Merge pull request #299 from SciML/new_nemo_compat

updating to the newest AA and Nemo

Project.toml

@@ -29,27 +29,27 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 ModelingToolkitSIExt = ["ModelingToolkit", "SymbolicUtils", "Symbolics"]
 
 [compat]
-AbstractAlgebra = "0.34.5, 0.35, 0.36, 0.37, 0.38, 0.39, 0.40"
+AbstractAlgebra = "0.40"
 Aqua = "0.8"
 CPUSummary = "0.2"
 Combinatorics = "1"
 DataStructures = "0.18"
 Dates = "1.6, 1.7"
-Groebner = "0.6.3, 0.7"
+Groebner = "0.7.3"
 IterTools = "1"
 LinearAlgebra = "1.6, 1.7"
 Logging = "1.6, 1.7"
 MacroTools = "0.5"
 ModelingToolkit = "8.75"
-Nemo = "0.38.3, 0.39, 0.40, 0.41, 0.42, 0.43"
-ParamPunPam = "0.3, 0.4"
+Nemo = "0.43"
+ParamPunPam = "0.4"
 Pkg = "1.6, 1.7"
 PrecompileTools = "1.2"
 Primes = "0.5"
 Random = "1.6, 1.7"
 SpecialFunctions = "2"
 SymbolicUtils = "1.4, 1.5"
-Symbolics = "5.16"
+Symbolics = "5.17"
 Test = "1.6, 1.7"
 TestSetExtensions = "2"
 TimerOutputs = "0.5"

ext/ModelingToolkitSIExt.jl

@@ -165,7 +165,7 @@ function __mtk_to_si(
     measured_quantities::Array{<:Tuple{String, <:SymbolicUtils.BasicSymbolic}},
 )
     polytype = StructuralIdentifiability.Nemo.QQMPolyRingElem
-    fractype = StructuralIdentifiability.Nemo.Generic.Frac{polytype}
+    fractype = StructuralIdentifiability.Nemo.Generic.FracFieldElem{polytype}
     diff_eqs =
         filter(eq -> !(ModelingToolkit.isoutput(eq.lhs)), ModelingToolkit.equations(de))
     # performing full structural simplification

src/ODE.jl

@@ -11,14 +11,14 @@ struct ODE{P} # P is the type of polynomials in the rhs of the ODE system
     y_vars::Array{P, 1}
     u_vars::Array{P, 1}
     parameters::Array{P, 1}
-    x_equations::Dict{P, <:Union{P, Generic.Frac{P}}}
-    y_equations::Dict{P, <:Union{P, Generic.Frac{P}}}
+    x_equations::Dict{P, <:ExtendedFraction{P}}
+    y_equations::Dict{P, <:ExtendedFraction{P}}
 
     function ODE{P}(
         x_vars::Array{P, 1},
         y_vars::Array{P, 1},
-        x_eqs::Dict{P, <:Union{P, Generic.Frac{P}}},
-        y_eqs::Dict{P, <:Union{P, Generic.Frac{P}}},
+        x_eqs::Dict{P, <:ExtendedFraction{P}},
+        y_eqs::Dict{P, <:ExtendedFraction{P}},
         inputs::Array{P, 1},
     ) where {P <: MPolyRingElem{<:FieldElem}}
         # Initialize ODE
@@ -37,8 +37,8 @@ struct ODE{P} # P is the type of polynomials in the rhs of the ODE system
     end
 
     function ODE{P}(
-        x_eqs::Dict{P, <:Union{P, Generic.Frac{P}}},
-        y_eqs::Dict{P, <:Union{P, Generic.Frac{P}}},
+        x_eqs::Dict{P, <:ExtendedFraction{P}},
+        y_eqs::Dict{P, <:ExtendedFraction{P}},
         inputs::Array{P, 1},
     ) where {P <: MPolyRingElem{<:FieldElem}}
         x_vars = collect(keys(x_eqs))
@@ -62,19 +62,19 @@ function add_outputs(
     new_ring, new_vars = Nemo.polynomial_ring(base_ring(ode.poly_ring), new_var_names)
 
     new_x = Array{P, 1}([parent_ring_change(x, new_ring) for x in ode.x_vars])
-    new_x_eqs = Dict{P, Union{P, Generic.Frac{P}}}(
+    new_x_eqs = Dict{P, ExtendedFraction{P}}(
         parent_ring_change(x, new_ring) => parent_ring_change(f, new_ring) for
         (x, f) in ode.x_equations
     )
     new_y = Array{P, 1}([parent_ring_change(y, new_ring) for y in ode.y_vars])
     for y in keys(extra_y)
         push!(new_y, str_to_var(y, new_ring))
     end
-    new_y_eqs = Dict{P, Union{P, Generic.Frac{P}}}(
+    new_y_eqs = Dict{P, ExtendedFraction{P}}(
         parent_ring_change(y, new_ring) => parent_ring_change(g, new_ring) for
         (y, g) in ode.y_equations
     )
-    extra_y_eqs = Dict{P, Union{P, Generic.Frac{P}}}(
+    extra_y_eqs = Dict{P, ExtendedFraction{P}}(
         str_to_var(y, new_ring) => parent_ring_change(g, new_ring) for (y, g) in extra_y
     )
     merge!(new_y_eqs, extra_y_eqs)
@@ -106,11 +106,11 @@ function set_parameter_values(
     merge!(eval_dict, Dict(p => small_ring(val) for (p, val) in param_values))
 
     return ODE{P}(
-        Dict{P, Union{P, Generic.Frac{P}}}(
+        Dict{P, ExtendedFraction{P}}(
             eval_at_dict(v, eval_dict) => eval_at_dict(f, eval_dict) for
             (v, f) in ode.x_equations
         ),
-        Dict{P, Union{P, Generic.Frac{P}}}(
+        Dict{P, ExtendedFraction{P}}(
             eval_at_dict(v, eval_dict) => eval_at_dict(f, eval_dict) for
             (v, f) in ode.y_equations
         ),
@@ -225,7 +225,7 @@ function _reduce_mod_p(poly::QQMPolyRingElem, p::Int)
     return change_base_ring(Nemo.Native.GF(p), num) * (1 // Nemo.Native.GF(p)(den))
 end
 
-function _reduce_mod_p(rat::Generic.Frac{QQMPolyRingElem}, p::Int)
+function _reduce_mod_p(rat::Generic.FracFieldElem{QQMPolyRingElem}, p::Int)
     num, den = map(poly -> _reduce_mod_p(poly, p), [numerator(rat), denominator(rat)])
     if den == 0
         throw(Base.ArgumentError("Prime $p divides the denominator of $rat"))
@@ -248,8 +248,8 @@ function reduce_ode_mod_p(ode::ODE{<:MPolyRingElem{Nemo.QQFieldElem}}, p::Int)
     new_inputs = map(u -> switch_ring(u, new_ring), ode.u_vars)
     new_x = map(x -> switch_ring(x, new_ring), ode.x_vars)
     new_y = map(y -> switch_ring(y, new_ring), ode.y_vars)
-    new_x_eqs = Dict{new_type, Union{new_type, Generic.Frac{new_type}}}()
-    new_y_eqs = Dict{new_type, Union{new_type, Generic.Frac{new_type}}}()
+    new_x_eqs = Dict{new_type, ExtendedFraction{new_type}}()
+    new_y_eqs = Dict{new_type, ExtendedFraction{new_type}}()
     for (old, new) in Dict(ode.x_equations => new_x_eqs, ode.y_equations => new_y_eqs)
         for (v, f) in old
             new_v = switch_ring(v, new_ring)

src/RationalFunctionFields/IdealMQS.jl

@@ -100,7 +100,7 @@ mutable struct IdealMQS{T} <: AbstractBlackboxIdeal
         end
         varnames = append_at_index(ystrs, sat_var_index, sat_varname)
         @debug "Saturating variable is $sat_varname, index is $sat_var_index"
-        R_sat, v_sat = Nemo.polynomial_ring(K, varnames, ordering = ordering)
+        R_sat, v_sat = Nemo.polynomial_ring(K, varnames, internal_ordering = ordering)
         # Saturation
         t_sat = v_sat[sat_var_index]
         den_lcm_orig = den_lcm
@@ -144,7 +144,7 @@ mutable struct IdealMQS{T} <: AbstractBlackboxIdeal
                 push!(nums_qq, num)
             end
         end
-        parent_ring_param, _ = polynomial_ring(ring, varnames, ordering = ordering)
+        parent_ring_param, _ = polynomial_ring(ring, varnames, internal_ordering = ordering)
         @debug "Constructed MQS ideal in $R_sat with $(length(nums_qq) + 1) elements"
         @assert length(pivots_indices) == length(dens_indices) == length(dens_qq)
         @assert length(pivots_indices) == length(funcs_den_nums)
@@ -202,7 +202,7 @@ function fractionfree_generators_raw(mqs::IdealMQS)
     end
     # NOTE: new variables go first!
     big_ring, big_vars =
-        polynomial_ring(K, vcat(new_varnames, old_varnames), ordering = :lex)
+        polynomial_ring(K, vcat(new_varnames, old_varnames), internal_ordering = :lex)
     @info "$(mqs.sat_var_index) $(varnames) $ring_params $(parent(mqs.sat_qq))"
     nums_qq, dens_qq, sat_qq = mqs.nums_qq, mqs.dens_qq, mqs.sat_qq
     nums_y = map(num -> parent_ring_change(num, big_ring, matching = :byindex), nums_qq)

src/RationalFunctionFields/RationalFunctionField.jl

@@ -26,7 +26,7 @@ mutable struct RationalFunctionField{T}
     function RationalFunctionField(polys::Vector{T}) where {T}
         RationalFunctionField(polys .// one(parent(first(polys))))
     end
-    function RationalFunctionField(fractions::Vector{Generic.Frac{T}}) where {T}
+    function RationalFunctionField(fractions::Vector{Generic.FracFieldElem{T}}) where {T}
         RationalFunctionField(fractions_to_dennums(fractions))
     end
     function RationalFunctionField(dennums::Vector{Vector{T}}) where {T}
@@ -156,7 +156,7 @@ end
 
 function field_contains(
     field::RationalFunctionField{T},
-    ratfuncs::Vector{Generic.Frac{T}},
+    ratfuncs::Vector{Generic.FracFieldElem{T}},
     prob_threshold,
 ) where {T}
     return field_contains(field, fractions_to_dennums(ratfuncs), prob_threshold)
@@ -200,7 +200,7 @@ function check_algebraicity(field, ratfuncs, p)
     eval_point = [Nemo.QQ(rand(1:D)) for x in base_vars]
 
     # Filling the jacobain for generators
-    S = MatrixSpace(Nemo.QQ, length(base_vars), length(fgens) + 1)
+    S = matrix_space(Nemo.QQ, length(base_vars), length(fgens) + 1)
     J = zero(S)
     for (i, f) in enumerate(fgens)
         for (j, x) in enumerate(base_vars)

src/RationalFunctionFields/normalforms.jl

@@ -291,7 +291,7 @@ Note: uses Monte-Carlo probabilistic algorithm. The probability of correctness
 is not specified but is assumed to be close to 1.
 """
 @timeit _to function linear_relations_between_normal_forms(
-    fracs::Vector{Generic.Frac{T}},
+    fracs::Vector{Generic.FracFieldElem{T}},
     up_to_degree::Integer;
     seed = 42,
 ) where {T}
@@ -391,7 +391,7 @@ is not specified but is assumed to be close to 1.
     end
     union!(complete_intersection_relations_ff, relations_ff_1)
     @debug "Reconstructing relations to rationals"
-    relations_qq = Vector{Generic.Frac{elem_type(ring_param)}}(
+    relations_qq = Vector{Generic.FracFieldElem{elem_type(ring_param)}}(
         undef,
         length(complete_intersection_relations_ff),
     )

src/RationalFunctionFields/util.jl

@@ -11,7 +11,7 @@ Output: an array of fractions
 `[f2/f1, f3/f1, ..., g2/g1, g3/g1, ...]`
 """
 function dennums_to_fractions(dennums::Vector{Vector{T}}) where {T}
-    fractions = Vector{AbstractAlgebra.Generic.Frac{T}}()
+    fractions = Vector{AbstractAlgebra.Generic.FracFieldElem{T}}()
     for dni in dennums
         den, nums = dni[1], dni[2:end]
         isempty(nums) && continue

src/StructuralIdentifiability.jl

@@ -47,6 +47,8 @@ export find_submodels
 # finding identifiabile reparametrizations
 export reparametrize_global
 
+ExtendedFraction{P} = Union{P, Generic.FracFieldElem{P}}
+
 include("logging.jl")
 include("util.jl")
 include("power_series_utils.jl")
@@ -102,7 +104,7 @@ The function returns an (ordered) dictionary from the functions to check to thei
 function assess_identifiability(
     ode::ODE{P};
     funcs_to_check = Vector(),
-    known_ic::Vector{<:Union{P, Generic.Frac{P}}} = Vector{Union{P, Generic.Frac{P}}}(),
+    known_ic::Vector{<:ExtendedFraction{P}} = Vector{ExtendedFraction{P}}(),
     prob_threshold::Float64 = 0.99,
     loglevel = Logging.Info,
 ) where {P <: MPolyRingElem{QQFieldElem}}

src/discrete.jl

@@ -10,8 +10,8 @@ struct DDS{P} # P is the type of polynomials in the rhs of the DDS system
     function DDS{P}(
         x_vars::Array{P, 1},
         y_vars::Array{P, 1},
-        x_eqs::Dict{P, <:Union{P, Generic.Frac{P}}},
-        y_eqs::Dict{P, <:Union{P, Generic.Frac{P}}},
+        x_eqs::Dict{P, <:ExtendedFraction{P}},
+        y_eqs::Dict{P, <:ExtendedFraction{P}},
         u_vars::Array{P, 1},
     ) where {P <: MPolyRingElem{<:FieldElem}}
         new{P}(ODE{P}(x_vars, y_vars, x_eqs, y_eqs, u_vars))

src/global_identifiability.jl

@@ -148,7 +148,7 @@ The function returns a tuple containing the following:
         param_ring, _ = polynomial_ring(
             base_ring(bring),
             map(string, ode.parameters),
-            ordering = Nemo.ordering(bring),
+            internal_ordering = Nemo.internal_ordering(bring),
         )
         id_funcs_no_states_param = map(
             polys -> map(poly -> parent_ring_change(poly, param_ring), polys),
@@ -218,7 +218,7 @@ Output: a list L of booleans with L[i] being the identifiability status of the i
         with_states = states_needed,
     )
 
-    funcs_to_check = Vector{Generic.Frac{P}}(
+    funcs_to_check = Vector{Generic.FracFieldElem{P}}(
         map(f -> parent_ring_change(f, bring) // one(bring), funcs_to_check),
     )
 

src/identifiable_functions.jl

@@ -40,15 +40,15 @@ ode = @ODEmodel(
 find_identifiable_functions(ode)
 
 # prints
-3-element Vector{AbstractAlgebra.Generic.Frac{Nemo.QQMPolyRingElem}}:
+3-element Vector{AbstractAlgebra.Generic.FracFieldElem{Nemo.QQMPolyRingElem}}:
  a12 + a01 + a21
  a12*a01
 ```
 
 """
 function find_identifiable_functions(
     ode::ODE{T};
-    known_ic::Vector{<:Union{T, Generic.Frac{T}}} = Vector{Union{T, Generic.Frac{T}}}(),
+    known_ic::Vector{<:ExtendedFraction{T}} = Vector{ExtendedFraction{T}}(),
     prob_threshold::Float64 = 0.99,
     seed = 42,
     with_states = false,

src/input_macro.jl

@@ -136,7 +136,7 @@ function generate_model_code(type, ex::Expr...)
             StructuralIdentifiability.Nemo.QQMPolyRingElem,
             Union{
                 StructuralIdentifiability.Nemo.QQMPolyRingElem,
-                StructuralIdentifiability.AbstractAlgebra.Generic.Frac{
+                StructuralIdentifiability.AbstractAlgebra.Generic.FracFieldElem{
                     StructuralIdentifiability.Nemo.QQMPolyRingElem,
                 },
             },
@@ -147,7 +147,7 @@ function generate_model_code(type, ex::Expr...)
             StructuralIdentifiability.Nemo.QQMPolyRingElem,
             Union{
                 StructuralIdentifiability.Nemo.QQMPolyRingElem,
-                StructuralIdentifiability.AbstractAlgebra.Generic.Frac{
+                StructuralIdentifiability.AbstractAlgebra.Generic.FracFieldElem{
                     StructuralIdentifiability.Nemo.QQMPolyRingElem,
                 },
             },
@@ -304,4 +304,4 @@ macro DDSmodel(ex::Expr...)
     return esc(generate_model_code(:dds, ex...))
 end
 
-#------------------------------------------------------------------------------
+#-----------------------------------------------------------------------------i

src/io_equation.jl

@@ -24,7 +24,7 @@ function diff_poly(poly::P, derivation::Dict{P, T}) where {P <: MPolyRingElem, T
     return sum(derivative(poly, x) * xd for (x, xd) in derivation)
 end
 
-function diff_frac(frac::Generic.Frac{F}, derivation::Dict{P, T}) where {F, P, T}
+function diff_frac(frac::Generic.FracFieldElem{F}, derivation::Dict{P, T}) where {F, P, T}
     num, den = unpack_fraction(frac)
     numd = den * diff_poly(num, derivation) - num * diff_poly(den, derivation)
     dend = den^2

src/known_ic.jl

@@ -28,12 +28,12 @@ This functions takes the following optional arguments:
 """
 function _find_identifiable_functions_kic(
     ode::ODE{T},
-    known_ic::Vector{<:Union{T, Generic.Frac{T}}};
+    known_ic::Vector{<:ExtendedFraction{T}};
     prob_threshold::Float64 = 0.99,
     seed = 42,
     simplify = :standard,
     rational_interpolator = :VanDerHoevenLecerf,
-) where {T <: MPolyElem{fmpq}}
+) where {T <: MPolyRingElem{Nemo.QQFieldElem}}
     Random.seed!(seed)
     @assert simplify in (:standard, :weak, :strong, :absent)
     half_p = 0.5 + prob_threshold / 2
@@ -80,10 +80,10 @@ The function returns an (ordered) dictionary from the functions to check to thei
 """
 function _assess_identifiability_kic(
     ode::ODE{P},
-    known_ic::Vector{<:Union{P, Generic.Frac{P}}};
+    known_ic::Vector{<:ExtendedFraction{P}};
     funcs_to_check = Vector(),
     prob_threshold::Float64 = 0.99,
-) where {P <: MPolyElem{fmpq}}
+) where {P <: MPolyRingElem{Nemo.QQFieldElem}}
     runtime_start = time_ns()
     if length(funcs_to_check) == 0
         funcs_to_check = vcat(ode.x_vars, ode.parameters)

src/lincomp.jl

@@ -51,9 +51,7 @@ function linear_compartment_model(
     )
     x_vars = @view vars[1:n]
     x_equations =
-        Dict{QQMPolyRingElem, Union{QQMPolyRingElem, Generic.Frac{QQMPolyRingElem}}}(
-            x => R(0) for x in x_vars
-        )
+        Dict{QQMPolyRingElem, ExtendedFraction{QQMPolyRingElem}}(x => R(0) for x in x_vars)
     for i in 1:n
         for j in graph[i]
             rate = str_to_var("a_$(j)_$(i)", R)
@@ -69,10 +67,9 @@ function linear_compartment_model(
         end
     end
 
-    y_equations =
-        Dict{QQMPolyRingElem, Union{QQMPolyRingElem, Generic.Frac{QQMPolyRingElem}}}(
-            str_to_var("y$i", R) => str_to_var("x$i", R) for i in outputs
-        )
+    y_equations = Dict{QQMPolyRingElem, ExtendedFraction{QQMPolyRingElem}}(
+        str_to_var("y$i", R) => str_to_var("x$i", R) for i in outputs
+    )
 
     return ODE{QQMPolyRingElem}(
         x_equations,

src/local_identifiability.jl

@@ -135,7 +135,9 @@ function get_degree_and_coeffsize(f::MPolyRingElem{Nemo.QQFieldElem})
     return (total_degree(f), max_coef)
 end
 
-function get_degree_and_coeffsize(f::Generic.Frac{<:MPolyRingElem{Nemo.QQFieldElem}})
+function get_degree_and_coeffsize(
+    f::Generic.FracFieldElem{<:MPolyRingElem{Nemo.QQFieldElem}},
+)
     num_deg, num_coef = get_degree_and_coeffsize(numerator(f))
     den_deg, den_coef = get_degree_and_coeffsize(denominator(f))
     return (max(num_deg, den_deg), max(num_coef, den_coef))