def operation(op, name, options=None):
if options is None:
options = {}
if name:
vmx = utils.locate_vmx(name)
if vmx:
mechfile = utils.load_mechfile(name)
m = Mech()
m.vmx = vmx
m.user = mechfile['user']
for key, value in options.iteritems():
setattr(m, key, value)
method = getattr(m, op)
method()
else:
puts(colored.red("Couldn't find a VMX in the specified directory"))
else:
mechfile = utils.load_mechfile()
vmx = mechfile.get('vmx')
if vmx:
m = Mech()
m.vmx = vmx
m.user = mechfile.get('user')
for key, value in options.iteritems():
setattr(m, key, value)
method = getattr(m, op)
method()
else:
puts(colored.red("Couldn't find a VMX in the mechfile"))
def main():
try:
import os
import sys
from mech import Mech
HOME = os.path.expanduser('~/.mech')
if not os.path.exists(HOME):
os.makedirs(HOME)
arguments = Mech.docopt(Mech.__doc__, argv=sys.argv[1:], version=__version__)
return Mech(arguments)()
except KeyboardInterrupt:
sys.stderr.write('\n')
def operation(op, name, options=None, kwargs=None):
if options is None:
options = {}
if name:
vmx = utils.locate_vmx(name)
if vmx:
mechfile = utils.load_mechfile(name)
m = Mech()
m.vmx = vmx
m.user = mechfile['user']
for key, value in options.iteritems():
setattr(m, key, value)
method = getattr(m, op)
if kwargs:
method(**kwargs)
else:
method()
else:
puts(colored.red("Couldn't find a VMX in the specified directory"))
return
else:
mechfile = utils.load_mechfile()
if mechfile is None:
puts(
colored.red(
"Couldn't find a mechfile in the current directory any deeper directories"
))
puts(
colored.red(
"You can specify the name of the VM you'd like to start with mech up <name>"
))
puts(
colored.red(
"Or run mech init to setup a tarball of your VM or download the VM"
))
return
vmx = mechfile.get('vmx')
if vmx:
m = Mech()
m.vmx = vmx
m.user = mechfile.get('user')
for key, value in options.iteritems():
setattr(m, key, value)
method = getattr(m, op)
if kwargs:
method(**kwargs)
else:
method()
else:
puts(colored.red("Couldn't find a VMX in the mechfile"))
return
def operation(op, name, options=None):
if options is None:
options = {}
if name:
vmx = utils.locate_vmx(name)
if vmx:
mechfile = utils.load_mechfile(name)
m = Mech()
m.vmx = vmx
m.user = mechfile['user']
for key, value in options.iteritems():
setattr(m, key, value)
method = getattr(m, op)
method()
else:
puts(colored.red("Couldn't find a VMX in the specified directory"))
else:
mechfile = utils.load_mechfile()
vmx = mechfile.get('vmx')
if vmx:
m = Mech()
m.vmx = vmx
m.user = mechfile.get('user')
for key, value in options.iteritems():
setattr(m, key, value)
method = getattr(m, op)
method()
else:
puts(colored.red("Couldn't find a VMX in the mechfile"))
def operation(op, name, options=None, kwargs=None):
if options is None:
options = {}
if name:
vmx = utils.locate_vmx(name)
if vmx:
mechfile = utils.load_mechfile(name)
m = Mech()
m.vmx = vmx
m.user = mechfile['user']
for key, value in options.iteritems():
setattr(m, key, value)
method = getattr(m, op)
if kwargs:
method(**kwargs)
else:
method()
else:
puts(colored.red("Couldn't find a VMX in the specified directory"))
return
else:
mechfile = utils.load_mechfile()
if mechfile is None:
puts(colored.red("Couldn't find a mechfile in the current directory any deeper directories"))
puts(colored.red("You can specify the name of the VM you'd like to start with mech up <name>"))
puts(colored.red("Or run mech init to setup a tarball of your VM or download the VM"))
return
vmx = mechfile.get('vmx')
if vmx:
m = Mech()
m.vmx = vmx
m.user = mechfile.get('user')
for key, value in options.iteritems():
setattr(m, key, value)
method = getattr(m, op)
if kwargs:
method(**kwargs)
else:
method()
else:
puts(colored.red("Couldn't find a VMX in the mechfile"))
return
parser.add_option("-k", "--keywords", dest = "keywords", type="string", default = 'hv,PROD,EMISSION', help = "List of keywords to be ignored in reactants or products (comma delimited; default='hv')")
parser.add_option("-o", "--outpath", dest = "outpath", type="string", default = None, help = "Output path.")
parser.add_option("-m", "--monitor", dest = "monitor", type="string", default = None, help = "Extra monitor values (comma separated string).")
parser.add_option("-s", "--solver", dest = "solver", default = None, help = "solver (default: lsoda; vode; zvode; dopri5; dop853)")
parser.add_option("-c", "--code", dest = "code", default = "", help = "code to solve (exec) after model is compiled and run (unless --norun); out is a keyword for the mechanism that has been generated")
(options, args) = parser.parse_args()
if len(args) == 0:
parser.print_help()
exit()
outs = []
for arg in args:
out = Mech(arg, verbose = options.verbose, keywords = [k_.strip() for k_ in options.keywords.split(',')])
if options.monitor is not None:
out.monitor = tuple([(None if k not in out.allspcs else out.allspcs.index(k), k) for k in options.monitor.split(',')]) + out.monitor
if not options.norun:
runtime = out.run(tstart = options.tstart, tend = options.tend, dt = options.dt, solver = options.solver, jac = options.jacobian, atol = options.atol, rtol = options.rtol)
print 'Solved in %f seconds' % runtime
out.output(options.outpath)
outs.append(out)
if os.path.exists(options.code):
options.code = file(options.code, 'r').read()
exec(options.code)
def main(args=None):
arguments = docopt(__doc__, version='mech 0.3')
DEBUG = arguments['--debug']
if not os.path.exists(HOME):
os.makedirs(HOME)
if arguments['init']:
puts(colored.green("Initializing mech"))
url = arguments['<url>']
name = arguments['--name']
Mech.setup(url, name)
exit()
elif arguments['list'] or arguments['ls']:
Mech.list()
exit()
elif arguments['status'] or arguments['ps']:
Mech.status()
exit()
elif arguments['up'] or arguments['start']:
name = arguments['<name>']
gui = arguments['--gui']
operation(op='start', name=name, options={'gui': gui})
exit()
elif arguments['down'] or arguments['stop']:
name = arguments['<name>']
operation(op='stop', name=name)
exit()
elif arguments['pause']:
name = arguments['<name>']
operation(op='pause', name=name)
exit()
elif arguments['suspend']:
name = arguments['<name>']
operation(op='suspend', name=name)
exit()
elif arguments['ssh']:
name = arguments['<name>']
user = arguments.get("--user")
if user:
options = {'user': user}
else:
options = {}
operation(op='ssh', name=name, options=options)
exit()
elif arguments['scp']:
name = arguments['<name>']
name = arguments.get("--user")
operation(op='scp', name=name, options={'user': user})
exit()
elif arguments['ip']:
name = arguments['<name>']
operation(op='ip', name=name, options={'user': user})
exit()
dest="code",
default="",
help=
"code to solve (exec) after model is compiled and run (unless --norun); out is a keyword for the mechanism that has been generated"
)
(options, args) = parser.parse_args()
if len(args) == 0:
parser.print_help()
exit()
outs = []
for arg in args:
out = Mech(arg,
verbose=options.verbose,
keywords=[k_.strip() for k_ in options.keywords.split(',')])
if options.monitor is not None:
out.monitor = tuple(
[(None if k not in out.allspcs else out.allspcs.index(k), k)
for k in options.monitor.split(',')]) + out.monitor
if not options.norun:
runtime = out.run(tstart=options.tstart,
tend=options.tend,
dt=options.dt,
solver=options.solver,
jac=options.jacobian,
atol=options.atol,
rtol=options.rtol)
print 'Solved in %f seconds' % runtime
out.output(options.outpath)
def main(args=None):
arguments = docopt(__doc__, version='mech 0.3')
DEBUG = arguments['--debug']
if not os.path.exists(HOME):
os.makedirs(HOME)
if arguments['init']:
puts(colored.green("Initializing mech"))
url = arguments['<url>']
name = arguments['--name']
Mech.setup(url, name)
exit()
elif arguments['list'] or arguments['ls']:
Mech.list()
exit()
elif arguments['status'] or arguments['ps']:
Mech.status()
exit()
elif arguments['up'] or arguments['start']:
name = arguments['<name>']
gui = arguments['--gui']
operation(op='start', name=name, options={'gui':gui})
exit()
elif arguments['down'] or arguments['stop']:
name = arguments['<name>']
operation(op='stop', name=name)
exit()
elif arguments['pause']:
name = arguments['<name>']
operation(op='pause', name=name)
exit()
elif arguments['suspend']:
name = arguments['<name>']
operation(op='suspend', name=name)
exit()
elif arguments['ssh']:
name = arguments['<name>']
user = arguments.get("--user")
if user:
options = {'user':user}
else:
options = {}
operation(op='ssh', name=name, options=options)
exit()
elif arguments['scp']:
name = arguments['<name>']
name = arguments.get("--user")
operation(op='scp', name=name, options={'user':user})
exit()
elif arguments['ip']:
name = arguments['<name>']
operation(op='ip', name=name, options={'user':user})
exit()
