize}(sys::AbstractODESystem, dvs = unknowns(sys),
+function DiffEqBase.ODEFunction{iip, specialize}(sys::AbstractODESystem,
+        dvs = unknowns(sys),
         ps = parameters(sys), u0 = nothing;
         version = nothing, tgrad = false,
         jac = false, p = nothing,
diff --git a/src/systems/diffeqs/sdesystem.jl b/src/systems/diffeqs/sdesystem.jl
@@ -260,7 +260,8 @@ function stochastic_integral_transform(sys::SDESystem, correction_factor)
         ∇σσ′ = simplify.(jac * get_noiseeqs(sys)[:, 1])
         for k in 2:m
             eqs = vcat([equations(sys)[i].lhs ~ get_noiseeqs(sys)[Int(i +
-                                                                      (k - 1) * dimunknowns)]
+                                                                      (k - 1) *
+                                                                      dimunknowns)]
                         for i in eachindex(unknowns(sys))]...)
             de = ODESystem(eqs, get_iv(sys), unknowns(sys), parameters(sys), name = name,
                 checks = false)
diff --git a/src/systems/jumps/jumpsystem.jl b/src/systems/jumps/jumpsystem.jl
@@ -102,7 +102,8 @@ struct JumpSystem{U <: ArrayPartition} <: AbstractTimeDependentSystem
     """
     complete::Bool
 
-    function JumpSystem{U}(tag, ap::U, iv, unknowns, ps, var_to_name, observed, name, systems,
+    function JumpSystem{U}(tag, ap::U, iv, unknowns, ps, var_to_name, observed, name,
+            systems,
             defaults, connector_type, devents,
             metadata = nothing, gui_metadata = nothing,
             complete = false;
@@ -119,7 +120,9 @@ struct JumpSystem{U <: ArrayPartition} <: AbstractTimeDependentSystem
             connector_type, devents, metadata, gui_metadata, complete)
     end
 end
-JumpSystem(tag, ap, iv, states, ps, var_to_name, args...; kwargs...) = JumpSystem{typeof(ap)}(tag, ap, iv, states, ps, var_to_name, args...; kwargs...)
+function JumpSystem(tag, ap, iv, states, ps, var_to_name, args...; kwargs...)
+    JumpSystem{typeof(ap)}(tag, ap, iv, states, ps, var_to_name, args...; kwargs...)
+end
 
 function JumpSystem(eqs, iv, unknowns, ps;
         observed = Equation[],
@@ -498,7 +501,7 @@ function (ratemap::JumpSysMajParamMapper{
         U,
         V,
         W,
-    })(params) where {U <: AbstractArray,
+})(params) where {U <: AbstractArray,
         V <: AbstractArray, W}
     updateparams!(ratemap, params)
     [convert(W, value(substitute(paramexpr, ratemap.subdict)))
diff --git a/src/systems/optimization/constraints_system.jl b/src/systems/optimization/constraints_system.jl
@@ -176,7 +176,8 @@ function generate_hessian(sys::ConstraintsSystem, vs = unknowns(sys), ps = param
     return build_function(hess, vs, ps; kwargs...)
 end
 
-function generate_function(sys::ConstraintsSystem, dvs = unknowns(sys), ps = parameters(sys);
+function generate_function(sys::ConstraintsSystem, dvs = unknowns(sys),
+        ps = parameters(sys);
         kwargs...)
     lhss = generate_canonical_form_lhss(sys)
     pre, sol_states = get_substitutions_and_solved_unknowns(sys)
diff --git a/src/systems/optimization/optimizationsystem.jl b/src/systems/optimization/optimizationsystem.jl
@@ -125,7 +125,8 @@ function calculate_gradient(sys::OptimizationSystem)
     expand_derivatives.(gradient(objective(sys), unknowns(sys)))
 end
 
-function generate_gradient(sys::OptimizationSystem, vs = unknowns(sys), ps = parameters(sys);
+function generate_gradient(sys::OptimizationSystem, vs = unknowns(sys),
+        ps = parameters(sys);
         kwargs...)
     grad = calculate_gradient(sys)
     pre = get_preprocess_constants(grad)
@@ -149,7 +150,8 @@ function generate_hessian(sys::OptimizationSystem, vs = unknowns(sys), ps = para
         kwargs...)
 end
 
-function generate_function(sys::OptimizationSystem, vs = unknowns(sys), ps = parameters(sys);
+function generate_function(sys::OptimizationSystem, vs = unknowns(sys),
+        ps = parameters(sys);
         kwargs...)
     eqs = subs_constants(objective(sys))
     return build_function(eqs, vs, ps;
diff --git a/src/systems/systems.jl b/src/systems/systems.jl
@@ -81,9 +81,9 @@ function __structural_simplify(sys::AbstractSystem, io = nothing; simplify = fal
         sys = state.sys
         @set! sys.eqs = new_eqs
         @set! sys.unknowns = [v
-                            for (i, v) in enumerate(fullvars)
-                                if !iszero(new_idxs[i]) &&
-                                   invview(var_to_diff)[i] === nothing]
+                              for (i, v) in enumerate(fullvars)
+                                  if !iszero(new_idxs[i]) &&
+                                     invview(var_to_diff)[i] === nothing]
         # TODO: IO is not handled.
         ode_sys = structural_simplify(sys, io; simplify, kwargs...)
         eqs = equations(ode_sys)
diff --git a/src/utils.jl b/src/utils.jl
@@ -445,7 +445,6 @@ function collect_vars!(unknowns, parameters, expr, iv)
     return nothing
 end
 
-
 function collect_var!(unknowns, parameters, var, iv)
     isequal(var, iv) && return nothing
     if isparameter(var) || (istree(var) && isparameter(operation(var)))
diff --git a/test/funcaffect.jl b/test/funcaffect.jl
@@ -223,7 +223,8 @@ balls = compose(balls, [ball1, ball2])
 @test ModelingToolkit.has_discrete_events(balls)
 @test length(ModelingToolkit.affects(ModelingToolkit.discrete_events(balls))) == 2
 
-prob = ODEProblem(complete(balls), [ball1.x => 10.0, ball1.v => 0, ball2.x => 10.0, ball2.v => 0],
+prob = ODEProblem(complete(balls),
+    [ball1.x => 10.0, ball1.v => 0, ball2.x => 10.0, ball2.v => 0],
     (0, 3.0))
 sol = solve(prob, Tsit5())
 
diff --git a/test/jacobiansparsity.jl b/test/jacobiansparsity.jl
@@ -45,7 +45,8 @@ sys = complete(modelingtoolkitize(prob_ode_brusselator_2d))
 # test sparse jacobian pattern only.
 prob = ODEProblem(sys, u0, (0, 11.5), sparse = true, jac = false)
 JP = prob.f.jac_prototype
-@test findnz(Symbolics.jacobian_sparsity(map(x -> x.rhs, equations(sys)), unknowns(sys)))[1:2] ==
+@test findnz(Symbolics.jacobian_sparsity(map(x -> x.rhs, equations(sys)),
+    unknowns(sys)))[1:2] ==
       findnz(JP)[1:2]
 
 # test sparse jacobian
diff --git a/test/nonlinearsystem.jl b/test/nonlinearsystem.jl
@@ -265,7 +265,8 @@ end
 
     sys_init_simple = structural_simplify(sys_init)
 
-    prob = NonlinearProblem(sys_init_simple, get_default_or_guess.(unknowns(sys_init_simple)))
+    prob = NonlinearProblem(sys_init_simple,
+        get_default_or_guess.(unknowns(sys_init_simple)))
 
     @test prob.u0 == [0.5, -0.5]
 
diff --git a/test/odesystem.jl b/test/odesystem.jl
@@ -270,15 +270,15 @@ sol_dpmap = solve(prob_dpmap, Rodas5())
 
 @testset "symbolic remake with nested system" begin
     function makesys(name)
-        @parameters a=1.0
+        @parameters a = 1.0
         @variables x(t) = 0.0
         ODESystem([D(x) ~ -a * x], t; name)
     end
 
     function makecombinedsys()
         sys1 = makesys(:sys1)
         sys2 = makesys(:sys2)
-        @parameters b=1.0
+        @parameters b = 1.0
         complete(ODESystem(Equation[], t, [], [b]; systems = [sys1, sys2], name = :foo))
     end
 
diff --git a/test/optimizationsystem.jl b/test/optimizationsystem.jl
diff --git a/test/reduction.jl b/test/reduction.jl
diff --git a/test/structural_transformation/tearing.jl b/test/structural_transformation/tearing.jl
