Merge pull request #142 from biosimulators/new-evalidate

New evalidate

biosimulators_utils/_version.py

@@ -1 +1 @@
-__version__ = '0.1.180'
+__version__ = '0.1.181'

biosimulators_utils/sedml/math.py

@@ -179,10 +179,12 @@ def compile_math(math):
             .replace('^', '**')
         )
 
-    math_node = evalidate.evalidate(math,
-                                    addnodes=VALID_MATH_EXPRESSION_NODES,
-                                    funcs=MATHEMATICAL_FUNCTIONS.keys())
-    compiled_math = compile(math_node, '<math>', 'eval')
+    model = evalidate.base_eval_model.clone()
+    model.nodes.extend(VALID_MATH_EXPRESSION_NODES)
+    model.allowed_functions.extend(MATHEMATICAL_FUNCTIONS.keys())
+
+    math_node = evalidate.Expr(math, model=model)
+    compiled_math = compile(math_node.node, '<math>', 'eval')
     return compiled_math
 
 

biosimulators_utils/sedml/validation.py

@@ -1771,8 +1771,8 @@ def validate_calculation(calculation):
 
         try:
             compiled_math = compile_math(calculation.math)
-        except TypeError:
-            errors.append(['The mathematical expression must be a `string`, not a `{}`.'.format(calculation.math.__class__)])
+        except TypeError as exception:
+            errors.append(['The mathematical expression must be a `string`, not a `{}`:'.format(calculation.math.__class__), [[str(exception)]]])
             return (errors, warnings)
         except (SyntaxError, CompilationException) as exception:
             errors.append(['The syntax of the mathematical expression `{}` is invalid.'.format(calculation.math), [[str(exception)]]])

requirements.txt

@@ -1,7 +1,7 @@
 appdirs
 biopython
 cement
-evalidate
+evalidate >= 2.0.0
 h5py
 kisao >= 2.32
 lxml