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Jun 10, 2024
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[v14 - Ready] Fixes latexify tests #933

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233 changes: 117 additions & 116 deletions test/visualisation/latexify.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,8 @@ include("../test_networks.jl")
### Just be sure to remove all such macros before you commit a change since it
### will cause issues with Travis.

# Generally, for all latexify tests, the lines after `@test latexify(rn) == replace(` must
# start without any tabs, hence the somewhat weird formatting.

### Basic Tests ###

Expand All @@ -48,68 +50,68 @@ let
(d1,d2,d3,d4,d5,d6), (X1,X2,X3,X4,X5,X6) ⟶ ∅
end

# Latexify.@generate_test latexify(rn)
@test_broken latexify(rn; expand_functions = false) == replace(
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just a simple error, expand_functions = false tested twice.
(true is the default, so don't really need it in the next one, but specified it anyway)

raw"\begin{align*}
\varnothing &\xrightarrow{\frac{X4^{n1} v1^{2} K1^{n1}}{\left( K1^{n1} + X4^{n1} \right) \left( K1^{n1} + X2^{n1} \right)}} \mathrm{X1} \\
\varnothing &\xrightarrow{\mathrm{hill}\left( X5, v2, K2, n2 \right)} \mathrm{X2} \\
\varnothing &\xrightarrow{\mathrm{hill}\left( X3, v3, K3, n3 \right)} \mathrm{X3} \\
\varnothing &\xrightarrow{\mathrm{hillr}\left( X1, v4, K4, n4 \right)} \mathrm{X4} \\
\varnothing &\xrightarrow{\mathrm{hill}\left( X2, v5, K5, n5 \right)} \mathrm{X5} \\
\varnothing &\xrightarrow{\mathrm{hillar}\left( X1, X6, v6, K6, n6 \right)} \mathrm{X6} \\
\mathrm{X2} &\xrightleftharpoons[k2]{k1} \mathrm{X1} + 2 \mathrm{X4} \\
\mathrm{X4} &\xrightleftharpoons[k4]{k3} \mathrm{X3} \\
3 \mathrm{X5} + \mathrm{X1} &\xrightleftharpoons[k6]{k5} \mathrm{X2} \\
\mathrm{X1} &\xrightarrow{d1} \varnothing \\
\mathrm{X2} &\xrightarrow{d2} \varnothing \\
\mathrm{X3} &\xrightarrow{d3} \varnothing \\
\mathrm{X4} &\xrightarrow{d4} \varnothing \\
\mathrm{X5} &\xrightarrow{d5} \varnothing \\
\mathrm{X6} &\xrightarrow{d6} \varnothing
\end{align*}
", "\r\n"=>"\n")

#Latexify.@generate_test latexify(rn; expand_functions=false)
@test_broken latexify(rn; expand_functions = false) == replace(
raw"\begin{align*}
\varnothing &\xrightarrow{\frac{X4^{n1} v1^{2} K1^{n1}}{\left( K1^{n1} + X4^{n1} \right) \left( K1^{n1} + X2^{n1} \right)}} \mathrm{X1} \\
\varnothing &\xrightarrow{\mathrm{mm}\left( X5, v2, K2 \right)} \mathrm{X2} \\
\varnothing &\xrightarrow{\mathrm{mmr}\left( X3, v3, K3 \right)} \mathrm{X3} \\
\varnothing &\xrightarrow{\mathrm{hillr}\left( X1, v4, K4, n4 \right)} \mathrm{X4} \\
\varnothing &\xrightarrow{\mathrm{hill}\left( X2, v5, K5, n5 \right)} \mathrm{X5} \\
\varnothing &\xrightarrow{\mathrm{hillar}\left( X1, X6, v6, K6, n6 \right)} \mathrm{X6} \\
\mathrm{X2} &\xrightleftharpoons[k2]{k1} \mathrm{X1} + 2 \mathrm{X4} \\
\mathrm{X4} &\xrightleftharpoons[k4]{k3} \mathrm{X3} \\
3 \mathrm{X5} + \mathrm{X1} &\xrightleftharpoons[k6]{k5} \mathrm{X2} \\
\mathrm{X1} &\xrightarrow{d1} \varnothing \\
\mathrm{X2} &\xrightarrow{d2} \varnothing \\
\mathrm{X3} &\xrightarrow{d3} \varnothing \\
\mathrm{X4} &\xrightarrow{d4} \varnothing \\
\mathrm{X5} &\xrightarrow{d5} \varnothing \\
\mathrm{X6} &\xrightarrow{d6} \varnothing
\end{align*}
", "\r\n"=>"\n")

# Latexify.@generate_test latexify(rn, mathjax=false)
@test_broken latexify(rn, mathjax = false) == replace(
raw"\begin{align*}
\varnothing &\xrightarrow{\frac{X4^{n1} v1^{2} K1^{n1}}{\left( K1^{n1} + X4^{n1} \right) \left( K1^{n1} + X2^{n1} \right)}} \mathrm{X1} \\
\varnothing &\xrightarrow{\frac{X5 v2}{K2 + X5}} \mathrm{X2} \\
\varnothing &\xrightarrow{\frac{K3 v3}{K3 + X3}} \mathrm{X3} \\
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This just seemed to be an error, not sure what's up here.

\varnothing &\xrightarrow{\frac{v4 K4^{n4}}{K4^{n4} + X1^{n4}}} \mathrm{X4} \\
\varnothing &\xrightarrow{\frac{v5 X2^{n5}}{X2^{n5} + K5^{n5}}} \mathrm{X5} \\
\varnothing &\xrightarrow{\frac{v6 X1^{n6}}{X6^{n6} + K6^{n6} + X1^{n6}}} \mathrm{X6} \\
\mathrm{X2} &\xrightleftharpoons[k2]{k1} \mathrm{X1} + 2 \mathrm{X4} \\
\mathrm{X4} &\xrightleftharpoons[k4]{k3} \mathrm{X3} \\
3 \mathrm{X5} + \mathrm{X1} &\xrightleftharpoons[k6]{k5} \mathrm{X2} \\
\mathrm{X1} &\xrightarrow{d1} \varnothing \\
\mathrm{X2} &\xrightarrow{d2} \varnothing \\
\mathrm{X3} &\xrightarrow{d3} \varnothing \\
\mathrm{X4} &\xrightarrow{d4} \varnothing \\
\mathrm{X5} &\xrightarrow{d5} \varnothing \\
\mathrm{X6} &\xrightarrow{d6} \varnothing
\end{align*}
", "\r\n"=>"\n")
# Latexify.@generate_test latexify(rn; expand_functions = false)
@test latexify(rn; expand_functions = false) == replace(
raw"\begin{align*}
\varnothing &\xrightarrow{\mathrm{hillr}\left( X2, v1, K1, n1 \right) \mathrm{hill}\left( X4, v1, K1, n1 \right)} \mathrm{X1} \\
\varnothing &\xrightarrow{\mathrm{hill}\left( X5, v2, K2, n2 \right)} \mathrm{X2} \\
\varnothing &\xrightarrow{\mathrm{hill}\left( X3, v3, K3, n3 \right)} \mathrm{X3} \\
\varnothing &\xrightarrow{\mathrm{hillr}\left( X1, v4, K4, n4 \right)} \mathrm{X4} \\
\varnothing &\xrightarrow{\mathrm{hill}\left( X2, v5, K5, n5 \right)} \mathrm{X5} \\
\varnothing &\xrightarrow{\mathrm{hillar}\left( X1, X6, v6, K6, n6 \right)} \mathrm{X6} \\
\mathrm{X2} &\xrightleftharpoons[k2]{k1} \mathrm{X1} + 2 \mathrm{X4} \\
\mathrm{X4} &\xrightleftharpoons[k4]{k3} \mathrm{X3} \\
3 \mathrm{X5} + \mathrm{X1} &\xrightleftharpoons[k6]{k5} \mathrm{X2} \\
\mathrm{X1} &\xrightarrow{d1} \varnothing \\
\mathrm{X2} &\xrightarrow{d2} \varnothing \\
\mathrm{X3} &\xrightarrow{d3} \varnothing \\
\mathrm{X4} &\xrightarrow{d4} \varnothing \\
\mathrm{X5} &\xrightarrow{d5} \varnothing \\
\mathrm{X6} &\xrightarrow{d6} \varnothing
\end{align*}
", "\r\n"=>"\n")

# Latexify.@generate_test latexify(rn; expand_functions = true)
@test latexify(rn; expand_functions = true) == replace(
raw"\begin{align*}
\varnothing &\xrightarrow{\frac{X4^{n1} v1^{2} K1^{n1}}{\left( K1^{n1} + X4^{n1} \right) \left( K1^{n1} + X2^{n1} \right)}} \mathrm{X1} \\
\varnothing &\xrightarrow{\frac{v2 X5^{n2}}{X5^{n2} + K2^{n2}}} \mathrm{X2} \\
\varnothing &\xrightarrow{\frac{v3 X3^{n3}}{X3^{n3} + K3^{n3}}} \mathrm{X3} \\
\varnothing &\xrightarrow{\frac{v4 K4^{n4}}{K4^{n4} + X1^{n4}}} \mathrm{X4} \\
\varnothing &\xrightarrow{\frac{v5 X2^{n5}}{X2^{n5} + K5^{n5}}} \mathrm{X5} \\
\varnothing &\xrightarrow{\frac{v6 X1^{n6}}{X6^{n6} + K6^{n6} + X1^{n6}}} \mathrm{X6} \\
\mathrm{X2} &\xrightleftharpoons[k2]{k1} \mathrm{X1} + 2 \mathrm{X4} \\
\mathrm{X4} &\xrightleftharpoons[k4]{k3} \mathrm{X3} \\
3 \mathrm{X5} + \mathrm{X1} &\xrightleftharpoons[k6]{k5} \mathrm{X2} \\
\mathrm{X1} &\xrightarrow{d1} \varnothing \\
\mathrm{X2} &\xrightarrow{d2} \varnothing \\
\mathrm{X3} &\xrightarrow{d3} \varnothing \\
\mathrm{X4} &\xrightarrow{d4} \varnothing \\
\mathrm{X5} &\xrightarrow{d5} \varnothing \\
\mathrm{X6} &\xrightarrow{d6} \varnothing
\end{align*}
", "\r\n"=>"\n")
# Latexify.@generate_test latexify(rn, mathjax = false)
@test latexify(rn, mathjax = false) == replace(
raw"\begin{align*}
\varnothing &\xrightarrow{\frac{X4^{n1} v1^{2} K1^{n1}}{\left( K1^{n1} + X4^{n1} \right) \left( K1^{n1} + X2^{n1} \right)}} \mathrm{X1} \\
\varnothing &\xrightarrow{\frac{v2 X5^{n2}}{X5^{n2} + K2^{n2}}} \mathrm{X2} \\
\varnothing &\xrightarrow{\frac{v3 X3^{n3}}{X3^{n3} + K3^{n3}}} \mathrm{X3} \\
\varnothing &\xrightarrow{\frac{v4 K4^{n4}}{K4^{n4} + X1^{n4}}} \mathrm{X4} \\
\varnothing &\xrightarrow{\frac{v5 X2^{n5}}{X2^{n5} + K5^{n5}}} \mathrm{X5} \\
\varnothing &\xrightarrow{\frac{v6 X1^{n6}}{X6^{n6} + K6^{n6} + X1^{n6}}} \mathrm{X6} \\
\mathrm{X2} &\xrightleftharpoons[k2]{k1} \mathrm{X1} + 2 \mathrm{X4} \\
\mathrm{X4} &\xrightleftharpoons[k4]{k3} \mathrm{X3} \\
3 \mathrm{X5} + \mathrm{X1} &\xrightleftharpoons[k6]{k5} \mathrm{X2} \\
\mathrm{X1} &\xrightarrow{d1} \varnothing \\
\mathrm{X2} &\xrightarrow{d2} \varnothing \\
\mathrm{X3} &\xrightarrow{d3} \varnothing \\
\mathrm{X4} &\xrightarrow{d4} \varnothing \\
\mathrm{X5} &\xrightarrow{d5} \varnothing \\
\mathrm{X6} &\xrightarrow{d6} \varnothing
\end{align*}
", "\r\n"=>"\n")
end

# Tests basic functions on simple network (2).
Expand All @@ -121,35 +123,49 @@ let
end

# Latexify.@generate_test latexify(rn)
@test_broken latexify(rn) == replace(
raw"\begin{align*}
\varnothing &\xrightleftharpoons[d_{a}]{\frac{p_{a} B^{n}}{k^{n} + B^{n}}} \mathrm{A} \\
\varnothing &\xrightleftharpoons[d_{b}]{p_{b}} \mathrm{B} \\
3 \mathrm{B} &\xrightleftharpoons[r_{b}]{r_{a}} \mathrm{A}
\end{align*}
", "\r\n"=>"\n")

# Latexify.@generate_test latexify(rn, mathjax=false)
@test_broken latexify(rn, mathjax = false) == replace(
raw"\begin{align*}
\varnothing &\xrightleftharpoons[d_{a}]{\frac{p_{a} B^{n}}{k^{n} + B^{n}}} \mathrm{A} \\
\varnothing &\xrightleftharpoons[d_{b}]{p_{b}} \mathrm{B} \\
3 \mathrm{B} &\xrightleftharpoons[r_{b}]{r_{a}} \mathrm{A}
\end{align*}
", "\r\n"=>"\n")
@test latexify(rn) == replace(
raw"\begin{align*}
\varnothing &\xrightleftharpoons[d_{a}]{\frac{p_{a} B^{n}}{k^{n} + B^{n}}} \mathrm{A} \\
\varnothing &\xrightleftharpoons[d_{b}]{p_{b}} \mathrm{B} \\
3 \mathrm{B} &\xrightleftharpoons[r_{b}]{r_{a}} \mathrm{A}
\end{align*}
", "\r\n"=>"\n")

# Latexify.@generate_test latexify(rn, mathjax = false)
@test latexify(rn, mathjax = false) == replace(
raw"\begin{align*}
\varnothing &\xrightleftharpoons[d_{a}]{\frac{p_{a} B^{n}}{k^{n} + B^{n}}} \mathrm{A} \\
\varnothing &\xrightleftharpoons[d_{b}]{p_{b}} \mathrm{B} \\
3 \mathrm{B} &\xrightleftharpoons[r_{b}]{r_{a}} \mathrm{A}
\end{align*}
", "\r\n"=>"\n")
end

# Tests for system with parametric stoichiometry.
let
rn = @reaction_network begin
p, 0 --> (m + n)*X
end

@test_broken latexify(rn) == replace(
raw"\begin{align*}
\varnothing &\xrightarrow{p} (m + n)\mathrm{X}
\end{align*}
", "\r\n"=>"\n")
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this just seem to be git getting confused. No tests have been moved (although tabs and empty liens were removed in places, which i presume is causing this).


# Latexify.@generate_test latexify(rn)
@test latexify(rn) == replace(
raw"\begin{align*}
\varnothing &\xrightarrow{p} (m + n)\mathrm{X}
\end{align*}
", "\r\n"=>"\n")
end

# Checks for systems with vector species/parameters.
# Technically tests would work, however, the display is non-ideal (https://github.com/SciML/Catalyst.jl/issues/932, https://github.com/JuliaSymbolics/Symbolics.jl/issues/1167).
let
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New test for vector stuff (don't work right now).

rn = @reaction_network begin
@parameters k[1:2] x[1:2] [isconstantspecies=true]
@species (X(t))[1:2] (K(t))[1:2]
(k[1]*K[1],k[2]*K[2]), X[1] + x[1] <--> X[2] + x[2]
end

# Latexify.@generate_test latexify(rn)
@test_broken false
end

### Tests the `form` Option ###
Expand All @@ -170,21 +186,15 @@ let
end

# Latexify.@generate_test latexify(rn; form=:ode)
@test_broken latexify(rn; form = :ode) == replace(
raw"$\begin{align}
\frac{\mathrm{d} X\left( t \right)}{\mathrm{d}t} =& p - \left( X\left( t \right) \right)^{2} kB - d X\left( t \right) + 2 kD \mathrm{X2}\left( t \right) \\
\frac{\mathrm{d} \mathrm{X2}\left( t \right)}{\mathrm{d}t} =& \frac{1}{2} \left( X\left( t \right) \right)^{2} kB - kD \mathrm{X2}\left( t \right)
\end{align}
$", "\r\n"=>"\n")

# Currently latexify doesn't handle SDE systems properly, and they look identical to ode systems.
# The "==" shoudl be a "!=", but due to latexify tests not working, for the broken test to work, I changed it.
@test_broken latexify(rn; form=:sde) == replace(
raw"$\begin{align}
\frac{\mathrm{d} X\left( t \right)}{\mathrm{d}t} =& p - \left( X\left( t \right) \right)^{2} kB - d X\left( t \right) + 2 kD \mathrm{X2}\left( t \right) \\
\frac{\mathrm{d} \mathrm{X2}\left( t \right)}{\mathrm{d}t} =& \frac{1}{2} \left( X\left( t \right) \right)^{2} kB - kD \mathrm{X2}\left( t \right)
\end{align}
$", "\r\n"=>"\n")
@test latexify(rn; form = :ode) == replace(
raw"$\begin{align}
\frac{\mathrm{d} X\left( t \right)}{\mathrm{d}t} =& p - d X\left( t \right) + 2 kD \mathrm{X2}\left( t \right) - \left( X\left( t \right) \right)^{2} kB \\
\frac{\mathrm{d} \mathrm{X2}\left( t \right)}{\mathrm{d}t} =& - kD \mathrm{X2}\left( t \right) + \frac{1}{2} \left( X\left( t \right) \right)^{2} kB
\end{align}
$", "\r\n"=>"\n")

# Currently latexify doesn't handle SDE systems properly, and they look identical to ode systems (https://github.com/SciML/ModelingToolkit.jl/issues/2782).
@test_broken false
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SDESystem latex printing is broken.


# Tests that erroneous form gives error.
@test_throws ErrorException latexify(rn; form=:xxx)
Expand Down Expand Up @@ -229,14 +239,15 @@ let
end

# Latexify.@generate_test latexify(rn)
@test_broken latexify(rn) == replace(
raw"\begin{align*}
\varnothing &\xrightarrow{p} (m + n)\mathrm{X}
\end{align*}
", "\r\n"=>"\n")
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This test seems to have used the wrong generated stuff? In source we got

let
    rn = @reaction_network begin
        k*Y, Y --> ∅
    end

    # Latexify.@generate_test latexify(rn)
    @test_broken latexify(rn) == replace(
    raw"\begin{align*}
    \varnothing &\xrightarrow{p} (m + n)\mathrm{X}  
    \end{align*}
    ", "\r\n"=>"\n")
end

@test latexify(rn) == replace(
raw"\begin{align*}
\mathrm{Y} &\xrightarrow{Y k} \varnothing
\end{align*}
", "\r\n"=>"\n")
end

# Checks when combined with equations (nonlinear system).
# Technically tests would work, however, the display is non-ideal (https://github.com/SciML/Catalyst.jl/issues/927).
let
t = default_t()
base_network = @reaction_network begin
Expand All @@ -247,18 +258,8 @@ let
extended = extend(decaying_rate, base_network)

# Latexify.@generate_test latexify(extended)
@test_broken latexify(extended) == replace(
raw"\begin{align*}
\mathrm{X} &\xrightarrow{k r} \varnothing
0 &= -1 - x\left( t \right)
\end{align*}
", "\r\n"=>"\n")
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While we could generate tests they would point towards LaTeX code we wouldn't want, so I removed it and just marked as something broken.

@test_broken false

# Latexify.@generate_test latexify(extended, mathjax=false)
@test_broken latexify(extended, mathjax = false) == replace(
raw"\begin{align*}
\mathrm{X} &\xrightarrow{k r} \varnothing
0 &= -1 - x\left( t \right)
\end{align*}
", "\r\n"=>"\n")
@test_broken false
end
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