worked around PY2 sympy bug and added numpy to package requirements

tclose · Apr 14, 2020 · 5a1eda1 · 5a1eda1
1 parent 4fb7690
commit 5a1eda1
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Showing 4 changed files with 19 additions and 13 deletions.
diff --git a/nineml/abstraction/expressions/parser.py b/nineml/abstraction/expressions/parser.py
@@ -86,14 +86,18 @@ def _parse_expr(self, expr):
         if self._logic_relation_re.search(expr):
             expr = self._parse_relationals(expr)
         self.escaped_names = set()
-        # try:
-        expr = sympy_parse(
-            expr, transformations=([self] + self._sympy_transforms),
-            local_dict=self.inline_randoms_dict)
-        # except Exception as e:
-        #     raise NineMLMathParseError(
-        #         "Could not parse math-inline expression: "
-        #         "{}\n\n{}".format(expr, e))
+        # This is a work around for a PY2 bug in Sympy where the inspect module
+        # can't get the argument spec of a Callable object (instead of a func.)
+        def parser(tokens, local_dict, global_dict):
+            return self(tokens, local_dict, global_dict)
+        try:
+            expr = sympy_parse(
+                expr, transformations=([parser] + self._sympy_transforms),
+                local_dict=self.inline_randoms_dict)
+        except Exception as e:
+            raise NineMLMathParseError(
+                "Could not parse math-inline expression: "
+                "{}\n\n{}".format(expr, e))
         return self._postprocess(expr)
 
     def _preprocess(self, tokens):

diff --git a/requirements.txt b/requirements.txt
@@ -2,5 +2,6 @@ lxml>=3.7.3
 pyyaml>=3.1
 h5py>=2.7.0
 future>=0.16.0
-sympy>=1.1
-numpydoc >= 0.7.0
+sympy>=1.5
+numpy>=1.11.0
+numpydoc>=0.7.0
diff --git a/setup.py b/setup.py
@@ -44,7 +44,8 @@
                       'future>=0.16.0',
                       'h5py>=2.7.0',
                       'PyYAML>=3.1',
-                      'sympy>=1.2'],
+                      'sympy>=1.5.1',
+                      'numpy>=1.11.0'],
     python_requires='>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, <4',
-    tests_require=['nose', 'numpy']
+    tests_require=['nose']
 )
diff --git a/test/unittests/abstraction_test/dynamics_test.py b/test/unittests/abstraction_test/dynamics_test.py
@@ -643,7 +643,7 @@ def test_trigger(self):
                             'V < (V+10',
                             'V (< V+10)',
                             'V (< V+10)',
-                            '1 / ( 1 + mg_conc * eta *  exp (( -1 * gamma*V))'
+                            '1 / ( 1 + mg_conc * eta *  exp(-1 * gamma*V))'
                             '1..0'
                             '..0']
         for tr in invalid_triggers: