Removed NSDF test.

moose-core/tests/python/test_nsdf.py

-# 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"