Merge pull request #116 from SciML/pl/updatedocs

update docs

.github/workflows/FormatCheck.yml

@@ -32,7 +32,7 @@ jobs:
       - name: Format check
         run: |
           julia -e '
-          out = Cmd(`git diff --name-only`) |> read |> String
+          out = Cmd(`git diff`) |> read |> String
           if out == ""
               exit(0)
           else

README.md

@@ -43,13 +43,14 @@ prob = ODEProblem(odesys, [], tspan, [])
 sol = solve(prob, Tsit5())
 ```
 
-Alternatively, we also provide more concise methods to import `SBML.Models`, `Catalyst.ReactionSystems`, and `ModelingToolkit.ODESystems`.
+Alternatively, SBMLToolkit also provides more concise methods to import `SBML.Models`, `Catalyst.ReactionSystems`, and `ModelingToolkit.ODESystems`.
 
 ```julia
 mdl = readSBML(sbmlfile, DefaultImporter())
 rs = readSBML(sbmlfile, ReactionSystemImporter())
 odesys = readSBML(sbmlfile, ODESystemImporter())
 ```
+
 ## License
 
 The package is released under the [MIT license](https://github.com/SciML/SBMLToolkit.jl/blob/main/LICENSE).

docs/src/index.md

@@ -53,6 +53,14 @@ prob = ODEProblem(odesys, [], tspan, [])
 sol = solve(prob, Tsit5())
 ```
 
+SBMLToolkit also provides the following convenience functions to import `SBML.Models`, `Catalyst.ReactionSystems` and `ModelingToolkit.ODESystems`:
+
+```julia
+mdl = readSBML(sbmlfile, DefaultImporter())
+rs = readSBML(sbmlfile, ReactionSystemImporter())
+odesys = readSBML(sbmlfile, ODESystemImporter())
+```
+
 ## License
 
 The package is released under the [MIT license](https://github.com/SciML/SBMLToolkit.jl/blob/main/LICENSE).

src/systems.jl

@@ -37,8 +37,10 @@ Create a `ModelingToolkit.ODESystem` from an SBML file, using default import set
 
 See also [`Model`](@ref) and [`ODESystemImporter`](@ref).
 """
-function SBML.readSBML(sbmlfile::String, ::ODESystemImporter; include_zero_odes::Bool=true, kwargs...)  # Returns an MTK.ODESystem
-    convert(ODESystem, readSBML(sbmlfile, ReactionSystemImporter(), kwargs...), include_zero_odes = include_zero_odes)
+function SBML.readSBML(sbmlfile::String, ::ODESystemImporter;
+                       include_zero_odes::Bool = true, kwargs...)  # Returns an MTK.ODESystem
+    convert(ODESystem, readSBML(sbmlfile, ReactionSystemImporter(), kwargs...),
+            include_zero_odes = include_zero_odes)
 end
 
 """
@@ -98,7 +100,8 @@ Create an `ODESystem` from an `SBML.Model`.
 
 See also [`ReactionSystem`](@ref).
 """
-function ModelingToolkit.ODESystem(model::SBML.Model; include_zero_odes::Bool = true, kwargs...)
+function ModelingToolkit.ODESystem(model::SBML.Model; include_zero_odes::Bool = true,
+                                   kwargs...)
     rs = ReactionSystem(model; kwargs...)
     convert(ODESystem, rs; include_zero_odes = include_zero_odes)
 end

src/utils.jl

@@ -63,6 +63,6 @@ function has_rule_type(id::String, m::SBML.Model, T::Type{<:SBML.Rule})
 end
 
 const importdefaults = doc -> begin
-                   set_level_and_version(3, 2)(doc)
-                   convert_promotelocals_expandfuns(doc)
+    set_level_and_version(3, 2)(doc)
+    convert_promotelocals_expandfuns(doc)
 end

test/reactions.jl

@@ -1,5 +1,5 @@
 using SBMLToolkit
-using Catalyst, SBML, ModelingToolkit
+using Catalyst, SBML
 using Test
 
 cd(@__DIR__)