Prepare for a future removal of scipy.weave (replaced by weave)

brian/connections/base.py

@@ -8,7 +8,11 @@
 from .. import magic
 from ..log import log_warn, log_info, log_debug
 from numpy import *
-from scipy import sparse, stats, rand, weave, linalg
+try:
+    import weave
+except ImportError:
+    from scipy import weave
+from scipy import sparse, stats, rand, linalg
 import scipy
 import scipy.sparse
 import numpy

brian/equations.py

@@ -35,14 +35,16 @@
 '''
 Differential equations for Brian models.
 '''
-#from scipy.weave import blitz
 from operator import isSequenceType
 import types
 from units import *
 from stdunits import *
 from inspection import *
 from scipy import exp
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 from globalprefs import *
 import re
 import inspect

brian/experimental/c_stdp.py

@@ -22,12 +22,15 @@
     from ..optimiser import freeze
     from ..utils.separate_equations import separate_equations
     from codegen.c_support_code import *
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 import re
 
 __all__ = ['CSTDP']
 
-
+
 class CSTDP(NetworkOperation):
     def __init__(self, C, eqs, pre, post, wmin=0, wmax=Inf, level=0,
                  clock=None, delay_pre=None, delay_post=None):

brian/experimental/codegen/reset.py

@@ -7,7 +7,10 @@
 from ...globalprefs import get_global_preference
 from ...log import log_warn
 from expressions import *
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 from c_support_code import *
 
 __all__ = ['generate_c_reset', 'generate_python_reset',
@@ -58,13 +61,13 @@ def generate_python_reset(eqs, inputcode, level=0, ns=None):
             code += line + '\n'
     return code
 
-
+
 class PythonReset(Reset):
     def __init__(self, inputcode, level=0):
         self._ns, unknowns = namespace(inputcode, level=level + 1, return_unknowns=True)
         self._inputcode = inputcode
         self._prepared = False
-
+
     def __call__(self, P):
         ns = self._ns
         if not self._prepared:
@@ -80,7 +83,7 @@ def __call__(self, P):
         ns['_spikes'] = spikes
         exec cc in ns
 
-
+
 class CReset(Reset):
     def __init__(self, inputcode, level=0):
         self._ns, unknowns = namespace(inputcode, level=level + 1, return_unknowns=True)
@@ -96,7 +99,7 @@ def __init__(self, inputcode, level=0):
             self._extra_link_args = ['-fopenmp']
         else:
             self._extra_link_args = []
-
+
     def __call__(self, P):
         if not self._prepared:
             vars = [var for var in P.var_index if isinstance(var, str)]

brian/experimental/codegen/stateupdaters.py

@@ -6,7 +6,10 @@
 from codegen_python import *
 from integration_schemes import *
 import time
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 import numpy, scipy
 import re
 from c_support_code import *
@@ -17,7 +20,7 @@
 
 __all__ = ['CStateUpdater', 'PythonStateUpdater']
 
-
+
 class CStateUpdater(StateUpdater):
     def __init__(self, eqs, scheme, clock=None, freeze=False):
         self.clock = guess_clock(clock)
@@ -51,7 +54,7 @@ def __init__(self, eqs, scheme, clock=None, freeze=False):
                             self._arrays_to_check.append((varname, varval))
                             self.code_c = re.sub(r'\b'+varname+r'\b', varname+'[_i]', self.code_c)
                             break
-
+
     def __call__(self, P):
         if self._arrays_to_check is not None:
             N = len(P)
@@ -77,7 +80,7 @@ def __call__(self, P):
             self.__init__(self.eqs, self.scheme, self.clock, self.freeze)
             self.__call__(P)
 
-
+
 class PythonStateUpdater(StateUpdater):
     def __init__(self, eqs, scheme, clock=None, freeze=False):
         eqs.prepare()
@@ -113,7 +116,7 @@ def __init__(self, eqs, scheme, clock=None, freeze=False):
         log_debug('brian.experimental.codegen.stateupdaters', 'Python state updater code:\n' + self.code_python)
         exec self.code_python in self.namespace
         self.state_update_func = self.namespace['_stateupdate']
-
+
     def __call__(self, P):
         self.state_update_func(P._S, P.clock._dt, P.clock._t, len(P))
 

brian/experimental/codegen/test_hh.py

@@ -2,7 +2,10 @@
 from brian.library.ionic_currents import *
 from brian.experimental.codegen import *
 import time
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 
 N = 1000
 record_and_plot = N == 1

brian/experimental/codegen/threshold.py

@@ -7,7 +7,10 @@
 from ...globalprefs import get_global_preference
 from ...log import log_warn
 from expressions import *
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 from c_support_code import *
 
 __all__ = ['generate_c_threshold', 'generate_python_threshold',

brian/experimental/codegen2/codeobject.py

@@ -3,7 +3,10 @@
 """
 from brian import *
 from brian.globalprefs import get_global_preference
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 from formatting import *
 
 __all__ = ['Code',

brian/experimental/cuda/gpucodegen.py

@@ -1,7 +1,10 @@
 #import brian_no_units
 from brian import *
 from brian import optimiser
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 try:
     import pycuda
     import pycuda.autoinit as autoinit
@@ -86,13 +89,13 @@ def __call__(self, P):
             P._S.sync_to_cpu()
             P._S.changed_cpu_data()
 
-
+
 class UserControlledGPUNonlinearStateUpdater(GPUNonlinearStateUpdater):
     def __init__(self, eqs, clock=None, freeze=False, precision='double', maxblocksize=512, gpu_to_cpu_vars=None, cpu_to_gpu_vars=None):
         GPUNonlinearStateUpdater.__init__(self, eqs, clock=clock, freeze=freeze, precision=precision, maxblocksize=maxblocksize, forcesync=False)
         self.gpu_to_cpu_vars = gpu_to_cpu_vars
         self.cpu_to_gpu_vars = cpu_to_gpu_vars
-
+
     def _prepare(self, P):
         GPUNonlinearStateUpdater._prepare(self, P)
         if isinstance(P._S._gpu_arr, pycuda.gpuarray.GPUArray):
@@ -101,7 +104,7 @@ def _prepare(self, P):
             self._gpuoffset = int(P._S._gpu_arr)
         self._cpuflat = array(P._S, copy=False)
         self._cpuflat.shape = self._cpuflat.size
-
+
     def __call__(self, P):
         if not self._prepared:
             self._prepare(P)
@@ -115,7 +118,7 @@ def __call__(self, P):
         P._S._cpu_data_changed = False # override any buffering
         P._S._gpu_data_changed = False # override any buffering
 
-
+
 class GPUNeuronGroup(NeuronGroup):
     '''
     Neuron group which performs numerical integration on the GPU.

brian/experimental/morphology/spatialneuron_remy.py

@@ -19,7 +19,10 @@
 import functools
 import warnings
 from math import ceil, log
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 from time import time
 import trace
 import numpy
@@ -33,7 +36,7 @@
 
 __all__ = ['SpatialNeuron', 'CompartmentalNeuron']
 
-
+
 class SpatialNeuron(NeuronGroup):
 	"""
 	Compartmental model with morphology.
@@ -126,7 +129,7 @@ def __getattr__(self, x):
 			return self[x]
 		else:
 			return NeuronGroup.__getattr__(self, x)
-
+
 class SpatialStateUpdater(StateUpdater):
 	"""
 	State updater for compartmental models.

brian/experimental/multilinearstateupdater.py

@@ -1,6 +1,10 @@
 from brian import *
 from brian.stateupdater import get_linear_equations_solution_numerically, get_linear_equations
-from scipy import linalg, weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
+from scipy import linalg
 import numpy
 import inspect
 from itertools import count
@@ -101,7 +105,7 @@ def get_multilinear_state_updater(eqs, subs, level=0, clock=None):
         B[:, i] = Bi.squeeze()
     return MultiLinearStateUpdater(A, B)
 
-
+
 class MultiLinearStateUpdater(StateUpdater):
     '''
     A StateUpdater with one differential equation for each neuron
@@ -121,7 +125,7 @@ def __init__(self, A, B=None):
         self._extra_compile_args = ['-O3']
         if self._cpp_compiler == 'gcc':
             self._extra_compile_args += get_global_preference('gcc_options') # ['-march=native', '-ffast-math']
-
+
     def __call__(self, P):
         if self._useaccel:
             n = len(P)
@@ -160,15 +164,15 @@ def __call__(self, P):
                 P._S[:] = AS
             if self.B is not None:
                 add(P._S, self.B, P._S)
-
+
     def __len__(self):
         return self.A.shape[0]
-
+
     def __repr__(self):
         return 'MultiLinearStateUpdater'
     __str__ = __repr__
 
-
+
 class MultiLinearNeuronGroup(NeuronGroup):
     '''
     Make a NeuronGroup with a linear differential equation for each neuron

brian/experimental/new_c_propagate.py

@@ -98,7 +98,10 @@
     from ..globalprefs import get_global_preference
     from codegen.c_support_code import *
 import numpy
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 import new
 
 __all__ = ['make_new_connection',
@@ -112,7 +115,7 @@
            'ConnectionCode',
            ]
 
-
+
 class ConnectionCode(object):
     def __init__(self, codestr, vars=None, pycodestr=None, pyvars=None):
         if pyvars is None:
@@ -134,7 +137,7 @@ def __init__(self, codestr, vars=None, pycodestr=None, pyvars=None):
         self._extra_compile_args = ['-O3']
         if self._weave_compiler == 'gcc':
             self._extra_compile_args += get_global_preference('gcc_options') # ['-march=native', '-ffast-math']
-
+
     def prepare(self):
         self.pyvars['vars'] = self.vars
         self.vars['_spikes'] = None
@@ -145,7 +148,7 @@ def prepare(self):
         else:
             self.compiled_pycode = None
         self.prepared = True
-
+
     def __call__(self, _spikes):
         if not self.prepared:
             self.prepare()
@@ -171,7 +174,7 @@ def __call__(self, _spikes):
                          support_code=c_support_code,
                          compiler=self._weave_compiler,
                          extra_compile_args=self._extra_compile_args)
-
+
     def __str__(self):
         s = 'C code:\n'
         spaces = 0

brian/hears/filtering/filterbank.py

@@ -1,5 +1,9 @@
 from brian import *
-from scipy import signal, weave, random
+try:
+    import weave
+except ImportError:
+    from scipy import weave
+from scipy import signal, random
 from ..bufferable import Bufferable
 from operator import isSequenceType
 from __builtin__ import all

brian/hears/filtering/filterbanklibrary.py

@@ -1,5 +1,9 @@
 from brian import *
-from scipy import signal, weave, random
+try:
+    import weave
+except ImportError:
+    from scipy import weave
+from scipy import signal, random
 from operator import isSequenceType
 from filterbank import Filterbank,RestructureFilterbank
 from linearfilterbank import *

brian/hears/filtering/linearfilterbank.py

@@ -1,5 +1,9 @@
 from brian import *
-from scipy import signal, weave, random
+try:
+    import weave
+except ImportError:
+    from scipy import weave
+from scipy import signal, random
 from filterbank import Filterbank, RestructureFilterbank
 from ..bufferable import Bufferable
 from itertools import izip

brian/monitor.py

@@ -68,7 +68,10 @@
 
 
 from globalprefs import *
-from scipy import weave
+try:
+    import weave
+except ImportError:
+    from scipy import weave
 
 
 class Monitor(object):