Merge pull request #2150 from mgxd/fix/py2functions

ref: isolate function handling from __future__ imports

Author: satra

doc/users/saving_workflows.rst

@@ -55,7 +55,7 @@ This will create a file "outputtestsave.py" with the following content:
 	from nipype.pipeline.engine import Workflow, Node, MapNode
 	from nipype.interfaces.utility import IdentityInterface
 	from nipype.interfaces.utility import Function
-	from nipype.utils.misc import getsource
+	from nipype.utils.functions import getsource
 	from nipype.interfaces.fsl.preprocess import BET
 	from nipype.interfaces.fsl.utils import ImageMaths
 	# Functions

nipype/interfaces/utility/wrappers.py

@@ -24,7 +24,7 @@
                     BaseInterfaceInputSpec)
 from ..io import IOBase, add_traits
 from ...utils.filemanip import filename_to_list
-from ...utils.misc import getsource, create_function_from_source
+from ...utils.functions import getsource, create_function_from_source
 
 logger = logging.getLogger('interface')
 

nipype/pipeline/engine/utils.py

@@ -29,7 +29,8 @@
 
 from ...utils.filemanip import (fname_presuffix, FileNotFoundError, to_str,
                                 filename_to_list, get_related_files)
-from ...utils.misc import create_function_from_source, str2bool
+from ...utils.misc import str2bool
+from ...utils.functions import create_function_from_source
 from ...interfaces.base import (CommandLine, isdefined, Undefined,
                                 InterfaceResult)
 from ...interfaces.utility import IdentityInterface
@@ -99,7 +100,7 @@ def _write_inputs(node):
                         lines[-1] = lines[-1].replace(' %s(' % funcname,
                                                       ' %s_1(' % funcname)
                         funcname = '%s_1' % funcname
-                    lines.append('from nipype.utils.misc import getsource')
+                    lines.append('from nipype.utils.functions import getsource')
                     lines.append("%s.inputs.%s = getsource(%s)" % (nodename,
                                                                    key,
                                                                    funcname))

nipype/pipeline/engine/workflows.py

@@ -36,8 +36,9 @@
 
 
 from ... import config, logging
-from ...utils.misc import (unflatten, str2bool,
-                               getsource, create_function_from_source)
+
+from ...utils.misc import (unflatten, str2bool)
+from ...utils.functions import (getsource, create_function_from_source)
 from ...interfaces.base import (traits, InputMultiPath, CommandLine,
                                 Undefined, TraitedSpec, DynamicTraitedSpec,
                                 Bunch, InterfaceResult, md5, Interface,

nipype/utils/functions.py

@@ -0,0 +1,47 @@
+# -*- coding: utf-8 -*-
+"""
+Handles custom functions used in Function interface. Future imports
+are avoided to keep namespace as clear as possible.
+"""
+from builtins import next, str
+from future.utils import raise_from
+import inspect
+from textwrap import dedent
+
+def getsource(function):
+    """Returns the source code of a function"""
+    return dedent(inspect.getsource(function))
+
+
+def create_function_from_source(function_source, imports=None):
+    """Return a function object from a function source
+
+    Parameters
+    ----------
+    function_source : unicode string
+        unicode string defining a function
+    imports : list of strings
+        list of import statements in string form that allow the function
+        to be executed in an otherwise empty namespace
+    """
+    ns = {}
+    import_keys = []
+
+    try:
+        if imports is not None:
+            for statement in imports:
+                exec(statement, ns)
+            import_keys = list(ns.keys())
+        exec(function_source, ns)
+
+    except Exception as e:
+        msg = 'Error executing function\n{}\n'.format(function_source)
+        msg += ("Functions in connection strings have to be standalone. "
+                "They cannot be declared either interactively or inside "
+                "another function or inline in the connect string. Any "
+                "imports should be done inside the function.")
+        raise_from(RuntimeError(msg), e)
+    ns_funcs = list(set(ns) - set(import_keys + ['__builtins__']))
+    assert len(ns_funcs) == 1, "Function or inputs are ill-defined"
+    func = ns[ns_funcs[0]]
+    return func

nipype/utils/misc.py

@@ -3,7 +3,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Miscellaneous utility functions
 """
-from __future__ import print_function, division, unicode_literals, absolute_import
+from __future__ import print_function, unicode_literals, division, absolute_import
 from future import standard_library
 standard_library.install_aliases()
 from builtins import next, str
@@ -66,47 +66,6 @@ def trim(docstring, marker=None):
     return '\n'.join(trimmed)
 
 
-def getsource(function):
-    """Returns the source code of a function"""
-    src = dedent(inspect.getsource(function))
-    return src
-
-
-def create_function_from_source(function_source, imports=None):
-    """Return a function object from a function source
-
-    Parameters
-    ----------
-    function_source : pickled string
-        string in pickled form defining a function
-    imports : list of strings
-        list of import statements in string form that allow the function
-        to be executed in an otherwise empty namespace
-    """
-    ns = {}
-    import_keys = []
-    try:
-        if imports is not None:
-            for statement in imports:
-                exec(statement, ns)
-            import_keys = list(ns.keys())
-        exec(function_source, ns)
-
-    except Exception as e:
-        msg = '\nError executing function:\n %s\n' % function_source
-        msg += '\n'.join(["Functions in connection strings have to be standalone.",
-                          "They cannot be declared either interactively or inside",
-                          "another function or inline in the connect string. Any",
-                          "imports should be done inside the function"
-                          ])
-        raise_from(RuntimeError(msg), e)
-    ns_funcs = list(set(ns) - set(import_keys + ['__builtins__']))
-    assert len(ns_funcs) == 1, "Function or inputs are ill-defined"
-    funcname = ns_funcs[0]
-    func = ns[funcname]
-    return func
-
-
 def find_indices(condition):
     "Return the indices where ravel(condition) is true"
     res, = np.nonzero(np.ravel(condition))

nipype/utils/tests/test_functions.py

@@ -0,0 +1,41 @@
+# -*- coding: utf-8 -*-
+import sys
+import pytest
+from nipype.utils.functions import (getsource, create_function_from_source)
+
+def _func1(x):
+    return x**3
+
+def test_func_to_str():
+
+    def func1(x):
+        return x**2
+
+    # Should be ok with both functions!
+    for f in _func1, func1:
+        f_src = getsource(f)
+        f_recreated = create_function_from_source(f_src)
+        assert f(2.3) == f_recreated(2.3)
+
+def test_func_to_str_err():
+    bad_src = "obbledygobbledygook"
+    with pytest.raises(RuntimeError): create_function_from_source(bad_src)
+
+def _print_statement():
+    try:
+        exec('print ""')
+        return True
+    except SyntaxError:
+        return False
+
+def test_func_string():
+    def is_string():
+        return isinstance('string', str)
+
+    wrapped_func = create_function_from_source(getsource(is_string))
+    assert is_string() == wrapped_func()
+
+@pytest.mark.skipif(sys.version_info[0] > 2, reason="breaks python 3")
+def test_func_print_py2():
+    wrapped_func = create_function_from_source(getsource(_print_statement))
+    assert wrapped_func()

nipype/utils/tests/test_misc.py

@@ -8,9 +8,8 @@
 
 import pytest
 
-from nipype.utils.misc import (container_to_string, getsource,
-                               create_function_from_source, str2bool, flatten,
-                               unflatten)
+from nipype.utils.misc import (container_to_string, str2bool,
+                               flatten, unflatten)
 
 
 def test_cont_to_str():
@@ -35,26 +34,6 @@ def test_cont_to_str():
     assert (container_to_string(123) == '123')
 
 
-def _func1(x):
-    return x**3
-
-
-def test_func_to_str():
-
-    def func1(x):
-        return x**2
-
-    # Should be ok with both functions!
-    for f in _func1, func1:
-        f_src = getsource(f)
-        f_recreated = create_function_from_source(f_src)
-        assert f(2.3) == f_recreated(2.3)
-
-def test_func_to_str_err():
-    bad_src = "obbledygobbledygook"
-    with pytest.raises(RuntimeError): create_function_from_source(bad_src)
-
-
 @pytest.mark.parametrize("string, expected", [
         ("yes", True), ("true", True), ("t", True), ("1", True),
         ("no", False), ("false", False), ("n", False), ("f", False), ("0", False)