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_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 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 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 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'])