add SciMLBase dependency

SciML · Jul 24, 2024 · 4ae6b61 · 4ae6b61
1 parent 2bc6bed
commit 4ae6b61
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Showing 2 changed files with 10 additions and 50 deletions.
diff --git a/Project.toml b/Project.toml
@@ -20,6 +20,7 @@ Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
+SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
@@ -28,15 +29,15 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 [weakdeps]
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
 GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
+HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
 StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 
 [extensions]
 CatalystBifurcationKitExtension = "BifurcationKit"
 CatalystCairoMakieExtension = "CairoMakie"
-CatalystHomotopyContinuationExtension = "HomotopyContinuation"
 CatalystGraphMakieExtension = "GraphMakie"
+CatalystHomotopyContinuationExtension = "HomotopyContinuation"
 CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
 
 [compat]
@@ -48,9 +49,9 @@ DiffEqBase = "6.83.0"
 DocStringExtensions = "0.8, 0.9"
 DynamicPolynomials = "0.5"
 DynamicQuantities = "0.13.2"
+GraphMakie = "0.5"
 Graphs = "1.4"
 HomotopyContinuation = "2.9"
-GraphMakie = "0.5"
 JumpProcesses = "9.3.2"
 LaTeXStrings = "1.3.0"
 Latexify = "0.14, 0.15, 0.16"
@@ -60,6 +61,7 @@ Parameters = "0.12"
 Reexport = "0.2, 1.0"
 Requires = "1.0"
 RuntimeGeneratedFunctions = "0.5.12"
+SciMLBase = "2.44, >=2.45.1"
 Setfield = "1"
 StructuralIdentifiability = "0.5.8"
 Symbolics = "5.30.1"
@@ -71,11 +73,11 @@ BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
+GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
-GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"

diff --git a/src/latexify_recipes.jl b/src/latexify_recipes.jl
@@ -48,7 +48,7 @@ function processsym(s)
     var
 end
 
-function chemical_arrows(rn::ReactionSystem; expand = true,
+function chemical_arrows(rn::ReactionSystem;
         double_linebreak = LATEX_DEFS.double_linebreak,
         starred = LATEX_DEFS.starred, mathrm = true,
         mathjax = LATEX_DEFS.mathjax, kwargs...)
@@ -87,8 +87,6 @@ function chemical_arrows(rn::ReactionSystem; expand = true,
 
         ### Expand functions to maths expressions
         rate = r.rate isa Symbolic ? subber(r.rate) : r.rate
-        rate = ModelingToolkit.prettify_expr(Symbolics._toexpr(rate))
-        expand && (rate = recursive_clean!(rate))
 
         ### Generate formatted string of substrates
         substrates = [make_stoich_str(substrate[1], substrate[2], subber; mathrm,
@@ -102,10 +100,7 @@ function chemical_arrows(rn::ReactionSystem; expand = true,
         if i + 1 <= length(rxs) && issetequal(r.products, rxs[i + 1].substrates) &&
            issetequal(r.substrates, rxs[i + 1].products)
             ### Bi-directional arrows
-            rate_backwards = MT.prettify_expr(Symbolics._toexpr(rxs[i + 1].rate))
-            #rate_backwards = rxs[i+1].rate isa Symbolic ? Expr(subber(rxs[i+1].rate)) : rxs[i+1].rate
-            expand && (rate_backwards = recursive_clean!(rate_backwards))
-            expand && (rate_backwards = recursive_clean!(rate_backwards))
+            rate_backwards = rxs[i + 1].rate isa Symbolic ? subber(rxs[i + 1].rate) : rxs[i + 1].rate
             str *= " &" * rev_arrow
             str *= "[" * latexraw(rate_backwards; kwargs...) * "]"
             str *= "{" * latexraw(rate; kwargs...) * "} "
@@ -121,8 +116,8 @@ function chemical_arrows(rn::ReactionSystem; expand = true,
                     for product in zip(r.products, r.prodstoich)]
         isempty(products) && (products = ["\\varnothing"])
         str *= join(products, " + ")
-        if (i == lastidx) ||
-           (((i + 1) == lastidx) && (backwards_reaction == true)) &&
+        if ((i == lastidx) ||
+           (((i + 1) == lastidx) && (backwards_reaction == true))) &&
            isempty(nonrxs)
             str *= "  \n "
         else
@@ -155,43 +150,6 @@ function any_nonrx_subsys(rn::MT.AbstractSystem)
     false
 end
 
-# Recursively traverses an expression and removes things like X^1, 1*X. Will not actually have any effect on the expression when used as a function, but will make it much easier to look at it for debugging, as well as if it is transformed to LaTeX code.
-function recursive_clean!(expr)
-    (expr isa Symbol) && (expr == :no___noise___scaling) && (return 1)
-    (typeof(expr) != Expr) && (return expr)
-    for i in 1:length(expr.args)
-        expr.args[i] = recursive_clean!(expr.args[i])
-    end
-    (expr.args[1] == :^) && (expr.args[3] == 1) && (return expr.args[2])
-    if expr.args[1] == :*
-        in(0, expr.args) && (return 0)
-        i = 1
-        while (i = i + 1) <= length(expr.args)
-            if (typeof(expr.args[i]) == Expr) && (expr.args[i].head == :call) &&
-               (expr.args[i].args[1] == :*)
-                for arg in expr.args[i].args
-                    (arg != :*) && push!(expr.args, arg)
-                end
-            end
-        end
-        for i in length(expr.args):-1:2
-            (typeof(expr.args[i]) == Expr) && (expr.args[i].head == :call) &&
-                (expr.args[i].args[1] == :*) && deleteat!(expr.args, i)
-            (expr.args[i] == 1) && deleteat!(expr.args, i)
-        end
-        (length(expr.args) == 2) && (return expr.args[2])                   # We have a multiplication of only one thing, return only that thing.
-        (length(expr.args) == 1) && (return 1)                              # We have only * and no real arguments.
-        (length(expr.args) == 3) && (expr.args[2] == -1) && return :(-$(expr.args[3]))
-        (length(expr.args) == 3) && (expr.args[3] == -1) && return :(-$(expr.args[2]))
-    end
-    if expr.head == :call
-        (expr.args[1] == :/) && (expr.args[3] == 1) && (return expr.args[2])
-        (expr.args[1] == :binomial) && (expr.args[3] == 1) && return expr.args[2]
-        #@isdefined($(expr.args[1])) || error("Function $(expr.args[1]) not defined.")
-    end
-    return expr
-end
-
 function make_stoich_str(spec, stoich, subber; mathrm = true, kwargs...)
     if mathrm
         prestr = "\\mathrm{"