rafactor: make all import explicit (#189)

Author: oameye

Project.toml

@@ -5,6 +5,7 @@ repo = "https://github.com/juliadynamics/CriticalTransitions.jl.git"
 version = "0.6.0"
 
 [deps]
+ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
@@ -21,6 +22,7 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StateSpaceSets = "40b095a5-5852-4c12-98c7-d43bf788e795"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
@@ -29,7 +31,6 @@ StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 Attractors = "f3fd9213-ca85-4dba-9dfd-7fc91308fec7"
 ChaosTools = "608a59af-f2a3-5ad4-90b4-758bdf3122a7"
 DelaunayTriangulation = "927a84f5-c5f4-47a5-9785-b46e178433df"
-StateSpaceSets = "40b095a5-5852-4c12-98c7-d43bf788e795"
 
 [extensions]
 AttractorsExt = ["Attractors"]
@@ -39,6 +40,7 @@ DistMesh2D = ["DelaunayTriangulation"]
 [compat]
 Attractors = "1.23.3"
 ChaosTools = "3.3.1"
+ConstructionBase = "1.6.0"
 DataStructures = "0.18.20, 0.19"
 DelaunayTriangulation = "1.6"
 DocStringExtensions = "0.9.3"

src/CriticalTransitions.jl

@@ -9,8 +9,7 @@ using DataStructures: CircularBuffer
 using Random: Random
 
 # Core
-using SciMLBase: EnsembleThreads, DiscreteCallback, remake, terminate!
-using StochasticDiffEq: StochasticDiffEq
+using SciMLBase: SciMLBase, EnsembleThreads, DiscreteCallback, remake, terminate!, isinplace
 using DynamicalSystemsBase:
     DynamicalSystemsBase,
     CoupledSDEs,
@@ -20,10 +19,13 @@ using DynamicalSystemsBase:
     set_state!,
     trajectory,
     jacobian,
-    StateSpaceSet
+    ContinuousTimeDynamicalSystem
+using ConstructionBase: ConstructionBase
+using StateSpaceSets: StateSpaceSets, dimension, StateSpaceSet
+using StochasticDiffEq: StochasticDiffEq
 
 using Interpolations: linear_interpolation
-using Optimization
+using Optimization: Optimization
 using OptimizationOptimisers: Optimisers
 using LinearSolve: LinearProblem, KLUFactorization, solve
 

src/largedeviations/geometric_min_action_method.jl

@@ -81,8 +81,8 @@ function geometric_min_action_method(
         #     next!(prog)
         # end
     else
-        optf = OptimizationFunction((x, _) -> S(x), AD)
-        prob = OptimizationProblem(optf, init, ())
+        optf = SciMLBase.OptimizationFunction((x, _) -> S(x), AD)
+        prob = SciMLBase.OptimizationProblem(optf, init, ())
 
         function callback(state, loss_val)
             interpolate_path!(state.u, alpha, arc)

src/largedeviations/min_action_method.jl

@@ -4,7 +4,7 @@
 Minimizes an action functional to obtain a minimum action path (instanton) between an
 initial state `x_i` and final state `x_f` in phase space.
 
-This algorithm uses the 
+This algorithm uses the
 [`Optimization.jl`](https://github.com/SciML/Optimization.jl) package to minimize the
 specified action functional (either [`fw_action`](@ref) or [`om_action`](@ref))
 for the system `sys` over paths connecting `x_i` to `x_f` in time `T`.
@@ -74,8 +74,8 @@ function min_action_method(
         sys, fix_ends(x, init[:, 1], init[:, end]), times, functional; noise_strength
     )
 
-    optf = OptimizationFunction((x, _) -> S(x), ad_type)
-    prob = OptimizationProblem(optf, init, ())
+    optf = SciMLBase.OptimizationFunction((x, _) -> S(x), ad_type)
+    prob = SciMLBase.OptimizationProblem(optf, init, ())
 
     prog = Progress(maxiter; enabled=show_progress)
     function callback(state, loss_val)

src/trajectories/transition.jl

@@ -59,7 +59,9 @@ function prepare_transition_problem(sys, x, radii, radius_directions, tmax)
     return prob, cb_ball
 end
 
-remove_start(sol, idx) = SciMLBase.setproperties(sol; u=sol.u[idx:end], t=sol.t[idx:end])
+function remove_start(sol, idx)
+    ConstructionBase.setproperties(sol; u=sol.u[idx:end], t=sol.t[idx:end])
+end
 function remove_start(sol, x_i, rad_i)
     idx = size(sol)[2]
     dist = norm(sol[:, idx] - x_i)
@@ -134,7 +136,7 @@ function transitions(
         return remake(prob; seed=rand(Random.MersenneTwister(seed + i + repeat), UInt32))
     end
 
-    ensemble = EnsembleProblem(prob; output_func=output_func, prob_func=prob_func)
+    ensemble = SciMLBase.EnsembleProblem(prob; output_func=output_func, prob_func=prob_func)
     sim = solve(
         ensemble, solver(sys), EnsembleAlg; callback=cb_ball, trajectories=N, kwargs...
     )

test/code_quality.jl

@@ -19,13 +19,26 @@ end
 @testset "ExplicitImports" begin
     using ExplicitImports
 
-    # @test check_no_implicit_imports(CriticalTransitions) == nothing
+    @test check_no_implicit_imports(CriticalTransitions) == nothing
     @test check_all_explicit_imports_via_owners(CriticalTransitions) == nothing
-    # @test check_all_explicit_imports_are_public(CriticalTransitions) == nothing
+    @test check_all_explicit_imports_are_public(CriticalTransitions) == nothing
     @test check_no_stale_explicit_imports(CriticalTransitions) == nothing
-    # @test check_all_qualified_accesses_via_owners(CriticalTransitions) == nothing
-    # @test check_all_qualified_accesses_are_public(KeldyshContraction) == nothing
-    # @test check_no_self_qualified_accesses(CriticalTransitions) == nothing
+    @test check_all_qualified_accesses_via_owners(CriticalTransitions) == nothing
+    @test isnothing(
+        check_all_qualified_accesses_are_public(
+            CriticalTransitions;
+            skip=(Base => Base.Experimental, Base => Core),
+            ignore=(
+                :EnsembleAlgorithm,
+                :Terminated,
+                :covariance_matrix,
+                :diffusion_matrix,
+                :get_extension,
+                :register_error_hint,
+            ),
+        ),
+    )
+    @test check_no_self_qualified_accesses(CriticalTransitions) == nothing
 end
 
 if isempty(VERSION.prerelease)