simplifying module name

.coveragerc

@@ -1,12 +1,12 @@
 [run]
 include =
 	# include these files
-	Sequential_WC_Simulator/*
+	wc_sim/*
 	tests/*
 	examples/*	
 omit =
     # omit these files
-	Sequential_WC_Simulator/multialgorithm/plot_specie_pop.py
-	Sequential_WC_Simulator/multialgorithm/species_counts.py
-	Sequential_WC_Simulator/multialgorithm/temp/analysis.py
-	Sequential_WC_Simulator/multialgorithm/temp/exercise.py
+	wc_sim/multialgorithm/plot_specie_pop.py
+	wc_sim/multialgorithm/species_counts.py
+	wc_sim/multialgorithm/temp/analysis.py
+	wc_sim/multialgorithm/temp/exercise.py

MANIFEST.in

@@ -8,4 +8,4 @@ include requirements.txt
 recursive-include examples *
 
 # configuration files
-recursive-include Sequential_WC_Simulator *.cfg
+recursive-include wc_sim *.cfg

README.md

@@ -1,16 +1,15 @@
-<!-- [![PyPI package](https://img.shields.io/pypi/v/Sequential_WC_Simulator.svg)](https://pypi.python.org/pypi/Karr-Lab-build-utils) -->
-[![Documentation](https://img.shields.io/badge/docs-latest-brightgreen.svg)](http://code.karrlab.org/Sequential_WC_Simulator/docs)
-[![Test results](https://circleci.com/gh/KarrLab/Sequential_WC_Simulator.svg?style=shield&circle-token=5f0ee7e437b91cbcac19a9b8526a7ea320ee61c7)](https://circleci.com/gh/KarrLab/Sequential_WC_Simulator)
-[![Test coverage](https://coveralls.io/repos/github/KarrLab/Sequential_WC_Simulator/badge.svg?t=EUFJ40)](https://coveralls.io/github/KarrLab/Sequential_WC_Simulator)
+<!-- [![PyPI package](https://img.shields.io/pypi/v/wc_sim.svg)](https://pypi.python.org/pypi/Karr-Lab-build-utils) -->
+[![Documentation](https://img.shields.io/badge/docs-latest-brightgreen.svg)](http://code.karrlab.org/wc_sim/docs)
+[![Test results](https://circleci.com/gh/KarrLab/wc_sim.svg?style=shield&circle-token=5f0ee7e437b91cbcac19a9b8526a7ea320ee61c7)](https://circleci.com/gh/KarrLab/wc_sim)
+[![Test coverage](https://coveralls.io/repos/github/KarrLab/wc_sim/badge.svg?t=EUFJ40)](https://coveralls.io/github/KarrLab/wc_sim)
 [![Code analysis](https://codeclimate.com/repos/57ab5e097ba8854f41000799/badges/54b4deadccf7944d38f6/gpa.svg)](https://codeclimate.com/repos/57ab5e097ba8854f41000799)
-[![License](https://img.shields.io/github/license/KarrLab/Sequential_WC_Simulator.svg)](LICENSE)
-![Analytics](https://ga-beacon.appspot.com/UA-86759801-1/Sequential_WC_Simulator/README.md?pixel)
-
-# Sequential_WC_Simulator
+[![License](https://img.shields.io/github/license/KarrLab/wc_sim.svg)](LICENSE)
+![Analytics](https://ga-beacon.appspot.com/UA-86759801-1/wc_sim/README.md?pixel)
 
+# wc_sim
 
 ## Documentation
-Please see the [API documentation](http://code.karrlab.org/Sequential_WC_Simulator/docs).
+Please see the [API documentation](http://code.karrlab.org/wc_sim/docs).
 
 ## License
 The build utilities are released under the [MIT license](LICENSE).

docs/conf.py

@@ -19,7 +19,7 @@
 import os
 import sys
 sys.path.insert(0, os.path.abspath('..'))
-import Sequential_WC_Simulator
+import wc_sim
 
 # -- General configuration ------------------------------------------------
 
@@ -65,7 +65,7 @@
 # built documents.
 #
 # The short X.Y version.
-version = Sequential_WC_Simulator.__version__
+version = wc_sim.__version__
 # The full version, including alpha/beta/rc tags.
 release = version
 

examples/PHOLD.py

@@ -15,8 +15,8 @@
 import datetime
 
 from .debug_logs import logs as debug_logs
-from Sequential_WC_Simulator.core.simulation_object import EventQueue, SimulationObject
-from Sequential_WC_Simulator.core.simulation_engine import SimulationEngine, MessageTypesRegistry
+from wc_sim.core.simulation_object import EventQueue, SimulationObject
+from wc_sim.core.simulation_engine import SimulationEngine, MessageTypesRegistry
 
 def obj_name( obj_num ):
     # create object name from index

examples/config/paths.py

@@ -11,4 +11,4 @@
 import os
 
 debug_logs = debug_logs_default_paths.deepcopy()
-debug_logs.default = resource_filename('Sequential_WC_Simulator', 'examples/config/debug.default.cfg')
+debug_logs.default = resource_filename('wc_sim', 'examples/config/debug.default.cfg')

setup.cfg

@@ -6,8 +6,8 @@ universal = 1
 
 [coverage:run]
 source = 
-    Sequential_WC_Simulator
+    wc_sim
 
 [sphinx-apidocs]
 packages = 
-    Sequential_WC_Simulator
+    wc_sim

setup.py

@@ -3,7 +3,7 @@
 
 from setuptools import setup, find_packages
 from wc_utils.util.install import parse_requirements, install_dependencies
-import Sequential_WC_Simulator
+import wc_sim
 
 # parse dependencies and links from requirements.txt files
 with open('requirements.txt', 'r') as file:
@@ -17,18 +17,18 @@
 
 # install package
 setup(
-    name="Sequential_WC_Simulator",
-    version=Sequential_WC_Simulator.__version__,
+    name="wc_sim",
+    version=wc_sim.__version__,
     description="Sequential whole-cell model simulator",
-    url="https://github.com/KarrLab/Sequential_WC_Simulator",
-    download_url='https://github.com/KarrLab/Sequential_WC_Simulator/tarball/{}'.format(Sequential_WC_Simulator.__version__),
+    url="https://github.com/KarrLab/wc_sim",
+    download_url='https://github.com/KarrLab/wc_sim/tarball/{}'.format(wc_sim.__version__),
     author="Arthur Goldberg",
     author_email="[email protected]",
     license="MIT",
     keywords='whole-cell systems cell molecular biology',
     packages=find_packages(exclude=['tests', 'tests.*']),
     package_data={
-        'Sequential_WC_Simulator': [
+        'wc_sim': [
             'core/config/core.default.cfg',
             'core/config/core.schema.cfg',
             'core/config/debug.default.cfg',

tests/all.sh

@@ -12,7 +12,7 @@ function usage {
     if [ -n "$1" ]; then echo $1 >&2; fi
 cat <<EOF >&2
 usage: $(basename $0) 
-  run all unittests for Sequential_WC_Simulator
+  run all unittests for wc_sim
   -c: perform coverage tests as well
   -h: produce this message 
 EOF
@@ -43,7 +43,7 @@ SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 
 if [[ -n "$OPT_COVERAGE" ]]
 then
-    nosetests $SCRIPT_DIR --with-coverage --cover-package=Sequential_WC_Simulator
+    nosetests $SCRIPT_DIR --with-coverage --cover-package=wc_sim
     coverage html
 else
     nosetests $SCRIPT_DIR

tests/test_CellState.py

@@ -6,12 +6,12 @@
 
 from wc_utils.util.rand import RandomStateManager
 
-from Sequential_WC_Simulator.core.simulation_object import EventQueue, SimulationObject
-from Sequential_WC_Simulator.core.simulation_engine import SimulationEngine, MessageTypesRegistry
-from Sequential_WC_Simulator.multialgorithm.cell_state import CellState
-from Sequential_WC_Simulator.multialgorithm.message_types import *
+from wc_sim.core.simulation_object import EventQueue, SimulationObject
+from wc_sim.core.simulation_engine import SimulationEngine, MessageTypesRegistry
+from wc_sim.multialgorithm.cell_state import CellState
+from wc_sim.multialgorithm.message_types import *
 from tests.universal_sender_receiver_simulation_object import UniversalSenderReceiverSimulationObject
-# from Sequential_WC_Simulator.core.logging_config import LOGGING_ROOT_DIR
+# from wc_sim.core.logging_config import LOGGING_ROOT_DIR
 
 class TestCellState(unittest.TestCase):
 

tests/test_CellStateMultiObj.py

@@ -15,10 +15,10 @@
 from wc_utils.util.rand import RandomStateManager
 
 # TODO(Arthur): test the exceptions in these modules
-from Sequential_WC_Simulator.core.simulation_object import EventQueue, SimulationObject
-from Sequential_WC_Simulator.core.simulation_engine import SimulationEngine, MessageTypesRegistry
-from Sequential_WC_Simulator.multialgorithm.message_types import *
-from Sequential_WC_Simulator.multialgorithm.cell_state import CellState
+from wc_sim.core.simulation_object import EventQueue, SimulationObject
+from wc_sim.core.simulation_engine import SimulationEngine, MessageTypesRegistry
+from wc_sim.multialgorithm.message_types import *
+from wc_sim.multialgorithm.cell_state import CellState
 from tests.universal_sender_receiver_simulation_object import UniversalSenderReceiverSimulationObject
 
 def parse_population_history( pop_history ):

tests/test_MessageTypes.py

@@ -2,7 +2,7 @@
 
 from wc_utils.util.misc import isclass_by_name
 
-from Sequential_WC_Simulator.multialgorithm.message_types import *
+from wc_sim.multialgorithm.message_types import *
 
 class TestMessageTypes(unittest.TestCase):
 

tests/test_MultiAlgorithm.py

@@ -4,11 +4,11 @@
 
 from argparse import Namespace
 
-from Sequential_WC_Simulator.multialgorithm.config import paths as config_paths
-from Sequential_WC_Simulator.multialgorithm.multi_algorithm import MultiAlgorithm
+from wc_sim.multialgorithm.config import paths as config_paths
+from wc_sim.multialgorithm.multi_algorithm import MultiAlgorithm
 from wc_utils.config.core import ConfigManager
 
-config = ConfigManager(config_paths.core).get_config()['Sequential_WC_Simulator']['multialgorithm']
+config = ConfigManager(config_paths.core).get_config()['wc_sim']['multialgorithm']
 
 
 class TestMultiAlgorithm(unittest.TestCase):

tests/test_SharedMemoryCellState.py

@@ -4,8 +4,8 @@
 
 from wc_utils.util.rand import RandomStateManager
 
-from Sequential_WC_Simulator.multialgorithm.specie import Specie
-from Sequential_WC_Simulator.multialgorithm.shared_memory_cell_state import SharedMemoryCellState
+from wc_sim.multialgorithm.specie import Specie
+from wc_sim.multialgorithm.shared_memory_cell_state import SharedMemoryCellState
 
 class TestSharedMemoryCellState(unittest.TestCase):
 

tests/test_SimpleStochasticSimulationAlgorithm.py

@@ -1,9 +1,9 @@
 import unittest
 
-from Sequential_WC_Simulator.core.simulation_object import (EventQueue, SimulationObject)
-from Sequential_WC_Simulator.core.simulation_engine import (SimulationEngine, MessageTypesRegistry)
-from Sequential_WC_Simulator.multialgorithm.submodels.simple_SSA_submodel import simple_SSA_submodel
-from Sequential_WC_Simulator.multialgorithm.message_types import *
+from wc_sim.core.simulation_object import (EventQueue, SimulationObject)
+from wc_sim.core.simulation_engine import (SimulationEngine, MessageTypesRegistry)
+from wc_sim.multialgorithm.submodels.simple_SSA_submodel import simple_SSA_submodel
+from wc_sim.multialgorithm.message_types import *
 from tests.universal_sender_receiver_simulation_object import UniversalSenderReceiverSimulationObject
 
 class Testsimple_SSA_submodel(unittest.TestCase):

tests/test_SimulationEngine.py

@@ -1,9 +1,9 @@
 from __future__ import print_function
 import unittest
 
-from Sequential_WC_Simulator.core.simulation_object import (EventQueue, SimulationObject)
-from Sequential_WC_Simulator.core.event import Event
-from Sequential_WC_Simulator.core.simulation_engine import (SimulationEngine, MessageTypesRegistry)
+from wc_sim.core.simulation_object import (EventQueue, SimulationObject)
+from wc_sim.core.event import Event
+from wc_sim.core.simulation_engine import (SimulationEngine, MessageTypesRegistry)
 from tests.some_message_types import *
 
 class ExampleSimulationObject(SimulationObject):

tests/test_SimulationObject.py

@@ -1,8 +1,8 @@
 from __future__ import print_function
 import unittest
 
-from Sequential_WC_Simulator.core.simulation_object import (EventQueue, SimulationObject)
-from Sequential_WC_Simulator.core.simulation_engine import (SimulationEngine, MessageTypesRegistry)
+from wc_sim.core.simulation_object import (EventQueue, SimulationObject)
+from wc_sim.core.simulation_engine import (SimulationEngine, MessageTypesRegistry)
 from tests.some_message_types import *
 
 class ExampleSimulationObject(SimulationObject):

tests/test_Specie.py

@@ -4,9 +4,9 @@
 import unittest
 
 from scipy.stats import binom
-from Sequential_WC_Simulator.core.simulation_object import EventQueue, SimulationObject
-from Sequential_WC_Simulator.core.simulation_engine import SimulationEngine, MessageTypesRegistry
-from Sequential_WC_Simulator.multialgorithm.specie import Specie
+from wc_sim.core.simulation_object import EventQueue, SimulationObject
+from wc_sim.core.simulation_engine import SimulationEngine, MessageTypesRegistry
+from wc_sim.multialgorithm.specie import Specie
 from wc_utils.util.rand import RandomStateManager
 
 

tests/test_utilities.py

@@ -1,6 +1,6 @@
 import unittest
 import re
-from Sequential_WC_Simulator.multialgorithm.utilities import get_species_and_compartment_from_name
+from wc_sim.multialgorithm.utilities import get_species_and_compartment_from_name
 
 class TestUtilities(unittest.TestCase):
 

tests/universal_sender_receiver_simulation_object.py

@@ -1,6 +1,6 @@
-from Sequential_WC_Simulator.core.simulation_object import SimulationObject
-from Sequential_WC_Simulator.core.simulation_engine import MessageTypesRegistry
-from Sequential_WC_Simulator.multialgorithm.message_types import *
+from wc_sim.core.simulation_object import SimulationObject
+from wc_sim.core.simulation_engine import MessageTypesRegistry
+from wc_sim.multialgorithm.message_types import *
 
 class UniversalSenderReceiverSimulationObject(SimulationObject):
 

Sequential_WC_Simulator/core/config/core.default.cfg → wc_sim/core/config/core.default.cfg

@@ -1,4 +1,4 @@
-[Sequential_WC_Simulator]
+[wc_sim]
     [[core]]
         copy_event_bodies = False
         default_center_of_mass = 10

Sequential_WC_Simulator/core/config/core.schema.cfg → wc_sim/core/config/core.schema.cfg

@@ -1,4 +1,4 @@
-[Sequential_WC_Simulator]
+[wc_sim]
     [[core]]
         copy_event_bodies = boolean(default=False)
         # whether to deepcopy each event_body in SimulationObject.send_event() before 

wc_sim/core/config/paths.py

@@ -0,0 +1,29 @@
+""" Configuration
+
+:Author: Arthur Goldberg <[email protected]>
+:Date: 2016-09-19
+:Copyright: 2016, Karr Lab
+:License: MIT
+"""
+
+from pkg_resources import resource_filename
+from wc_utils.config.core import ConfigPaths
+from wc_utils.debug_logs.config import paths as debug_logs_default_paths
+import os
+
+
+core = ConfigPaths(
+    default=resource_filename('wc_sim', 'core/config/core.default.cfg'),
+    schema=resource_filename('wc_sim', 'core/config/core.schema.cfg'),
+    user=(
+        'wc_sim.core.core.cfg',
+        os.path.expanduser('~/.wc/wc_sim.core.core.cfg'),
+    ),
+)
+
+debug_logs = debug_logs_default_paths.deepcopy()
+debug_logs.default = resource_filename('wc_sim', 'core/config/debug.default.cfg')
+debug_logs.user = (
+    'wc_sim.core.debug.cfg',
+    os.path.expanduser('~/.wc/wc_sim.core.debug.cfg'),
+)

Sequential_WC_Simulator/core/simulation_engine.py → wc_sim/core/simulation_engine.py

@@ -16,7 +16,7 @@
 
 import datetime
 
-from Sequential_WC_Simulator.core.event import Event
+from wc_sim.core.event import Event
 
 # configure logging
 from .debug_logs import logs as debug_logs