"""`Seminar` for running `sawsim` and parsing the results.
"""
+from __future__ import with_statement
+
try:
from collections import namedtuple
except ImportError: # work around Python < 2.6
from ._collections import namedtuple
+from distutils.spawn import find_executable
import hashlib
from optparse import Option
import os
import os.path
+from random import shuffle
import shutil
from uuid import uuid4
+from . import __version__
from .manager import MANAGERS, get_manager, InvokeJob
-SAWSIM = 'sawsim' # os.path.expand(os.path.join('~', 'bin', 'sawsim'))
-CACHE_DIR = os.path.expanduser(os.path.join('~', '.sawsim_cache'))
+_multiprocess_can_split_ = True
+"""Allow nosetests to split tests between processes.
+"""
+
+SAWSIM = find_executable('sawsim')
+if SAWSIM == None:
+ SAWSIM = os.path.join('bin', 'sawsim')
+
+CACHE_DIR = os.path.expanduser(os.path.join('~', '.sawsim-cache'))
DEFAULT_PARAM_STRING = (
'-s cantilever,hooke,0.05 -N1 '
'-s folded,null -N8 '
class SawsimRunner (object):
"""
- >>> from .manager.thread import ThreadManager
- >>> m = ThreadManager()
- >>> sr = SawsimRunner(sawsim='bin/sawsim', manager=m)
+ >>> m = get_manager()()
+ >>> sr = SawsimRunner(manager=m)
>>> for run in sr(param_string=DEFAULT_PARAM_STRING, N=2):
... print 'New run'
... for i,event in enumerate(run):
"""
optparse_options = [
- Option("-s","--sawsim", dest="sawsim",
- metavar="PATH",
- help="Set sawsim binary (%default).",
+ Option('-s','--sawsim', dest='sawsim',
+ metavar='PATH',
+ help='Set sawsim binary (%default).',
default=SAWSIM),
- Option("-p","--params", dest="param_string",
- metavar="PARAMS",
- help="Initial params for fitting (%default).",
+ Option('-p','--params', dest='param_string',
+ metavar='PARAMS',
+ help='Initial params for fitting (%default).',
default=DEFAULT_PARAM_STRING),
- Option("-N", "--number-of-runs", dest="N",
- metavar="INT", type='int',
- help="Number of sawsim runs at each point in parameter space (%default).",
+ Option('-N', '--number-of-runs', dest='N',
+ metavar='INT', type='int',
+ help='Number of sawsim runs at each point in parameter space (%default).',
default=400),
- Option("-m", "--manager", dest="manager",
- metavar="STRING",
- help="Job manager name (one of %s) (%%default)."
+ Option('-m', '--manager', dest='manager',
+ metavar='STRING',
+ help='Job manager name (one of %s) (default: auto-select).'
% (', '.join(MANAGERS)),
- default=MANAGERS[0]),
- Option("-C","--use-cache", dest="use_cache",
- help="Use cached simulations if they exist (vs. running new simulations) (%default)",
- default=False, action="store_true"),
- Option("--clean-cache", dest="clean_cache",
- help="Remove previously cached simulations if they exist (%default)",
- default=False, action="store_true"),
- Option("-d","--cache-dir", dest="cache_dir",
- metavar="STRING",
- help="Cache directory for sawsim unfolding forces (%default).",
+ default=None),
+ Option('-C','--use-cache', dest='use_cache',
+ help='Use cached simulations if they exist (vs. running new simulations) (%default)',
+ default=False, action='store_true'),
+ Option('--clean-cache', dest='clean_cache',
+ help='Remove previously cached simulations if they exist (%default)',
+ default=False, action='store_true'),
+ Option('-d','--cache-dir', dest='cache_dir',
+ metavar='STRING',
+ help='Cache directory for sawsim unfolding forces (%default).',
default=CACHE_DIR),
]
[job.id for job in jobs.itervalues()])
for i,job in jobs.iteritems():
j = complete_jobs[job.id]
- assert j.status == 0, j.data
+ assert j.status == 0, j.data['error']
if self._use_cache == True:
self._cache_run(d, j.data['stdout'])
yield self.parse(j.data['stdout'])
"""
>>> s = SawsimRunner()
>>> s._param_cache_dir(DEFAULT_PARAM_STRING) # doctest: +ELLIPSIS
- '/.../.sawsim_cache/...'
+ '/.../.sawsim-cache/...'
"""
return os.path.join(
self._cache_dir, hashlib.sha256(param_string).hexdigest())
def _load_cached_data(self, param_string):
pcd = self._param_cache_dir(param_string)
- for filename in os.listdir(pcd):
+ filenames = os.listdir(pcd)
+ shuffle(filenames)
+ for filename in filenames:
if not filename.endswith('.dat'):
continue
with open(os.path.join(pcd, filename), 'r') as f:
Options:
-h, --help show this help message and exit
-s PATH, --sawsim=PATH
- Set sawsim binary (sawsim).
+ Set sawsim binary (...sawsim).
...
>>> print e
0
- >>> main(['--sawsim', 'bin/sawsim', '-N', '2'])
+ >>> main(['-N', '2'])
... # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
#Force (N) Initial state Final state
... folded unfolded
sr = SawsimRunner()
- usage = "%prog [options]"
- parser = OptionParser(usage)
+ usage = '%prog [options]'
+ epilog = '\n'.join([
+ 'Python wrapper around `sawsim`. Distribute `N` runs using',
+ 'one of the possible job "managers". Also supports caching',
+ 'results to speed future runs.'
+ ])
+ parser = OptionParser(usage, epilog=epilog)
for option in sr.optparse_options:
parser.add_option(option)
projects / sawsim.git / blobdiff