def is_installed(version, silent=False):
if is_verbose():
inform(
"Checking whether the engine %s has been installed correctly..."
% NetPyNEEngine.name,
indent=1)
ret = True
try:
ret_str = sp.check_output(
['python -c "import netpyne; print(netpyne.__version__)"'],
shell=True,
stderr=sp.STDOUT)
ret = len(ret_str) > 0
if ret and is_verbose():
inform("%s is correctly installed..." % (NetPyNEEngine.name),
indent=2)
except Exception as err:
inform("Couldn't import netpyne into Python: ", err, indent=1)
ret = False
installed = ret and PyNRNEngine.is_installed(
None) and PyNeuroMLEngine.is_installed(None)
if not silent:
inform("NetPyNE is_installed: %s" % ret, "", indent=1)
return installed
def is_installed(version):
if is_verbose():
inform("Checking whether the engine %s has been installed correctly..." %
MooseEngine.name, indent=1)
ret = True
try:
ret_str = sp.check_output(['python -c "import moose; print(moose.__version__)"'], shell=True,stderr=sp.STDOUT)
ret = len(ret_str) > 0
if ret and is_verbose():
inform("%s is correctly installed..." % (MooseEngine.name), indent=2)
if ret:
import moose
ret = 'v%s'%moose.__version__
except Exception as err:
inform("Couldn't import moose into Python: ", err, indent=1)
ret = False
if not ret or not PyNeuroMLEngine.is_installed(None):
ret = False
inform("Moose is_installed(): %s"%ret, "", indent=1, verbosity=2)
return ret
def is_installed(version):
PyNestEngine.environment_vars = NestEngine.get_nest_environment()
ret = True
try:
ret_str = check_output(['python -c "import nest; print(nest.version())"'], shell=True, verbosity=2)
ret = len(ret_str) > 0
if ret:
ret = 'v%s'%ret_str.split('Version')[-1].split()[0]
if ret and is_verbose():
inform("%s is correctly installed..." % (PyNestEngine.name), indent=2)
if is_verbose():
inform("NEST is installed with Python support...", indent=2)
inform("Env vars: %s" % PyNestEngine.environment_vars, indent=2)
except Exception as err:
inform("Couldn't import NEST into Python: ", err, indent=1)
inform("NEST env vars: %s" % PyNestEngine.environment_vars, indent=1)
ret = False
return ret
def is_installed(version, silent=True):
if is_verbose():
inform("Checking whether the engine %s has been installed correctly..." %
NetPyNEEngine.name, indent=1)
ret = True
try:
ret_str = sp.check_output(['python -c "import netpyne; print(netpyne.__version__)"'], shell=True,stderr=sp.STDOUT)
ret = len(ret_str) > 0
if ret and is_verbose():
inform("%s is correctly installed..." % (NetPyNEEngine.name), indent=2)
if ret:
ret = 'v%s'%str(ret_str.strip())
except Exception as err:
inform("Couldn't import netpyne into Python: ", err, indent=1)
ret = False
if not PyNRNEngine.is_installed(None) or not PyNeuroMLEngine.is_installed(None):
ret = False
if not silent:
inform("NetPyNE is_installed: %s"%ret, "", indent=1)
return ret
def is_installed(version):
PyNestEngine.environment_vars = NestEngine.get_nest_environment()
ret = True
try:
ret_str = check_output(
['python -c "import nest; print(nest.version())"'], shell=True)
ret = len(ret_str) > 0
if ret and is_verbose():
inform("%s is correctly installed..." % (PyNestEngine.name),
indent=2)
if is_verbose():
inform("NEST is installed with Python support...", indent=2)
inform("Env vars: %s" % PyNestEngine.environment_vars,
indent=2)
except Exception as err:
inform("Couldn't import NEST into Python: ", err, indent=1)
inform("NEST env vars: %s" % PyNestEngine.environment_vars,
indent=1)
ret = False
return ret
def is_installed(version):
ret = True
if is_verbose():
inform("Checking whether %s is installed..." % NeuronEngine.name,
indent=1)
try:
output = check_output(['nrniv', '--version'], verbosity=2)
if is_verbose():
inform('%s is installed' % output.strip(), indent=2)
ret = 'v%s' % output.split()[3]
except OSError:
try:
environment_vars, path = NeuronEngine.get_nrn_environment()
inform('Testing NEURON with env: %s and path: %s' %
(environment_vars, path),
indent=2)
output = check_output([path + '/nrniv', '--version'])
if is_verbose():
inform('%s was already installed (by OMV..?)' %
output.strip(),
indent=2)
ret = 'v%s' % output.split()[3]
except OSError:
inform('NEURON not currently installed', indent=2)
ret = False
return ret
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 is_installed(version):
if is_verbose():
inform("Checking whether %s is installed..." %
PyNNBrian1Engine.name,
indent=1)
return PyNNEngine.is_installed(None) and Brian1Engine.is_installed(
None)
def is_installed(version):
ret = True
try:
ret_str = sp.check_output(
['python -c "import numba; print(numba.__version__)"'],
shell=True,
stderr=sp.STDOUT)
ret = len(ret_str) > 0
if isinstance(ret_str, bytes):
ret_str = ret_str.decode('utf-8')
ret = 'v%s' % ret_str.strip()
if is_verbose():
inform("numba %s is correctly installed..." % ret,
indent=2,
verbosity=2)
except Exception as err:
inform("Couldn't import numba into Python: ",
err,
indent=1,
verbosity=2)
ret = False
return ret
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 is_installed(version):
ret = True
try:
if is_verbose():
inform("Checking whether %s is installed..." %
PyNRNEngine.name,
indent=1)
import neuron
if is_verbose():
inform("PyNEURON version %s is correctly installed..." %
neuron.sys.version,
indent=2)
except Exception as err:
inform("Couldn't import NEURON into Python: ", err, indent=1)
ret = False
return ret
def is_installed(version):
if is_verbose():
inform("Checking whether %s is installed..." %
PyLemsNeuroML2Engine.name,
indent=1)
nml2_installed = os.path.isdir(default_nml2_dir)
return PyLemsEngine.is_installed(None) and nml2_installed
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 is_installed(cls, version):
ret = True
try:
output = check_output(['nrniv', '--version'])
if is_verbose():
inform('%s was already installed locally'%output.strip(), indent=2)
except OSError:
try:
environment_vars, path = NeuronEngine.get_nrn_environment()
inform('Testing NEURON with env: %s and path: %s'%(environment_vars, path), indent=2)
output = check_output([path+'/nrniv', '--version'])
if is_verbose():
inform('%s was already installed (by OMV..?)'%output.strip(), indent=2)
except OSError:
inform('NEURON not currently installed', indent=2)
ret = False
return ret
def is_installed(version):
ret = True
try:
if is_verbose():
inform("Checking whether %s is installed..." %
PyNeuroMLEngine.name, indent=1)
FNULL = open(os.devnull, 'w')
sp.check_call(['pynml' if os.name != 'nt' else 'pynml.bat', '-h'], stdout=FNULL)
except OSError:
ret = False
return ret
def is_installed(version):
ret = True
try:
import pyNN
if is_verbose():
inform("pyNN version %s is correctly installed..." % pyNN.__version__, indent=2)
except Exception as err:
inform("Couldn't import pyNN into Python: ", err, indent=1)
ret = False
return ret
def is_installed(version):
ret = True
try:
if is_verbose():
inform("Checking whether %s is installed..." %
JNeuroMLEngine.name,
indent=1)
FNULL = open(os.devnull, 'w')
jnml = JNeuroMLEngine.get_executable()
r = check_output([jnml, '-v'],
verbosity=2,
env=JNeuroMLEngine.get_environment())
ret = '%s' % r.split()[1]
if is_verbose():
inform("%s %s is installed..." % (JNeuroMLEngine.name, ret),
indent=2)
except OSError as err:
inform("Couldn't execute/import jNeuroML: ", err, indent=1)
ret = False
return ret
def is_installed(version):
ret = True
try:
if is_verbose():
inform("Checking whether %s is installed..." %
JNeuroMLEngine.name, indent=1)
FNULL = open(os.devnull, 'w')
r = check_output(['jnml' if os.name != 'nt' else 'jnml.bat', '-v'], verbosity=2)
ret = '%s'%r.split()[1]
except OSError:
ret = False
return ret
def is_installed(version):
ret = True
try:
if is_verbose():
inform("Checking whether %s is installed..." %
PyNeuroMLEngine.name,
indent=1)
FNULL = open(os.devnull, 'w')
sp.check_call(['pynml' if os.name != 'nt' else 'pynml.bat', '-h'],
stdout=FNULL)
except OSError:
ret = False
return ret
def is_installed(version):
PyNestEngine.environment_vars = NestEngine.get_nest_environment()
ret = True
try:
ret_str = check_output(
['python -c "import nest; print(nest.version())"'],
shell=True,
verbosity=2)
ret = len(ret_str) > 0
if ret:
ret_str = ret_str.strip().split('\n')[-1]
#print('NEST info: %s; <<%s>>'%(ret, ret_str))
if 'Version' in ret_str:
ret = 'v%s' % ret_str.split('Version')[-1].split()[0]
elif '-' in ret_str:
ret = 'v%s' % ret_str.split('-')[-1].split()[0]
else:
ret = 'v%s' % ret_str.split()[-1]
if ret and is_verbose():
inform("%s is correctly installed..." % (PyNestEngine.name),
indent=2)
if is_verbose():
inform("NEST is installed with Python support...", indent=2)
inform("Env vars: %s" % PyNestEngine.environment_vars,
indent=2)
except Exception as err:
inform("Couldn't import NEST into Python: ", err, indent=1)
inform("NEST env vars: %s" % PyNestEngine.environment_vars,
indent=1)
ret = False
return ret
def test_one(omt_fname):
tally = parse_omt(omt_fname)
inform('')
if tally.all_passed():
inform("Test passed: %s" % omt_fname, overline='=', center=True)
else:
inform("Test failed: %s" % (omt_fname), underline='=', center=True)
if is_verbose():
th = TallyHolder()
th.add(tally)
print('\n' + th.summary() + '\n')
assert (tally.all_passed())
def is_installed(version):
ret = True
environment_vars = NestEngine.get_nest_environment()
try:
FNULL = open(os.devnull, 'w')
check_output([environment_vars['NEST_HOME'] + 'bin/nest', '-v'],
verbosity=is_verbose())
except OSError as err:
inform("Couldn't execute NEST: ", err, indent=1)
ret = False
return ret
def is_installed(version):
ret = True
try:
ret_str = sp.check_output(['python -c "import pyNN; print(pyNN.__version__)"'], shell=True,stderr=sp.STDOUT)
ret = len(ret_str) > 0
ret = 'v%s'%ret_str.strip()
if is_verbose():
inform("pyNN %s is correctly installed..." % ret, indent=2)
except Exception as err:
inform("Couldn't import pyNN into Python: ", err, indent=1)
ret = False
return ret
def is_installed(version):
ret = False
try:
import brian
if is_verbose():
inform("Brian version %s is correctly installed..." %
brian.__version__,
indent=2)
ret = 'v%s' % brian.__version__
except Exception as err:
inform("Couldn't import Brian into Python: ", err, indent=1)
ret = False
return ret
def is_installed(version):
ret = True
try:
inform("Checking whether %s is installed..." % PyNRNEngine.name, indent=1, verbosity=2)
### Prints to stderr!!
#ret_str = check_output(['python -c "import neuron; print(neuron.h.nrnversion())"'], shell=True, verbosity=2)
import neuron
ret_str = neuron.h.nrnversion()
ret = 'v%s'%ret_str.split()[3]
if is_verbose():
inform("PyNEURON version %s is correctly installed..." % ret, indent=2)
except Exception as err:
inform("Couldn't import NEURON into Python: ", err, indent=1)
ret = False
return ret
def is_installed(version):
ret = True
try:
inform("Checking whether %s is installed..." % PyNRNEngine.name, indent=1, verbosity=2)
### Prints to stderr!!
#ret_str = check_output(['python -c "import neuron; print(neuron.h.nrnversion())"'], shell=True, verbosity=2)
import neuron
ret_str = neuron.h.nrnversion()
ret = 'v%s'%ret_str.split()[3]
if is_verbose():
inform("PyNEURON version %s is correctly installed..." % ret, indent=2)
except Exception as err:
inform("Couldn't import NEURON into Python: ", err, indent=1)
ret = False
return ret
def is_installed(version):
if is_verbose():
inform("Checking whether %s is installed..." %
PyNNNestEngine.name, indent=1)
return PyNNEngine.is_installed(None) and PyNestEngine.is_installed(None)
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 test_all(do_not_run=False,
only_this_engine=None,
include_temp_tests=False):
cwd = Path(getcwd())
all_omts = [p.as_posix() for p in cwd.glob('**/*.omt')]
if include_temp_tests:
all_omts += [p.as_posix() for p in cwd.glob('**/*.omt_')]
th = TallyHolder()
if environ.get('TRAVIS'):
if not environ.get('OMV_ENGINE'):
tallies = [parse_omt(t) for t in all_omts]
else:
engine = environ.get('OMV_ENGINE').lower()
tallies = [
parse_omt(t) for t in all_omts
if load_yaml(t)['engine'].lower() == engine
]
elif only_this_engine:
inform('Only running tests for engine: %s' % only_this_engine)
tallies = [
parse_omt(t) for t in all_omts
if load_yaml(t)['engine'].lower() == only_this_engine.lower()
]
else:
tallies = []
failed = 0
for i in range(len(all_omts)):
t = all_omts[i]
inform('')
tally = parse_omt(t, do_not_run)
if not tally.all_passed(): failed += 1
if not do_not_run:
inform('')
inform('')
inform(' [ Test %i of %i complete - failed so far: %s ]' %
(i + 1, len(all_omts), failed))
tallies.append(tally)
tallies.sort()
if not do_not_run:
for t in tallies:
th.add(t)
results = []
for i in range(len(tallies)):
t = tallies[i]
results.append(t.all_passed())
inform('')
inform("%i test(s) run" % len(tallies),
overline='-',
underline='-',
center=True)
inform('')
if len(results) == 0:
inform("No tests found!", underline='=', center=True)
elif all(results):
inform("All tests passing!", underline='=', center=True)
else:
failed = [trim_path(t.omt) for t in tallies if not t.all_passed()]
inform("Some test(s) failed: ", failed, underline='=')
if is_verbose():
print('\n' + th.summary() + '\n')
assert len(results) > 0
assert all(results)
else:
engs = {}
tot_tests = 0
for t in tallies:
if not t.engine in engs:
engs[t.engine] = 0
engs[t.engine] += 1
tot_tests += 1
inform('')
for e in sorted(engs):
inform(' Engine %s has %s tests' % (e, engs[e]))
inform('')
inform(' %s OMV tests in total' % (tot_tests))
inform('')
