Merge pull request #397 from brian-team/unknown_attributes

Raise an error when setting a new attribute for a `Group`

LICENSE

@@ -618,4 +618,32 @@ subject to the following conditions:
     HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
     WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
     FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-    OTHER DEALINGS IN THE SOFTWARE.
+    OTHER DEALINGS IN THE SOFTWARE.
+
+-------------------------------------------------------------------------------
+
+The spelling corrector code in brian2.utils.stringtools is based on the spelling
+corrector by Peter Norvig, available at: http://norvig.com/spell.py
+It is published under the MIT license:
+
+The MIT License (MIT)
+
+Copyright (c) 2007 Peter Norvig
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

brian2/groups/group.py

@@ -27,7 +27,7 @@
                                            get_unit)
 from brian2.units.allunits import second
 from brian2.utils.logger import get_logger
-from brian2.utils.stringtools import get_identifiers
+from brian2.utils.stringtools import get_identifiers, SpellChecker
 
 __all__ = ['Group', 'CodeRunner']
 
@@ -371,8 +371,55 @@ def __setattr__(self, name, val, level=0):
             var.get_addressable_value(name[:-1], self).set_item(slice(None),
                                                                 val,
                                                                 level=level+1)
-        else:
+        elif hasattr(self, name) or name.startswith('_'):
             object.__setattr__(self, name, val)
+        else:
+            # Try to suggest the correct name in case of a typo
+            checker = SpellChecker([varname for varname, var in self.variables.iteritems()
+                                    if not (varname.startswith('_') or var.read_only)])
+            if name.endswith('_'):
+                suffix = '_'
+                name = name[:-1]
+            else:
+                suffix = ''
+            error_msg = 'Could not find a state variable with name "%s".' % name
+            suggestions = checker.suggest(name)
+            if len(suggestions) == 1:
+                suggestion, = suggestions
+                error_msg += ' Did you mean to write "%s%s"?' % (suggestion,
+                                                                 suffix)
+            elif len(suggestions) > 1:
+                error_msg += (' Did you mean to write any of the following: %s ?' %
+                              (', '.join(['"%s%s"' % (suggestion, suffix)
+                                          for suggestion in suggestions])))
+            error_msg += (' Use the add_attribute method if you intend to add '
+                          'a new attribute to the object.')
+            raise AttributeError(error_msg)
+
+    def add_attribute(self, name):
+        '''
+        Add a new attribute to this group. Using this method instead of simply
+        assigning to the new attribute name is necessary because Brian will
+        raise an error in that case, to avoid bugs passing unnoticed
+        (misspelled state variable name, un-declared state variable, ...).
+
+        Parameters
+        ----------
+        name : str
+            The name of the new attribute
+
+        Raises
+        ------
+        AttributeError
+            If the name already exists as an attribute or a state variable.
+        '''
+        if name in self.variables:
+            raise AttributeError('Cannot add an attribute "%s", it is already '
+                                 'a state variable of this group.' % name)
+        if hasattr(self, name):
+            raise AttributeError('Cannot add an attribute "%s", it is already '
+                                 'an attribute of this group.' % name)
+        object.__setattr__(self, name, None)
 
     def get_states(self, vars=None, units=True, format='dict', level=0):
         '''
@@ -856,6 +903,7 @@ def __init__(self, group, template, code='', user_code=None,
         if codeobj_class is None:
             codeobj_class = group.codeobj_class
         self.codeobj_class = codeobj_class
+        self.codeobj = None
 
     def update_abstract_code(self, run_namespace=None, level=0):
         '''

brian2/groups/poissongroup.py

@@ -73,15 +73,15 @@ def __init__(self, N, rates, dt=None, clock=None, when='thresholds',
 
         self._refractory = False
 
-        #
-        self._enable_group_attributes()
         # To avoid a warning about the local variable rates, we set the real
         # threshold condition only after creating the object
         self.threshold = 'False'
         self.thresholder = Thresholder(self)
         self.threshold = 'rand() < rates * dt'
         self.contained_objects.append(self.thresholder)
 
+        self._enable_group_attributes()
+
         # Here we want to use the local namespace, but at the level where the
         # constructor was called
         self.rates.set_item(slice(None), rates, level=2)

brian2/groups/spikegeneratorgroup.py

@@ -117,9 +117,6 @@ def __init__(self, N, indices, times, dt=None, clock=None,
                                  dtype=np.int32, read_only=True)
         self.variables.create_clock_variables(self._clock)
 
-        # Activate name attribute access
-        self._enable_group_attributes()
-
         #: Remember the dt we used the last time when we checked the spike bins
         #: to not repeat the work for multiple runs with the same dt
         self._previous_dt = None
@@ -132,6 +129,9 @@ def __init__(self, N, indices, times, dt=None, clock=None,
                             order=order,
                             name=None)
 
+        # Activate name attribute access
+        self._enable_group_attributes()
+
     def before_run(self, run_namespace=None, level=0):
         # Do some checks on the period vs. dt
         if self.period < np.inf*second:

brian2/spatialneuron/spatialneuron.py

@@ -212,6 +212,13 @@ def __init__(self, morphology=None, model=None, threshold=None,
         """)
         # Possibilities for the name: characteristic_length, electrotonic_length, length_constant, space_constant
 
+        # Insert morphology
+        self.morphology = morphology
+
+        # Link morphology variables to neuron's state variables
+        self.morphology_data = MorphologyData(len(morphology))
+        self.morphology.compress(self.morphology_data)
+
         NeuronGroup.__init__(self, len(morphology), model=model + eqs_constants,
                              threshold=threshold, refractory=refractory,
                              reset=reset,
@@ -220,13 +227,6 @@ def __init__(self, morphology=None, model=None, threshold=None,
 
         self.Cm = Cm
         self.Ri = Ri
-
-        # Insert morphology
-        self.morphology = morphology
-
-        # Link morphology variables to neuron's state variables
-        self.morphology_data = MorphologyData(self.N)
-        self.morphology.compress(self.morphology_data)
         # TODO: View instead of copy for runtime?
         self.diameter_ = self.morphology_data.diameter
         self.distance_ = self.morphology_data.distance
@@ -237,6 +237,7 @@ def __init__(self, morphology=None, model=None, threshold=None,
         self.z_ = self.morphology_data.z
 
         # Performs numerical integration step
+        self.add_attribute('diffusion_state_updater')
         self.diffusion_state_updater = SpatialStateUpdater(self, method,
                                                            clock=self.clock,
                                                            order=order)
@@ -323,8 +324,8 @@ class SpatialSubgroup(Subgroup):
     '''
 
     def __init__(self, source, start, stop, morphology, name=None):
-        Subgroup.__init__(self, source, start, stop, name)
         self.morphology = morphology
+        Subgroup.__init__(self, source, start, stop, name)
 
     def __getattr__(self, x):
         return SpatialNeuron.spatialneuron_attribute(self, x)

brian2/synapses/synapses.py

@@ -746,10 +746,11 @@ def __init__(self, source, target=None, model=None, pre=None, post=None,
         # Support 2d indexing
         self._indices = SynapticIndexing(self)
 
+        self._initial_connect = connect
+
         # Activate name attribute access
         self._enable_group_attributes()
 
-        self._initial_connect = connect
         if not connect is False:
             self.connect(connect, level=1)
 

brian2/tests/test_neurongroup.py

@@ -856,6 +856,23 @@ def test_state_variable_access_strings():
     assert_equal(G.v[:], np.arange(10)*volt)
 
 
+@attr('codegen-independent')
+def test_unknown_state_variables():
+    # Test how setting attribute names that do not correspond to a state
+    # variable are handled
+    G = NeuronGroup(10, 'v : 1')
+    assert_raises(AttributeError, lambda: setattr(G, 'unknown', 42))
+
+    # Creating a new private attribute should be fine
+    G._unknown = 42
+    assert G._unknown == 42
+
+    # Explicitly create the attribute
+    G.add_attribute('unknown')
+    G.unknown = 42
+    assert G.unknown == 42
+
+
 def test_subexpression():
     G = NeuronGroup(10, '''dv/dt = freq : 1
                            freq : Hz
@@ -1123,6 +1140,7 @@ def test_random_vector_values():
     test_state_variables()
     test_state_variable_access()
     test_state_variable_access_strings()
+    test_unknown_state_variables()
     test_subexpression()
     test_subexpression_with_constant()
     test_scalar_parameter_access()

brian2/tests/test_utils.py

@@ -1,7 +1,7 @@
 from nose.plugins.attrib import attr
 
 from brian2.utils.environment import running_from_ipython
-
+from brian2.utils.stringtools import SpellChecker
 
 @attr('codegen-independent')
 def test_environment():
@@ -29,5 +29,14 @@ def test_environment():
         del builtins.__IPYTHON__
 
 
+def test_spell_check():
+    checker = SpellChecker(['vm', 'alpha', 'beta'])
+    assert checker.suggest('Vm') == set(['vm'])
+    assert checker.suggest('alphas') == set(['alpha'])
+    assert checker.suggest('bta') == set(['beta'])
+    assert checker.suggest('gamma') == set()
+
+
 if __name__ == '__main__':
     test_environment()
+    test_spell_check()

brian2/utils/stringtools.py

@@ -3,6 +3,7 @@
 """
 
 import re
+import string
 
 __all__ = ['indent',
            'deindent',
@@ -13,6 +14,7 @@
            'stripped_deindented_lines',
            'strip_empty_leading_and_trailing_lines',
            'code_representation',
+           'SpellChecker'
            ]
 
 def indent(text, numtabs=1, spacespertab=4, tab=None):
@@ -230,3 +232,42 @@ def code_representation(code):
         msg += indent(str(v))
         output.append(msg)
     return strip_empty_leading_and_trailing_lines('\n'.join(output))
+
+
+# The below is adapted from Peter Norvig's spelling corrector
+# http://norvig.com/spell.py (MIT licensed)
+class SpellChecker(object):
+    '''
+    A simple spell checker that will be used to suggest the correct name if the
+    user made a typo (e.g. for state variable names).
+
+    Parameters
+    ----------
+    words : iterable of str
+        The known words
+    alphabet : iterable of str, optional
+        The allowed characters. Defaults to the characters allowed for
+        identifiers, i.e. ascii characters, digits and the underscore.
+    '''
+    def __init__(self, words,
+                 alphabet=string.ascii_lowercase+string.digits+'_'):
+        self.words = words
+        self.alphabet = alphabet
+
+    def edits1(self, word):
+       s = [(word[:i], word[i:]) for i in range(len(word) + 1)]
+       deletes    = [a + b[1:] for a, b in s if b]
+       transposes = [a + b[1] + b[0] + b[2:] for a, b in s if len(b)>1]
+       replaces   = [a + c + b[1:] for a, b in s for c in self.alphabet if b]
+       inserts    = [a + c + b     for a, b in s for c in self.alphabet]
+       return set(deletes + transposes + replaces + inserts)
+
+    def known_edits2(self, word):
+        return set(e2 for e1 in self.edits1(word)
+                   for e2 in self.edits1(e1) if e2 in self.words)
+
+    def known(self, words):
+        return set(w for w in words if w in self.words)
+
+    def suggest(self, word):
+        return self.known(self.edits1(word)) or self.known_edits2(word) or set()