Merge pull request #1771 from SciML/myb/strong_alias

WIP: Strong alias elimination

Author: YingboMa

Project.toml

@@ -36,6 +36,7 @@ RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
+SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -72,6 +73,7 @@ Reexport = "0.2, 1"
 RuntimeGeneratedFunctions = "0.4.3, 0.5"
 SciMLBase = "1.58.0"
 Setfield = "0.7, 0.8, 1"
+SimpleWeightedGraphs = "1"
 SpecialFunctions = "0.7, 0.8, 0.9, 0.10, 1.0, 2"
 StaticArrays = "0.10, 0.11, 0.12, 1.0"
 SymbolicUtils = "0.19"
@@ -93,9 +95,9 @@ OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ReferenceTests = "324d217c-45ce-50fc-942e-d289b448e8cf"
+SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"

src/bipartite_graph.jl

@@ -470,19 +470,23 @@ function set_neighbors!(g::BipartiteGraph, i::Integer, new_neighbors)
         for n in old_neighbors
             @inbounds list = g.badjlist[n]
             index = searchsortedfirst(list, i)
-            deleteat!(list, index)
+            if 1 <= index <= length(list) && list[index] == i
+                deleteat!(list, index)
+            end
         end
         for n in new_neighbors
             @inbounds list = g.badjlist[n]
             index = searchsortedfirst(list, i)
-            insert!(list, index, i)
+            if !(1 <= index <= length(list) && list[index] == i)
+                insert!(list, index, i)
+            end
         end
     end
     if iszero(new_nneighbors) # this handles Tuple as well
         # Warning: Aliases old_neighbors
         empty!(g.fadjlist[i])
     else
-        g.fadjlist[i] = copy(new_neighbors)
+        g.fadjlist[i] = unique!(sort(new_neighbors))
     end
 end
 

src/structural_transformation/utils.jl

@@ -218,7 +218,7 @@ highest_order_variable_mask(ts) =
 
 lowest_order_variable_mask(ts) =
     let v2d = ts.structure.var_to_diff
-        v -> isempty(outneighbors(v2d, v))
+        v -> isempty(inneighbors(v2d, v))
     end
 
 function but_ordered_incidence(ts::TearingState, varmask = highest_order_variable_mask(ts))

src/systems/abstractsystem.jl

@@ -1031,7 +1031,7 @@ function linearization_function(sys::AbstractSystem, inputs,
         input_idxs = input_idxs,
         sts = states(sys),
         fun = ODEFunction{true, SciMLBase.FullSpecialize}(sys),
-        h = ModelingToolkit.build_explicit_observed_function(sys, outputs),
+        h = build_explicit_observed_function(sys, outputs),
         chunk = ForwardDiff.Chunk(input_idxs)
 
         function (u, p, t)