Correct mpi4py URL.

[sawsim.git] / pysawsim / sawsim.py

diff --git a/pysawsim/sawsim.py b/pysawsim/sawsim.py
index ccac6f3308da100724ed7d97e0dd1eb7529f33ea..0f85869dd634111a0ce0f64d65a9700895f6d8f1 100644 (file)
--- a/pysawsim/sawsim.py
+++ b/pysawsim/sawsim.py
@@ -27,6 +27,7 @@ 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
@@ -43,7 +44,10 @@ _multiprocess_can_split_ = True
 """Allow nosetests to split tests between processes.
 """
 
-SAWSIM = 'sawsim'  # os.path.expand(os.path.join('~', 'bin', 'sawsim'))
+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 '
@@ -61,9 +65,8 @@ Event = namedtuple(
 
 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):
@@ -104,9 +107,9 @@ class SawsimRunner (object):
                default=400),
         Option('-m', '--manager', dest='manager',
                metavar='STRING',
-               help='Job manager name (one of %s) (%%default).'
+               help='Job manager name (one of %s) (default: auto-select).'
                % (', '.join(MANAGERS)),
-               default=MANAGERS[0]),
+               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'),
@@ -273,11 +276,11 @@ def main(argv=None):
     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