def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
inform("%s installed JNeuroML..." % JNeuroMLNetPyNEEngine.name,
indent=2,
verbosity=1)
if not NetPyNEEngine.is_installed(None):
NetPyNEEngine.install(None)
inform("%s installed NetPyNE (& NEURON)..." %
JNeuroMLNetPyNEEngine.name,
indent=2,
verbosity=1)
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
JNeuroMLNetPyNEEngine.path = JNeuroMLEngine.path + ":" + path_nrn
JNeuroMLNetPyNEEngine.environment_vars = {}
JNeuroMLNetPyNEEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
JNeuroMLNetPyNEEngine.environment_vars.update(
NetPyNEEngine.environment_vars)
JNeuroMLNetPyNEEngine.environment_vars.update(environment_vars_nrn)
inform("PATH: " + JNeuroMLNetPyNEEngine.path)
inform("Env vars: %s" % JNeuroMLNetPyNEEngine.environment_vars)
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)
pynn_loc = sp.check_output(['python -c "import pyNN,os; print(os.path.dirname(pyNN.__file__))"'], shell=True,stderr=sp.STDOUT).strip()
pynn_mod_dir = '%s/neuron/nmodl/'%pynn_loc
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(version) # interpret version as version of NEURON!
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 install(version):
if not NeuronEngine.is_installed(None):
NeuronEngine.install(version) # interpret version as version of NEURON!
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 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 JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
inform("%s installed JNeuroML..." % JNeuroMLNetPyNEEngine.name, indent=2, verbosity =1)
if not NetPyNEEngine.is_installed(None):
NetPyNEEngine.install(None)
inform("%s installed NetPyNE (& NEURON)..." % JNeuroMLNetPyNEEngine.name, indent=2, verbosity =1)
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
JNeuroMLNetPyNEEngine.path = JNeuroMLEngine.path+":"+path_nrn
JNeuroMLNetPyNEEngine.environment_vars = {}
JNeuroMLNetPyNEEngine.environment_vars.update(JNeuroMLEngine.environment_vars)
JNeuroMLNetPyNEEngine.environment_vars.update(NetPyNEEngine.environment_vars)
JNeuroMLNetPyNEEngine.environment_vars.update(environment_vars_nrn)
inform("PATH: " + JNeuroMLNetPyNEEngine.path)
inform("Env vars: %s" % JNeuroMLNetPyNEEngine.environment_vars)
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 get_jnmlnrnenv():
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)
JNeuroMLNRNEngine.environment_vars.update(
JNeuroMLEngine.get_environment())
inform("PATH: " + JNeuroMLNRNEngine.path)
inform("Env vars: %s" % JNeuroMLNRNEngine.environment_vars)
del JNeuroMLNRNEngine.environment_vars['PYTHONPATH']
return JNeuroMLNRNEngine.environment_vars
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))