Fixing how the working directory is handled in kernel.

* Changed working_dir -> work_dir.
* Now, ipcluster does not try to set the work dir for the controller
  and engine. To set it, just use the engine/controller config or
  pass the command line arg to the engine_args/controller_args
  attribute of a launcher.

IPython/config/default/ipcluster_config.py

@@ -47,22 +47,19 b' c = get_config()'
 
 # The working directory for the process. The application will use os.chdir
 # to change to this directory before starting.
-# c.Global.working_dir = os.getcwd()
+# c.Global.work_dir = os.getcwd()
 
 
 #-----------------------------------------------------------------------------
 # Local process launchers
 #-----------------------------------------------------------------------------
 
-# The working directory for the controller
-# c.LocalControllerLauncher.working_dir = u''
-
 # The command line arguments to call the controller with.
 # c.LocalControllerLauncher.controller_args = \
 #    ['--log-to-file','--log-level', '40']
 
 # The working directory for the controller
-# c.LocalEngineSetLauncher.working_dir = u''
+# c.LocalEngineSetLauncher.work_dir = u''
 
 # Command line argument passed to the engines.
 # c.LocalEngineSetLauncher.engine_args = ['--log-to-file','--log-level', '40']
@@ -71,9 +68,6 b' c = get_config()'
 # MPIExec launchers
 #-----------------------------------------------------------------------------
 
-# The working directory for the controller
-# c.MPIExecControllerLauncher.working_dir = u''
-
 # The mpiexec/mpirun command to use in started the controller.
 # c.MPIExecControllerLauncher.mpi_cmd = ['mpiexec']
 
@@ -85,9 +79,6 b' c = get_config()'
 #     ['--log-to-file','--log-level', '40']
 
 
-# The working directory for the controller
-# c.MPIExecEngineSetLauncher.working_dir = u''
-
 # The mpiexec/mpirun command to use in started the controller.
 # c.MPIExecEngineSetLauncher.mpi_cmd = ['mpiexec']
 
@@ -111,9 +102,6 b' c = get_config()'
 # Unix batch (PBS) schedulers launchers
 #-----------------------------------------------------------------------------
 
-# The working directory for the controller
-# c.PBSControllerLauncher.working_dir = u''
-
 # The command line program to use to submit a PBS job.
 # c.PBSControllerLauncher.submit_command = 'qsub'
 
@@ -125,8 +113,8 b' c = get_config()'
 
 # The batch submission script used to start the controller. This is where
 # environment variables would be setup, etc. This string is interpolated using
-# the Itpl module in IPython.external. Basically, you can use ${profile} for 
-# the controller profile or ${cluster_dir} for the cluster_dir.
+# the Itpl module in IPython.external. Basically, you can use ${n} for the
+# number of engine and ${cluster_dir} for the cluster_dir.
 # c.PBSControllerLauncher.batch_template = """"""
 
 # The name of the instantiated batch script that will actually be used to
@@ -134,9 +122,6 b' c = get_config()'
 # c.PBSControllerLauncher.batch_file_name = u'pbs_batch_script_controller'
 
 
-# The working directory for the controller
-# c.PBSEngineSetLauncher.working_dir = u''
-
 # The command line program to use to submit a PBS job.
 # c.PBSEngineSetLauncher.submit_command = 'qsub'
 
@@ -149,8 +134,7 b' c = get_config()'
 # The batch submission script used to start the engines. This is where
 # environment variables would be setup, etc. This string is interpolated using
 # the Itpl module in IPython.external. Basically, you can use ${n} for the
-# number of engine, ${profile} or the engine profile and ${cluster_dir} 
-# for the cluster_dir.
+# number of engine and ${cluster_dir} for the cluster_dir.
 # c.PBSEngineSetLauncher.batch_template = """"""
 
 # The name of the instantiated batch script that will actually be used to
@@ -173,7 +157,6 b' c = get_config()'
 # c.IPControllerTask.controller_args = ['--log-to-file', '--log-level', '40']
 # c.IPControllerTask.environment_variables = {}
 
-# c.WindowsHPCControllerLauncher.working_dir = u''
 # c.WindowsHPCControllerLauncher.scheduler = 'HEADNODE'
 # c.WindowsHPCControllerLauncher.job_file_name = u'ipcontroller_job.xml'
 
@@ -190,7 +173,6 b' c = get_config()'
 # c.IPEngineTask.engine_args = ['--log-to-file', '--log-level', '40']
 # c.IPEngineTask.environment_variables = {}
 
-# c.WindowsHPCEngineSetLauncher.working_dir = u''
 # c.WindowsHPCEngineSetLauncher.scheduler = 'HEADNODE'
 # c.WindowsHPCEngineSetLauncher.job_file_name = u'ipengineset_job.xml'
 

IPython/config/default/ipcontroller_config.py

@@ -37,7 +37,7 b' c = get_config()'
 
 # The working directory for the process. The application will use os.chdir
 # to change to this directory before starting.
-# c.Global.working_dir = os.getcwd()
+# c.Global.work_dir = os.getcwd()
 
 #-----------------------------------------------------------------------------
 # Configure the client services

IPython/config/default/ipengine_config.py

@@ -36,7 +36,7 b' c = get_config()'
 
 # The working directory for the process. The application will use os.chdir
 # to change to this directory before starting.
-# c.Global.working_dir = os.getcwd()
+# c.Global.work_dir = os.getcwd()
 
 #-----------------------------------------------------------------------------
 # MPI configuration

IPython/kernel/clusterdir.py

@@ -257,11 +257,11 b' class AppWithClusterDirArgParseConfigLoader(ArgParseConfigLoader):'
             default=NoConfigDefault,
             metavar='Global.cluster_dir'
         ),
-        self.parser.add_argument('--working-dir',
-            dest='Global.working_dir',type=unicode,
+        self.parser.add_argument('--work-dir',
+            dest='Global.work_dir',type=unicode,
             help='Set the working dir for the process.',
             default=NoConfigDefault,
-            metavar='Global.working_dir'
+            metavar='Global.work_dir'
         )
         self.parser.add_argument('--clean-logs',
             dest='Global.clean_logs', action='store_true',
@@ -299,7 +299,7 b' class ApplicationWithClusterDir(Application):'
         super(ApplicationWithClusterDir, self).create_default_config()
         self.default_config.Global.profile = u'default'
         self.default_config.Global.cluster_dir = u''
-        self.default_config.Global.working_dir = os.getcwd()
+        self.default_config.Global.work_dir = os.getcwd()
         self.default_config.Global.log_to_file = False
         self.default_config.Global.clean_logs = False
 
@@ -405,13 +405,13 b' class ApplicationWithClusterDir(Application):'
         pdir = self.cluster_dir_obj.pid_dir
         self.pid_dir = config.Global.pid_dir = pdir
         self.log.info("Cluster directory set to: %s" % self.cluster_dir)
-        config.Global.working_dir = unicode(genutils.expand_path(config.Global.working_dir))
+        config.Global.work_dir = unicode(genutils.expand_path(config.Global.work_dir))
         # Change to the working directory. We do this just before construct
         # is called so all the components there have the right working dir.
-        self.to_working_dir()
+        self.to_work_dir()
 
-    def to_working_dir(self):
-        wd = self.master_config.Global.working_dir
+    def to_work_dir(self):
+        wd = self.master_config.Global.work_dir
         if unicode(wd) != unicode(os.getcwd()):
             os.chdir(wd)
             self.log.info("Changing to working dir: %s" % wd)

IPython/kernel/ipclusterapp.py

@@ -86,11 +86,11 b' class IPClusterCLLoader(ArgParseConfigLoader):'
             '--profile option.',
             default=NoConfigDefault,
             metavar='Global.cluster_dir'),
-        parent_parser2.add_argument('--working-dir',
-            dest='Global.working_dir',type=unicode,
+        parent_parser2.add_argument('--work-dir',
+            dest='Global.work_dir',type=unicode,
             help='Set the working dir for the process.',
             default=NoConfigDefault,
-            metavar='Global.working_dir')
+            metavar='Global.work_dir')
         parent_parser2.add_argument('--log-to-file',
             action='store_true', dest='Global.log_to_file', 
             default=NoConfigDefault,
@@ -247,7 +247,7 b' class IPClusterApp(ApplicationWithClusterDir):'
                     print start_cmd + " ==> " + full_path
 
     def pre_construct(self):
-        # This is where we cd to the working directory.
+        # IPClusterApp.pre_construct() is where we cd to the working directory.
         super(IPClusterApp, self).pre_construct()
         config = self.master_config
         try:
@@ -272,14 +272,17 b' class IPClusterApp(ApplicationWithClusterDir):'
     def start_launchers(self):
         config = self.master_config
 
-        # Create the launchers
+        # Create the launchers. In both bases, we set the work_dir of
+        # the launcher to the cluster_dir. This is where the launcher's
+        # subprocesses will be launched. It is not where the controller
+        # and engine will be launched.
         el_class = import_item(config.Global.engine_launcher)
         self.engine_launcher = el_class(
-            self.cluster_dir, config=config
+            work_dir=self.cluster_dir, config=config
         )
         cl_class = import_item(config.Global.controller_launcher)
         self.controller_launcher = cl_class(
-            self.cluster_dir, config=config
+            work_dir=self.cluster_dir, config=config
         )
 
         # Setup signals

IPython/kernel/launcher.py

@@ -99,11 +99,18 b' class UnknownStatus(LauncherError):'
 class BaseLauncher(Component):
     """An asbtraction for starting, stopping and signaling a process."""
 
-    working_dir = Unicode(u'')
-
-    def __init__(self, working_dir, parent=None, name=None, config=None):
+    # In all of the launchers, the work_dir is where child processes will be
+    # run. This will usually be the cluster_dir, but may not be. any work_dir
+    # passed into the __init__ method will override the config value.
+    # This should not be used to set the work_dir for the actual engine
+    # and controller. Instead, use their own config files or the
+    # controller_args, engine_args attributes of the launchers to add
+    # the --work-dir option.
+    work_dir = Unicode(u'')
+
+    def __init__(self, work_dir, parent=None, name=None, config=None):
         super(BaseLauncher, self).__init__(parent, name, config)
-        self.working_dir = working_dir
+        self.work_dir = work_dir
         self.state = 'before' # can be before, running, after
         self.stop_deferreds = []
         self.start_data = None
@@ -270,16 +277,16 b' class LocalProcessLauncher(BaseLauncher):'
     """Start and stop an external process in an asynchronous manner.
 
     This will launch the external process with a working directory of
-    ``self.working_dir``.
+    ``self.work_dir``.
     """
 
     # This is used to to construct self.args, which is passed to 
     # spawnProcess.
     cmd_and_args = List([])
 
-    def __init__(self, working_dir, parent=None, name=None, config=None):
+    def __init__(self, work_dir, parent=None, name=None, config=None):
         super(LocalProcessLauncher, self).__init__(
-            working_dir, parent, name, config
+            work_dir, parent, name, config
         )
         self.process_protocol = None
         self.start_deferred = None
@@ -296,7 +303,7 b' class LocalProcessLauncher(BaseLauncher):'
                 str(self.args[0]),  # twisted expects these to be str, not unicode
                 [str(a) for a in self.args],  # str expected, not unicode
                 env=os.environ,
-                path=self.working_dir  # start in the working_dir
+                path=self.work_dir  # start in the work_dir
             )
             return self.start_deferred
         else:
@@ -331,8 +338,7 b' class LocalControllerLauncher(LocalProcessLauncher):'
     controller_args = List(['--log-to-file','--log-level', '40'], config=True)
 
     def find_args(self):
-        return self.controller_cmd + self.controller_args + \
-            ['--working-dir', self.working_dir]
+        return self.controller_cmd + self.controller_args
 
     def start(self, cluster_dir):
         """Start the controller by cluster_dir."""
@@ -352,8 +358,7 b' class LocalEngineLauncher(LocalProcessLauncher):'
     )
 
     def find_args(self):
-        return self.engine_cmd + self.engine_args + \
-            ['--working-dir', self.working_dir]
+        return self.engine_cmd + self.engine_args
 
     def start(self, cluster_dir):
         """Start the engine by cluster_dir."""
@@ -370,9 +375,9 b' class LocalEngineSetLauncher(BaseLauncher):'
         ['--log-to-file','--log-level', '40'], config=True
     )
 
-    def __init__(self, working_dir, parent=None, name=None, config=None):
+    def __init__(self, work_dir, parent=None, name=None, config=None):
         super(LocalEngineSetLauncher, self).__init__(
-            working_dir, parent, name, config
+            work_dir, parent, name, config
         )
         self.launchers = []
 
@@ -381,7 +386,7 b' class LocalEngineSetLauncher(BaseLauncher):'
         self.cluster_dir = unicode(cluster_dir)
         dlist = []
         for i in range(n):
-            el = LocalEngineLauncher(self.working_dir, self)
+            el = LocalEngineLauncher(self.work_dir, self)
             # Copy the engine args over to each engine launcher.
             import copy
             el.engine_args = copy.deepcopy(self.engine_args)
@@ -471,8 +476,7 b' class MPIExecControllerLauncher(MPIExecLauncher):'
 
     def find_args(self):
         return self.mpi_cmd + ['-n', self.n] + self.mpi_args + \
-               self.controller_cmd + self.controller_args + \
-               ['--working-dir', self.working_dir]
+               self.controller_cmd + self.controller_args
 
 
 class MPIExecEngineSetLauncher(MPIExecLauncher):
@@ -481,20 +485,20 b' class MPIExecEngineSetLauncher(MPIExecLauncher):'
     # Command line arguments for ipengine.
     engine_args = List(
         ['--log-to-file','--log-level', '40'], config=True
-    )    
+    )
     n = Int(1, config=True)
 
     def start(self, n, cluster_dir):
         """Start n engines by profile or cluster_dir."""
         self.engine_args.extend(['--cluster-dir', cluster_dir])
         self.cluster_dir = unicode(cluster_dir)
+        self.n = n
         log.msg('Starting MPIExecEngineSetLauncher: %r' % self.args)
         return super(MPIExecEngineSetLauncher, self).start(n)
 
     def find_args(self):
         return self.mpi_cmd + ['-n', self.n] + self.mpi_args + \
-               self.engine_cmd + self.engine_args + \
-               ['--working-dir', self.working_dir]
+               self.engine_cmd + self.engine_args
 
 
 #-----------------------------------------------------------------------------
@@ -565,20 +569,20 b' class WindowsHPCLauncher(BaseLauncher):'
     # The filename of the instantiated job script.
     job_file_name = Unicode(u'ipython_job.xml', config=True)
     # The full path to the instantiated job script. This gets made dynamically
-    # by combining the working_dir with the job_file_name.
+    # by combining the work_dir with the job_file_name.
     job_file = Unicode(u'')
     # The hostname of the scheduler to submit the job to
     scheduler = Str('', config=True)
     job_cmd = Str(find_job_cmd(), config=True)
 
-    def __init__(self, working_dir, parent=None, name=None, config=None):
+    def __init__(self, work_dir, parent=None, name=None, config=None):
         super(WindowsHPCLauncher, self).__init__(
-            working_dir, parent, name, config
+            work_dir, parent, name, config
         )
 
     @property
     def job_file(self):
-        return os.path.join(self.working_dir, self.job_file_name)
+        return os.path.join(self.work_dir, self.job_file_name)
 
     def write_job_file(self, n):
         raise NotImplementedError("Implement write_job_file in a subclass.")
@@ -611,7 +615,7 b' class WindowsHPCLauncher(BaseLauncher):'
         output = yield getProcessOutput(str(self.job_cmd),
             [str(a) for a in args],
             env=dict((str(k),str(v)) for k,v in os.environ.items()),
-            path=self.working_dir
+            path=self.work_dir
         )
         job_id = self.parse_job_id(output)
         self.notify_start(job_id)
@@ -630,7 +634,7 b' class WindowsHPCLauncher(BaseLauncher):'
             output = yield getProcessOutput(str(self.job_cmd),
                 [str(a) for a in args],
                 env=dict((str(k),str(v)) for k,v in os.environ.items()),
-                path=self.working_dir
+                path=self.work_dir
             )
         except:
             output = 'The job already appears to be stoppped: %r' % self.job_id
@@ -651,7 +655,7 b' class WindowsHPCControllerLauncher(WindowsHPCLauncher):'
         # the controller. It is used as the base path for the stdout/stderr
         # files that the scheduler redirects to.
         t.work_directory = self.cluster_dir
-        # Add the --cluster-dir and --working-dir from self.start().
+        # Add the --cluster-dir and from self.start().
         t.controller_args.extend(self.extra_args)
         job.add_task(t)
 
@@ -664,9 +668,7 b' class WindowsHPCControllerLauncher(WindowsHPCLauncher):'
 
     def start(self, cluster_dir):
         """Start the controller by cluster_dir."""
-        self.extra_args = [
-            '--cluster-dir', cluster_dir, '--working-dir', self.working_dir
-        ]
+        self.extra_args = ['--cluster-dir', cluster_dir]
         self.cluster_dir = unicode(cluster_dir)
         return super(WindowsHPCControllerLauncher, self).start(1)
 
@@ -685,7 +687,7 b' class WindowsHPCEngineSetLauncher(WindowsHPCLauncher):'
             # the engine. It is used as the base path for the stdout/stderr
             # files that the scheduler redirects to.
             t.work_directory = self.cluster_dir
-            # Add the --cluster-dir and --working-dir from self.start().
+            # Add the --cluster-dir and from self.start().
             t.engine_args.extend(self.extra_args)
             job.add_task(t)
 
@@ -698,9 +700,7 b' class WindowsHPCEngineSetLauncher(WindowsHPCLauncher):'
 
     def start(self, n, cluster_dir):
         """Start the controller by cluster_dir."""
-        self.extra_args = [
-            '--cluster-dir', cluster_dir, '--working-dir', self.working_dir
-        ]
+        self.extra_args = ['--cluster-dir', cluster_dir]
         self.cluster_dir = unicode(cluster_dir)
         return super(WindowsHPCEngineSetLauncher, self).start(n)
 
@@ -739,11 +739,11 b' class BatchSystemLauncher(BaseLauncher):'
     # The full path to the instantiated batch script.
     batch_file = Unicode(u'')
 
-    def __init__(self, working_dir, parent=None, name=None, config=None):
+    def __init__(self, work_dir, parent=None, name=None, config=None):
         super(BatchSystemLauncher, self).__init__(
-            working_dir, parent, name, config
+            work_dir, parent, name, config
         )
-        self.batch_file = os.path.join(self.working_dir, self.batch_file_name)
+        self.batch_file = os.path.join(self.work_dir, self.batch_file_name)
         self.context = {}
 
     def parse_job_id(self, output):
@@ -758,7 +758,7 b' class BatchSystemLauncher(BaseLauncher):'
         return job_id
 
     def write_batch_script(self, n):
-        """Instantiate and write the batch script to the working_dir."""
+        """Instantiate and write the batch script to the work_dir."""
         self.context['n'] = n
         script_as_string = Itpl.itplns(self.batch_template, self.context)
         log.msg('Writing instantiated batch script: %s' % self.batch_file)

IPython/quarantine/InterpreterExec.py

@@ -14,7 +14,7 b' executed.'
 #  the file COPYING, distributed as part of this software.
 #*****************************************************************************
 
-# TODO: deprecated
+
 def prefilter_shell(self,line,continuation):
     """Alternate prefilter, modified for shell-like functionality.