Merge branch 'master' into known_ic_generic

.github/workflows/CI.yml

@@ -13,6 +13,7 @@ jobs:
       matrix:
         group:
           - Core
+          - ModelingToolkitSIExt
         version:
           - '1'
           - '1.6'
@@ -21,7 +22,7 @@ jobs:
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:

.github/workflows/Downgrade.yml

@@ -0,0 +1,31 @@
+name: Downgrade
+on:
+  pull_request:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        version: ['1']
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+      - uses: cjdoris/julia-downgrade-compat-action@v1
+#        if: ${{ matrix.version == '1.6' }}
+        with:
+        # skip standard libraries..
+          skip: Aqua,Compat,Dates,IterTools,LinearAlgebra,Logging,Pkg,Random,Test,TOML
+          strict: 'false'
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1

.github/workflows/SpellCheck.yml

@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request]
+
+jobs:
+   typos-check:
+     name: Spell Check with Typos
+     runs-on: ubuntu-latest
+     steps:
+       - name: Checkout Actions Repository
+         uses: actions/checkout@v3
+       - name: Check spelling
+         uses: crate-ci/[email protected]

.typos.toml

@@ -0,0 +1,2 @@
+[default.extend-words]
+ numer = "numer"

Project.toml

@@ -1,11 +1,10 @@
 name = "StructuralIdentifiability"
 uuid = "220ca800-aa68-49bb-acd8-6037fa93a544"
 authors = ["Alexander Demin, Ruiwen Dong, Christian Goodbrake, Heather Harrington, Gleb Pogudin <[email protected]>"]
-version = "0.4.15"
+version = "0.5.3"
 
 [deps]
 AbstractAlgebra = "c3fe647b-3220-5bb0-a1ea-a7954cac585d"
-BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -14,45 +13,58 @@ 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"
 ParamPunPam = "3e851597-e36f-45a9-af0a-b7781937992f"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 Primes = "27ebfcd6-29c5-5fa9-bf4b-fb8fc14df3ae"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
+
+[weakdeps]
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
-TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
+
+[extensions]
+ModelingToolkitSIExt = ["ModelingToolkit", "SymbolicUtils", "Symbolics"]
 
 [compat]
-AbstractAlgebra = "0.13, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30, 0.31, 0.32, 0.33"
-BenchmarkTools = "1"
+AbstractAlgebra = "0.34.5, 0.35"
+Aqua = "0.8"
 Combinatorics = "1"
+CPUSummary = "0.2"
 DataStructures = "0.18"
 Dates = "1.6, 1.7"
-Groebner = "0.4, 0.5"
+Groebner = "0.6.3"
 IterTools = "1"
 LinearAlgebra = "1.6, 1.7"
 Logging = "1.6, 1.7"
 MacroTools = "0.5"
-ModelingToolkit = "7, 8"
-Nemo = "0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30, 0.31, 0.32, 0.33, 0.34, 0.35, 0.36, 0.37"
-ParamPunPam = "0.2"
-PrecompileTools = "1"
+ModelingToolkit = "8.75"
+Nemo = "0.38.3, 0.39"
+ParamPunPam = "0.3.1"
+Pkg = "1.6, 1.7"
+PrecompileTools = "1.2"
 Primes = "0.5"
 Random = "1.6, 1.7"
-SpecialFunctions = "1, 2"
-SymbolicUtils = "1"
-Symbolics = "5"
+SpecialFunctions = "2"
+SymbolicUtils = "1.4, 1.5"
+Symbolics = "5.16"
+Test = "1.6, 1.7"
 TestSetExtensions = "2"
 TimerOutputs = "0.5"
 julia = "1.6, 1.7"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 CPUSummary = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
+Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TestSetExtensions = "98d24dd4-01ad-11ea-1b02-c9a08f80db04"
 
 [targets]
-test = ["CPUSummary", "Test", "TestSetExtensions"]
+test = ["Aqua", "CPUSummary", "Pkg", "SpecialFunctions", "Test", "TestSetExtensions"]

README.md

@@ -56,7 +56,7 @@ In this example:
   - `y(t)` is the **output variable** which is assumed to be observed in the experiments and, thus, known;
   - `a01, a21, a12, b` are unknown scalar **parameters**.
 
-Note that there may be mulitple inputs and outputs.
+Note that there may be multiple inputs and outputs.
 
 ### Assessing identifiability
 

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)

benchmarking/IdentifiableFunctions/param.jl

@@ -31,7 +31,7 @@ function check_constructive_field_membership(generators::AbstractVector, to_be_r
     $(join(map(x -> string(x[1]) * " -> " * string(x[2]),  zip(fracs_gen, tag_strings)), "\t\n"))
     """
     var_strings = vcat(sat_string, map(string, gens(ring)), tag_strings)
-    ring_tag, xs_tag = PolynomialRing(K, var_strings, ordering = Nemo.ordering(ring))
+    ring_tag, xs_tag = polynomial_ring(K, var_strings, ordering = Nemo.ordering(ring))
     orig_vars = xs_tag[2:(nvars(ring) + 1)]
     tag_vars = xs_tag[(nvars(ring) + 2):end]
     sat_var = xs_tag[1]
@@ -121,12 +121,12 @@ rem_tags, tag_to_gen = check_constructive_field_membership(fracs_generators, to_
 #=
 ┌ Info: 
 │   rem_tags =
-│    3-element Vector{AbstractAlgebra.Generic.Frac{fmpq_mpoly}}:
+│    3-element Vector{AbstractAlgebra.Generic.Frac{QQMPolyRingElem}}:
 │     T1^2
 │     -5*T1 + T2
 │     T2//T1^10
 │   tag_to_gen =
-│    Dict{fmpq_mpoly, AbstractAlgebra.Generic.Frac{fmpq_mpoly}} with 2 entries:
+│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 2 entries:
 │      T1 => a^2
 └      T2 => (a + b)//b
 =#
@@ -205,10 +205,10 @@ new_vector_field, new_outputs, new_vars =
 │    Dict{Any, Any} with 1 entry:
 │      T1 => 2*T1 + T2
 │   new_outputs =
-│    Dict{fmpq_mpoly, AbstractAlgebra.Generic.Frac{fmpq_mpoly}} with 1 entry:
+│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 1 entry:
 │      y => T1
 │   new_vars =
-│    Dict{fmpq_mpoly, AbstractAlgebra.Generic.Frac{fmpq_mpoly}} with 2 entries:
+│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 2 entries:
 │      T2 => a + b
 └      T1 => x2 + x1
 =#
@@ -230,7 +230,7 @@ id_funcs = StructuralIdentifiability.find_identifiable_functions(
 #=
 ┌ Info: 
 │   id_funcs =
-│    2-element Vector{AbstractAlgebra.Generic.Frac{fmpq_mpoly}}:
+│    2-element Vector{AbstractAlgebra.Generic.Frac{QQMPolyRingElem}}:
 │     x2*x1
 └     a + b
 =#
@@ -246,10 +246,10 @@ new_vector_field, new_outputs, new_vars = reparametrize_with_respect_to(ode, new
 │    Dict{Any, Any} with 1 entry:
 │      T1 => T1*T2
 │   new_outputs =
-│    Dict{fmpq_mpoly, AbstractAlgebra.Generic.Frac{fmpq_mpoly}} with 1 entry:
+│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 1 entry:
 │      y => T1
 │   new_vars =
-│    Dict{fmpq_mpoly, AbstractAlgebra.Generic.Frac{fmpq_mpoly}} with 2 entries:
+│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 2 entries:
 │      T2 => a + b
 └      T1 => x2*x1
 =#
@@ -271,7 +271,7 @@ id_funcs = StructuralIdentifiability.find_identifiable_functions(
 #=
 ┌ Info: 
 │   id_funcs =
-│    5-element Vector{AbstractAlgebra.Generic.Frac{fmpq_mpoly}}:
+│    5-element Vector{AbstractAlgebra.Generic.Frac{QQMPolyRingElem}}:
 │     x2*x1
 │     a*b
 │     x2 + x1
@@ -292,10 +292,10 @@ new_vector_field, new_iutputs, new_vars = reparametrize_with_respect_to(ode, new
 │      T2 => T2*T4
 │      T3 => -1//2*T1*T4^2 + 2*T1*T5 + 1//2*T3*T4
 │   new_outputs =
-│    Dict{fmpq_mpoly, AbstractAlgebra.Generic.Frac{fmpq_mpoly}} with 1 entry:
+│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 1 entry:
 │      y => T1
 │   new_vars =
-│    Dict{fmpq_mpoly, AbstractAlgebra.Generic.Frac{fmpq_mpoly}} with 5 entries:
+│    Dict{QQMPolyRingElem, AbstractAlgebra.Generic.Frac{QQMPolyRingElem}} with 5 entries:
 │      T1 => x2 + x1
 │      T2 => x2*x1
 │      T3 => a*x2 - a*x1 - b*x2 + b*x1

docs/Project.toml

@@ -7,5 +7,5 @@ StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 [compat]
 BenchmarkTools = "1.3"
 Documenter = "0.27, 1"
-ModelingToolkit = "8.34"
-StructuralIdentifiability = "0.4"
+ModelingToolkit = "8.74"
+StructuralIdentifiability = "0.5"

docs/pages.jl

@@ -5,6 +5,7 @@ pages = [
         "tutorials/identifiability.md",
         "tutorials/identifiable_functions.md",
         "tutorials/discrete_time.md",
+        "tutorials/reparametrization.md",
     ],
     "Basics" => Any["input/input.md", "identifiability/identifiability.md"],
     "Library" => Any[

docs/src/assets/Project.toml

@@ -7,5 +7,5 @@ StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 [compat]
 BenchmarkTools = "1.3"
 Documenter = "0.27, 1"
-ModelingToolkit = "8.34"
-StructuralIdentifiability = "0.4"
+ModelingToolkit = "8.74"
+StructuralIdentifiability = "0.5"

docs/src/input/input.md

@@ -1,4 +1,4 @@
-# Parsing input ODE system
+# Parsing input system
 
 ```@docs
 @ODEmodel(ex::Expr...)
@@ -11,3 +11,9 @@ set_parameter_values
 ```@docs
 linear_compartment_model
 ```
+
+## Discrete-time systems
+
+```@docs
+@DDSmodel
+```

docs/src/tutorials/creating_ode.md

@@ -12,7 +12,7 @@ which involves
 
   - a vector $\mathbf{x}(t)$ of the state variables of the system,
 
-  - a vector $\mathbf{u}(t)$ of extermal inputs,
+  - a vector $\mathbf{u}(t)$ of external inputs,
   - a vector $\mathbf{p}$ of scalar parameters,
   - a vector $\mathbf{y}(t)$ of outputs (i.e., observations),
   - and vectors of rational functions $\mathbf{f}$ and $\mathbf{g}$ (for discussion of the non-rational case, see this [issue](https://github.com/SciML/StructuralIdentifiability.jl/issues/144)).
@@ -54,7 +54,9 @@ assess_identifiability(ode)
 
 ## Defining using `ModelingToolkit`
 
-Alternatively, one can use `ModelingToolkit`: encode the equations for the states as `ODESystem` and specify the outputs separately.
+`StructuralIdentifiability` has an extension `ModelingToolkitSIExt` which allows to use `ODESystem` from `ModelingToolkit` to describe
+a model. The extension is loaded automatically once `ModelingToolkit` is loaded via `using ModelingToolkit`.
+In this case, one should encode the equations for the states as `ODESystem` and specify the outputs separately.
 In order to do this, we first introduce all functions and scalars:
 
 ```@example 2; continued = true