clean up documentation and types

docs/src/index.md

@@ -89,7 +89,14 @@ Modules = [SBML]
 Pages = ["utils.jl"]
 ```
 
-## Internal math manipulation
+## Math and `Symbolics.jl` compatibility
+
+```@autodocs
+Modules = [SBML]
+Pages = ["symbolics.jl"]
+```
+
+### Internal math helpers
 
 ```@autodocs
 Modules = [SBML]

src/SBML.jl

@@ -16,6 +16,6 @@ include("symbolics.jl")
 sbml = (sym::Symbol) -> dlsym(SBML_jll.libsbml_handle, sym)
 
 export SBMLVersion, readSBML, getS, getLBs, getUBs, getOCs
-export convert_level_and_version, libsbml_convert, convert_simplify_math
+export set_level_and_version, libsbml_convert, convert_simplify_math
 
 end # module

src/readsbml.jl

@@ -2,7 +2,7 @@
 const VPtr = Ptr{Cvoid}
 
 """
-    function get_string(x::VPtr, fn_sym)::Maybe{String}
+    get_string(x::VPtr, fn_sym)::Maybe{String}
 
 C-call the SBML function `fn_sym` with a single parameter `x`, interpret the
 result as a string and return it, or throw exception in case the pointer is
@@ -18,9 +18,9 @@ function get_string(x::VPtr, fn_sym)::String
 end
 
 """
-    function get_optional_string(x::VPtr, fn_sym)::Maybe{String}
+    get_optional_string(x::VPtr, fn_sym)::Maybe{String}
 
-Like [`get_string`](@Ref), but returns `nothing` instead of throwing an
+Like [`get_string`](@ref), but returns `nothing` instead of throwing an
 exception.
 
 This is used to get notes and annotations and several other things (see
@@ -82,7 +82,7 @@ Read the SBML from a XML file in `fn` and return the contained `SBML.Model`.
 The `sbml_conversion` is a function that does an in-place modification of the
 single parameter, which is the C pointer to the loaded SBML document (C type
 `SBMLDocument*`). Several functions for doing that are prepared, including
-[`convert_level_and_version`](@ref), [`libsbml_convert`](@ref), and
+[`set_level_and_version`](@ref), [`libsbml_convert`](@ref), and
 [`convert_simplify_math`](@ref).
 
 # Example

src/symbolics.jl

 
-default_symbolics_mapping = Dict(
+"""
+    default_symbolics_mapping :: Dict{String,Any}
+
+Default mapping of SBML function names to Julia functions, represented as a
+dictionary from Strings (SBML names) to anything `eval`uable as Julia&Symbolics
+functions, such as symbols and expressions.
+
+The default mapping only contains the basic SBML functions that are
+unambiguously represented in Julia; it is supposed to be extended by the user
+if more functions need to be supported.
+"""
+default_symbolics_mapping = Dict{String,Any}(
     "+" => :+,
     "-" => :-,
     "*" => :*,
@@ -12,7 +23,6 @@ default_symbolics_mapping = Dict(
     "ceiling" => :ceil,
     "floor" => :floor,
     "piecewise" => :(Core.ifelse),
-    #TODO extend this in the future
 )
 
 allowed_sym(x, allowed_funs) =