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 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)
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))
def main():
arguments = docopt(__doc__, version='OpenSourceBrain Model Validation 0.0')
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:
test_all(only_this_engine=arguments['--engine'])
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)
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)
engine = arguments['<engine>']
if engine not in OMVEngines:
inform('Engine ' + engine + ' unknown!')
else:
eng = arguments['<engine>']
inform('Trying to install: %s' % eng)
already_installed = False
if eng == 'NEURON':
from engines.neuron_ import NeuronEngine
if not NeuronEngine.is_installed(''):
from engines.getnrn import install_neuron
install_neuron(get_latest=True)
else:
already_installed = True
elif eng == 'PyNEURON':
from engines.pyneuron import PyNRNEngine
if not PyNRNEngine.is_installed(''):
from engines.getnrn import install_neuron
install_neuron()
else:
already_installed = True
elif eng == 'jLEMS':
from engines.jlems import JLemsEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from engines.getjlems import install_jlems
install_jlems()
elif eng == 'jNeuroML':
from engines.jneuroml import JNeuroMLEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from engines.getjnml import install_jnml
install_jnml()
elif eng == 'neuroConstruct' or eng == 'Py_neuroConstruct':
from engines.pyneuroconstruct import PyneuroConstructEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from engines.getneuroconstruct import install_neuroconstruct
install_neuroconstruct()
elif eng == 'pyNeuroML':
from engines.pyneuroml_ import PyNeuroMLEngine as ee
if ee.is_installed(None):
already_installed = True
else:
from engines.getpyneuroml import install_pynml
install_pynml()
elif eng == 'PyLEMS_NeuroML2':
from engines.getpylems import install_pylems
install_pylems()
from engines.getnml2 import install_nml2
install_nml2()
elif eng == 'genesis':
from engines.getgenesis import install_genesis
install_genesis()
elif eng == 'Moose':
from engines.getmoose import install_moose
install_moose()
elif eng == 'NetPyNE':
from engines.getnetpyne import install_netpyne
install_netpyne()
elif eng == 'Brian':
from engines.getbrian1 import install_brian
install_brian()
elif eng == 'Brian2':
from engines.getbrian2 import install_brian2
install_brian2()
elif eng == 'NEST':
from engines.getnest import install_nest
install_nest()
elif eng == 'PyNN':
from engines.getpynn import install_pynn
install_pynn()
elif eng == 'PyNN':
from engines.getpynn import install_pynn
install_pynn()
elif eng == 'Py_neuroConstruct' or eng == 'neuroConstruct':
from engines.getneuroconstruct import install_neuroconstruct
install_neuroconstruct()
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']:
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:
inform(' %s%s(installed: %s)' %
(engine, ' ' * (30 - len(engine)), installed[engine]))
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)