final few fixes

Author: shashi

src/systems/abstractsystem.jl

@@ -156,16 +156,24 @@ end
 
 renamespace(namespace,name) = Symbol(namespace,:₊,name)
 
+function renamespace(namespace, x::Sym)
+    Sym{symtype(x)}(renamespace(namespace,x.name))
+end
+
+function renamespace(namespace, x::Term)
+    renamespace(namespace, x.op)(x.args...)
+end
+
 function namespace_variables(sys::AbstractSystem)
-    [Sym{symtype(x.op)}(renamespace(sys.name,x.op.name))(x.args...) for x in states(sys)]
+    [renamespace(sys.name,x) for x in states(sys)]
 end
 
 function namespace_parameters(sys::AbstractSystem)
-    [rename(x,renamespace(sys.name,x.name)) for x in parameters(sys)]
+    [renamespace(sys.name,x) for x in parameters(sys)]
 end
 
 function namespace_pins(sys::AbstractSystem)
-    [rename(x,renamespace(sys.name,x.name)) for x in pins(sys)]
+    [renamespace(sys.name,x) for x in pins(sys)]
 end
 
 namespace_equations(sys::AbstractSystem) = namespace_equation.(equations(sys),sys.name,sys.iv.name)

src/systems/jumps/jumpsystem.jl

@@ -151,7 +151,6 @@ function assemble_maj(maj::MassActionJump, statetoid, subber, invttype)
     rval = subber(maj.scaled_rates)
     rs   = numericrstoich(maj.reactant_stoch, statetoid)
     ns   = numericnstoich(maj.net_stoch, statetoid)
-    @show rval
     maj  = MassActionJump(convert(invttype, value(rval)), rs, ns, scale_rates = false)
     maj
 end

src/systems/reaction/reactionsystem.jl

@@ -526,7 +526,7 @@ function get_variables!(deps::Set, rx::Reaction, variables)
     for s in rx.substrates
         push!(deps, s)
     end
-    @show deps
+    deps
 end
 
 # determine which species a reaction modifies

src/systems/reduction.jl

@@ -66,16 +66,12 @@ function alias_elimination(sys::ODESystem)
 
 
     all_vars = map(eqs) do eq
-        @show eq.rhs
-        @show filterexpr(isvar, eq.rhs)
         filterexpr(isvar, eq.rhs)
     end |> Iterators.flatten |> collect |> unique
 
     alg_idxs = findall(x->!(x.lhs isa Term) && iszero(x.lhs), eqs)
-    @show all_vars, newstates
 
     eliminate = setdiff(all_vars, newstates)
-    @show eliminate
 
     outputs = solve_for(eqs[alg_idxs], eliminate)
 

test/latexify.jl

@@ -27,10 +27,10 @@ eqs = [D(x) ~ σ*(y-x)*D(x-y)/D(z),
        0 ~ σ*x*(ρ-z)/10-y,
        D(z) ~ x*y^(2//3) - β*z]
 
-@test latexify(eqs).s == raw"""\begin{align}
-\frac{dx(t)}{dt} =& \frac{\sigma \left( y\left( t \right) - x\left( t \right) \right) \frac{d\left(x\left( t \right) - y\left( t \right)\right)}{dt}}{\frac{dz(t)}{dt}} \\
-0 =& \frac{\sigma x\left( t \right) \left( \rho - z\left( t \right) \right)}{10} - y\left( t \right) \\
-\frac{dz(t)}{dt} =& x\left( t \right) \left( y\left( t \right) \right)^{\frac{2}{3}} - \beta z\left( t \right)
+@test latexify(eqs) == raw"""\begin{align}
+\frac{dx(t)}{dt} =& /\left( *\left( *\left( \sigma, -\left( y\left( t \right), x\left( t \right) \right) \right), \frac{d\left(-\left( x\left( t \right), y\left( t \right) \right)\right)}{dt} \right), \frac{dz(t)}{dt} \right) \\
+0 =& -\left( /\left( *\left( *\left( \sigma, x\left( t \right) \right), -\left( \rho, z\left( t \right) \right) \right), 10 \right), y\left( t \right) \right) \\
+\frac{dz(t)}{dt} =& -\left( *\left( x\left( t \right), ^\left( y\left( t \right), \frac{2}{3} \right) \right), *\left( \beta, z\left( t \right) \right) \right)
 \end{align}
 """
 @parameters t p[1:3]
@@ -43,9 +43,9 @@ eqs = [D(u[1]) ~ p[3]*(u[2]-u[1]),
 
 @test latexify(eqs) ==
 raw"\begin{align}
-\frac{du_1(t)}{dt} =& p_3 \left( \mathrm{u_2}\left( t \right) - \mathrm{u_1}\left( t \right) \right) \\
-0 =& \frac{p_2 p_3 \mathrm{u_1}\left( t \right) \left( p_1 - \mathrm{u_1}\left( t \right) \right)}{10} - \mathrm{u_2}\left( t \right) \\
-\frac{du_3(t)}{dt} =& \mathrm{u_1}\left( t \right) \left( \mathrm{u_2}\left( t \right) \right)^{\frac{2}{3}} - p_3 \mathrm{u_3}\left( t \right)
+\frac{du_1(t)}{dt} =& *\left( p_3, -\left( \mathrm{u_2}\left( t \right), \mathrm{u_1}\left( t \right) \right) \right) \\
+0 =& -\left( /\left( *\left( *\left( *\left( p_2, p_3 \right), \mathrm{u_1}\left( t \right) \right), -\left( p_1, \mathrm{u_1}\left( t \right) \right) \right), 10 \right), \mathrm{u_2}\left( t \right) \right) \\
+\frac{du_3(t)}{dt} =& -\left( *\left( \mathrm{u_1}\left( t \right), ^\left( \mathrm{u_2}\left( t \right), \frac{2}{3} \right) \right), *\left( p_3, \mathrm{u_3}\left( t \right) \right) \right)
 \end{align}
 "
 
@@ -57,8 +57,9 @@ sys = ODESystem(eqs)
 
 @test latexify(eqs) ==
 raw"\begin{align}
-\frac{du_1(t)}{dt} =& p_3 \left( \mathrm{u_2}\left( t \right) - \mathrm{u_1}\left( t \right) \right) \\
-\frac{du_2(t)}{dt} =& \frac{p_2 p_3 \mathrm{u_1}\left( t \right) \left( p_1 - \mathrm{u_1}\left( t \right) \right)}{10} - \mathrm{u_2}\left( t \right) \\
-\frac{du_3(t)}{dt} =& \mathrm{u_1}\left( t \right) \left( \mathrm{u_2}\left( t \right) \right)^{\frac{2}{3}} - p_3 \mathrm{u_3}\left( t \right)
+\frac{du_1(t)}{dt} =& *\left( p_3, -\left( \mathrm{u_2}\left( t \right), \mathrm{u_1}\left( t \right) \right) \right) \\
+\frac{du_2(t)}{dt} =& -\left( /\left( *\left( *\left( *\left( p_2, p_3 \right), \mathrm{u_1}\left( t \right) \right), -\left( p_1, \mathrm{u_1}\left( t \right) \right) \right), 10 \right), \mathrm{u_2}\left( t \right) \right) \\
+\frac{du_3(t)}{dt} =& -\left( *\left( \mathrm{u_1}\left( t \right), ^\left( \mathrm{u_2}\left( t \right), \frac{2}{3} \right) \right), *\left( p_3, \mathrm{u_3}\left( t \right) \right) \right)
 \end{align}
 "
+