Fix type piracy

Project.toml

@@ -26,28 +26,28 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 
 [compat]
-AbstractAlgebra = "0.27, 0.28, 0.29, 0.30, 0.31, 0.32, 0.33, 0.34, 0.35"
+AbstractAlgebra = "0.34.5, 0.35"
 BenchmarkTools = "1"
 Combinatorics = "1"
 DataStructures = "0.18"
-Dates = "1.6, 1.7"
-Groebner = "0.4, 0.5, 0.6"
+Dates = "1.6"
+Groebner = "0.6.3"
 IterTools = "1"
-LinearAlgebra = "1.6, 1.7"
-Logging = "1.6, 1.7"
+LinearAlgebra = "1.6"
+Logging = "1.6"
 MacroTools = "0.5"
-ModelingToolkit = "8.51"
-Nemo = "0.32, 0.33, 0.34, 0.35, 0.36, 0.37, 0.38, 0.39"
-ParamPunPam = "0.2"
-PrecompileTools = "1.1, 1.2"
+ModelingToolkit = "8.75"
+Nemo = "0.38.3, 0.39"
+ParamPunPam = "0.3.1"
+PrecompileTools = "1.2"
 Primes = "0.5"
-Random = "1.6, 1.7"
-SpecialFunctions = "1, 2"
-SymbolicUtils = "1"
-Symbolics = "5.5"
+Random = "1.6"
+SpecialFunctions = "2"
+SymbolicUtils = "1.5"
+Symbolics = "5.16"
 TestSetExtensions = "2"
 TimerOutputs = "0.5"
-julia = "1.6, 1.7"
+julia = "1.6"
 
 [extras]
 CPUSummary = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"

benchmarking/IdentifiableFunctions/experiments.jl

@@ -1116,7 +1116,7 @@ end
 #! format: off
 
 new_rff = StructuralIdentifiability.RationalFunctionField(funcs1)
-cfs = StructuralIdentifiability.beautifuly_generators(new_rff)
+cfs = StructuralIdentifiability.beautiful_generators(new_rff)
 gb_rff = StructuralIdentifiability.RationalFunctionField(cfs)
 
 K = GF(2^31 - 1)

benchmarking/IdentifiableFunctions/homogenization.jl

@@ -15,7 +15,7 @@ Bilirubin2_io = @ODEmodel(
 funcs = find_identifiable_functions(Bilirubin2_io, with_states = true, strategy = (:gb,))
 
 rff = StructuralIdentifiability.RationalFunctionField(funcs)
-cfs = StructuralIdentifiability.beautifuly_generators(rff)
+cfs = StructuralIdentifiability.beautiful_generators(rff)
 rff = StructuralIdentifiability.RationalFunctionField(cfs)
 
 K = GF(2^31 - 1)

src/RationalFunctionFields/RationalFunctionField.jl

@@ -212,7 +212,7 @@ end
 # ------------------------------------------------------------------------------
 
 """
-    beautifuly_generators(rff::RationalFunctionField)
+    beautiful_generators(rff::RationalFunctionField)
 
 Given a field of rational functions `rff` returns a set of "simpler" and
 standardized generators for `rff`.
@@ -221,7 +221,7 @@ Applies the following passes:
 1. Filter constants,
 2. Remove redundant generators.
 """
-@timeit _to function beautifuly_generators(
+@timeit _to function beautiful_generators(
     rff::RationalFunctionField;
     discard_redundant = true,
     reversed_order = false,
@@ -402,7 +402,7 @@ Returns a set of Groebner bases for multiple different rankings of variables.
     # The first basis in some ordering
     ord = InputOrdering()
     new_rff = groebner_basis_coeffs(rff, seed = seed, ordering = ord)
-    cfs = beautifuly_generators(new_rff)
+    cfs = beautiful_generators(new_rff)
     ordering_to_generators[ord] = cfs
     if isempty(cfs)
         return ordering_to_generators
@@ -427,7 +427,7 @@ Returns a set of Groebner bases for multiple different rankings of variables.
                 ordering = ord,
                 up_to_degree = up_to_degree,
             )
-            cfs = beautifuly_generators(new_rff, discard_redundant = false)
+            cfs = beautiful_generators(new_rff, discard_redundant = false)
             ordering_to_generators[ord] = cfs
         end
     end
@@ -444,7 +444,7 @@ Returns a set of Groebner bases for multiple different rankings of variables.
                 ordering = ord,
                 up_to_degree = up_to_degree,
             )
-            cfs = beautifuly_generators(new_rff, discard_redundant = false)
+            cfs = beautiful_generators(new_rff, discard_redundant = false)
             ordering_to_generators[ord] = cfs
         end
     end
@@ -462,7 +462,7 @@ Returns a set of Groebner bases for multiple different rankings of variables.
                 ordering = ord,
                 up_to_degree = up_to_degree,
             )
-            cfs = beautifuly_generators(new_rff, discard_redundant = false)
+            cfs = beautiful_generators(new_rff, discard_redundant = false)
             ordering_to_generators[ord] = cfs
         end
     end
@@ -479,7 +479,7 @@ function monomial_generators_up_to_degree(
 ) where {T}
     @assert strategy in (:monte_carlo,)
     relations = linear_relations_between_normal_forms(
-        beautifuly_generators(rff),
+        beautiful_generators(rff),
         up_to_degree,
         seed = seed,
     )
@@ -544,7 +544,7 @@ Result is correct (in the Monte-Carlo sense) with probability at least `prob_thr
         seed = seed,
         rational_interpolator = rational_interpolator,
     )
-    new_fracs = beautifuly_generators(new_rff)
+    new_fracs = beautiful_generators(new_rff)
     if isempty(new_fracs)
         return new_fracs
     end
@@ -568,10 +568,9 @@ Result is correct (in the Monte-Carlo sense) with probability at least `prob_thr
 Final cleaning and simplification of generators. 
 Out of $(length(new_fracs)) fractions $(length(new_fracs_unique)) are syntactically unique."""
     runtime =
-        @elapsed new_fracs = beautifuly_generators(RationalFunctionField(new_fracs_unique))
+        @elapsed new_fracs = beautiful_generators(RationalFunctionField(new_fracs_unique))
     @debug "Checking inclusion with probability $prob_threshold"
-    runtime =
-        @elapsed result = issubfield(rff, RationalFunctionField(new_fracs), prob_threshold)
+    runtime = @elapsed result = issubfield(rff, RationalFunctionField(new_fracs), p)
     _runtime_logger[:id_inclusion_check] = runtime
     if !result
         @warn "Field membership check failed. Error will follow."

src/discrete.jl

@@ -215,7 +215,7 @@ function _assess_local_identifiability_discrete_aux(
     deg_x = _degree_with_common_denom(values(dds.x_equations))
     deg_y = _degree_with_common_denom(values(dds.y_equations))
     deg_known = reduce(+, map(total_degree, known_ic), init = 0)
-    deg_to_check = max(map(total_degree, funcs_to_check)...)
+    deg_to_check = max(map(total_degree_frac, funcs_to_check)...)
     Jac_degree = deg_to_check + deg_known
     if deg_x > 1
         Jac_degree += 2 * deg_y * ((deg_x^prec - 1) ÷ (deg_x - 1))

src/util.jl

@@ -1,10 +1,6 @@
 # ------------------------------------------------------------------------------
 
-function Nemo.vars(f::Generic.Frac{<:MPolyElem})
-    return collect(union(Set(vars(numerator(f))), Set(vars(denominator(f)))))
-end
-
-function Nemo.total_degree(f::Generic.Frac{<:MPolyElem})
+function total_degree_frac(f::Generic.Frac{<:MPolyElem})
     return sum(map(total_degree, unpack_fraction(f)))
 end