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 run(self): try: path_s = resolve_paths(self.modelpath) from omv.engines.jneuroml import JNeuroMLEngine jnml = JNeuroMLEngine.get_executable() cmds = [jnml, '-validatev1'] for p in path_s: cmds.append(p) inform("Running with %s, using %s..." % (JNeuroMLValidateV1Engine.name, cmds), indent=1) self.stdout = sp.check_output(cmds, cwd=os.path.dirname(self.modelpath), env=JNeuroMLEngine.get_environment()) inform("Success with running ", JNeuroMLValidateV1Engine.name, indent=1, verbosity=1) self.returncode = 0 except sp.CalledProcessError as err: self.returncode = err.returncode self.stdout = err.output raise EngineExecutionError
def run(self): np = 2 try: inform("Running file %s with %s" % (trim_path(self.modelpath), JNeuroMLNetPyNEEngine.name), indent=1) from omv.engines.jneuroml import JNeuroMLEngine jnml = JNeuroMLEngine.get_executable() self.stdout = check_output([ jnml, self.modelpath, '-netpyne', '-nogui', '-run', '-np', '%s' % np ], cwd=os.path.dirname(self.modelpath), env=JNeuroMLEngine.get_environment()) inform("Success with running ", JNeuroMLNetPyNEEngine.name, indent=1) self.returncode = 0 except sp.CalledProcessError as err: inform("Error with ", JNeuroMLNetPyNEEngine.name, indent=1) self.returncode = err.returncode self.stdout = err.output raise EngineExecutionError
def install(version): if not JNeuroMLEngine.is_installed(None): JNeuroMLEngine.install(None) if not NeuronEngine.is_installed(None): NeuronEngine.install(None) JNeuroMLNRNEngine.get_jnmlnrnenv()
def install(version): if not JNeuroMLEngine.is_installed(None): JNeuroMLEngine.install(None) JNeuroMLValidateEngine.path = JNeuroMLEngine.path JNeuroMLValidateEngine.environment_vars = {} JNeuroMLValidateEngine.environment_vars.update( JNeuroMLEngine.environment_vars)
def is_installed(version): if is_verbose(): inform("Checking whether %s is installed..." % JNeuroMLPyNNNRNEngine.name, indent=1) return JNeuroMLEngine.is_installed( None) and PyNNNRNEngine.is_installed(None)
def install(version): if not JNeuroMLEngine.is_installed(None): JNeuroMLEngine.install(None) if not Brian1Engine.is_installed(None): Brian1Engine.install(None) JNeuroMLBrianEngine.path = JNeuroMLEngine.path + \ ":" + Brian1Engine.path JNeuroMLBrianEngine.environment_vars = {} JNeuroMLBrianEngine.environment_vars.update( JNeuroMLEngine.environment_vars) JNeuroMLBrianEngine.environment_vars.update( Brian1Engine.environment_vars) inform("PATH: " + JNeuroMLBrianEngine.path) inform("Env vars: %s" % JNeuroMLBrianEngine.environment_vars)
def install(version): if not JNeuroMLEngine.is_installed(None): JNeuroMLEngine.install(None) if not MooseEngine.is_installed(None): MooseEngine.install(None) JNeuroMLMooseEngine.path = JNeuroMLEngine.path + \ ":" + JNeuroMLMooseEngine.path JNeuroMLMooseEngine.environment_vars = {} JNeuroMLMooseEngine.environment_vars.update( JNeuroMLEngine.environment_vars) JNeuroMLMooseEngine.environment_vars.update( MooseEngine.environment_vars) inform("PATH: " + JNeuroMLMooseEngine.path) inform("Env vars: %s" % JNeuroMLMooseEngine.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 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 run(self): try: inform("Running file %s with %s" % (trim_path(self.modelpath), JNeuroMLBrian2Engine.name), indent=1) from omv.engines.jneuroml import JNeuroMLEngine jnml = JNeuroMLEngine.get_executable() self.stdout = check_output([jnml, self.modelpath, '-brian2'], cwd=os.path.dirname(self.modelpath), env=JNeuroMLEngine.get_environment()) self.stdout += check_output([ 'python', self.modelpath.replace('.xml', '_brian2.py'), '-nogui' ], cwd=os.path.dirname(self.modelpath)) inform("Success with running ", JNeuroMLBrian2Engine.name, indent=1) self.returncode = 0 except sp.CalledProcessError as err: inform("Error with ", JNeuroMLBrian2Engine.name, indent=1) self.returncode = err.returncode self.stdout = err.output raise EngineExecutionError
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 run_using_jnmlnrn_env(engine, modelpath, args): try: env = JNeuroMLNRNEngine.get_jnmlnrnenv() inform("Running file %s with %s, env: %s" % (trim_path(modelpath), engine, env), indent=1) from omv.engines.jneuroml import JNeuroMLEngine jnml = JNeuroMLEngine.get_executable() cmds = [jnml, modelpath] cmds.extend(args) stdout = check_output(cmds, cwd=os.path.dirname(modelpath), env=env) inform("Success with running ", engine, indent=1) returncode = 0 return stdout, returncode except sp.CalledProcessError as err: inform("Error with ", engine, indent=1) returncode = err.returncode stdout = err.output return stdout, returncode
def is_installed(version): if is_verbose(): inform("Checking whether %s is installed..." % JNeuroMLMooseEngine.name, indent=1) return JNeuroMLEngine.is_installed(None) and MooseEngine.is_installed(None)
def is_installed(version): return JNeuroMLEngine.is_installed(None)