Merge 4ae72c5 into 74d8917

pycalphad/core/cache.py

@@ -6,7 +6,11 @@
 http://code.activestate.com/recipes/578078-py26-and-py30-backport-of-python-33s-lru-cache/
 """
 
-from collections import Iterable, Mapping, namedtuple
+try:
+    from collections.abc import Iterable, Mapping
+except ImportError:
+    from collections import Iterable, Mapping
+from collections import namedtuple
 from threading import RLock
 from functools import update_wrapper
 

pycalphad/core/utils.py

@@ -6,13 +6,16 @@
 from pycalphad.core.halton import halton
 from pycalphad.core.constants import MIN_SITE_FRACTION
 from sympy.utilities.lambdify import lambdify
-from sympy.printing.lambdarepr import LambdaPrinter
 from sympy import Symbol
 import numpy as np
 import operator
 import functools
 import itertools
 import collections
+try:
+    from collections.abc import Iterable, Mapping
+except ImportError:
+    from collections import Iterable, Mapping
 
 try:
     # Only available in numpy 1.10 and newer
@@ -137,7 +140,7 @@ def unpack_condition(tup):
             return np.arange(tup[0], tup[1], tup[2], dtype=np.float)
         else:
             raise ValueError('Condition tuple is length {}'.format(len(tup)))
-    elif isinstance(tup, collections.Iterable):
+    elif isinstance(tup, Iterable):
         return [float(x) for x in tup]
     else:
         return [float(tup)]
@@ -242,14 +245,14 @@ def unpack_kwarg(kwarg_obj, default_arg=None):
     """
     new_dict = collections.defaultdict(lambda: default_arg)
 
-    if isinstance(kwarg_obj, collections.Mapping):
+    if isinstance(kwarg_obj, Mapping):
         new_dict.update(kwarg_obj)
     # kwarg_obj is a list containing a dict and a default
     # For now at least, we don't treat ndarrays the same as other iterables
     # ndarrays are assumed to be numeric arrays containing "default values", so don't match here
-    elif isinstance(kwarg_obj, collections.Iterable) and not isinstance(kwarg_obj, np.ndarray):
+    elif isinstance(kwarg_obj, Iterable) and not isinstance(kwarg_obj, np.ndarray):
         for element in kwarg_obj:
-            if isinstance(element, collections.Mapping):
+            if isinstance(element, Mapping):
                 new_dict.update(element)
             else:
                 # element=element syntax to silence var-from-loop warning

pycalphad/io/tdb.py

@@ -11,6 +11,7 @@
 from sympy import sympify, And, Or, Not, Intersection, Union, EmptySet, Interval, Piecewise
 from sympy import Symbol, GreaterThan, StrictGreaterThan, LessThan, StrictLessThan, Complement, S
 from sympy import Mul, Pow, Rational
+from sympy.abc import _clash
 from sympy.printing.str import StrPrinter
 from sympy.core.mul import _keep_coeff
 from sympy.printing.precedence import precedence
@@ -36,6 +37,16 @@
                   ast.Load, ast.Mult, ast.Name, ast.Num, ast.Pow, ast.Sub,
                   ast.UAdd, ast.UnaryOp, ast.USub]
 
+# Avoid symbol names clashing with objects in sympy (gh-233)
+clashing_namespace = {}
+clashing_namespace.update(_clash)
+clashing_namespace['CC'] = Symbol('CC')
+clashing_namespace['FF'] = Symbol('FF')
+clashing_namespace['T'] = v.T
+clashing_namespace['P'] = v.P
+clashing_namespace['R'] = v.R
+
+
 def _sympify_string(math_string):
     "Convert math string into SymPy object."
     # drop pound symbols ('#') since they denote function names
@@ -49,12 +60,7 @@ def _sympify_string(math_string):
     expr_string = \
         re.sub(r'(?<!\w)EXP(?!\w)', 'exp', expr_string,
                flags=re.IGNORECASE)
-    # Convert raw variables into StateVariable objects
-    variable_fixes = {
-        Symbol('T'): v.T,
-        Symbol('P'): v.P,
-        Symbol('R'): v.R
-    }
+
     # sympify uses eval, so we need to sanitize the input
     nodes = ast.parse(expr_string)
     nodes = ast.Expression(nodes.body[0].value)
@@ -63,7 +69,8 @@ def _sympify_string(math_string):
         if type(node) not in _AST_WHITELIST: #pylint: disable=W1504
             raise ValueError('Expression from TDB file not in whitelist: '
                              '{}'.format(expr_string))
-    return sympify(expr_string).xreplace(variable_fixes)
+
+    return sympify(expr_string, locals=clashing_namespace)
 
 def _parse_action(func):
     """
@@ -84,7 +91,13 @@ def _parse_action(func):
     Source: Florian Brucker on StackOverflow
     http://stackoverflow.com/questions/10177276/pyparsing-setparseaction-function-is-getting-no-arguments
     """
-    num_args = len(inspect.getargspec(func).args)
+    if sys.version_info[0] > 2:
+        func_items = inspect.signature(func).parameters.items()
+        func_args = [name for name, param in func_items
+                     if param.kind == param.POSITIONAL_OR_KEYWORD]
+    else:
+        func_args = inspect.getargspec(func).args
+    num_args = len(func_args)
     if num_args > 3:
         raise ValueError('Input function must take at most 3 parameters.')
 
@@ -628,7 +641,7 @@ def _apply_new_symbol_names(dbf, symbol_name_map):
     dbf.symbols = {name: S(expr).xreplace({Symbol(s): Symbol(v) for s, v in symbol_name_map.items()}) for name, expr in dbf.symbols.items()}
     # finally propagate through to the parameters
     for p in dbf._parameters.all():
-        dbf._parameters.update({'parameter': S(p['parameter']).xreplace({Symbol(s): Symbol(v) for s, v in symbol_name_map.items()})}, eids=[p.eid])
+        dbf._parameters.update({'parameter': S(p['parameter']).xreplace({Symbol(s): Symbol(v) for s, v in symbol_name_map.items()})}, doc_ids=[p.doc_id])
 
 
 def write_tdb(dbf, fd, groupby='subsystem', if_incompatible='warn'):
@@ -914,7 +927,7 @@ def read_tdb(dbf, fd):
         try:
             tokens = grammar.parseString(command)
             _TDB_PROCESSOR[tokens[0]](dbf, *tokens[1:])
-        except ParseException:
+        except:
             print("Failed while parsing: " + command)
             print("Tokens: " + str(tokens))
             raise

pycalphad/tests/test_database.py

@@ -560,3 +560,8 @@ def test_database_parameter_with_species_that_is_not_a_stoichiometric_formula():
     sbminus3 = dbf._parameters.search(tinydb.where('constituent_array') == ((species_dict['SB-3'],),))
     assert len(sbminus3) == 1
     assert sbminus3[0]['parameter'].args[0][0] == 10000
+
+
+def test_database_sympy_namespace_clash():
+    """Symbols that clash with sympy special objects are replaced (gh-233)"""
+    Database.from_string("""FUNCTION TEST 0.01 T*LN(CC)+FF; 6000 N TW !""", fmt='tdb')