Merge pull request #423 from brian-team/windows_testing

Windows testing

README.rst

@@ -13,14 +13,17 @@ Documentation for Brian2 can be found at http://brian2.readthedocs.org
 
 Brian2 is released under the terms of the CeCILL 2.1 license.
 
-.. image:: https://pypip.in/v/Brian2/badge.png
-        :target: https://crate.io/packages/Brian2
+.. image:: https://img.shields.io/pypi/v/Brian2.svg?style=flat-square
+        :target: https://pypi.python.org/pypi/Brian2
 
 Testing status for master branch
 --------------------------------
 
-.. image:: https://travis-ci.org/brian-team/brian2.png?branch=master
+.. image:: https://img.shields.io/travis/brian-team/brian2/master.svg?style=flat-square
   :target: https://travis-ci.org/brian-team/brian2?branch=master
 
-.. image:: https://coveralls.io/repos/brian-team/brian2/badge.png?branch=master
+.. image:: https://img.shields.io/appveyor/ci/brianteam/brian2/master.svg?style=flat-square
+  :target: https://ci.appveyor.com/project/brianteam/brian2/branch/master
+
+.. image:: https://img.shields.io/coveralls/brian-team/brian2/master.svg?style=flat-square
   :target: https://coveralls.io/r/brian-team/brian2?branch=master

appveyor.yml

@@ -0,0 +1,69 @@
+ # CI configuration for Windows tests on appveyor
+ # Based on Olivier Grisel's python-appveyor-demo
+
+environment:
+  global:
+    # SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the
+    # /E:ON and /V:ON options are not enabled in the batch script intepreter
+    # See: http://stackoverflow.com/a/13751649/163740
+    CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\dev\\appveyor\\run_with_env.cmd"
+
+  matrix:
+    - PYTHON: "C:\\Python27-conda32"
+      PYTHON_VERSION: "2.7.8"
+      PYTHON_ARCH: "32"
+      STANDALONE: "FALSE"
+
+    - PYTHON: "C:\\Python27-conda64"
+      PYTHON_VERSION: "2.7.8"
+      PYTHON_ARCH: "64"
+      STANDALONE: "FALSE"
+
+    - PYTHON: "C:\\Python34-conda32"
+      PYTHON_VERSION: "3.4.1"
+      PYTHON_ARCH: "32"
+      STANDALONE: "FALSE"
+
+    - PYTHON: "C:\\Python34-conda64"
+      PYTHON_VERSION: "3.4.1"
+      PYTHON_ARCH: "64"
+      STANDALONE: "FALSE"
+
+    - PYTHON: "C:\\Python27-conda32"
+      PYTHON_VERSION: "2.7.8"
+      PYTHON_ARCH: "32"
+      STANDALONE: "TRUE"
+
+    - PYTHON: "C:\\Python27-conda64"
+      PYTHON_VERSION: "2.7.8"
+      PYTHON_ARCH: "64"
+      STANDALONE: "TRUE"
+
+install:
+  # Install Python and miniconda
+  - "powershell .\\dev\\appveyor\\install_python.ps1"
+
+  # Prepend newly installed Python to the PATH of this build (this cannot be
+  # done from inside the powershell script as it would require to restart
+  # the parent CMD process).
+  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+
+  # Check that we have the expected version and architecture for Python
+  - "python --version"
+  - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
+
+  # Install the build dependencies of the project via conda
+  - "conda install --yes --quiet numpy scipy nose sphinx sympy pyparsing jinja2 ipython setuptools"
+  - "pip install py-cpuinfo"
+
+build: false  # Not a C# project, build stuff at the test step instead.
+
+test_script:
+  # Run the test suite
+  - "%CMD_IN_ENV% python -c \"import sys; print(sys.executable)\""
+  - "%CMD_IN_ENV% python setup.py install"
+  - "if \"%STANDALONE%\" == \"TRUE\" (
+        %CMD_IN_ENV% python .\\dev\\tools\\run_nose_tests_standalone.py
+    ) ELSE (
+        %CMD_IN_ENV% python .\\dev\\tools\\run_nose_tests.py
+    )"

brian2/devices/cpp_standalone/device.py

@@ -477,7 +477,20 @@ def build(self, directory='output',
                     if net().name != '_fake_network']
         synapses = []
         for net in networks:
-            synapses.extend(s for s in net.objects if isinstance(s, Synapses))
+            net_synapses = [s for s in net.objects if isinstance(s, Synapses)]
+            synapses.extend(net_synapses)
+            # We don't currently support pathways with scalar delays
+            for synapse_obj in net_synapses:
+                for pathway in synapse_obj._pathways:
+                    if not isinstance(pathway.variables['delay'],
+                                      DynamicArrayVariable):
+                        error_msg = ('The "%s" pathway  uses a scalar '
+                                     'delay (instead of a delay per synapse). '
+                                     'This is not yet supported. Do not '
+                                     'specify a delay in the Synapses(...) '
+                                     'call but instead set its delay attribute '
+                                     'afterwards.') % (pathway.name)
+                        raise NotImplementedError(error_msg)
 
         # Not sure what the best place is to call Network.after_run -- at the
         # moment the only important thing it does is to clear the objects stored
@@ -642,9 +655,10 @@ def build(self, directory='output',
                 writer.header_files.append('brianlib/'+file)
 
         # Copy the CSpikeQueue implementation
-        spikequeue_h = os.path.join(directory, 'brianlib', 'spikequeue.h')
         shutil.copy2(os.path.join(os.path.split(inspect.getsourcefile(Synapses))[0], 'cspikequeue.cpp'),
-                     spikequeue_h)
+                     os.path.join(directory, 'brianlib', 'spikequeue.h'))
+        shutil.copy2(os.path.join(os.path.split(inspect.getsourcefile(Synapses))[0], 'stdint_compat.h'),
+                     os.path.join(directory, 'brianlib', 'stdint_compat.h'))
 
         writer.source_files.extend(additional_source_files)
         writer.header_files.extend(additional_header_files)

brian2/devices/device.py

@@ -442,5 +442,4 @@ def restore_device():
 
     for device in all_devices.itervalues():
         device.reinit()
-    set_device('runtime')
     restore_initial_state()

brian2/synapses/cspikequeue.cpp

@@ -2,7 +2,7 @@
 #include<vector>
 #include<map>
 #include<algorithm>
-#include<stdint.h>
+#include"stdint_compat.h"
 #include<assert.h>
 using namespace std;
 

brian2/synapses/cythonspikequeue.pyx

@@ -4,6 +4,7 @@
 from libcpp.vector cimport vector
 from libcpp.string cimport string
 
+import cython
 from cython.operator import dereference
 from cython.operator cimport dereference
 
@@ -12,11 +13,13 @@ import numpy as np
 
 np.import_array()
 
-cdef extern from "inttypes.h":
+
+cdef extern from "stdint_compat.h":
     # Note that this does not actually define int32_t as int (which might be
-    # wrong on a 64bit system), it only tells Cython that int32_t is an int-like
-    # type
+    # wrong on a 64bit system), it only tells Cython that int32_t and int_64t
+    # are int-like types
     ctypedef int int32_t
+    ctypedef int int64_t
 
 cdef extern from "cspikequeue.cpp":
     cdef cppclass CSpikeQueue[T]:

brian2/synapses/stdint_compat.h

@@ -0,0 +1,7 @@
+// Work around the fact that older MSVC versions don't have stdint.h
+#ifdef _MSC_VER
+typedef __int32 int32_t;
+typedef __int64 int64_t;
+#else
+#include <stdint.h>
+#endif

brian2/tests/test_cpp_standalone.py

@@ -13,6 +13,7 @@
 @attr('cpp_standalone', 'standalone-only')
 @with_setup(teardown=restore_device)
 def test_cpp_standalone(with_output=False):
+    previous_device = get_device()
     set_device('cpp_standalone')
     ##### Define the model
     tau = 1*ms
@@ -49,10 +50,12 @@ def test_cpp_standalone(with_output=False):
     assert len(M.t) == len(M.i)
     assert M.t[0] == 0.
     assert M.t[-1] == 100*ms - defaultclock.dt
+    set_device(previous_device)
 
 @attr('cpp_standalone', 'standalone-only')
 @with_setup(teardown=restore_device)
 def test_multiple_connects(with_output=False):
+    previous_device = get_device()
     set_device('cpp_standalone')
     G = NeuronGroup(10, 'v:1')
     S = Synapses(G, G, 'w:1')
@@ -65,10 +68,12 @@ def test_multiple_connects(with_output=False):
     device.build(directory=tempdir, compile=True, run=True,
                  with_output=True)
     assert len(S) == 2 and len(S.w[:]) == 2
+    set_device(previous_device)
 
 @attr('cpp_standalone', 'standalone-only')
 @with_setup(teardown=restore_device)
 def test_storing_loading(with_output=False):
+    previous_device = get_device()
     set_device('cpp_standalone')
     G = NeuronGroup(10, '''v : volt
                            x : 1
@@ -103,11 +108,12 @@ def test_storing_loading(with_output=False):
     assert_allclose(S.n_syn[:], n)
     assert_allclose(G.b[:], b)
     assert_allclose(S.b_syn[:], b)
+    set_device(previous_device)
 
 @attr('cpp_standalone', 'standalone-only')
 @with_setup(teardown=restore_device)
 def test_openmp_consistency(with_output=False):
-
+    previous_device = get_device()
     n_cells    = 100
     n_recorded = 10
     numpy.random.seed(42)
@@ -201,10 +207,12 @@ def test_openmp_consistency(with_output=False):
         assert_allclose(results[key1]['v'], results[key2]['v'])
         assert_allclose(results[key1]['r'], results[key2]['r'])
         assert_allclose(results[key1]['s'], results[key2]['s'])
+    set_device(previous_device)
 
 @attr('cpp_standalone', 'standalone-only')
 @with_setup(teardown=restore_device)
 def test_timedarray(with_output=True):
+    previous_device = get_device()
     set_device('cpp_standalone')
 
     defaultclock.dt = 0.1*ms
@@ -233,6 +241,8 @@ def test_timedarray(with_output=True):
     # only NaN
     assert_equal(mon[3].y[:], np.nan)
 
+    set_device(previous_device)
+
 
 if __name__=='__main__':
     # Print the debug output when testing this file only but not when running

brian2/tests/test_monitor.py

@@ -33,6 +33,26 @@ def test_spike_monitor():
     assert_array_equal(t, mon.t)
     assert_array_equal(t_, mon.t_)
 
+
+def test_synapses_state_monitor():
+    G = NeuronGroup(2, '')
+    S = Synapses(G, G, 'w: siemens')
+    S.connect(True)
+    S.w = 'j*nS'
+
+    # record from a Synapses object (all synapses connecting to neuron 1)
+    synapse_mon = StateMonitor(S, 'w', record=S[:, 1])
+    synapse_mon2 = StateMonitor(S, 'w', record=S['j==1'])
+
+    net = Network(G, S, synapse_mon, synapse_mon2)
+    net.run(10*ms)
+    # Synaptic variables
+    assert_allclose(synapse_mon[S[0, 1]].w, 1*nS)
+    assert_allclose(synapse_mon.w[1], 1*nS)
+    assert_allclose(synapse_mon2[S[0, 1]].w, 1*nS)
+    assert_allclose(synapse_mon2[S['i==0 and j==1']].w, 1*nS)
+    assert_allclose(synapse_mon2.w[1], 1*nS)
+
 @attr('standalone-compatible')
 @with_setup(teardown=restore_device)
 def test_state_monitor():
@@ -63,16 +83,14 @@ def test_state_monitor():
     # Use a StateMonitor recording everything
     all_mon = StateMonitor(G, True, record=True)
 
-    # record from a Synapses object (all synapses connecting to neuron 1)
-    synapse_mon = StateMonitor(S, 'w', record=S[:, 1])
-    synapse_mon2 = StateMonitor(S, 'w', record=S['j==1'])
-
+    # Record synapses with explicit indices (the only way allowed in standalone)
+    synapse_mon = StateMonitor(S, 'w', record=np.arange(len(G)**2))
 
     net = Network(G, S, nothing_mon,
                   v_mon, v_mon1,
                   multi_mon, multi_mon1,
                   all_mon,
-                  synapse_mon, synapse_mon2)
+                  synapse_mon)
     net.run(10*ms)
 
     # Check time recordings
@@ -102,12 +120,9 @@ def test_state_monitor():
 
     assert all(all_mon[0].not_refractory[:] == True)
 
-    # Synaptic variables
-    assert_allclose(synapse_mon[S[0, 1]].w, 1*nS)
-    assert_allclose(synapse_mon.w[1], 1*nS)
-    assert_allclose(synapse_mon2[S[0, 1]].w, 1*nS)
-    assert_allclose(synapse_mon2[S['i==0 and j==1']].w, 1*nS)
-    assert_allclose(synapse_mon2.w[1], 1*nS)
+    # Synapses
+    assert_allclose(synapse_mon.w[:], np.tile(S.j[:]*nS,
+                                              (synapse_mon.w[:].shape[1], 1)).T)
 
 @attr('standalone-compatible')
 @with_setup(teardown=restore_device)
@@ -151,14 +166,12 @@ def test_rate_monitor():
     assert_allclose(rate_mon.rate_, np.asarray(np.ones(10) / defaultclock.dt))
 
     G = NeuronGroup(10, 'v : 1', threshold='v>1') # no reset
-    G.v[:5] = 1.1 # Half of the neurons fire every time step
+    G.v['i<5'] = 1.1  # Half of the neurons fire every time step
     rate_mon = PopulationRateMonitor(G)
     net = Network(G, rate_mon)
     net.run(10*defaultclock.dt)
     assert_allclose(rate_mon.rate, 0.5 * np.ones(10) / defaultclock.dt)
     assert_allclose(rate_mon.rate_, 0.5 *np.asarray(np.ones(10) / defaultclock.dt))
-    assert_array_equal(rate_mon.rate['t>0.5*ms'],
-                 rate_mon.rate[np.nonzero(rate_mon.t>0.5*ms)[0]])
 
 @attr('standalone-compatible')
 @with_setup(teardown=restore_device)

brian2/tests/test_spatialneuron.py

@@ -98,7 +98,7 @@ def test_infinitecable():
     assert_allclose(v[t>0.5*ms],theory[t>0.5*ms],rtol=0.01) # 1% error tolerance (not exact because not infinite cable)
 
 
-@attr('long', 'standalone-compatible')
+@attr('long')
 @with_setup(teardown=restore_initial_state)
 def test_finitecable():
     '''

brian2/tests/test_spikegenerator.py

@@ -52,7 +52,7 @@ def test_spikegenerator_basic():
     net.run(5*ms)
     for idx in xrange(5):
         generator_spikes = sorted([(idx, time) for time in times[indices==idx]])
-        recorded_spikes = sorted([(idx, time) for time in s_mon.t['i==%d' % idx]])
+        recorded_spikes = sorted([(idx, time) for time in s_mon.t[s_mon.i==idx]])
         assert generator_spikes == recorded_spikes
 
 @attr('standalone-compatible')
@@ -69,7 +69,7 @@ def test_spikegenerator_basic_sorted():
     net.run(5*ms)
     for idx in xrange(5):
         generator_spikes = sorted([(idx, time) for time in times[indices==idx]])
-        recorded_spikes = sorted([(idx, time) for time in s_mon.t['i==%d' % idx]])
+        recorded_spikes = sorted([(idx, time) for time in s_mon.t[s_mon.i==idx]])
         assert generator_spikes == recorded_spikes
 
 @attr('standalone-compatible')
@@ -87,7 +87,7 @@ def test_spikegenerator_period():
     net.run(10*ms)
     for idx in xrange(5):
         generator_spikes = sorted([(idx, time) for time in times[indices==idx]] + [(idx, time+5*ms) for time in times[indices==idx]])
-        recorded_spikes = sorted([(idx, time) for time in s_mon.t['i==%d' % idx]])
+        recorded_spikes = sorted([(idx, time) for time in s_mon.t[s_mon.i==idx]])
         assert generator_spikes == recorded_spikes
 
 @attr('standalone-compatible')

brian2/tests/test_subgroup.py

@@ -327,7 +327,7 @@ def test_subexpression_no_references():
 @with_setup(teardown=restore_device)
 def test_synaptic_propagation():
     G1 = NeuronGroup(10, 'v:1', threshold='v>1', reset='v=0')
-    G1.v[1::2] = 1.1 # odd numbers should spike
+    G1.v['i%2==1'] = 1.1 # odd numbers should spike
     G2 = NeuronGroup(20, 'v:1')
     SG1 = G1[1:6]
     SG2 = G2[10:]
@@ -421,7 +421,7 @@ def test_no_reference_4():
     Using subgroups without keeping an explicit reference. Synapses
     '''
     G1 = NeuronGroup(10, 'v:1', threshold='v>1', reset='v=0')
-    G1.v[1::2] = 1.1 # odd numbers should spike
+    G1.v['i%2==1'] = 1.1 # odd numbers should spike
     G2 = NeuronGroup(20, 'v:1')
     S = Synapses(G1[1:6], G2[10:], pre='v+=1')
     S.connect('i==j')