Remove Groebner Basis dependency

Project.toml

@@ -8,13 +8,13 @@ AbstractAlgebra = "c3fe647b-3220-5bb0-a1ea-a7954cac585d"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
-GroebnerBasis = "e39c9192-ea4d-5e15-9584-a488c6d614bd"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 Nemo = "2edaba10-b0f1-5616-af89-8c11ac63239a"
+Oscar = "f1435218-dba5-11e9-1e4d-f1a5fab5fc13"
 Primes = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae"
 Singular = "bcd08a7b-43d2-5ff7-b6d4-c458787f915c"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
@@ -24,11 +24,11 @@ TestSetExtensions = "98d24dd4-01ad-11ea-1b02-c9a08f80db04"
 [compat]
 AbstractAlgebra = "0.13, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23"
 DataStructures = "0.18"
-GroebnerBasis = "0.1, 0.2, 0.3"
 IterTools = "1"
 MacroTools = "0.5"
 ModelingToolkit = "7, 8"
 Nemo = "0.24, 0.25, 0.26, 0.27, 0.28"
+Oscar = "0.7"
 Primes = "0.5"
 Singular = "0.4, 0.5, 0.6, 0.7, 0.8, 0.9"
 SpecialFunctions = "1, 2"

examples/CRN.jl

@@ -5,8 +5,8 @@ using Logging
 
 using StructuralIdentifiability
 
-logger = Logging.SimpleLogger(stdout, Logging.Info)
-global_logger(logger)
+# logger = Logging.SimpleLogger(stdout, Logging.Info)
+# global_logger(logger)
 
 ode = @ODEmodel(
     x1'(t) = -k1 * x1(t) * x2(t) + k2 * x4(t) + k4 * x6(t),

src/StructuralIdentifiability.jl

@@ -13,7 +13,8 @@ using DataStructures
 # Algebra packages
 using AbstractAlgebra
 using Nemo
-using GroebnerBasis
+# using GroebnerBasis
+using Oscar
 using Singular
 
 # For testing (TODO: move to the test-specific dependencies)

src/global_identifiability.jl

@@ -52,9 +52,9 @@ function check_field_membership(
     @debug "\tPoint is $point"
 
     @debug "Constructing the equations"
-    eqs_sing = Array{Singular.spoly{Singular.n_Q},1}()
-    ring_sing, vars_sing = Singular.PolynomialRing(
-                               Singular.QQ, 
+    eqs_sing = Array{Nemo.gfp_mpoly,1}()
+    ring_sing, vars_sing = Oscar.PolynomialRing(
+                               Oscar.FiniteField(536870909), #Singular.QQ, 
                                vcat(map(var_to_str, gens(ring)), ["sat_aux$i" for i in 1:length(generators)]);
                                # vcat(map(var_to_str, gens(ring)), ["sat_aux"]);
                                ordering=:degrevlex
@@ -82,11 +82,10 @@ function check_field_membership(
     if method == :Singular
         gb = Singular.std(Singular.Ideal(ring_sing, eqs_sing))
     elseif method == :GroebnerBasis
-        gb = GroebnerBasis.f4(Singular.Ideal(ring_sing, eqs_sing))
+        gb = Oscar.f4(Oscar.ideal(ring_sing, eqs_sing))
     else
         throw(Base.ArgumentError("Unknown method $method"))
     end
-    # @debug gens(gb)
 
     @debug "Producing the result"
     flush(stdout)
@@ -95,7 +94,7 @@ function check_field_membership(
         num, den = unpack_fraction(f)
         poly = num * evaluate(den, point) - den * evaluate(num, point)
         poly_sing = parent_ring_change(poly, ring_sing)
-        push!(result, iszero(Singular.reduce(poly_sing, gb)))
+        push!(result, iszero(Oscar.reduce(poly_sing, gb)))
     end
     return result
 end