def install_pynn():
try:
pip.main([
'install', 'lazyarray'
]) # This should ideally be automatically installed with PyNN...
pip.main([
'install', 'neo'
]) # This should ideally be automatically installed with PyNN...
install_root = os.environ['HOME']
with working_dir(install_root):
check_output(
['git', 'clone', 'https://github.com/NeuralEnsemble/PyNN.git'])
path = os.path.join(install_root, 'PyNN')
with working_dir(path):
check_output(['python', 'setup.py', 'install'])
import pyNN
m = 'Successfully installed pyNN...'
except Exception as e:
m = 'ERROR installing pyNN: ' + str(e)
finally:
inform(m)
def install_nml2():
with working_dir(install_root):
print co(['git', 'clone', 'https://github.com/NeuroML/NeuroML2.git'])
with working_dir(default_nml2_dir):
print co(['git', 'checkout', 'development'])
inform('Successfully cloned NeuroML2', indent=2, verbosity=1)
def install_nml2():
with working_dir(install_root):
print co(['git', 'clone', 'https://github.com/NeuroML/NeuroML2.git'])
with working_dir(default_nml2_dir):
print co(['git', 'checkout', 'development'])
inform('Successfully cloned NeuroML2', indent=2, verbosity=1)
def install_jlems():
install_root = os.environ['HOME']
with working_dir(install_root):
print co(['git', 'clone', 'https://github.com/LEMS/jLEMS.git'])
inform('Successfully cloned jLEMS', indent=2, verbosity=1)
path = os.path.join(install_root, 'jLEMS')
with working_dir(path):
print co(['mvn', 'install'])
inform('Successfully installed jLEMS', indent=2, verbosity=1)
def install_jlems():
install_root = os.environ['HOME']
with working_dir(install_root):
print co(['git', 'clone', 'https://github.com/LEMS/jLEMS.git'])
inform('Successfully cloned jLEMS', indent=2, verbosity=1)
path = os.path.join(install_root,'jLEMS')
with working_dir(path):
print co(['mvn', 'install'])
inform('Successfully installed jLEMS', indent=2, verbosity=1)
def install_pylems():
install_root = os.environ['HOME']
with working_dir(install_root):
check_output(['git', 'clone', 'https://github.com/LEMS/pylems.git'])
inform('Successfully cloned PyLEMS', indent=2, verbosity=1)
path = os.path.join(install_root, 'pylems')
with working_dir(path):
check_output(['python', 'setup.py', 'install'])
inform('Successfully installed PyLEMS', indent=2, verbosity=1)
def install_neuron(get_latest=False):
nrnpath = os.path.join(os.environ['HOME'], 'neuron')
os.mkdir(nrnpath)
with working_dir(nrnpath):
if get_latest:
print co(
['hg', 'clone', 'http://www.neuron.yale.edu/hg/neuron/nrn'])
os.chdir('nrn')
print co(['./build.sh'])
else:
print co([
'wget',
'http://www.neuron.yale.edu/ftp/neuron/versions/v7.3/nrn-7.3.tar.gz'
])
print co(['tar', 'xzvf', 'nrn-7.3.tar.gz'])
print co(['mv', 'nrn-7.3', 'nrn'])
os.chdir('nrn')
path = os.getcwd()
pyexec = sys.executable
co([
"./configure --prefix=%s --without-iv --with-nrnpython=%s" %
(path, pyexec)
],
shell=True)
print co(['make'])
print co(['make', 'install'])
os.chdir('src/nrnpython')
run_setup('./setup.py', ['install'])
def run(self):
try:
self.stdout = NeuronEngine.compile_modfiles(self.modelpath)
except sp.CalledProcessError as err:
self.stderr = err.output
self.returncode = err.returncode
inform('Error compiling modfiles:', self.stderr, indent=2)
with working_dir(dirname(self.modelpath)):
inform("Running %s on %s..." % (self.name, self.modelpath),
indent=1)
p = sp.Popen(['nrniv', '-python', self.modelpath, '-nogui'],
stdin=sp.PIPE,
stdout=sp.PIPE,
stderr=sp.PIPE)
cmd = '''\
%s
''' % ('\n'.join(self.extra_pars))
stdout, stderr = p.communicate(dedent(cmd))
# with open('/tmp/omv_test.nrn.stdout', 'w') as f:
# f.write(stdout)
self.stdout = stdout
self.stderr = stderr
inform("OUT: ", stdout, verbosity=1, indent=2)
inform("ERR: ", stderr, verbosity=1, indent=2)
inform("returncode: ", p.returncode, verbosity=1, indent=2)
self.returncode = p.returncode
if self.returncode is not 0:
raise EngineExecutionError
def run(self):
with working_dir(dirname(self.modelpath)):
inform("Running %s on %s..." % (self.name, self.modelpath),
indent=1)
p = sp.Popen(['nrniv'],
stdin=sp.PIPE,
stdout=sp.PIPE,
stderr=sp.PIPE)
cmd = '''\
load_file("noload.hoc")
//cvode_active(1)
load_file("%s")
%s
''' % (self.modelpath, '\n'.join(self.extra_pars))
stdout, stderr = p.communicate(dedent(cmd))
# with open('/tmp/omv_test.nrn.stdout', 'w') as f:
# f.write(stdout)
self.stdout = stdout
self.stderr = stderr
inform("OUT: ", stdout, verbosity=1, indent=2)
inform("ERR: ", stderr, verbosity=1, indent=2)
inform("returncode: ", p.returncode, verbosity=1, indent=2)
self.returncode = p.returncode
if self.returncode is not 0:
raise EngineExecutionError
def run(self):
try:
self.stdout = self.compile_modfiles()
except sp.CalledProcessError as err:
self.stderr = err.output
self.returncode = err.returncode
inform('Error compiling modfiles:', self.stderr, indent=2)
with working_dir(dirname(self.modelpath)):
inform("Running %s on %s..." % (self.name, self.modelpath),
indent=1)
p = sp.Popen(['nrniv', '-python', self.modelpath, '-nogui'],
stdin=sp.PIPE, stdout=sp.PIPE, stderr=sp.PIPE)
cmd = '''\
%s
''' % ('\n'.join(self.extra_pars))
stdout, stderr = p.communicate(dedent(cmd))
# with open('/tmp/omv_test.nrn.stdout', 'w') as f:
# f.write(stdout)
self.stdout = stdout
self.stderr = stderr
inform("OUT: ", stdout, verbosity=1, indent=2)
inform("ERR: ", stderr, verbosity=1, indent=2)
inform("returncode: ", p.returncode, verbosity=1, indent=2)
self.returncode = p.returncode
if self.returncode is not 0:
raise EngineExecutionError
def run(self):
with working_dir(dirname(self.modelpath)):
inform("Running %s on %s..." % (self.name, self.modelpath),
indent=1)
p = sp.Popen(['nrniv'],
stdin=sp.PIPE, stdout=sp.PIPE, stderr=sp.PIPE)
cmd = '''\
load_file("noload.hoc")
//cvode_active(1)
load_file("%s")
%s
''' % (self.modelpath, '\n'.join(self.extra_pars))
stdout, stderr = p.communicate(dedent(cmd))
# with open('/tmp/omv_test.nrn.stdout', 'w') as f:
# f.write(stdout)
self.stdout = stdout
self.stderr = stderr
inform("OUT: ", stdout, verbosity=1, indent=2)
inform("ERR: ", stderr, verbosity=1, indent=2)
inform("returncode: ", p.returncode, verbosity=1, indent=2)
self.returncode = p.returncode
if self.returncode is not 0:
raise EngineExecutionError
def install_jnml():
jnmlpath = os.path.join(os.environ['HOME'], 'jnml')
os.mkdir(jnmlpath)
with working_dir(jnmlpath):
print co([
'svn', 'checkout',
'svn://svn.code.sf.net/p/neuroml/code/jNeuroMLJar'
])
def compile_modfiles(cls, modelpath):
with working_dir(dirname(modelpath)):
out = 0
if len(glob('*.mod')) > 0:
inform('Compiling all modfiles in: %s'%modelpath, indent=1)
out = sp.check_output(['nrnivmodl'])
inform(out, indent=2)
return out
def compile_modfiles(self):
with working_dir(dirname(self.modelpath)):
out = 0
if len(glob('*.mod')) > 0:
inform('Compiling modfiles', indent=1)
out = sp.check_output(['nrnivmodl'])
inform(out, indent=2)
return out
def compile_modfiles(self):
with working_dir(dirname(self.modelpath)):
out = 0
if len(glob('*.mod')) > 0:
inform('Compiling modfiles', indent=1)
out = sp.check_output(['nrnivmodl'])
inform(out, indent=2)
return out
def install_netpyne():
try:
install_root = os.environ['HOME']
with working_dir(install_root):
check_output(['git', 'clone', 'https://github.com/Neurosim-lab/netpyne.git'])
path = os.path.join(install_root,'netpyne')
with working_dir(path):
check_output(['git', 'checkout', 'neuroml_export'])
check_output(['python', 'setup.py', 'install'])
import netpyne
m = 'Successfully installed NetPyNE...'
except Exception as e:
m = 'ERROR installing NetPyNE: ' + str(e)
finally:
inform(m)
def install_netpyne():
try:
install_root = os.environ['HOME']
with working_dir(install_root):
check_output([
'git', 'clone', 'https://github.com/Neurosim-lab/netpyne.git'
])
path = os.path.join(install_root, 'netpyne')
with working_dir(path):
check_output(['git', 'checkout', 'neuroml_export'])
check_output(['python', 'setup.py', 'install'])
import netpyne
m = 'Successfully installed NetPyNE...'
except Exception as e:
m = 'ERROR installing NetPyNE: ' + str(e)
finally:
inform(m)
def install_genesis(get_latest=False):
genpath = os.path.join(os.environ['HOME'], 'genesis')
os.mkdir(genpath)
with working_dir(genpath):
print co(['wget',
'https://github.com/borismarin/genesis2.4gamma/archive/master.zip'])
print co(['unzip', 'master.zip'])
print co(['ls', '-la', 'genesis2.4gamma-master'])
os.chdir('genesis2.4gamma-master/src')
print co(['./configure'])
print co(['make'])
open(os.path.join(os.environ['HOME'], '.simrc'), 'w').write(simrc)
def install_pynn():
try:
pip.main(['install', 'lazyarray']) # This should ideally be automatically installed with PyNN...
pip.main(['install', 'neo']) # This should ideally be automatically installed with PyNN...
install_root = os.environ['HOME']
with working_dir(install_root):
check_output(['git', 'clone', 'https://github.com/NeuralEnsemble/PyNN.git'])
path = os.path.join(install_root,'PyNN')
with working_dir(path):
check_output(['python', 'setup.py', 'install'])
import pyNN
m = 'Successfully installed pyNN...'
except Exception as e:
m = 'ERROR installing pyNN: ' + str(e)
finally:
inform(m)
def install_genesis(get_latest=False):
genpath = os.path.join(os.environ['HOME'], 'genesis')
os.mkdir(genpath)
with working_dir(genpath):
print co([
'wget',
'https://github.com/borismarin/genesis2.4gamma/archive/master.zip'
])
print co(['unzip', 'master.zip'])
print co(['ls', '-la', 'genesis2.4gamma-master'])
os.chdir('genesis2.4gamma-master/src')
print co(['./configure'])
print co(['make'])
open(os.path.join(os.environ['HOME'], '.simrc'), 'w').write(simrc)
def run(self):
with working_dir(dirname(self.modelpath)):
p = sp.Popen(['nrniv'], stdin=sp.PIPE, stdout=sp.PIPE, stderr=sp.PIPE)
cmd = '''\
load_file("noload.hoc")
cvode_active(1)
load_file("%s")
%s
''' % (self.modelpath, '\n'.join(self.extra_pars))
stdout, stderr = p.communicate(dedent(cmd))
with open('/tmp/omv_test.nrn.stdout', 'w') as f:
f.write(stdout)
self.stdout = stdout
self.stderr = stderr
self.returncode = p.returncode
def install_nest():
inform('Installing NEST', indent=2, verbosity=1)
nestpath = os.path.join(os.environ['HOME'],'nest')
nestpath2 = os.path.join(os.environ['HOME'],'nest/nest')
os.mkdir(nestpath)
with working_dir(nestpath):
version='2.6.0'
check_output(['wget', 'http://www.nest-simulator.org/downloads/gplreleases/nest-%s.tar.gz'%version])
#check_output(['cp', '/home/padraig/temp/nest-2.4.2.tar.gz', '.'])
check_output(['tar', 'xzvf', 'nest-%s.tar.gz'%version])
check_output(['mv', 'nest-%s'%version, 'nest'], cwd=nestpath)
check_output(["./configure", "--prefix=%s"%(nestpath2)], cwd=nestpath2)
check_output(['make'], cwd=nestpath2)
check_output(['make', 'install'], cwd=nestpath2)
def run(self):
with working_dir(dirname(self.modelpath)):
p = sp.Popen(['nrniv'],
stdin=sp.PIPE,
stdout=sp.PIPE,
stderr=sp.PIPE)
cmd = '''\
load_file("noload.hoc")
cvode_active(1)
load_file("%s")
%s
''' % (self.modelpath, '\n'.join(self.extra_pars))
stdout, stderr = p.communicate(dedent(cmd))
with open('/tmp/omv_test.nrn.stdout', 'w') as f:
f.write(stdout)
self.stdout = stdout
self.stderr = stderr
self.returncode = p.returncode
def install_neuron(get_latest=False):
nrnpath = os.path.join(os.environ['HOME'],'neuron')
os.mkdir(nrnpath)
with working_dir(nrnpath):
if get_latest:
print co(['hg', 'clone', 'http://www.neuron.yale.edu/hg/neuron/nrn'])
os.chdir('nrn')
print co(['./build.sh'])
else:
print co(['wget', 'http://www.neuron.yale.edu/ftp/neuron/versions/v7.3/nrn-7.3.tar.gz'])
print co(['tar', 'xzvf', 'nrn-7.3.tar.gz'])
print co(['mv', 'nrn-7.3', 'nrn'])
os.chdir('nrn')
path = os.getcwd()
pyexec = sys.executable
co(["./configure --prefix=%s --without-iv --with-nrnpython=%s"%(path,pyexec)], shell=True)
print co(['make'])
print co(['make', 'install'])
os.chdir('src/nrnpython')
run_setup('./setup.py', ['install'])
def run(self):
from pkg_resources import resource_filename
with working_dir(os.path.dirname(self.modelpath)):
try:
temp = NamedTemporaryFile(suffix='.g')
temp.write('include %s\n' % self.modelpath)
temp.write('include %s\n' %
resource_filename('omv', 'engines/utils/genesis_utils.g'))
temp.write('\n'.join(self.extra_pars) + '\n')
temp.seek(0)
with open('/tmp/omv.gen.err', 'w+') as se:
self.stdout = sp.check_output(['genesis', '-nox',
'-batch', '-notty', temp.name],
stderr=se)
se.seek(0)
self.stderr = se.readlines()
self.returncode = 0
except sp.CalledProcessError as e:
self.returncode = e.returncode
raise EngineExecutionError
finally:
temp.close()
def run(self):
from pkg_resources import resource_filename
with working_dir(os.path.dirname(self.modelpath)):
try:
temp = NamedTemporaryFile(suffix='.g')
temp.write('include %s\n' % self.modelpath)
temp.write(
'include %s\n' %
resource_filename('omv', 'engines/utils/genesis_utils.g'))
temp.write('\n'.join(self.extra_pars) + '\n')
temp.seek(0)
with open('/tmp/omv.gen.err', 'w+') as se:
self.stdout = sp.check_output(
['genesis', '-nox', '-batch', '-notty', temp.name],
stderr=se)
se.seek(0)
self.stderr = se.readlines()
self.returncode = 0
except sp.CalledProcessError as e:
self.returncode = e.returncode
raise EngineExecutionError
finally:
temp.close()
def install_pynml():
pynmlpath = os.path.join(os.environ['HOME'],'pynml')
os.mkdir(pynmlpath)
with working_dir(pynmlpath):
print co(['git', 'clone', 'https://github.com/NeuroML/pyNeuroML.git'])
def install_jnml():
jnmlpath = os.path.join(os.environ['HOME'],'jnml')
os.mkdir(jnmlpath)
with working_dir(jnmlpath):
print co(['svn', 'checkout', 'svn://svn.code.sf.net/p/neuroml/code/jNeuroMLJar'])
def install_pynml():
pynmlpath = os.path.join(os.environ['HOME'], 'pynml')
os.mkdir(pynmlpath)
with working_dir(pynmlpath):
print co(['git', 'clone', 'https://github.com/NeuroML/pyNeuroML.git'])
