fix doc builds

Author: isaacsas

README.md

@@ -9,7 +9,7 @@ Finite State Projection [[1]](#1)  algorithms for chemical reaction networks bas
 - FSP equations are generated as `ODEFunction`/`ODEProblem`s and can be solved with [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl), with on-the-fly generation of targeted functions for improved performance
 - The Chemical Master Equation can be represented as a `SparseMatrixCSC`
 
-More information is available in the [documentation](https://kaandocal.github.io/FiniteStateProjection.jl/dev/). Please feel free to open issues and submit pull requests! 
+More information is available in the [documentation](https://kaandocal.github.io/FiniteStateProjection.jl/dev/). Please feel free to open issues and submit pull requests!
 
 ## Examples
 ### Birth-Death System
@@ -20,7 +20,7 @@ using OrdinaryDiffEq
 rn = @reaction_network begin
     σ, 0 --> A
     d, A --> 0
-end σ d
+end
 
 sys = FSPSystem(rn)
 
@@ -30,7 +30,7 @@ ps = [ 10.0, 1.0 ]
 # Initial distribution (over 1 species)
 # Here we start with 0 copies of A
 u0 = zeros(50)
-u0[1] = 1.0 
+u0[1] = 1.0
 
 prob = convert(ODEProblem, sys, u0, (0, 10.0), ps)
 sol = solve(prob, Vern7())
@@ -47,7 +47,7 @@ rn = @reaction_network begin
     σ_off, G_on --> 0
     ρ, G_on --> G_on + M
     d, M --> 0
-end σ_on σ_off ρ d
+end
 
 sys = FSPSystem(rn)
 

demo/birth_death.jl

@@ -7,7 +7,7 @@ using PyPlot
 rs = @reaction_network begin
     r1, 0 --> A
     r2, A --> 0
-end r1 r2
+end
 
 ##
 

demo/telegraph.jl

@@ -9,7 +9,7 @@ rs = @reaction_network begin
     r2, G_on --> 0
     r3, G_on --> G_on + M
     r4, M --> 0
-end r1 r2 r3 r4
+end
 
 ##
 
@@ -20,9 +20,9 @@ ps = [ 0.25, 0.15, 15.0, 1.0 ]
 
 # Initial values
 # Since G_on + G_off = const. we do not have to model the two
-# separately. Use reduced_species(sys) to get the list of 
+# separately. Use reduced_species(sys) to get the list of
 # species we actually have to model:
-# 
+#
 # julia> reduced_species(sys)
 # 2-element Vector{Int64}:
 #  1

docs/Project.toml

@@ -1,2 +1,5 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+Documenter = "0.27"

docs/src/examples.md

@@ -11,7 +11,7 @@ using OrdinaryDiffEq
 rn = @reaction_network begin
     σ, 0 --> A
     d, A --> 0
-end σ d
+end
 
 sys = FSPSystem(rn)
 
@@ -21,7 +21,7 @@ ps = [ 10.0, 1.0 ]
 # Initial distribution (over 1 species)
 # Here we start with 0 copies of A
 u0 = zeros(50)
-u0[1] = 1.0 
+u0[1] = 1.0
 
 prob = ODEProblem(sys, u0, (0, 10.0), ps)
 sol = solve(prob, Vern7())
@@ -47,7 +47,7 @@ rn = @reaction_network begin
     σ_off, G_on --> 0
     ρ, G_on --> G_on + M
     d, M --> 0
-end σ_on σ_off ρ d
+end
 
 sys = FSPSystem(rn)
 

docs/src/troubleshoot.md

@@ -42,7 +42,7 @@ This point might seem obvious, but errors in the rate functions, or an incorrect
 rn = @reaction_network begin
    σ * (N - I), I --> 2I
    ρ, I --> 0
-end σ ρ N
+end
 
 sys_fsp = FSPSystem(rn)
 ```