diff --git a/Makefile b/Makefile
index c2c637fe0b52a17434b6363ea44acbe9973e0f44..6c29ab0d52e6b7f1b8b4a1d05b3c1e394360968f 100644
--- a/Makefile
+++ b/Makefile
@@ -40,9 +40,11 @@ coverage: tests
docs:
rm -f docs/pulsar.rst
+ rm -f docs/galaxy.rst
rm -f docs/modules.rst
- sphinx-apidoc -o docs/ pulsar
- sphinx-apidoc -o docs/ galaxy
+ sphinx-apidoc -f -o docs/ pulsar
+ sphinx-apidoc -f -o docs/ galaxy
+ cp docs/fixed_modules.rst docs/modules.rst
$(MAKE) -C docs clean
$(MAKE) -C docs html
diff --git a/README.rst b/README.rst
index 613053b8d7f7bd3c3b0f51201334ec043c8f351b..6d6bba54106b5b4341080a99b00d8869e42c171e 100644
--- a/README.rst
+++ b/README.rst
@@ -16,7 +16,7 @@ Full documentation for the project can be found on `Read The Docs
Configuring Galaxy
------------------
-Galaxy job runners are configured in Galaxy's ``job_conf.xml`` file. Some small examples of how to configure this can be found `here <https://pulsar.readthedocs.org/en/latest/#galaxy-configuration>`_, but be sure to checkout ``job_conf.xml.sample_advanced``
+Galaxy job runners are configured in Galaxy's ``job_conf.xml`` file. Some small examples of how to configure this can be found `here <https://pulsar.readthedocs.org/en/latest/#galaxy-configuration>`__, but be sure to checkout ``job_conf.xml.sample_advanced``
in your Galaxy code base or on
`Bitbucket <https://bitbucket.org/galaxy/galaxy-dist/src/tip/job_conf.xml.sample_advanced?at=default>`_
for complete information.
@@ -76,7 +76,7 @@ easy_install
------------
Install python setuptools for your platform, more details on how to do
-this can be found `here <http://pypi.python.org/pypi/setuptools>`_.
+this can be found `here <http://pypi.python.org/pypi/setuptools>`__.
The ``easy_install`` command line application will be installed as
part of setuptools. Use the following command to install the needed
@@ -123,8 +123,7 @@ Alternative Cross Platform Instructions (Windows and \*nix)
The ``paster`` command line application will be installed as part of the
previous dependency installation process. This application can be used to
-start and stop a paste web server running the Pulsar. This can be done by
-executing the following command::
+start and stop a paste web server running the Pulsar.
The server may be ran as a daemon via the command::
@@ -225,7 +224,7 @@ documentation
even more information.
Customizing the Pulsar Environment
--------------------------------
+-----------------------------------
In more sophisticated deployments, the Pulsar's environment will need to be
tweaked - for instance to define a ``DRMAA_LIBRARY_PATH`` environment variable
diff --git a/docs/fixed_modules.rst b/docs/fixed_modules.rst
new file mode 100644
index 0000000000000000000000000000000000000000..3207736d33c2c08995de1ddeaf2497b2295c8dd5
--- /dev/null
+++ b/docs/fixed_modules.rst
@@ -0,0 +1,15 @@
+galaxy
+======
+
+.. toctree::
+ :maxdepth: 4
+
+ galaxy
+
+pulsar
+======
+
+.. toctree::
+ :maxdepth: 4
+
+ pulsar
diff --git a/docs/galaxy.tools.deps.resolvers.rst b/docs/galaxy.tools.deps.resolvers.rst
index f31ad4d9ad9fabfdf55835654f4110ad92426c21..0061887e4045bd00fda71ce884ad1a5562ad7ffd 100644
--- a/docs/galaxy.tools.deps.resolvers.rst
+++ b/docs/galaxy.tools.deps.resolvers.rst
@@ -4,6 +4,14 @@ galaxy.tools.deps.resolvers package
Submodules
----------
+galaxy.tools.deps.resolvers.brewed_tool_shed_packages module
+------------------------------------------------------------
+
+.. automodule:: galaxy.tools.deps.resolvers.brewed_tool_shed_packages
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
galaxy.tools.deps.resolvers.galaxy_packages module
--------------------------------------------------
@@ -28,6 +36,14 @@ galaxy.tools.deps.resolvers.modules module
:undoc-members:
:show-inheritance:
+galaxy.tools.deps.resolvers.resolver_mixins module
+--------------------------------------------------
+
+.. automodule:: galaxy.tools.deps.resolvers.resolver_mixins
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
galaxy.tools.deps.resolvers.tool_shed_packages module
-----------------------------------------------------
diff --git a/docs/modules.rst b/docs/modules.rst
index 8e92bfb370a0768f2bc70748794ce89113a20d8e..3207736d33c2c08995de1ddeaf2497b2295c8dd5 100644
--- a/docs/modules.rst
+++ b/docs/modules.rst
@@ -1,3 +1,11 @@
+galaxy
+======
+
+.. toctree::
+ :maxdepth: 4
+
+ galaxy
+
pulsar
======
diff --git a/docs/public_server.rst b/docs/public_server.rst
index 63f0cbc71d3e9fd6e7edb95caccdeeee403663ee..85f91938dc95e687aa2a7d88eeca801756490086 100644
--- a/docs/public_server.rst
+++ b/docs/public_server.rst
@@ -16,7 +16,7 @@ disadvantages (lack of reproducibility if the Pulsar server goes away,
potential lack of transparency).
Securing a Public Pulsar
----------------------
+-----------------------------
The following options should be set in ``server.ini`` to configure a
public `Pulsar` server.
diff --git a/galaxy/jobs/metrics/collectl/cli.py b/galaxy/jobs/metrics/collectl/cli.py
index dc2c7e07d8b958ae95d8baa92a18b3cffc98f413..e30b316898046fbe4a05bfe3da1eca21aa8fd4bc 100644
--- a/galaxy/jobs/metrics/collectl/cli.py
+++ b/galaxy/jobs/metrics/collectl/cli.py
@@ -12,7 +12,8 @@ MODE_PLAYBACK = "playback"
class CollectlCli( object ):
- """ Abstraction over (some of) the command-line arguments of collectl.
+ """
+ Abstraction over (some of) the command-line arguments of collectl.
Ideally this will be useful for building up command line arguments for
remote execution as well as runnning directly on local host.
@@ -20,33 +21,43 @@ class CollectlCli( object ):
collectl CLI - logic more directly related to the Galaxy job metric plugin
plugin should be placed in other modules.
- Keyword Arguments:
- collectl_path: Path to collectl executable (defaults to collectl - i.e.
- search the PATH).
-
- playback_path (defaults to None): If this is None collectl will run in
- record mode, else it will playback specified file.
-
- Playback Mode Options:
-
- sep : Separator used in playback mode (set to 9 to produce tsv)
- (defaults to None).
-
- Record Mode Options (some of these may work in playback mode also):
-
- destination_path: Location of path files to write to (defaults to None
- and collectl will just use cwd). Really this is just to prefix -
- collectl will append hostname and datetime to file.
- interval: Setup polling interval (secs) for most subsystems (defaults
- to None and when unspecified collectl will use default of 1 second).
- interval2: Setup polling interval (secs) for process information
- (defaults to None and when unspecified collectl will use default to
- 60 seconds).
- interval3: Setup polling interval (secs) for environment information
- (defaults to None and when unspecified collectl will use default to
- 300 seconds).
- procfilt: Optional argument to procfilt. (defaults to None).
- flush : Optional flush interval (defaults to None).
+ **Keyword Arguments:**
+
+ ``collectl_path``
+ Path to collectl executable (defaults to collectl - i.e.
+ search the PATH).
+
+ ``playback_path`` (defaults to ``None``)
+ If this is ``None``, collectl will run in
+ record mode, else it will playback specified file.
+
+ **Playback Mode Options:**
+
+ ``sep``
+ Separator used in playback mode (set to 9 to produce tsv)
+ (defaults to None).
+
+ **Record Mode Options** (some of these may work in playback mode also)
+
+ ``destination_path``
+ Location of path files to write to (defaults to None
+ and collectl will just use cwd). Really this is just to prefix -
+ collectl will append hostname and datetime to file.
+ ``interval``
+ Setup polling interval (secs) for most subsystems (defaults
+ to None and when unspecified collectl will use default of 1 second).
+ ``interval2``
+ Setup polling interval (secs) for process information
+ (defaults to None and when unspecified collectl will use default to
+ 60 seconds).
+ ``interval3``
+ Setup polling interval (secs) for environment information
+ (defaults to None and when unspecified collectl will use default to
+ 300 seconds).
+ ``procfilt``
+ Optional argument to procfilt. (defaults to None).
+ ``flush``
+ Optional flush interval (defaults to None).
"""
def __init__( self, **kwargs ):
@@ -125,4 +136,4 @@ class CollectlCli( object ):
if return_code:
raise Exception( "Problem running collectl command." )
-__all__ = [ CollectlCli ]
+__all__ = [ 'CollectlCli' ]
diff --git a/galaxy/jobs/metrics/collectl/processes.py b/galaxy/jobs/metrics/collectl/processes.py
index 2660c144d9dc4a8b9fd636668045711b576c7187..3e7da0e20f0e29c11f34cf345b3d1d898744db50 100644
--- a/galaxy/jobs/metrics/collectl/processes.py
+++ b/galaxy/jobs/metrics/collectl/processes.py
@@ -26,7 +26,7 @@ log = logging.getLogger( __name__ )
#
# Process data dumped one row per process per interval.
-#http://collectl.sourceforge.net/Data-detail.html
+# http://collectl.sourceforge.net/Data-detail.html
PROCESS_COLUMNS = [
"#Date", # Date of interval - e.g. 20140322
"Time", # Time of interval - 12:18:58
@@ -36,7 +36,7 @@ PROCESS_COLUMNS = [
"PPID", # Parent PID of process.
"THRD", # Thread???
"S", # Process state - S - Sleeping, D - Uninterruptable Sleep, R - Running, Z - Zombie or T - Stopped/Traced
- ## Memory options - http://ewx.livejournal.com/579283.html
+ # Memory options - http://ewx.livejournal.com/579283.html
"VmSize",
"VmLck",
"VmRSS",
@@ -93,7 +93,7 @@ def parse_process_statistics( statistics ):
statistics = DEFAULT_STATISTICS
statistics = util.listify( statistics )
- statistics = map( __tuplize_statistic, statistics )
+ statistics = map( _tuplize_statistic, statistics )
# Check for validity...
for statistic in statistics:
if statistic[ 0 ] not in STATISTIC_TYPES:
@@ -109,10 +109,10 @@ def generate_process_statistics( collectl_playback_cli, pid, statistics=DEFAULT_
with tempfile.NamedTemporaryFile( ) as tmp_tsv:
collectl_playback_cli.run( stdout=tmp_tsv )
with open( tmp_tsv.name, "r" ) as tsv_file:
- return __read_process_statistics( tsv_file, pid, statistics )
+ return _read_process_statistics( tsv_file, pid, statistics )
-def __read_process_statistics( tsv_file, pid, statistics ):
+def _read_process_statistics( tsv_file, pid, statistics ):
process_summarizer = CollectlProcessSummarizer( pid, statistics )
current_interval = None
@@ -167,7 +167,7 @@ class CollectlProcessSummarizer( object ):
to_num = float
else:
to_num = long
-
+
interval_stat = sum( to_num( r[ column_index ] ) for r in rows )
self.tree_statistics[ column_name ].track( interval_stat )
@@ -228,7 +228,7 @@ class CollectlProcessInterval( object ):
ability to filter out just rows corresponding to the process tree
corresponding to a given pid.
"""
-
+
def __init__( self ):
self.rows = []
@@ -242,11 +242,11 @@ class CollectlProcessInterval( object ):
self.rows.append( row )
-def __tuplize_statistic( statistic ):
+def _tuplize_statistic( statistic ):
if not isinstance( statistic, tuple ):
statistic_split = statistic.split( "_", 1 )
statistic = ( statistic_split[ 0 ].lower(), statistic_split[ 1 ] )
return statistic
-__all__ = [ generate_process_statistics ]
+__all__ = [ 'generate_process_statistics' ]
diff --git a/galaxy/jobs/metrics/collectl/subsystems.py b/galaxy/jobs/metrics/collectl/subsystems.py
index 2ccbfd4cf3f518b6e59523d6c712eafa5850325c..28e2bece559e557da0c5f03b89bd859e12f6cc27 100644
--- a/galaxy/jobs/metrics/collectl/subsystems.py
+++ b/galaxy/jobs/metrics/collectl/subsystems.py
@@ -69,4 +69,4 @@ def get_subsystem( name ):
"""
return SUBSYSTEM_DICT[ name ]
-__all__ = [ get_subsystem ]
+__all__ = [ 'get_subsystem' ]
diff --git a/galaxy/jobs/metrics/instrumenters/collectl.py b/galaxy/jobs/metrics/instrumenters/collectl.py
index 15109f77170cde43456aa93a02499d14986dadde..e91a9273bec15905f41ba6a54a05d3a7c96c388d 100644
--- a/galaxy/jobs/metrics/instrumenters/collectl.py
+++ b/galaxy/jobs/metrics/instrumenters/collectl.py
@@ -211,4 +211,4 @@ def procfilt_argument( procfilt_on ):
return ""
-__all__ = [ CollectlPlugin ]
+__all__ = [ 'CollectlPlugin' ]
diff --git a/pulsar/__init__.py b/pulsar/__init__.py
index c1d47377493b2190c3ea38bf758e24bda6c63c91..c0f6f2877d524ff03ef110625f11b25f97b940c6 100644
--- a/pulsar/__init__.py
+++ b/pulsar/__init__.py
@@ -1,99 +1,2 @@
"""
-
-:mod:`pulsar.managers` Module
---------------------------
-
-.. automodule:: pulsar.managers
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.core` Module
----------------------
-
-.. automodule:: pulsar.core
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.daemon` Module
----------------------
-
-.. automodule:: pulsar.daemon
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.scripts` Module
----------------------
-
-.. automodule:: pulsar.scripts
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.web` Module
----------------------------
-
-.. automodule:: pulsar.web
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.messaging` Module
----------------------------
-
-.. automodule:: pulsar.messaging
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.mesos` Module
----------------------------
-
-.. automodule:: pulsar.mesos
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.app` Module
----------------------
-
-.. automodule:: pulsar.app
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.manager_endpoint_util` Module
----------------------------------
-
-.. automodule:: pulsar.manager_endpoint_util
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.manager_factory` Module
----------------------------------
-
-.. automodule:: pulsar.manager_factory
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.locks` Module
------------------------
-
-.. automodule:: pulsar.locks
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.tools` Module
------------------------
-
-.. automodule:: pulsar.tools
- :members:
- :undoc-members:
- :show-inheritance:
-
"""
diff --git a/pulsar/cache/__init__.py b/pulsar/cache/__init__.py
index a95325b64917b7df7e476268360d53e5a5de9525..7a97262b38b32fd89252660931e9f38ad4c702d9 100644
--- a/pulsar/cache/__init__.py
+++ b/pulsar/cache/__init__.py
@@ -62,4 +62,4 @@ class Cache(PersistenceStore):
return sha256(for_hash.encode('UTF-8')).hexdigest()
-__all__ = [Cache]
+__all__ = ['Cache']
diff --git a/pulsar/client/__init__.py b/pulsar/client/__init__.py
index 4f84a01bde8adeb67267cbf2e58be7accedd885b..5ada39334bc8f35a051a9ad624dd702f9bf7683d 100644
--- a/pulsar/client/__init__.py
+++ b/pulsar/client/__init__.py
@@ -1,6 +1,6 @@
"""
pulsar client
-======
+=================
This module contains logic for interfacing with an external Pulsar server.
@@ -50,13 +50,13 @@ from .destination import url_to_destination_params
from .path_mapper import PathMapper
__all__ = [
- build_client_manager,
- OutputNotFoundException,
- url_to_destination_params,
- finish_job,
- submit_job,
- ClientJobDescription,
- PulsarOutputs,
- ClientOutputs,
- PathMapper,
+ 'build_client_manager',
+ 'OutputNotFoundException',
+ 'url_to_destination_params',
+ 'finish_job',
+ 'submit_job',
+ 'ClientJobDescription',
+ 'PulsarOutputs',
+ 'ClientOutputs',
+ 'PathMapper',
]
diff --git a/pulsar/client/action_mapper.py b/pulsar/client/action_mapper.py
index 03db77b9309e2196bb9089329dbdab5f31baacd4..be2adea487f1648126a5db4a6100db8df1371123 100644
--- a/pulsar/client/action_mapper.py
+++ b/pulsar/client/action_mapper.py
@@ -617,10 +617,10 @@ MAPPER_CLASS_DICT = dict(map(lambda c: (c.match_type, c), MAPPER_CLASSES))
def mappers_from_dicts(mapper_def_list):
- return map(lambda m: __mappper_from_dict(m), mapper_def_list)
+ return map(lambda m: _mappper_from_dict(m), mapper_def_list)
-def __mappper_from_dict(mapper_dict):
+def _mappper_from_dict(mapper_dict):
map_type = mapper_dict.get('match_type', DEFAULT_PATH_MAPPER_TYPE)
return MAPPER_CLASS_DICT[map_type](mapper_dict)
@@ -661,9 +661,9 @@ actions = dict([(clazz.action_type, clazz) for clazz in ACTION_CLASSES])
__all__ = [
- FileActionMapper,
- path_type,
- from_dict,
- MessageAction,
- RemoteTransferAction, # For testing
+ 'FileActionMapper',
+ 'path_type',
+ 'from_dict',
+ 'MessageAction',
+ 'RemoteTransferAction', # For testing
]
diff --git a/pulsar/client/manager.py b/pulsar/client/manager.py
index 066d9a126c15ae1f9eea6c70dc2fde869d65b6a9..25e28ee559e78d138194cea25fcb6917ebbd83a9 100644
--- a/pulsar/client/manager.py
+++ b/pulsar/client/manager.py
@@ -220,4 +220,8 @@ def _environ_default_int(variable, default="0"):
int_val = int(val)
return int_val
-__all__ = [ClientManager, ObjectStoreClientManager, HttpPulsarInterface]
+__all__ = [
+ 'ClientManager',
+ 'ObjectStoreClientManager',
+ 'HttpPulsarInterface'
+]
diff --git a/pulsar/client/path_mapper.py b/pulsar/client/path_mapper.py
index 02089117b5a032bbef21926d02b9ef196b0b8fd6..97c1a770311e51ab9b4c5c77dc54f0815fba6cf3 100644
--- a/pulsar/client/path_mapper.py
+++ b/pulsar/client/path_mapper.py
@@ -95,4 +95,4 @@ class PathMapper(object):
message = "PathMapper cannot handle path type %s" % dataset_path_type
raise Exception(message)
-__all__ = [PathMapper]
+__all__ = ['PathMapper']
diff --git a/pulsar/client/setup_handler.py b/pulsar/client/setup_handler.py
index 29382dffa4ff7369cac093f338d815dfe6b15a46..2cc9d1afcc4ee38f8ba84ae7e3f481117f3eb317 100644
--- a/pulsar/client/setup_handler.py
+++ b/pulsar/client/setup_handler.py
@@ -101,4 +101,4 @@ def build_job_config(job_id, job_directory, system_properties={}, tool_id=None,
return job_config
-__all__ = [build_job_config, build]
+__all__ = ['build_job_config', 'build']
diff --git a/pulsar/client/staging/down.py b/pulsar/client/staging/down.py
index e3adf9d7fa3bd17d10b1a6da26c4650a1cc0bb0d..cfb901d5eb07a145fb580d4bc036741f756ec7ef 100644
--- a/pulsar/client/staging/down.py
+++ b/pulsar/client/staging/down.py
@@ -152,4 +152,4 @@ def __clean(collection_failure_exceptions, cleanup_job, client):
except Exception:
log.warn("Failed to cleanup remote Pulsar job")
-__all__ = [finish_job]
+__all__ = ['finish_job']
diff --git a/pulsar/client/staging/up.py b/pulsar/client/staging/up.py
index 63d5435612f4b67afc3e3307e4b19d8de548c56e..3daf124085e31b7ee8127af5bd5152f04f25be27 100644
--- a/pulsar/client/staging/up.py
+++ b/pulsar/client/staging/up.py
@@ -421,4 +421,4 @@ def _read(path):
input.close()
-__all__ = [submit_job]
+__all__ = ['submit_job']
diff --git a/pulsar/client/transport/__init__.py b/pulsar/client/transport/__init__.py
index 98e5d12abcd30d4016bdee62fd2cf378026d81c6..4ff9c7df25f95b48374f2242f0e1b81759a3d563 100644
--- a/pulsar/client/transport/__init__.py
+++ b/pulsar/client/transport/__init__.py
@@ -38,5 +38,12 @@ def _get_transport_type(transport_type, os_module):
transport_type = 'curl'
return transport_type
-__all__ = [get_transport, get_file, post_file, rsync_get_file, rsync_post_file,
- scp_get_file, scp_post_file]
+__all__ = [
+ 'get_transport',
+ 'get_file',
+ 'post_file',
+ 'rsync_get_file',
+ 'rsync_post_file',
+ 'scp_get_file',
+ 'scp_post_file'
+]
diff --git a/pulsar/client/transport/curl.py b/pulsar/client/transport/curl.py
index d22a30b25592f06d2dcb857b1095065137e799d8..983b9786f0bf6e7145c7a844af13c0750f1ab38d 100644
--- a/pulsar/client/transport/curl.py
+++ b/pulsar/client/transport/curl.py
@@ -91,4 +91,8 @@ def _new_curl_object():
except NameError:
raise ImportError(PYCURL_UNAVAILABLE_MESSAGE)
-___all__ = [PycurlTransport, post_file, get_file]
+__all__ = [
+ 'PycurlTransport',
+ 'post_file',
+ 'get_file'
+]
diff --git a/pulsar/client/transport/ssh.py b/pulsar/client/transport/ssh.py
index 22c10785d5960b9d1f843f58c9b2f305cda3db44..0dbf4cd144e683e1ee1a9ae5a16866c79eb3b31b 100644
--- a/pulsar/client/transport/ssh.py
+++ b/pulsar/client/transport/ssh.py
@@ -56,4 +56,9 @@ def scp_post_file(uri_from, uri_to, user, host, port, key):
raise Exception("scp exited with code %s" % exit_code)
-___all__ = [rsync_post_file, rsync_get_file, scp_post_file, scp_get_file]
+___all__ = [
+ 'rsync_post_file',
+ 'rsync_get_file',
+ 'scp_post_file',
+ 'scp_get_file'
+]
diff --git a/pulsar/managers/__init__.py b/pulsar/managers/__init__.py
index c8a51b27a018b5558cf574feda2054aff646ac1f..7e19a192d899555edf1c2f4fb0eeccf663dd303d 100644
--- a/pulsar/managers/__init__.py
+++ b/pulsar/managers/__init__.py
@@ -1,96 +1,4 @@
"""
-
-Job Managers
-
-:mod:`pulsar.managers.base` Module
--------------------------------
-
-.. automodule:: pulsar.managers.base
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.queued` Module
----------------------------------
-
-.. automodule:: pulsar.managers.queued
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.queued_drmaa` Module
-------------------------------
-
-.. automodule:: pulsar.managers.queued_drmaa
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.queued_external_drmaa` Module
-------------------------------
-
-.. automodule:: pulsar.managers.queued_external_drmaa
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.queued_condor` Module
-------------------------------
-
-.. automodule:: pulsar.managers.queued_condor
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.queued_pbs` Module
-------------------------------
-
-.. automodule:: pulsar.managers.queued_pbs
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.unqueued` Module
-------------------------------
-
-.. automodule:: pulsar.managers.unqueued
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.stateful` Module
-------------------------------
-
-.. automodule:: pulsar.managers.stateful
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.status` Module
-------------------------------
-
-.. automodule:: pulsar.managers.status
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.util` Module
-------------------------------
-
-.. automodule:: pulsar.managers.util
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-:mod:`pulsar.managers.staging` Module
-------------------------------
-
-.. automodule:: pulsar.managers.staging
- :members:
- :undoc-members:
- :show-inheritance:
-
"""
from abc import ABCMeta, abstractmethod
diff --git a/pulsar/managers/base/__init__.py b/pulsar/managers/base/__init__.py
index e5c68cc4f837d22f18d7ac53ecd3b0b06335caf8..4f4bcbf80d03a924d46a92e2b56a4f85f48bf105 100644
--- a/pulsar/managers/base/__init__.py
+++ b/pulsar/managers/base/__init__.py
@@ -1,32 +1,6 @@
"""
-
Base Classes and Infrastructure Supporting Concret Manager Implementations.
-
-:mod:`pulsar.managers.base.base_drmaa` Module
--------------------------------
-
-.. automodule:: pulsar.managers.base.base_drmaa
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.base.directory` Module
--------------------------------
-
-.. automodule:: pulsar.managers.base.directory
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.managers.base.external` Module
--------------------------------
-
-.. automodule:: pulsar.managers.base.external
- :members:
- :undoc-members:
- :show-inheritance:
-
"""
from collections import deque
import logging
diff --git a/pulsar/managers/staging/__init__.py b/pulsar/managers/staging/__init__.py
index 3d7934c93b4103ed9a378c8e2915a369e0f7887f..366cb343b80667a95d41762a8113fd657cd288e4 100644
--- a/pulsar/managers/staging/__init__.py
+++ b/pulsar/managers/staging/__init__.py
@@ -1,24 +1,9 @@
""" This module contains the code that allows the Pulsar to stage file's during
preprocessing (currently this means downloading or copying files) and then unstage
or send results back to client during postprocessing.
-
-:mod:`pulsar.managers.staging.preprocess` Module
--------------------------------
-
-.. automodule:: pulsar.managers.staging.preprocess
-
- .. autofunction:: preprocess
-
-:mod:`pulsar.managers.staging.postprocess` Module
--------------------------------
-
-.. automodule:: pulsar.managers.staging.postprocess
-
- .. autofunction:: postprocess
-
"""
from .postprocess import postprocess
from .preprocess import preprocess
-__all__ = [preprocess, postprocess]
+__all__ = ['preprocess', 'postprocess']
diff --git a/pulsar/managers/staging/postprocess.py b/pulsar/managers/staging/postprocess.py
index ac3590824fe18f8c0cfdd71deb446c5c42a03a8b..b90c771414aa344ca1e04c749e55cf0fbd3bf4ef 100644
--- a/pulsar/managers/staging/postprocess.py
+++ b/pulsar/managers/staging/postprocess.py
@@ -66,4 +66,4 @@ def __pulsar_outputs(job_directory):
output_directory_contents,
)
-__all__ = [postprocess]
+__all__ = ['postprocess']
diff --git a/pulsar/managers/staging/preprocess.py b/pulsar/managers/staging/preprocess.py
index cb9e1b8151fc9246450e78d2cfd9090ac75ccfae..668897d8fc1544c0c119c9025df517fd435a84e6 100644
--- a/pulsar/managers/staging/preprocess.py
+++ b/pulsar/managers/staging/preprocess.py
@@ -1,3 +1,5 @@
+"""
+"""
from pulsar.client.action_mapper import from_dict
import logging
@@ -13,4 +15,4 @@ def preprocess(job_directory, setup_actions, action_executor):
log.debug("Staging %s '%s' via %s to %s", input_type, name, action.__class__.__name__, path)
action_executor.execute(lambda: action.write_to_path(path))
-__all__ = [preprocess]
+__all__ = ['preprocess']
diff --git a/pulsar/managers/stateful.py b/pulsar/managers/stateful.py
index 0e8eea5d25f12db4fc6a61bdb1a02bd29f61b36a..0b027080b4c10db1c16fbd4d432c5dc6318e16a0 100644
--- a/pulsar/managers/stateful.py
+++ b/pulsar/managers/stateful.py
@@ -269,4 +269,4 @@ def new_thread_for_manager(manager, name, target, daemon):
thread.start()
return thread
-__all__ = [StatefulManagerProxy]
+__all__ = ['StatefulManagerProxy']
diff --git a/pulsar/managers/unqueued.py b/pulsar/managers/unqueued.py
index 4a298957b0bd639ce134b1cda35718c2ac70a0bb..705b72e1aa0dd18d150cccffb71684d01ee62fee 100644
--- a/pulsar/managers/unqueued.py
+++ b/pulsar/managers/unqueued.py
@@ -171,4 +171,4 @@ def execute(command_line, working_directory, stdout, stderr):
return proc
-__all__ = [Manager]
+__all__ = ['Manager']
diff --git a/pulsar/managers/util/__init__.py b/pulsar/managers/util/__init__.py
index aff63231255a5b81b3310b58435e8c2a309485c9..d197ae6c9d70e33cbdb00cc12f2fa324440ac59c 100644
--- a/pulsar/managers/util/__init__.py
+++ b/pulsar/managers/util/__init__.py
@@ -7,4 +7,4 @@ from galaxy.util.bunch import Bunch
from .kill import kill_pid
-__all__ = [kill_pid, Bunch]
+__all__ = ['kill_pid', 'Bunch']
diff --git a/pulsar/managers/util/drmaa/__init__.py b/pulsar/managers/util/drmaa/__init__.py
index b46ccb2c50487e557ab8bc462d6568d79843a341..d9e155a1b6a3111850cba0f1de762bd49cfe40af 100644
--- a/pulsar/managers/util/drmaa/__init__.py
+++ b/pulsar/managers/util/drmaa/__init__.py
@@ -53,4 +53,4 @@ class DrmaaSession(object):
return self.session.exit()
-__all__ = [DrmaaSessionFactory]
+__all__ = ['DrmaaSessionFactory']
diff --git a/pulsar/mesos/__init__.py b/pulsar/mesos/__init__.py
index e16273b208d427ff55225ed392f69cff802d9f52..469c4a8d1313a7703b4418993436e703f10bfe8c 100644
--- a/pulsar/mesos/__init__.py
+++ b/pulsar/mesos/__init__.py
@@ -1,13 +1,4 @@
""" This module and submodules contain code for interfacing the Apache Mesos framework.
-
-:mod:`pulsar.mesos.framework` Module
--------------------------------
-
-.. automodule:: pulsar.mesos.framework
- :members:
- :undoc-members:
- :show-inheritance:
-
"""
try:
from mesos import (
diff --git a/pulsar/messaging/__init__.py b/pulsar/messaging/__init__.py
index aa7981f6d84c3fbed44658f8c4788782965010a5..024d017339cdf85fd4259366bd3e4894e01888d7 100644
--- a/pulsar/messaging/__init__.py
+++ b/pulsar/messaging/__init__.py
@@ -1,16 +1,6 @@
""" This module contains the server-side only code for interfacing with
message queues. Code shared between client and server can be found in
submodules of ``pulsar.client``.
-
-
-:mod:`pulsar.messaging.bind_amqp` Module
-------------------------------
-
-.. automodule:: pulsar.messaging.bind_amqp
- :members:
- :undoc-members:
- :show-inheritance:
-
"""
from ..messaging import bind_amqp
diff --git a/pulsar/scripts/__init__.py b/pulsar/scripts/__init__.py
index ab3b0fc1332a3f30044fd704577ee7f4c032d517..d6f9a3ba61ef1b276aae7b9c18ad2c418501819b 100644
--- a/pulsar/scripts/__init__.py
+++ b/pulsar/scripts/__init__.py
@@ -1,57 +1,4 @@
""" This module contains entry points into various Pulsar scripts. Corresponding
shell scripts that setup the deployment specific environments and then
delegate to these Python scripts can be found in ``PULSAR_ROOT/scripts``.
-
-
-:mod:`pulsar.scripts.chown_working_directory` Module
---------------------------
-
-.. automodule:: pulsar.scripts.chown_working_directory
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.scripts.drmaa_kill` Module
---------------------------
-
-.. automodule:: pulsar.scripts.drmaa_kill
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.scripts.drmaa_launch` Module
---------------------------
-
-.. automodule:: pulsar.scripts.drmaa_launch
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-:mod:`pulsar.scripts.submit` Module
---------------------------
-
-.. automodule:: pulsar.scripts.submit
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-:mod:`pulsar.scripts.mesos_executor` Module
---------------------------
-
-.. automodule:: pulsar.scripts.mesos_executor
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-:mod:`pulsar.scripts.mesos_framework` Module
---------------------------
-
-.. automodule:: pulsar.scripts.mesos_framework
- :members:
- :undoc-members:
- :show-inheritance:
-
"""
diff --git a/pulsar/tools/__init__.py b/pulsar/tools/__init__.py
index 2d7577f83235d2982d086ef92a30ecc8421c253f..b1013e30244a4550c517bedc5668005a2dd58d0c 100644
--- a/pulsar/tools/__init__.py
+++ b/pulsar/tools/__init__.py
@@ -2,30 +2,6 @@
Tools
-:mod:`pulsar.tools.toolbox` Module
--------------------------------
-
-.. automodule:: pulsar.tools.toolbox
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.tools.authorization` Module
---------------------------------
-
-.. automodule:: pulsar.tools.authorization
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.tools.validator` Module
-------------------------------
-
-.. automodule:: pulsar.tools.validator
- :members:
- :undoc-members:
- :show-inheritance:
-
"""
from .toolbox import ToolBox
diff --git a/pulsar/tools/authorization.py b/pulsar/tools/authorization.py
index bec80b5334539f16c432c24d4d293d48a4226421..1a6a8bfbe08f6e7fe8a401bafc79c627cb8f6943 100644
--- a/pulsar/tools/authorization.py
+++ b/pulsar/tools/authorization.py
@@ -87,4 +87,4 @@ def get_authorizer(toolbox):
authorizer = AllowAnyAuthorizer()
return authorizer
-__all__ = [get_authorizer]
+__all__ = ['get_authorizer']
diff --git a/pulsar/tools/toolbox.py b/pulsar/tools/toolbox.py
index a02fbe42ca84c246ec95e82245ed211e2c14b33d..6386d578e3015d6d769bfc8b55326e20fe353377 100644
--- a/pulsar/tools/toolbox.py
+++ b/pulsar/tools/toolbox.py
@@ -126,15 +126,17 @@ class ToolShedToolConfig(SimpleToolConfig):
toolbox with the `tool` tag, i.e. one from the
toolshed.
- <tool file="../shed_tools/gvk.bx.psu.edu/repos/test/column_maker/f06aa1bf1e8a/column_maker/column_maker.xml" guid\
-="gvk.bx.psu.edu:9009/repos/test/column_maker/Add_a_column1/1.1.0">
- <tool_shed>gvk.bx.psu.edu:9009</tool_shed>
- <repository_name>column_maker</repository_name>
- <repository_owner>test</repository_owner>
- <installed_changeset_revision>f06aa1bf1e8a</installed_changeset_revision
- <id>gvk.bx.psu.edu:9009/repos/test/column_maker/Add_a_column1/1.1.0</id>
- <version>1.1.0</version>
- </tool>
+ ::
+
+ <tool file="../shed_tools/gvk.bx.psu.edu/repos/test/column_maker/f06aa1bf1e8a/column_maker/column_maker.xml" guid\
+ ="gvk.bx.psu.edu:9009/repos/test/column_maker/Add_a_column1/1.1.0">
+ <tool_shed>gvk.bx.psu.edu:9009</tool_shed>
+ <repository_name>column_maker</repository_name>
+ <repository_owner>test</repository_owner>
+ <installed_changeset_revision>f06aa1bf1e8a</installed_changeset_revision
+ <id>gvk.bx.psu.edu:9009/repos/test/column_maker/Add_a_column1/1.1.0</id>
+ <version>1.1.0</version>
+ </tool>
"""
def __init__(self, tool_el, tool_path):
diff --git a/pulsar/web/__init__.py b/pulsar/web/__init__.py
index a9a657ada4b98c14b9c85fdf9d69a66d82f9f59f..dcf718029462c31cd2c92bfcf9a787c3c8e4bcad 100644
--- a/pulsar/web/__init__.py
+++ b/pulsar/web/__init__.py
@@ -1,29 +1,3 @@
""" The code explicitly related to the Pulsar web server can be found in this
module and its submodules.
-
-
-
-:mod:`pulsar.web.framework` Module
---------------------------
-
-.. automodule:: pulsar.web.framework
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.web.routes` Module
---------------------------
-
-.. automodule:: pulsar.web.routes
- :members:
- :undoc-members:
- :show-inheritance:
-
-:mod:`pulsar.web.wsgi` Module
---------------------------
-
-.. automodule:: pulsar.web.wsgi
- :members:
- :undoc-members:
- :show-inheritance:
"""