Make brian ready for python 3

.travis.yml

@@ -2,16 +2,23 @@ language: python
 python:
   - "2.6"
   - "2.7"
+  - "3.2"
+  - "3.3"
 # install build dependencies
 before_install:
   - sudo apt-get update -qq
   - sudo apt-get build-dep -qq python-scipy python-sympy python-pyparsing
 # command to install dependencies
 install:
-  - "pip install numpy==1.6.2"
-  - "pip install scipy sympy pyparsing==1.5.7 sphinx ipython --use-mirrors"
+  # install different versions of numpy for python 2 and 3
+  - "if [ ${TRAVIS_PYTHON_VERSION:0:1} == '2' ]; then pip install numpy==1.6.2 --use-mirrors; else pip install numpy --use-mirrors; fi"
+  - "pip install scipy sphinx ipython --use-mirrors"
+  # Make sure to use the python 3 version for sympy
+  - "if [ ${TRAVIS_PYTHON_VERSION:0:1} == '2' ]; then pip install sympy --use-mirrors; else pip install http://sympy.googlecode.com/files/sympy-0.7.2-py3.2.tar.gz; fi"
+  # install different pyparsing versions for python 2 and 3
+  - "if [ ${TRAVIS_PYTHON_VERSION:0:1} == '2' ]; then pip install pyparsing==1.5.7 --use-mirrors; else pip install pyparsing --use-mirrors; fi"
   - "pip install . --use-mirrors"
-# command to run tests
-script: nosetests --with-doctest brian2
+# command to run tests (make sure to not run it from the source directory)
+script: "cd ~;nosetests --with-doctest brian2"
 notifications:
   email: false

brian2/__init__.py

@@ -13,22 +13,22 @@
 try:
     import numpy
 except ImportError as ex:
-    print >>sys.stderr, 'Importing numpy failed:', ex
+    sys.stderr.write('Importing numpy failed: %s\n' % ex)
     missing.append('numpy')
 try:
     import scipy
 except ImportError as ex:
-    print >>sys.stderr, 'Importing scipy failed:', ex
+    sys.stderr.write('Importing scipy failed: %s\n' % ex)
     missing.append('scipy')
 try:
     import sympy
 except ImportError as ex:
-    print >>sys.stderr, 'Importing sympy failed:', ex
+    sys.stderr.write('Importing sympy failed: %s\n' % ex)
     missing.append('sympy')
 try:
     import pyparsing
 except ImportError as ex:
-    print >>sys.stderr, 'Importing pyparsing failed:', ex
+    sys.stderr.write('Importing pyparsing failed: %s\n' % ex)
     missing.append('pyparsing')
 
 if len(missing):

brian2/codegen/languages/cpp.py

@@ -1,20 +1,24 @@
 '''
 TODO: restrict keyword optimisations
 '''
-import itertools
+import re
 
 from sympy.printing.ccode import CCodePrinter
 import numpy
-from scipy import weave
-import re
 
 from brian2.utils.stringtools import deindent
 from brian2.utils.parsing import parse_to_sympy
-
 from brian2.codegen.functions.base import Function
-from .base import Language, CodeObject
+from brian2.utils.logger import get_logger
 
+from .base import Language, CodeObject
 
+logger = get_logger(__name__)
+try:
+    from scipy import weave
+except ImportError as ex:
+    logger.warn('Importing scipy.weave failed: %s' % ex)
+    weave = None
 
 __all__ = ['CPPLanguage', 'CPPCodeObject',
            'c_data_type',

brian2/core/clocks.py

@@ -45,10 +45,10 @@ class Clock(Nameable):
 
     @check_units(dt=second, t=second)
     def __init__(self, dt=None, name=None):
-        Nameable.__init__(self, name)
         self._dt_spec = dt
         self.i = 0  #: The time step of the simulation as an integer.
         self.i_end = 0  #: The time step the simulation will end as an integer
+        Nameable.__init__(self, name)
         logger.debug("Created clock {self.name} with dt={self._dt_spec}".format(self=self))
 
     def reinit(self):
@@ -153,21 +153,5 @@ def running(self):
         return self.i<self.i_end
 
     epsilon = 1e-14
-
-    def __lt__(self, other):
-        selft = self.t_
-        othert = other.t_
-        if selft==othert or abs(selft-othert)<=self.epsilon*abs(selft):
-            return False
-        return selft<othert
-
-    def __eq__(self, other):
-        selft = self.t_
-        othert = other.t_
-        if selft==othert or abs(selft-othert)<=self.epsilon*abs(selft):
-            return True
-        else:
-            return False
-
 
 defaultclock = Clock(name='defaultclock')

brian2/core/network.py

@@ -3,6 +3,7 @@
 from brian2.utils.logger import get_logger
 from brian2.core.names import Nameable
 from brian2.core.base import BrianObject
+from brian2.core.clocks import Clock
 from brian2.units.fundamentalunits import check_units
 from brian2.units.allunits import second 
 from brian2.core.preferences import brian_prefs
@@ -236,8 +237,10 @@ def prepare(self):
         self._prepared = True
 
     def _nextclocks(self):
-        minclock = min(self._clocks)
-        curclocks = set(clock for clock in self._clocks if clock==minclock)
+        minclock = min(self._clocks, key=lambda c: c.t_)
+        curclocks = set(clock for clock in self._clocks if
+                        (clock.t_ == minclock.t_ or
+                         abs(clock.t_ - minclock.t_)<Clock.epsilon))
         return minclock, curclocks
 
     @check_units(duration=second, report_period=second)

brian2/core/operations.py

@@ -63,15 +63,15 @@ def network_operation(*args, **kwds):
     >>> from brian2 import *
     >>> @network_operation
     ... def f():
-    ...   print 'something'
+    ...   print('something')
     ...
     >>> net = Network(f)
 
     Print the time each time step:
 
     >>> @network_operation
     ... def f(t):
-    ...   print 'The time is', t
+    ...   print('The time is', t)
     ...
     >>> net = Network(f)
 
@@ -80,7 +80,7 @@ def network_operation(*args, **kwds):
     >>> myclock = Clock(dt=0.5*ms) 
     >>> @network_operation(when=(myclock, 'start', 0))
     ... def f():
-    ...   print 'This will happen at the start of each timestep.'
+    ...   print('This will happen at the start of each timestep.')
     ...
     >>> net = Network(f)
 

brian2/memory/dynamicarray.py

@@ -60,11 +60,11 @@ class DynamicArray(object):
     >>> x.resize((4, 4))
     >>> x[:] += 1
     >>> x.data[:] = x.data**2
-    >>> print x.data
-    [[16 16 16  4]
-     [16 16 16  4]
-     [ 9  9  9  4]
-     [ 1  1  1  1]]
+    >>> x.data
+    array([[16, 16, 16,  4],
+           [16, 16, 16,  4],
+           [ 9,  9,  9,  4],
+           [ 1,  1,  1,  1]])
 
     Notes
     -----

brian2/stateupdaters/integration.py

@@ -61,11 +61,11 @@ def split_expression(expr):
 
     Examples
     --------
-    >>> print split_expression('dt * f(x, t)')
+    >>> split_expression('dt * f(x, t)')
     (dt*f(x, t), None)
-    >>> print split_expression('dt * f(x, t) + dW * g(x, t)')
+    >>> split_expression('dt * f(x, t) + dW * g(x, t)')
     (dt*f(x, t), dW*g(x, t))
-    >>> print split_expression('1/(2*dt**.5)*(g_support - g(x, t))*(dW**2)')
+    >>> split_expression('1/(2*dt**.5)*(g_support - g(x, t))*(dW**2)')
     (0, dW**2*dt**(-0.5)*g_support/2 - dW**2*dt**(-0.5)*g(x, t)/2)
     '''
 
@@ -255,7 +255,7 @@ def replace_func(x, t, expr, temp_vars):
             replacements (see `_generate_RHS`).
             '''
             try:
-                s_expr = parse_to_sympy(expr, local_dict=symbols)
+                s_expr = parse_to_sympy(unicode(expr), local_dict=symbols)
             except SympifyError as ex:
                 raise ValueError('Error parsing the expression "%s": %s' %
                                  (expr, str(ex)))

brian2/tests/test_functions.py

@@ -11,8 +11,15 @@ def test_math_functions():
     '''
     test_array = np.array([-1, -0.5, 0, 0.5, 1])
 
-    with catch_logs() as _:  # Let's suppress warnings about illegal values
+    # We can only test C++ if weave is availabe
+    try:
+        import scipy.weave
         languages = [PythonLanguage(), CPPLanguage()]
+    except ImportError:
+        # Can't test C++
+        languages = [PythonLanguage()]
+
+    with catch_logs() as _:  # Let's suppress warnings about illegal values        
         for lang in languages:
 
             # Functions with a single argument

brian2/tests/test_units.py

@@ -1,7 +1,6 @@
 import itertools
 import warnings
 import pickle
-from exceptions import RuntimeWarning
 
 import numpy as np
 from numpy.testing import assert_raises, assert_equal
@@ -14,6 +13,7 @@
                                            Unit,
                                            have_same_dimensions,
                                            get_dimensions,
+                                           is_scalar_type,
                                            DimensionMismatchError,
                                            check_units,
                                            in_unit,
@@ -99,6 +99,17 @@ def test_get_dimensions():
     assert_equal(dims.get_dimension('length'), 0)
 
     assert get_dimensions(5) is DIMENSIONLESS
+    assert get_dimensions(5.0) is DIMENSIONLESS
+    assert get_dimensions(np.array(5, dtype=np.int)) is DIMENSIONLESS
+    assert get_dimensions(np.array(5.0)) is DIMENSIONLESS
+    assert get_dimensions(np.float32(5.0)) is DIMENSIONLESS
+    assert get_dimensions(np.float64(5.0)) is DIMENSIONLESS
+    assert is_scalar_type(5)
+    assert is_scalar_type(5.0)
+    assert is_scalar_type(np.array(5, dtype=np.int))
+    assert is_scalar_type(np.array(5.0))
+    assert is_scalar_type(np.float32(5.0))
+    assert is_scalar_type(np.float64(5.0))
     assert_raises(TypeError, lambda: get_dimensions('a string'))
 
     # wrong number of indices

brian2/tests/test_utils.py

@@ -4,20 +4,25 @@ def test_environment():
     '''
     Test information about the environment we are running under.
     '''
-    import __builtin__
+    try:
+        # Python 2
+        import __builtin__ as builtins
+    except ImportError:
+        # Python 3
+        import builtins
 
-    if hasattr(__builtin__, '__IPYTHON__'):
+    if hasattr(builtins, '__IPYTHON__'):
         testing_under_ipython = True
-        del __builtin__.__IPYTHON__
+        del builtins.__IPYTHON__
     else:
         testing_under_ipython = False
 
     assert not running_from_ipython()
-    __builtin__.__IPYTHON__ = True
+    builtins.__IPYTHON__ = True
     assert running_from_ipython()
 
     if not testing_under_ipython:
-        del __builtin__.__IPYTHON__
+        del builtins.__IPYTHON__
 
 
 if __name__ == '__main__':