Adjust pysawsim.manager.pbs to skip most doctests if pbs mod is missing.

diff --git a/pysawsim/manager/pbs.py b/pysawsim/manager/pbs.py
index f0487c126fac6ed16588168c9c442de35048a198..f98a0aaf9897bf9eb6800636a7fbd75c3d03e214 100644 (file)
--- a/pysawsim/manager/pbs.py
+++ b/pysawsim/manager/pbs.py
@@ -40,8 +40,10 @@ import types
 
 try:
     import pbs
 
 try:
     import pbs

+    _SKIP = ''

 except ImportError, pbs_error:
     pbs = None
 except ImportError, pbs_error:
     pbs = None

+    _SKIP = '  # doctest: +SKIP'

 
 from .. import invoke
 from . import Job, JobManager
 
 from .. import invoke
 from . import Job, JobManager


@@ -51,28 +53,28 @@ SCRATCH_DIR = os.path.expanduser('~')
 
 
 class PBSManager (JobManager):
 
 
 class PBSManager (JobManager):

-    """Manage asynchronous `Job` execution via :mod:`pbs`.
+    __doc__ = """Manage asynchronous `Job` execution via :mod:`pbs`.

 
     >>> from math import sqrt
 
     >>> from math import sqrt

-    >>> m = PBSManager()
+    >>> m = PBSManager()%(skip)s

     >>> group_A = []
     >>> for i in range(10):
     >>> group_A = []
     >>> for i in range(10):

-    ...     group_A.append(m.async_invoke(Job(target=sqrt, args=[i])))
+    ...     group_A.append(m.async_invoke(Job(target=sqrt, args=[i])))%(skip)s

     >>> group_B = []
     >>> for i in range(10):
     ...     group_B.append(m.async_invoke(Job(target=sqrt, args=[i],
     >>> group_B = []
     >>> for i in range(10):
     ...     group_B.append(m.async_invoke(Job(target=sqrt, args=[i],

-    ...                 blocks_on=[j.id for j in group_A])))
-    >>> jobs = m.wait(ids=[j.id for j in group_A[5:8]])
-    >>> print sorted(jobs.values(), key=lambda j: j.id)
+    ...                 blocks_on=[j.id for j in group_A])))%(skip)s
+    >>> jobs = m.wait(ids=[j.id for j in group_A[5:8]])%(skip)s
+    >>> print sorted(jobs.values(), key=lambda j: j.id)%(skip)s

     [<Job 5>, <Job 6>, <Job 7>]
     [<Job 5>, <Job 6>, <Job 7>]

-    >>> jobs = m.wait()
-    >>> print sorted(jobs.values(), key=lambda j: j.id)
+    >>> jobs = m.wait()%(skip)s
+    >>> print sorted(jobs.values(), key=lambda j: j.id)%(skip)s

     ... # doctest: +NORMALIZE_WHITESPACE
     [<Job 0>, <Job 1>, <Job 2>, <Job 3>, <Job 4>, <Job 8>, <Job 9>, <Job 10>,
      <Job 11>, <Job 12>, <Job 13>, <Job 14>, <Job 15>, <Job 16>, <Job 17>,
      <Job 18>, <Job 19>]
     ... # doctest: +NORMALIZE_WHITESPACE
     [<Job 0>, <Job 1>, <Job 2>, <Job 3>, <Job 4>, <Job 8>, <Job 9>, <Job 10>,
      <Job 11>, <Job 12>, <Job 13>, <Job 14>, <Job 15>, <Job 16>, <Job 17>,
      <Job 18>, <Job 19>]

-    >>> m.teardown()
-    """
+    >>> m.teardown()%(skip)s
+    """ % {'skip': _SKIP}

     def __init__(self, workdir=None):
         super(PBSManager, self).__init__()
         self._cleanup = True
     def __init__(self, workdir=None):
         super(PBSManager, self).__init__()
         self._cleanup = True


@@ -146,15 +148,36 @@ class PBSManager (JobManager):
         self._post_submit = True
 
     def _write_script(self, job, stream):
         self._post_submit = True
 
     def _write_script(self, job, stream):

-        """
+        stream.write('#!/usr/bin/env python\n')
+        stream.write('#PBS -l walltime:%s\n' % self._walltime)
+        #stream.write('#PBS -l minwclimit:...')
+        if len(job.blocks_on) > 0:
+            blockers = [self._jobs.get(id, None) for id in job.blocks_on]
+            stream.write(
+                '#PBS -w afterok:%s\n'
+                % ':'.join([j._pbs_id for j in blockers if j != None]))
+        stream.write('from __future__ import with_statement\n')
+        stream.write('import os\n')
+        stream.write('import pickle\n')
+        stream.write('import sys\n')
+        stream.write('sys.path = [%s]\n' % ', '.join(
+                ["'%s'" % p for p in sys.path]))
+        stream.write("os.chdir(os.environ['PBS_O_WORKDIR'])\n")
+        stream.write("with open('%s', 'r') as f:\n" % job._pbs_paths['job'])
+        stream.write('    job = pickle.load(f)\n')
+        stream.write('job.run()\n')
+        stream.write("with open('%s', 'w') as f:\n" % job._pbs_paths['data'])
+        stream.write('    pickle.dump(job.data, f)\n')
+        stream.write('sys.exit(job.status)\n')
+    _write_script.__doc__ = """

         >>> from . import InvokeJob
         >>> from . import InvokeJob

-        >>> m = PBSManager()
-        >>> j = InvokeJob(id=7, target='echo "testing %s"' % m)
+        >>> m = PBSManager()%(skip)s
+        >>> j = InvokeJob(id=7, target='echo "testing %%s"' %% m)%(skip)s

         >>> j._pbs_paths = {
         >>> j._pbs_paths = {

-        ...     'job': os.path.join(m._workdir, '%d.job.pkl' % j.id),
-        ...     'data': os.path.join(m._workdir, '%d.pkl' % j.id),
-        ...     }
-        >>> m._write_script(j, sys.stdout)
+        ...     'job': os.path.join(m._workdir, '%%d.job.pkl' %% j.id),
+        ...     'data': os.path.join(m._workdir, '%%d.pkl' %% j.id),
+        ...     }%(skip)s
+        >>> m._write_script(j, sys.stdout)%(skip)s

         ... # doctest: +ELLIPSIS, +REPORT_UDIFF
         #!/usr/bin/env python
         #PBS -l walltime:3:00:00
         ... # doctest: +ELLIPSIS, +REPORT_UDIFF
         #!/usr/bin/env python
         #PBS -l walltime:3:00:00


@@ -171,16 +194,16 @@ class PBSManager (JobManager):
             pickle.dump(job.data, f)
         sys.exit(job.status)
 
             pickle.dump(job.data, f)
         sys.exit(job.status)
 

-        >>> for id in [3, 4]:
+        >>> for id in [3, 4]:%(skip)s

         ...     m._jobs[id] = Job(id=id)
         ...     m._jobs[id] = Job(id=id)

-        ...     m._jobs[id]._pbs_id = '%d.big.iron.com' % id
-        >>> j = InvokeJob(id=8, target='echo "testing %s"' % m,
-        ...               blocks_on=[1,2,3,4])
+        ...     m._jobs[id]._pbs_id = '%%d.big.iron.com' %% id
+        >>> j = InvokeJob(id=8, target='echo "testing %%s"' %% m,
+        ...               blocks_on=[1,2,3,4])%(skip)s

         >>> j._pbs_paths = {
         >>> j._pbs_paths = {

-        ...     'job': os.path.join(m._workdir, '%d.job.pkl' % j.id),
-        ...     'data': os.path.join(m._workdir, '%d.pkl' % j.id),
-        ...     }
-        >>> m._write_script(j, sys.stdout)
+        ...     'job': os.path.join(m._workdir, '%%d.job.pkl' %% j.id),
+        ...     'data': os.path.join(m._workdir, '%%d.pkl' %% j.id),
+        ...     }%(skip)s
+        >>> m._write_script(j, sys.stdout)%(skip)s

         ... # doctest: +ELLIPSIS, +REPORT_UDIFF
         #!/usr/bin/env python
         #PBS -l walltime:3:00:00
         ... # doctest: +ELLIPSIS, +REPORT_UDIFF
         #!/usr/bin/env python
         #PBS -l walltime:3:00:00


@@ -197,29 +220,8 @@ class PBSManager (JobManager):
         with open('/.../tmp-PBSManager-.../8.pkl', 'w') as f:
             pickle.dump(job.data, f)
         sys.exit(job.status)
         with open('/.../tmp-PBSManager-.../8.pkl', 'w') as f:
             pickle.dump(job.data, f)
         sys.exit(job.status)

-        >>> m.teardown()
-        """
-        stream.write('#!/usr/bin/env python\n')
-        stream.write('#PBS -l walltime:%s\n' % self._walltime)
-        #stream.write('#PBS -l minwclimit:...')
-        if len(job.blocks_on) > 0:
-            blockers = [self._jobs.get(id, None) for id in job.blocks_on]
-            stream.write(
-                '#PBS -w afterok:%s\n'
-                % ':'.join([j._pbs_id for j in blockers if j != None]))
-        stream.write('from __future__ import with_statement\n')
-        stream.write('import os\n')
-        stream.write('import pickle\n')
-        stream.write('import sys\n')
-        stream.write('sys.path = [%s]\n' % ', '.join(
-                ["'%s'" % p for p in sys.path]))
-        stream.write("os.chdir(os.environ['PBS_O_WORKDIR'])\n")
-        stream.write("with open('%s', 'r') as f:\n" % job._pbs_paths['job'])
-        stream.write('    job = pickle.load(f)\n')
-        stream.write('job.run()\n')
-        stream.write("with open('%s', 'w') as f:\n" % job._pbs_paths['data'])
-        stream.write('    pickle.dump(job.data, f)\n')
-        stream.write('sys.exit(job.status)\n')
+        >>> m.teardown()%(skip)s
+        """ % {'skip': _SKIP}

 
     def _environ(self):
         """Mimic the environment you would get with `qsub -V`.
 
     def _environ(self):
         """Mimic the environment you would get with `qsub -V`.