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 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 is_installed(version):
if is_verbose():
inform("Checking whether %s is installed correctly..." %
PyNNNRNEngine.name, indent=1)
installed = PyNNEngine.is_installed(None) and NeuronEngine.is_installed(None)
return installed
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 is_installed(version):
if is_verbose():
inform("Checking whether %s is installed correctly..." %
PyNNNRNEngine.name,
indent=1)
installed = PyNNEngine.is_installed(
None) and NeuronEngine.is_installed(None)
return installed
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)
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..." % 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 main():
arguments = docopt(__doc__,
version='OpenSourceBrain Model Validation %s' % version)
set_env_vars()
if arguments['--verbose']:
set_verbosity(1)
if arguments['test']:
try:
test_one(arguments['<testMe.omt>'])
except AssertionError:
inform("Failed due to non passing tests")
exit(1)
elif arguments['all']:
try:
if platform.python_version_tuple()[0] == '3':
inform(
"Python 3. Ignoring tests for non Py3 compatible engines: %s"
% arguments['--ignore-non-py3'])
test_all(only_this_engine=arguments['--engine'],
ignore_non_py3=arguments['--ignore-non-py3'])
except AssertionError:
inform("Failed due to non passing tests")
exit(1)
# Includes *.omt_, i.e. temporary test files
elif arguments['all_']:
try:
test_all(only_this_engine=arguments['--engine'],
include_temp_tests=True,
ignore_non_py3=arguments['--ignore-non-py3'])
except AssertionError:
inform("Failed due to non passing tests")
exit(1)
elif arguments['find']:
try:
test_all(do_not_run=True)
except AssertionError:
inform("Failed due to non passing tests")
exit(1)
elif arguments['validate-mep']:
validate_mep.validate(arguments['<mepfile>'])
elif arguments['validate-omt']:
inform('OMT validation not implemented yet!')
exit(1)
elif arguments['install']:
set_verbosity(1)
eng = arguments['<engine>']
engine_version = None
if ':' in eng:
ee = eng.split(':')
eng = ee[0]
engine_version = ee[1]
inform('Engine %s version %s will be used...' %
(eng, engine_version))
else:
inform('Engine %s, default version will be used...' % (eng))
if eng.lower() not in [e.lower() for e in OMVEngines]:
inform('Engine ' + eng + ' unknown!')
else:
inform('Trying to install: %s' % eng)
already_installed = False
if eng.lower() == 'NEURON'.lower():
from omv.engines.neuron_ import NeuronEngine
if not NeuronEngine.is_installed(None):
from omv.engines.getnrn import install_neuron
install_neuron(engine_version)
else:
already_installed = True
elif eng.lower() == 'PyNEURON'.lower():
from omv.engines.pyneuron import PyNRNEngine
if not PyNRNEngine.is_installed(None):
from omv.engines.getnrn import install_neuron
install_neuron(engine_version)
else:
already_installed = True
elif eng.lower() == 'jLEMS'.lower():
from omv.engines.jlems import JLemsEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from omv.engines.getjlems import install_jlems
install_jlems()
elif eng.lower() == 'jNeuroML'.lower():
from omv.engines.jneuroml import JNeuroMLEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from omv.engines.getjnml import install_jnml
install_jnml()
elif eng.lower(
) == 'neuroConstruct' or eng == 'Py_neuroConstruct'.lower():
from omv.engines.pyneuroconstruct import PyneuroConstructEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from omv.engines.getneuroconstruct import install_neuroconstruct
install_neuroconstruct()
elif eng.lower() == 'pyNeuroML'.lower():
from omv.engines.pyneuroml_ import PyNeuroMLEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from omv.engines.getpyneuroml import install_pynml
install_pynml()
elif eng.lower() == 'PyLEMS'.lower():
from omv.engines.pylems import PyLemsEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from omv.engines.getpylems import install_pylems
install_pylems()
elif eng.lower() == 'PyLEMS_NeuroML2'.lower():
pylems_already_installed = False
nml2_already_installed = False
from omv.engines.pylems import PyLemsEngine as ee
if ee.is_installed(None):
pylems_already_installed = True
else:
from omv.engines.getpylems import install_pylems
install_pylems()
from omv.engines.getnml2 import install_nml2, is_nml2_installed
if is_nml2_installed():
nml2_already_installed = True
else:
install_nml2()
already_installed = nml2_already_installed and pylems_already_installed
elif eng.lower() == 'Py_neuroConstruct'.lower():
from omv.engines.pyneuroconstruct import PyneuroConstructEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from omv.engines.getneuroconstruct import install_neuroconstruct
install_neuroconstruct()
elif eng.lower() == 'genesis'.lower():
from omv.engines.getgenesis import install_genesis
install_genesis()
elif eng.lower() == 'Moose'.lower():
from omv.engines.getmoose import install_moose
install_moose()
elif eng.lower() == 'NetPyNE'.lower():
from omv.engines.getnetpyne import install_netpyne
install_netpyne()
elif eng.lower() == 'Brian'.lower():
from omv.engines.getbrian1 import install_brian
install_brian()
elif eng.lower() == 'Brian2'.lower():
from omv.engines.getbrian2 import install_brian2
install_brian2(engine_version)
elif eng.lower() == 'NEST'.lower():
from omv.engines.getnest import install_nest
install_nest(engine_version)
elif eng.lower() == 'PyNEST'.lower():
from omv.engines.getnest import install_nest
install_nest(engine_version)
elif eng.lower() == 'PyNN'.lower():
from omv.engines.getpynn import install_pynn
install_pynn()
else:
inform(
'Code not implemented yet for installing %s using: omv install! Try running a test using this engine.'
% eng)
exit(1)
if already_installed:
inform('Engine %s was already installed' % eng)
elif arguments['list-engines'] or arguments['list']:
inform('OMV is checking which engines are currently installed...')
set_verbosity(0)
engines = sorted(OMVEngines.keys())
installed = {}
for engine in engines:
installed[engine] = OMVEngines[engine].is_installed('')
inform('')
inform('The following engines are currently supported by OMV (v%s):' %
version)
inform('')
for engine in engines:
py3_info = '' if OMVEngines[
engine].python3_compatible else '; non Py3 compatible'
inform(' %s%s(installed: %s%s)' %
(engine, ' ' *
(30 - len(engine)), installed[engine], py3_info))
inform('')
if arguments['--verbose']:
inform('Additional Python (v%s) packages:' %
platform.python_version())
inform('')
for m in [
'matplotlib', 'numpy', 'pandas', 'scipy', 'sympy',
'tables', 'h5py', 'neo', 'lazyarray', 'pyelectro',
'pyneuroml', 'neuroml', 'neuromllite'
]:
installed_ver = False
try:
exec('import %s' % m)
installed_ver = 'v%s' % eval('%s.__version__' % m)
except:
pass
inform(' %s%s(installed: %s)' %
(m, ' ' * (30 - len(m)), installed_ver))
inform('')
elif arguments['autogen']:
inform('Automatically generating model validation files')
dry = arguments['--dryrun']
auto = arguments['-y']
autogen(auto, dry)
def main():
arguments = docopt(__doc__, version='OpenSourceBrain Model Validation %s'%version)
set_env_vars()
if arguments['--verbose']:
set_verbosity(1)
if arguments['test']:
try:
test_one(arguments['<testMe.omt>'])
except AssertionError:
inform("Failed due to non passing tests")
exit(1)
elif arguments['all']:
try:
if platform.python_version_tuple()[0]=='3':
inform("Python 3. Ignoring tests for non Py3 compatible engines: %s"%arguments['--ignore-non-py3'])
test_all(only_this_engine=arguments['--engine'], ignore_non_py3=arguments['--ignore-non-py3'])
except AssertionError:
inform("Failed due to non passing tests")
exit(1)
# Includes *.omt_, i.e. temporary test files
elif arguments['all_']:
try:
test_all(only_this_engine=arguments['--engine'],include_temp_tests=True, ignore_non_py3=arguments['--ignore-non-py3'])
except AssertionError:
inform("Failed due to non passing tests")
exit(1)
elif arguments['find']:
try:
test_all(do_not_run=True)
except AssertionError:
inform("Failed due to non passing tests")
exit(1)
elif arguments['validate-mep']:
validate_mep.validate(arguments['<mepfile>'])
elif arguments['validate-omt']:
inform('OMT validation not implemented yet!')
exit(1)
elif arguments['install']:
set_verbosity(1)
eng = arguments['<engine>']
engine_version=None
if ':' in eng:
ee = eng.split(':')
eng = ee[0]
engine_version = ee[1]
inform('Engine %s version %s will be used...'%(eng, engine_version))
else:
inform('Engine %s, default version will be used...'%(eng))
if eng.lower() not in [e.lower() for e in OMVEngines]:
inform('Engine ' + eng + ' unknown!')
else:
inform('Trying to install: %s'% eng)
already_installed = False
if eng.lower() == 'NEURON'.lower():
from omv.engines.neuron_ import NeuronEngine
if not NeuronEngine.is_installed(None):
from omv.engines.getnrn import install_neuron
install_neuron(engine_version)
else:
already_installed = True
elif eng.lower() == 'PyNEURON'.lower():
from omv.engines.pyneuron import PyNRNEngine
if not PyNRNEngine.is_installed(None):
from omv.engines.getnrn import install_neuron
install_neuron(engine_version)
else:
already_installed = True
elif eng.lower() == 'jLEMS'.lower():
from omv.engines.jlems import JLemsEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from omv.engines.getjlems import install_jlems
install_jlems()
elif eng.lower() == 'jNeuroML'.lower():
from omv.engines.jneuroml import JNeuroMLEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from omv.engines.getjnml import install_jnml
install_jnml()
elif eng.lower() == 'neuroConstruct' or eng == 'Py_neuroConstruct'.lower():
from omv.engines.pyneuroconstruct import PyneuroConstructEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from omv.engines.getneuroconstruct import install_neuroconstruct
install_neuroconstruct()
elif eng.lower() == 'pyNeuroML'.lower():
from omv.engines.pyneuroml_ import PyNeuroMLEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from omv.engines.getpyneuroml import install_pynml
install_pynml()
elif eng.lower() == 'PyLEMS_NeuroML2'.lower():
from omv.engines.getpylems import install_pylems
install_pylems()
from omv.engines.getnml2 import install_nml2
install_nml2()
elif eng.lower() == 'genesis'.lower():
from omv.engines.getgenesis import install_genesis
install_genesis()
elif eng.lower() == 'Moose'.lower():
from omv.engines.getmoose import install_moose
install_moose()
elif eng.lower() == 'NetPyNE'.lower():
from omv.engines.getnetpyne import install_netpyne
install_netpyne()
elif eng.lower() == 'Brian'.lower():
from omv.engines.getbrian1 import install_brian
install_brian()
elif eng.lower() == 'Brian2'.lower():
from omv.engines.getbrian2 import install_brian2
install_brian2(engine_version)
elif eng.lower() == 'NEST'.lower():
from omv.engines.getnest import install_nest
install_nest(engine_version)
elif eng.lower() == 'PyNN'.lower():
from omv.engines.getpynn import install_pynn
install_pynn()
else:
inform('Code not implemented yet for installing %s using: omv install! Try running a test using this engine.'%eng)
exit(1)
if already_installed:
inform('Engine %s was already installed'%eng)
elif arguments['list-engines'] or arguments['list']:
inform('OMV is checking which engines are currently installed...')
set_verbosity(0)
engines = sorted(OMVEngines.keys())
installed = {}
for engine in engines:
installed[engine] = OMVEngines[engine].is_installed('')
inform('')
inform('The following engines are currently supported by OMV:')
inform('')
for engine in engines:
py3_info = '' if OMVEngines[engine].python3_compatible else '; non Py3 compatible'
inform(' %s%s(installed: %s%s)'%(engine, ' '*(30-len(engine)), installed[engine], py3_info))
inform('')
if arguments['--verbose']:
inform('Additional Python (v%s) packages:'%platform.python_version())
inform('')
for m in ['matplotlib','numpy','pandas','scipy','sympy','tables','neo','lazyarray','pyelectro','pyneuroml','neuroml']:
installed_ver = False
try:
exec('import %s'%m)
installed_ver = eval('%s.__version__'%m)
except:
pass
inform(' %s%s(installed: %s)'%(m, ' '*(30-len(m)), installed_ver))
inform('')
elif arguments['autogen']:
inform('Automatically generating model validation files')
dry = arguments['--dryrun']
auto = arguments['-y']
autogen(auto, dry)
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)