def install(version):
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
inform("%s installed NEURON..." % NetPyNEEngine.name,
indent=2,
verbosity=1)
from getnetpyne import install_netpyne
home = os.environ['HOME']
inform('Will fetch and install the latest NetPyNE', indent=2)
install_netpyne()
inform('Done, NetPyNE is correctly installed...', indent=2)
NetPyNEEngine.path = NeuronEngine.path
NetPyNEEngine.environment_vars = {}
NetPyNEEngine.environment_vars.update(NeuronEngine.environment_vars)
inform("PATH: " + NetPyNEEngine.path, indent=2, verbosity=1)
inform("Env vars: %s" % NetPyNEEngine.environment_vars,
indent=2,
verbosity=1)
'''
import pyNN
pynn_mod_dir = os.path.dirname(pyNN.__file__)+'/neuron/nmodl/'
inform("Attempting to compile PyNN mod files for standard models in %s..."%pynn_mod_dir, indent=2, verbosity =1)
print check_output(['ls', pynn_mod_dir], cwd=pynn_mod_dir)'''
environment_vars, path = NeuronEngine.get_nrn_environment()
inform("Using NEURON with env %s at %s..." % (environment_vars, path),
indent=2,
verbosity=1)
def install(version):
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
inform("%s installed NEURON..." % PyNNNRNEngine.name,
indent=2,
verbosity=1)
if not PyNNEngine.is_installed(None):
PyNNEngine.install(None)
inform("%s installed PyNN..." % PyNNNRNEngine.name,
indent=2,
verbosity=1)
PyNNNRNEngine.path = PyNNEngine.path + \
":" + NeuronEngine.path
PyNNNRNEngine.environment_vars = {}
PyNNNRNEngine.environment_vars.update(PyNNEngine.environment_vars)
PyNNNRNEngine.environment_vars.update(NeuronEngine.environment_vars)
inform("PATH: " + PyNNNRNEngine.path, indent=2, verbosity=1)
inform("Env vars: %s" % PyNNNRNEngine.environment_vars,
indent=2,
verbosity=1)
import pyNN
pynn_mod_dir = os.path.dirname(pyNN.__file__) + '/neuron/nmodl/'
inform(
"Attempting to compile PyNN mod files for standard models in %s..."
% pynn_mod_dir,
indent=2,
verbosity=1)
print check_output(['ls', pynn_mod_dir], cwd=pynn_mod_dir)
print check_output(
[NeuronEngine.environment_vars['NEURON_HOME'] + '/bin/nrnivmodl'],
cwd=pynn_mod_dir)
def install(version):
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
inform("%s installed NEURON..." % PyNNNRNEngine.name, indent=2, verbosity =1)
if not PyNNEngine.is_installed(None):
PyNNEngine.install(None)
inform("%s installed PyNN..." % PyNNNRNEngine.name, indent=2, verbosity =1)
PyNNNRNEngine.path = PyNNEngine.path + \
":" + NeuronEngine.path
PyNNNRNEngine.environment_vars = {}
PyNNNRNEngine.environment_vars.update(
PyNNEngine.environment_vars)
PyNNNRNEngine.environment_vars.update(
NeuronEngine.environment_vars)
inform("PATH: " + PyNNNRNEngine.path, indent=2, verbosity =1)
inform("Env vars: %s" % PyNNNRNEngine.environment_vars, indent=2, verbosity =1)
import pyNN
pynn_mod_dir = os.path.dirname(pyNN.__file__)+'/neuron/nmodl/'
inform("Attempting to compile PyNN mod files for standard models in %s..."%pynn_mod_dir, indent=2, verbosity =1)
print check_output(['ls', pynn_mod_dir], cwd=pynn_mod_dir)
environment_vars, path = NeuronEngine.get_nrn_environment()
inform("Using NEURON with env %s at %s..."%(environment_vars, path), indent=2, verbosity =1)
print check_output([environment_vars['NEURON_HOME']+'/bin/nrnivmodl'], cwd=pynn_mod_dir)
def install(version):
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
inform("%s installed NEURON..." % NetPyNEEngine.name, indent=2, verbosity =1)
from getnetpyne import install_netpyne
home = os.environ['HOME']
inform('Will fetch and install the latest NetPyNE', indent=2)
install_netpyne()
inform('Done, NetPyNE is correctly installed...', indent=2)
NetPyNEEngine.path = NeuronEngine.path
NetPyNEEngine.environment_vars = {}
NetPyNEEngine.environment_vars.update(
NeuronEngine.environment_vars)
inform("PATH: " + NetPyNEEngine.path, indent=2, verbosity =1)
inform("Env vars: %s" % NetPyNEEngine.environment_vars, indent=2, verbosity =1)
'''
import pyNN
pynn_mod_dir = os.path.dirname(pyNN.__file__)+'/neuron/nmodl/'
inform("Attempting to compile PyNN mod files for standard models in %s..."%pynn_mod_dir, indent=2, verbosity =1)
print check_output(['ls', pynn_mod_dir], cwd=pynn_mod_dir)'''
environment_vars, path = NeuronEngine.get_nrn_environment()
inform("Using NEURON with env %s at %s..."%(environment_vars, path), indent=2, verbosity =1)
def install(version):
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
inform("%s installed NEURON..." % PyNRNEngine.name, indent=2, verbosity =1)
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
PyNRNEngine.path = path_nrn
PyNRNEngine.environment_vars = {}
PyNRNEngine.environment_vars.update(environment_vars_nrn)
inform("PATH: " + PyNRNEngine.path, indent=2, verbosity =1)
inform("Env vars: %s" % PyNRNEngine.environment_vars, indent=2, verbosity =1)
def is_installed(version):
if is_verbose():
inform("Checking whether %s is installed correctly..." %
PyNRNEngine.name, indent=1)
installed = NeuronEngine.is_installed(None)
return installed
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)
try:
inform("Running file %s with %s" %
(trim_path(self.modelpath), self.name),
indent=1)
self.stdout = check_output(['python', self.modelpath, 'neuron'],
cwd=os.path.dirname(self.modelpath))
self.returncode = 0
except sp.CalledProcessError as err:
self.returncode = err.returncode
self.stdout = err.output
raise EngineExecutionError
except Exception as err:
inform("Another error with running %s: " % self.name,
err,
indent=1)
self.returncode = -1
self.stdout = "???"
def is_installed(version):
if is_verbose():
inform("Checking whether %s is installed..." %
JNeuroMLNRNEngine.name,
indent=1)
return JNeuroMLEngine.is_installed(None) and NeuronEngine.is_installed(
None)
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 install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
JNeuroMLNRNEngine.path = JNeuroMLEngine.path + \
":" + NeuronEngine.path
JNeuroMLNRNEngine.environment_vars = {}
JNeuroMLNRNEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
JNeuroMLNRNEngine.environment_vars.update(
NeuronEngine.environment_vars)
inform("PATH: " + JNeuroMLNRNEngine.path)
inform("Env vars: %s" % JNeuroMLNRNEngine.environment_vars)
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
JNeuroMLNRNEngine.path = JNeuroMLEngine.path + \
":" + NeuronEngine.path
JNeuroMLNRNEngine.environment_vars = {}
JNeuroMLNRNEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
JNeuroMLNRNEngine.environment_vars.update(
NeuronEngine.environment_vars)
inform("PATH: " + JNeuroMLNRNEngine.path)
inform("Env vars: %s" % JNeuroMLNRNEngine.environment_vars)
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 install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
JNeuroMLNRNEngine.path = JNeuroMLEngine.path + \
":" + path_nrn
JNeuroMLNRNEngine.environment_vars = {}
JNeuroMLNRNEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
JNeuroMLNRNEngine.environment_vars.update(environment_vars_nrn)
inform("PATH: " + JNeuroMLNRNEngine.path)
inform("Env vars: %s" % JNeuroMLNRNEngine.environment_vars)
def install(version):
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
inform("%s installed NEURON..." % PyNRNEngine.name,
indent=2,
verbosity=1)
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
PyNRNEngine.path = path_nrn
PyNRNEngine.environment_vars = {}
PyNRNEngine.environment_vars.update(environment_vars_nrn)
inform("PATH: " + PyNRNEngine.path, indent=2, verbosity=1)
inform("Env vars: %s" % PyNRNEngine.environment_vars,
indent=2,
verbosity=1)
def is_installed(version):
if is_verbose():
inform("Checking whether %s is installed correctly..." %
PyNRNEngine.name,
indent=1)
installed = NeuronEngine.is_installed(None)
return installed
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
JNeuroMLNRNEngine.path = JNeuroMLEngine.path + \
":" + path_nrn
JNeuroMLNRNEngine.environment_vars = {}
JNeuroMLNRNEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
JNeuroMLNRNEngine.environment_vars.update(
environment_vars_nrn)
inform("PATH: " + JNeuroMLNRNEngine.path)
inform("Env vars: %s" % JNeuroMLNRNEngine.environment_vars)
def is_installed(version):
if is_verbose():
inform("Checking whether %s is installed correctly..." %
NetPyNEEngine.name, indent=1)
ret = True
try:
import netpyne
if is_verbose():
inform("%s version %s is correctly installed..." % (NetPyNEEngine.name,netpyne.__version__), indent=2)
except Exception as err:
inform("Couldn't import netpyne into Python: ", err, indent=1)
ret = False
installed = ret and NeuronEngine.is_installed(None)
return installed
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
inform("%s installed JNeuroML..." % JNeuroMLPyNNNRNEngine.name, indent=2, verbosity =1)
if not PyNNNRNEngine.is_installed(None):
PyNNNRNEngine.install(None)
inform("%s installed PyNN & NRN..." % JNeuroMLPyNNNRNEngine.name, indent=2, verbosity =1)
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
JNeuroMLPyNNNRNEngine.path = JNeuroMLEngine.path+":"+path_nrn
JNeuroMLPyNNNRNEngine.environment_vars = {}
JNeuroMLPyNNNRNEngine.environment_vars.update(JNeuroMLEngine.environment_vars)
JNeuroMLPyNNNRNEngine.environment_vars.update(PyNNEngine.environment_vars)
JNeuroMLPyNNNRNEngine.environment_vars.update(environment_vars_nrn)
inform("PATH: " + JNeuroMLPyNNNRNEngine.path)
inform("Env vars: %s" % JNeuroMLPyNNNRNEngine.environment_vars)
def is_installed(version):
if is_verbose():
inform("Checking whether %s is installed correctly..." %
NetPyNEEngine.name,
indent=1)
ret = True
try:
import netpyne
if is_verbose():
inform("%s version %s is correctly installed..." %
(NetPyNEEngine.name, netpyne.__version__),
indent=2)
except Exception as err:
inform("Couldn't import netpyne into Python: ", err, indent=1)
ret = False
installed = ret and NeuronEngine.is_installed(None)
return installed
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)
try:
inform("Running file %s with %s" % (trim_path(self.modelpath), self.name), indent=1)
self.stdout = check_output(['python', self.modelpath, '-nogui'],
cwd=os.path.dirname(self.modelpath))
self.returncode = 0
except sp.CalledProcessError as err:
self.returncode = err.returncode
self.stdout = err.output
raise EngineExecutionError
except Exception as err:
inform("Another error with running %s: "%self.name, err, indent=1)
self.returncode = -1
self.stdout = "???"
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
inform("%s installed JNeuroML..." % JNeuroMLPyNNNRNEngine.name,
indent=2,
verbosity=1)
if not PyNNNRNEngine.is_installed(None):
PyNNNRNEngine.install(None)
inform("%s installed PyNN & NRN..." % JNeuroMLPyNNNRNEngine.name,
indent=2,
verbosity=1)
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
JNeuroMLPyNNNRNEngine.path = JNeuroMLEngine.path + ":" + path_nrn
JNeuroMLPyNNNRNEngine.environment_vars = {}
JNeuroMLPyNNNRNEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
JNeuroMLPyNNNRNEngine.environment_vars.update(
PyNNEngine.environment_vars)
JNeuroMLPyNNNRNEngine.environment_vars.update(environment_vars_nrn)
inform("PATH: " + JNeuroMLPyNNNRNEngine.path)
inform("Env vars: %s" % JNeuroMLPyNNNRNEngine.environment_vars)
def is_installed(version):
if is_verbose():
inform("Checking whether %s is installed..." %
JNeuroMLNRNEngine.name, indent=1)
return JNeuroMLEngine.is_installed(None) and NeuronEngine.is_installed(None)
