Update tests and fix infinite loop

Author: YingboMa

src/systems/alias_elimination.jl

@@ -743,6 +743,9 @@ function alias_eliminate_graph!(state::TransformationState, mm_orig::SparseMatri
             end
             if r === nothing
                 isempty(reach₌) && break
+                let stem_set = stem_set
+                    any(x -> x[2] in stem_set, reach₌) && break
+                end
                 # See example in the box above where D(D(D(z))) doesn't appear
                 # in the original system and needs to added, so we can alias to it.
                 # We do that here.
@@ -907,8 +910,9 @@ function alias_eliminate_graph!(state::TransformationState, mm_orig::SparseMatri
         merged_ag[v] = c => a
     end
     ag = merged_ag
-    echelon_mm = resize_cols(echelon_mm, length(var_to_diff))
-    mm = reduce!(echelon_mm, mm_orig, ag, size(echelon_mm, 1))
+    @set! echelon_mm.ncols = length(var_to_diff)
+    @set! mm_orig.ncols = length(var_to_diff)
+    mm = reduce!(copy(echelon_mm), mm_orig, ag, size(echelon_mm, 1))
 
     # Step 5: Reflect our update decisions back into the graph, and make sure
     # that the RHS of observable variables are defined.

src/systems/sparsematrixclil.jl

@@ -41,11 +41,6 @@ function SparseMatrixCLIL(mm::AbstractMatrix)
     SparseMatrixCLIL(nrows, ncols, Int[1:length(row_cols);], row_cols, row_vals)
 end
 
-function resize_cols(mm::SparseMatrixCLIL, nc)
-    @set! mm.ncols = nc
-    copy(mm)
-end
-
 struct CLILVector{T, Ti} <: AbstractSparseVector{T, Ti}
     vec::SparseVector{T, Ti}
 end

test/reduction.jl

@@ -256,7 +256,7 @@ eqs = [a ~ D(w)
 @named sys = ODESystem(eqs, t, vars, [])
 ss = alias_elimination(sys)
 @test equations(ss) == [0 ~ D(D(phi)) - a, 0 ~ sin(t) - D(phi)]
-@test observed(ss) == [w ~ D(phi)]
+@test observed(ss) == [w ~ D(phi), D(w) ~ D(D(phi))]
 
 @variables t x(t) y(t)
 D = Differential(t)