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) 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 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)