Dependencies fix during build target. bdist is build by default.

Author: Dilawar Singh

CMakeLists.txt

@@ -441,7 +441,7 @@ add_custom_command(TARGET bdist POST_BUILD
 # Copy python files from source to current binary directory. Make sure to call
 # this before building bdist.
 file(GLOB_RECURSE PYTHON_SRCS "${CMAKE_SOURCE_DIR}/python/*")
-add_custom_target(copy_pymoose DEPENDS ${PYTHON_SRCS}
+add_custom_target(copy_pymoose DEPENDS ${PYTHON_SRCS} _moose
     COMMAND ${CMAKE_COMMAND} -E copy_directory
         ${CMAKE_CURRENT_SOURCE_DIR}/python ${CMAKE_CURRENT_BINARY_DIR}/python
         COMMENT "Copying required python files from

tests/python/temp.npy

@@ -0,0 +1,92 @@
+# test_nsdf.py --- 
+# Changed from nsdf.py from
+# https://github.com/BhallaLab/moose-examples/snippets/nsdf.py
+
+from __future__ import print_function
+import numpy as np
+from datetime import datetime
+import getpass
+import os
+
+# Use in-repo moose to install.
+import moose
+print('using moose from: %s' % moose.__file__)
+
+global nsdf
+
+def setup_model():
+    """Setup a dummy model with a PulseGen and a SpikeGen. The SpikeGen
+    detects the leading edges of the pulses created by the PulseGen
+    and sends out the event times. We record the PulseGen outputValue
+    as Uniform data and leading edge time as Event data in the NSDF
+    file.
+
+    """
+    global nsdf
+    simtime = 100.0
+    dt = 1e-3
+    model = moose.Neutral('/model')
+    pulse = moose.PulseGen('/model/pulse')
+    pulse.level[0] = 1.0
+    pulse.delay[0] = 10
+    pulse.width[0] = 20
+    t_lead = moose.SpikeGen('/model/t_lead')
+    t_lead.threshold = 0.5
+    moose.connect(pulse, 'output', t_lead,'Vm');
+    nsdf = moose.NSDFWriter('/model/writer')
+    nsdf.filename = 'nsdf_demo.h5'
+    nsdf.mode = 2 #overwrite existing file
+    nsdf.flushLimit = 100
+    moose.connect(nsdf, 'requestOut', pulse, 'getOutputValue')
+    print('event input', nsdf.eventInput, nsdf.eventInput.num)
+    print(nsdf)
+
+    nsdf.eventInput.num = 1
+    ei = nsdf.eventInput[0]
+    print(ei.path)
+    moose.connect(t_lead, 'spikeOut', nsdf.eventInput[0], 'input')
+    tab = moose.Table('spiketab')
+    tab.threshold = t_lead.threshold
+    clock = moose.element('/clock')
+    for ii in range(32):
+        moose.setClock(ii, dt)
+    moose.connect(pulse, 'output', tab, 'spike')
+    print(datetime.now().isoformat())
+    moose.reinit()
+    moose.start(simtime)
+    print(datetime.now().isoformat())
+    np.savetxt('nsdf.txt', tab.vector)
+    ###################################
+    # Set the environment attributes
+    ###################################
+    nsdf.stringAttr['title'] = 'NSDF writing demo for moose'
+    nsdf.stringAttr['description'] = '''An example of writing data to NSDF file from MOOSE simulation. In
+this simulation we generate square pules from a PulseGen object and
+use a SpikeGen to detect the threshold crossing events of rising
+edges. We store the pulsegen output as Uniform data and the threshold
+crossing times as Event data. '''    
+    nsdf.stringAttr['creator'] = getpass.getuser()
+    nsdf.stringVecAttr['software'] = ['python2.7', 'moose3' ]
+    nsdf.stringVecAttr['method'] = ['']
+    nsdf.stringAttr['rights'] = ''
+    nsdf.stringAttr['license'] = 'CC-BY-NC'
+    # Specify units. MOOSE is unit agnostic, so we explicitly set the
+    # unit attibutes on individual datasets
+    nsdf.stringAttr['/data/uniform/PulseGen/outputValue/tunit'] = 's'
+    nsdf.stringAttr['/data/uniform/PulseGen/outputValue/unit'] = 'A'
+    eventDataPath = '/data/event/SpikeGen/spikeOut/{}_{}_{}/unit'.format(t_lead.vec.value,
+                                                                         t_lead.getDataIndex(), 
+                                                                         t_lead.fieldIndex)
+    nsdf.stringAttr[eventDataPath] = 's'
+
+if __name__ == '__main__':
+    setup_model()
+    # Very basic tests
+    nsdfFile = 'nsdf.txt'
+    if not os.path.exists( nsdf.filename ):
+        raise Exception("Test failed. No files : %s" % nsdfFile)
+    if not os.path.exists( nsdfFile ):
+        raise Exception("Test failed. No file : %s" % nsdfFile)
+
+    data = np.loadtxt( nsdfFile )
+    assert len(data) == 60001, "Expected 60001 entries"