Merge pull request #107 from LCSB-BioCore/mk-cleaning-055

0.5.5 release prep (cleaning)

docs/src/index.md

@@ -59,6 +59,13 @@ julia> Matrix(S)
 
 # Function reference
 
+## Helper types
+
+```@autodocs
+Modules = [SBML]
+Pages = ["types.jl"]
+```
+
 ## Data structures
 
 ```@autodocs

src/SBML.jl

@@ -4,14 +4,15 @@ using SBML_jll, Libdl
 using SparseArrays
 using Symbolics
 
+include("types.jl")
 include("structs.jl")
 include("version.jl")
 
-include("utils.jl")
-include("readsbml.jl")
 include("converters.jl")
 include("math.jl")
+include("readsbml.jl")
 include("symbolics.jl")
+include("utils.jl")
 
 sbml(sym::Symbol) = dlsym(SBML_jll.libsbml_handle, sym)
 

src/converters.jl

@@ -6,11 +6,18 @@ A converter to pass into [`readSBML`](@ref) that enforces certain SBML level
 and version.
 """
 set_level_and_version(level, version) =
-    doc -> check_errors(ccall(sbml(:SBMLDocument_setLevelAndVersion), Cint,
-                              (VPtr, Cint, Cint),
-                              doc, level, version),
-                        doc,
-                        ErrorException("Setting of level and version did not succeed"))
+    doc -> check_errors(
+        ccall(
+            sbml(:SBMLDocument_setLevelAndVersion),
+            Cint,
+            (VPtr, Cint, Cint),
+            doc,
+            level,
+            version,
+        ),
+        doc,
+        ErrorException("Setting of level and version did not succeed"),
+    )
 
 """
     libsbml_convert(conversion_options::Vector{Pair{String, Dict{String, String}}})
@@ -38,8 +45,11 @@ libsbml_convert(
                     opt,
                 )
             end
-            check_errors(ccall(sbml(:SBMLDocument_convert), Cint, (VPtr, VPtr), doc, props),
-                         doc, ErrorException("Conversion returned errors"))
+            check_errors(
+                ccall(sbml(:SBMLDocument_convert), Cint, (VPtr, VPtr), doc, props),
+                doc,
+                ErrorException("Conversion returned errors"),
+            )
         end
     end
 

src/readsbml.jl

@@ -93,8 +93,7 @@ end)
 function readSBML(fn::String, sbml_conversion = document -> nothing)::SBML.Model
     doc = ccall(sbml(:readSBML), VPtr, (Cstring,), fn)
     try
-        get_error_messages(doc,
-                           AssertionError("Opening SBML document has reported errors"))
+        get_error_messages(doc, AssertionError("Opening SBML document has reported errors"))
 
         sbml_conversion(doc)
 

src/structs.jl

 
-"""
-    Maybe{X}
-
-Type shortcut for "`X` or nothing" or "nullable `X`" in javaspeak. Name
-got inspired by our functional friends.
-"""
-const Maybe{X} = Union{Nothing,X}
-
 """
 Part of a measurement unit definition that corresponds to the SBML definition
 of `Unit`. For example, the unit "per square megahour", Mh^(-2), is written as:

src/types.jl

+
+"""
+    Maybe{X}
+
+Type shortcut for "`X` or nothing" or "nullable `X`" in javaspeak. Name
+got inspired by our functional friends.
+"""
+const Maybe{X} = Union{Nothing,X}
+
+"""
+    VPtr
+
+A convenience wrapper for "any" (C `void`) pointer.
+"""
+const VPtr = Ptr{Cvoid}

src/utils.jl

-const VPtr = Ptr{Cvoid}
-
 """
     function getS(m::SBML.Model; zeros=spzeros)::Tuple{Vector{String},Vector{String},AbstractMatrix{Float64}}
 
@@ -142,7 +140,7 @@ Show the error messages reported by SBML in the `doc` document and throw the
 function get_error_messages(doc::VPtr, error::Exception)
     n_errs = ccall(sbml(:SBMLDocument_getNumErrors), Cuint, (VPtr,), doc)
     for i = 1:n_errs
-        err = ccall(sbml(:SBMLDocument_getError), VPtr, (VPtr, Cuint), doc, i-1)
+        err = ccall(sbml(:SBMLDocument_getError), VPtr, (VPtr, Cuint), doc, i - 1)
         msg = string(strip(get_string(err, :XMLError_getMessage)))
         @error "SBML reported error: $(msg)"
     end

test/loadmodels.jl

@@ -134,7 +134,7 @@ end
     @test isequal(convert(Num, m.reactions["J29"].kinetic_math), 2.0 * S29 * S29b)
 end
 
-@testset "converters fail gracefully" begin
+@testset "converters work and fail gracefully" begin
     @test_logs (:error, r"^SBML reported error:") (:error, r"^SBML reported error:") @test_throws ErrorException readSBML(
         joinpath(@__DIR__, "data", "sbml01289.xml"),
         doc -> begin
@@ -142,4 +142,13 @@ end
             convert_simplify_math(doc)
         end,
     )
+
+    test_math =
+        readSBML(
+            joinpath(@__DIR__, "data", "sbml01565.xml"),
+            libsbml_convert("expandInitialAssignments"),
+        ).reactions["J31"].kinetic_math
+
+    @test test_math.args[2].fn == "sin"
+    @test test_math.args[2].args[1].val == 2.1
 end