def install_nest(version):
if not version:
version='2.12.0'
inform('Installing NEST', indent=2, verbosity=1)
nestpath = os.path.join(os.environ['HOME'],'nest')
nestpath2 = os.path.join(os.environ['HOME'],'nest/nest')
nestinstallpath = os.path.join(os.environ['HOME'],'nest/nest')
if 'NEST_INSTALL_DIR' in os.environ:
nestinstallpath = os.environ['NEST_INSTALL_DIR']+'/'
inform('Installing NEST (src: %s), (tgt: %s)'%(nestpath, nestinstallpath), indent=2, verbosity=1)
os.mkdir(nestpath)
with working_dir(nestpath):
#version='2.10.0'
check_output(['wget', 'https://github.com/nest/nest-simulator/archive/v%s.tar.gz'%(version)])
check_output(['tar', 'xzvf', 'v%s.tar.gz'%version])
check_output(['mv', 'nest-simulator-%s'%version, 'nest'], cwd=nestpath)
with working_dir(nestpath2):
check_output(["cmake", "-DCMAKE_INSTALL_PREFIX:PATH=%s"%(nestinstallpath)])
check_output(['make'])
check_output(['make', 'install'])
def install_pynn():
try:
print(check_output(['pip', 'install', 'lazyarray'])) # This should ideally be automatically installed with PyNN...
print(check_output(['pip', 'install', 'neo==0.5.1'])) # This should ideally be automatically installed with PyNN...
install_root = os.environ['HOME']
pyNN_src = 'PyNN_src'
with working_dir(install_root):
check_output(['git', 'clone', 'https://github.com/NeuralEnsemble/PyNN.git', pyNN_src])
path = os.path.join(install_root, pyNN_src)
with working_dir(path):
print(check_output(['git','checkout','neuroml'])) # neuroml branch has the latest NML2 import/export code!
#check_output(['git','checkout','master'])
print(check_output(['python', 'setup.py', 'install']))
print(check_output(['pwd']))
print("Finished attempting to install PyNN")
#import pyNN
m = 'Successfully installed pyNN...'
except Exception as e:
m = 'ERROR during install_pynn: %s'%e
finally:
inform(m)
def install_netpyne():
install_root = os.environ['HOME']
install_dir = 'netpyneInstall'
path = os.path.join(install_root, install_dir)
if not os.path.isdir(path):
with working_dir(install_root):
print(
check_output([
'git', 'clone',
'https://github.com/Neurosim-lab/netpyne.git', install_dir
]))
with working_dir(path):
print(check_output(['git', 'checkout', 'neuroml_updates']))
print(check_output(['pwd']))
with working_dir(path):
if sys.version_info.major == 2:
#pip_install([]'setuptools==42.0.1')
pip_install([
'kiwisolver==1.0.1', 'matplotlib==2.2.4', 'pandas==0.23.4',
'bokeh==1.4.0', 'Pillow==5.4.1', 'matplotlib-scalebar==0.5.1',
'scipy==1.2.2', 'python-dateutil==2.8.0'
])
print(check_output([sys.executable, 'setup.py', 'install']))
m = 'Successfully installed NetPyNE...'
def install_nest(version):
if not version:
version='2.18.0'
inform('Installing NEST', indent=2, verbosity=1)
nestpath = os.path.join(os.environ['HOME'],'nest')
nestpath2 = os.path.join(os.environ['HOME'],'nest/nest')
nestinstallpath = os.path.join(os.environ['HOME'],'nest/nest')
if 'NEST_INSTALL_DIR' in os.environ:
nestinstallpath = os.environ['NEST_INSTALL_DIR']+'/'
inform('Installing NEST (src: %s), (tgt: %s)'%(nestpath, nestinstallpath), indent=2, verbosity=1)
os.mkdir(nestpath)
with working_dir(nestpath):
#version='2.10.0'
check_output(['wget', 'https://github.com/nest/nest-simulator/archive/v%s.tar.gz'%(version)])
check_output(['tar', 'xzvf', 'v%s.tar.gz'%version])
check_output(['mv', 'nest-simulator-%s'%version, 'nest'], cwd=nestpath)
with working_dir(nestpath2):
check_output(["cmake", "-DCMAKE_INSTALL_PREFIX:PATH=%s"%(nestinstallpath)])
check_output(['make','-j4'])
check_output(['make', 'install'])
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_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_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_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_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(['git', 'checkout', 'development']))
print(co(['mvn', 'install']))
inform('Successfully installed jLEMS', indent=2, verbosity=1)
def install_brian():
install_root = os.environ['HOME']
with working_dir(install_root):
check_output(['git', 'clone', 'https://github.com/brian-team/brian.git'])
inform('Successfully cloned Brian', indent=2, verbosity=1)
path = os.path.join(install_root,'brian')
with working_dir(path):
check_output(['git','checkout','master'])
check_output(['python', 'setup.py', 'install'])
inform('Successfully installed Brian', indent=2, verbosity=1)
def install_netpyne():
install_root = os.environ['HOME']
with working_dir(install_root):
print(check_output(['git', 'clone', 'https://github.com/Neurosim-lab/netpyne.git', 'netpyneInstall']))
path = os.path.join(install_root,'netpyneInstall')
with working_dir(path):
print(check_output(['git', 'checkout', 'neuroml_updates']))
print(check_output(['pwd']))
print(check_output(['python', 'setup.py', 'install']))
m = 'Successfully installed NetPyNE...'
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(['git', 'checkout', 'development']))
print(co(['mvn', 'install']))
inform('Successfully installed jLEMS', indent=2, verbosity=1)
def install_neuron(version):
if not version:
version = '7.6'
nrnpath = os.path.join(os.environ['HOME'], 'neuron')
inform('Installing NEURON %s into %s' % (version, nrnpath), indent=1)
os.mkdir(nrnpath)
with working_dir(nrnpath):
print(
co([
'wget',
'https://www.neuron.yale.edu/ftp/neuron/versions/v%s/nrn-%s.tar.gz'
% (version, version)
]))
print(co(['tar', 'xzvf', 'nrn-%s.tar.gz' % version]))
print(co(['mv', 'nrn-%s' % version, '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', '-j4']))
print(co(['make', 'install']))
os.chdir('src/nrnpython')
run_setup('./setup.py', ['install'])
def compile_modfiles(cls, modelpath):
with working_dir(dirname(modelpath)):
out = 0
if len(glob('*.mod')) > 0:
environment_vars, path = NeuronEngine.get_nrn_environment()
inform('Compiling all mod files in directory: %s' %
dirname(modelpath),
indent=1)
out = check_output([path + '/nrnivmodl'])
inform(out, indent=2)
elif len(glob('modfiles/*.mod')) > 0:
environment_vars, path = NeuronEngine.get_nrn_environment()
mod_file_path = dirname(modelpath) + "/modfiles"
inform('Compiling all mod files in directory: %s' %
mod_file_path,
indent=1)
out = check_output([path + '/nrnivmodl', 'modfiles'])
inform(out, indent=2)
elif len(glob('mod_files/*.mod')) > 0:
environment_vars, path = NeuronEngine.get_nrn_environment()
mod_file_path = dirname(modelpath) + "/mod_files"
inform('Compiling all mod files in directory: %s' %
mod_file_path,
indent=1)
out = check_output([path + '/nrnivmodl', 'mod_files'])
inform(out, indent=2)
return out
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):
try:
self.stdout = self.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'],
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 = 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))
if sys.version_info[0]==3:
c = dedent(cmd).encode()
else:
c = dedent(cmd)
stdout, stderr = p.communicate(c)
# with open('/tmp/omv_test.nrn.stdout', 'w') as f:
# f.write(stdout)
self.stdout = str(stdout.decode())
self.stderr = str(stderr.decode())
inform("OUT: %s"% self.stdout, verbosity=1, indent=2)
inform("ERR: %s"% self.stderr, verbosity=1, indent=2)
inform("returncode: [%s]"% p.returncode, verbosity=1, indent=2)
self.returncode = p.returncode
if self.returncode != 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',
'https://svn.code.sf.net/p/neuroml/code/jNeuroMLJar'
]))
def install_moose():
install_root = os.environ['HOME']
with working_dir(install_root):
print(check_output(['git', 'clone', 'https://github.com/pgleeson/moose-core.git']))
with working_dir(os.path.join(install_root,'moose-core')):
print(check_output(['mkdir', 'build_']))
with working_dir(os.path.join(install_root,'moose-core/build_')):
print(check_output(['cmake', '..']))
print(check_output(['make']))
print(check_output(['make', 'install']))
with working_dir(os.path.join(install_root,'moose-core/build_/python')):
print(check_output(['pwd']))
print(check_output(['python', 'setup.py', 'install']))
m = 'Successfully installed Moose...'
def is_installed(version):
inform('Checking whether neuroConstruct is installed', indent=2)
ret = True
try:
with working_dir(PyneuroConstructEngine.get_nC_environment()['NC_HOME']):
print(co(['./nC.sh','-v']))
except Exception as err:
inform("Couldn't execute neuroConstruct:", err, indent=1)
ret = False
return ret
def install_neuroconstruct():
try:
install_root = os.environ['HOME']
with working_dir(install_root):
print(co(['git', 'clone', 'https://github.com/NeuralEnsemble/neuroConstruct.git']))
path = os.path.join(install_root,'neuroConstruct')
with working_dir(path):
print(co(['./updatenC.sh']))
print(co(['./nC.sh', '-make']))
m = 'Successfully installed neuroConstruct...'
except Exception as e:
m = 'ERROR installing neuroConstruct: ' + str(e)
finally:
inform(m)
def is_installed(version):
inform('Checking whether neuroConstruct is installed', indent=2, verbosity=2)
ret = True
try:
with working_dir(PyneuroConstructEngine.get_nC_environment()['NC_HOME']):
r = co(['./nC.sh','-v'], verbosity=1)
ret = 'v%s'%r.split()[-1]
except Exception as err:
inform("Couldn't execute neuroConstruct:", err, indent=1)
ret = False
return ret
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 is_installed(version):
nChome = PyneuroConstructEngine.get_nC_environment()['NC_HOME']
inform('Checking whether neuroConstruct is installed (in %s)'%nChome, indent=2, verbosity=2)
ret = True
try:
with working_dir(nChome):
r = co(['./nC.sh','-v'], verbosity=1)
ret = 'v%s'%r.split('neuroConstruct, version: ')[-1].split()[0]
except Exception as err:
inform("Couldn't execute neuroConstruct:", err, indent=1)
ret = False
return ret
def install_moose():
install_root = os.environ['HOME']
with working_dir(install_root):
print(
check_output(
['git', 'clone',
'https://github.com/pgleeson/moose-core.git']))
with working_dir(os.path.join(install_root, 'moose-core')):
print(check_output(['mkdir', 'build_']))
with working_dir(os.path.join(install_root, 'moose-core/build_')):
print(check_output(['cmake', '..']))
print(check_output(['make', '-j4']))
print(check_output(['make', 'install']))
with working_dir(os.path.join(install_root, 'moose-core/build_/python')):
print(check_output(['pwd']))
print(check_output(['python', 'setup.py', 'install']))
m = 'Successfully installed Moose...'
def install_pynn():
try:
pip.main(['install', 'lazyarray']) # This should ideally be automatically installed with PyNN...
pip.main(['install', 'neo==0.5.1']) # 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(['git','checkout','tags/0.9.2'])
#check_output(['git','checkout','master'])
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_neuroconstruct():
try:
install_root = os.environ['HOME']
with working_dir(install_root):
print(
co([
'git', 'clone',
'https://github.com/NeuralEnsemble/neuroConstruct.git'
]))
path = os.path.join(install_root, 'neuroConstruct')
with working_dir(path):
print(co(['./updatenC.sh']))
print(co(['./nC.sh', '-make']))
m = 'Successfully installed neuroConstruct...'
except Exception as e:
m = 'ERROR installing neuroConstruct: ' + 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_jnml():
version = '0.10.1'
jnmlpath = os.path.join(os.environ['HOME'], 'jnml')
if not os.path.isdir(jnmlpath):
os.mkdir(jnmlpath)
with working_dir(jnmlpath):
check_output([
'wget',
'https://github.com/NeuroML/jNeuroML/releases/download/v%s/jNeuroML.zip'
% (version)
])
check_output(['unzip', 'jNeuroML.zip'])
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_neuron(get_latest=False):
nrnpath = os.path.join(os.environ['HOME'],'neuron')
inform('Installing NEURON into %s'%nrnpath, indent=1)
os.mkdir(nrnpath)
with working_dir(nrnpath):
if get_latest:
print(co(['git', 'clone', 'https://github.com/neuronsimulator/nrn']))
os.chdir('nrn')
print(co(['./build.sh']))
else:
print(co(['wget', 'https://www.neuron.yale.edu/ftp/neuron/versions/v7.4/nrn-7.4.tar.gz']))
print(co(['tar', 'xzvf', 'nrn-7.4.tar.gz']))
print(co(['mv', 'nrn-7.4', 'nrn']))
os.chdir('nrn')
path = os.getcwd()
pyexec = 'python2' #sys.executable
co(["./configure --prefix=%s --without-iv --without-paranrn --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()
raw_url = github_repo.link_to_raw_file_in_repo(".travis.yml")
print(" .travis.yml found at %s\n" % raw_url)
contents = osb.utils.get_page(raw_url)
if 'omv' not in contents:
print("That .travis.yml does not look like it uses OMV...")
non_omv_tests += 1
else:
testable_projects += 1
test_it = True
else:
print(" (No .travis.yml)")
if test_it:
target_dir = '%s/%s' % (test_dir, proj_id)
print co(['git', 'clone', str(github_repo.clone_url), target_dir])
with working_dir(target_dir):
if proj_id in branches.keys():
print co(['git', 'checkout', branches[proj_id]])
print "Running 'omv all' on", target_dir
test_all()
passing_projects += 1
print("\nSo far: %i projects with OMV tests which pass\n" % (passing_projects))
end = datetime.datetime.now()
print("\n%i projects checked, of which %i have OMV tests (%i non-OMV tested projects) and %i passed with OMV in %s seconds\n" %
(projects, testable_projects, non_omv_tests, passing_projects, (end - start).seconds))
contents = osb.utils.get_page(raw_url)
if 'omv' not in contents:
print("That .travis.yml does not look like it uses OMV...")
non_omv_tests += 1
else:
testable_projects += 1
test_it = True
else:
print(" (No .travis.yml)")
if test_it:
target_dir = '%s/%s' % (test_dir, proj_id)
print co(['git', 'clone', str(github_repo.clone_url), target_dir])
with working_dir(target_dir):
if proj_id in branches.keys():
print co(['git', 'checkout', branches[proj_id]])
print "Running 'omv all' on", target_dir
test_all()
passing_projects += 1
print("\nSo far: %i projects with OMV tests which pass\n" %
(passing_projects))
end = datetime.datetime.now()
print(
"\n%i projects checked, of which %i have OMV tests (%i non-OMV tested projects) and %i passed with OMV in %s seconds\n"
% (projects, testable_projects, non_omv_tests, passing_projects,
(end - start).seconds))
def install_jnml():
jnmlpath = os.path.join(os.environ['HOME'],'jnml')
os.mkdir(jnmlpath)
with working_dir(jnmlpath):
print(co(['svn', 'checkout', 'https://svn.code.sf.net/p/neuroml/code/jNeuroMLJar']))
