Merge pull request #21 from anandijain/aj/fix2

#19 with test fixes

Author: anandijain

src/maps.jl

@@ -18,6 +18,11 @@ applymap = Dict{String,Function}(
     "geq" => x -> H(x[1] - x[2]),
     "gt" => x -> H(x[1] - x[2] - ϵ),
 
+    # equal nodes are not part of the MathML specification and
+    # are generated by disambiguate_equality!
+    "equal" => x -> H(x[1] - x[2]) * H(x[2] - x[1]),
+    "neq" => x -> 1 - H(x[1] - x[2]) * H(x[2] - x[1]),
+
     # "lt" => x -> Base.foldl(Base.:<, x),
     # "leq" => x -> Base.foldl(Base.:≤, x),
     # "geq" => x -> Base.foldl(Base.:≥, x),
@@ -114,4 +119,4 @@ tagmap = Dict{String,Function}(
     "math" => x -> map(parse_node, elements(x)),
     "vector" => x -> map(parse_node, elements(x)),
     "lambda" => parse_lambda,
-)
+)

src/parse.jl

@@ -33,7 +33,7 @@ function parse_cn(node)
     if haskey(node, "type") && elements(node) != EzXML.Node[]
         parse_cn_w_sep(node)
     else
-        Meta.parse(node.content)
+        Float64(Meta.parse(node.content))   # convert to Float64 for CellML compatibility
     end
 end
 
@@ -136,6 +136,7 @@ parse a <diff>
 """
 function parse_diff(a)
     (iv, deg), x = a
+    deg = trunc(Int, deg)
     # num = Num(Symbolics.Sym{Symbolics.FnType{Tuple{Real},Real}}(Symbol(x))(iv))
     D = Differential(iv)^deg
     D(x)
@@ -149,14 +150,14 @@ parse a <lambda> node
 ```xml
 <lambda>
   <bvar> x1 </bvar><bvar> xn </bvar>
-   expression-in-x1-xn 
+   expression-in-x1-xn
 </lambda>
 ```
 """
 function parse_lambda(node)
     es = elements(node)
     vars = findall("//x:bvar | //bvar", node, ["x" => MathML.mathml_ns])
-    # vars2 = findall("//bvar", node) # works in tests 
+    # vars2 = findall("//bvar", node) # works in tests
     # vars = union(vars, vars2) # FIX
 
     args = first.(parse_bvar.(vars))

src/utils.jl

@@ -3,12 +3,12 @@ const mathml_ns = "http://www.w3.org/1998/Math/MathML"
 """
     mathml_to_nums()
 
-given a filename or an `EzXML.Document` or `EzXML.Node`, 
+given a filename or an `EzXML.Document` or `EzXML.Node`,
 finds all of the <ci>s and defines them as Symbolics.jl Nums
 returns a Vector{Num}.
 Note, the root namespace needs to be MathML
 """
-function mathml_to_nums end 
+function mathml_to_nums end
 
 function mathml_to_nums(fn::AbstractString)
     doc = readxml(fn)
@@ -32,8 +32,8 @@ end
 """
     extract_mathml()
 
-given a filename, `EzXML.Document`, or `EzXML.Node` 
-returns all of the MathML nodes. 
+given a filename, `EzXML.Document`, or `EzXML.Node`
+returns all of the MathML nodes.
 """
 function extract_mathml end
 
@@ -46,9 +46,23 @@ function extract_mathml(doc::EzXML.Document)
 end
 
 function extract_mathml(node::EzXML.Node)
+    disambiguate_equality!(node)
     findall("//x:math", node, ["x" => mathml_ns])
 end
 
+"""
+    @disambiguate_equality!
+
+utility function to replace <eq> inside piecewise subtrees to
+disambiguate from the assignement <eq>
+"""
+function disambiguate_equality!(node)
+    nodes = findall("//x:piecewise//x:eq", node, ["x" => mathml_ns])
+    for n in nodes
+        setnodename!(n, "equal")
+    end
+end
+
 """
     @xml_str(s)
 
@@ -58,7 +72,7 @@ macro xml_str(s)
     parsexml(s).root
 end
 
-""" 
+"""
     @MathML_str(s)
 
 utility macro for parsing xml strings into symbolics
@@ -82,8 +96,8 @@ function check_ivs(node)
     all(y -> y.content == x[1].content, x)
 end
 
-# conditional hack
-H(x) = IfElse.ifelse(x > 0, one(x), zero(x))
+# conditional and rounding hacks
+H(x) = IfElse.ifelse(x >= 0, one(x), zero(x))
 const ϵ = eps(Float64)
 frac(x) = 0.5 - atan(cot(π * x)) / π
 heaviside_or(x) = length(x) == 1 ? x[1] : x[1] + heaviside_or(x[2:end]) - x[1] * heaviside_or(x[2:end])

test/parse.jl

@@ -99,8 +99,8 @@ str = """
 """
 @test isequal(MathML.parse_str(str), 
   IfElse.ifelse(
-    IfElse.ifelse(1 - t > 0, 1, 0) > 0.5,
-     x * (y + a * z) * ((1 - (b * z))^-1),
+    IfElse.ifelse(1. - t >= 0, 1, 0) > 0.5,
+     x * (y + a * z) * ((1.0 - (b * z))^-1),
       x * y))
 
 # factorial