Rename package name lie_workflow to mdstudio_workflow and lie_graph t…

…o graphit

lie_workflow/__init__.py → mdstudio_workflow/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__module__ = 'lie_workflow'
+__module__ = 'mdstudio_workflow'
 __docformat__ = 'restructuredtext'
 __version__ = '{major:d}.{minor:d}'.format(major=1, minor=0)
 __author__ = 'Marc van Dijk'

lie_workflow/wamp_services.py → mdstudio_workflow/wamp_services.py

@@ -7,7 +7,7 @@
 """
 
 from autobahn import wamp
-from lie_system import LieApplicationSession
+from mdstudio_system import LieApplicationSession
 
 
 class WorkflowWampApi(LieApplicationSession):
@@ -18,7 +18,7 @@ class WorkflowWampApi(LieApplicationSession):
     upon WAMP session setup
     """
 
-    require_config = ['system', 'lie_db']
+    require_config = ['system', 'mdstudio_db']
 
     @wamp.register(u'liestudio.workflow.run')
     def retrieve_structures(self, workflow, session=None):

lie_workflow/workflow_common.py → mdstudio_workflow/workflow_common.py

@@ -80,7 +80,7 @@ def validate_workflow(workflow):
     Validate the constructed workflow
 
     :param workflow: Workflow graph to validate
-    :type workflow:  :lie_graph:GraphAxis
+    :type workflow:  :graphit:GraphAxis
 
     :return: Validated or not
     :rtype:  :py:bool

lie_workflow/workflow_runner.py → mdstudio_workflow/workflow_runner.py

@@ -4,8 +4,8 @@
 import threading
 import random
 
-from lie_workflow.workflow_common import WorkflowError, validate_workflow
-from lie_workflow.workflow_spec import WorkflowSpec
+from mdstudio_workflow.workflow_common import WorkflowError, validate_workflow
+from mdstudio_workflow.workflow_spec import WorkflowSpec
 
 # Set twisted logger
 from twisted.logger import Logger
@@ -136,7 +136,7 @@ def output_callback(self, output, tid):
 
         # No more new tasks
         if not next_task_nids:
-            
+
             # Not finished but no active tasks anymore/breakpoint
             if not self.active_tasks and not self.is_completed:
                 breakpoints = self.active_breakpoints
@@ -197,7 +197,7 @@ def run_task(self, tid):
                 if unfinished.status == 'failed':
                     self.is_running = False
                     break
-            
+
             return
 
         # Run the task if status is 'ready'

lie_workflow/workflow_spec.py → mdstudio_workflow/workflow_spec.py

@@ -18,12 +18,12 @@
 from graphit.graph_py2to3 import to_unicode, prepaire_data_dict
 from graphit.graph_helpers import renumber_id
 
-from lie_workflow import __version__
-from lie_workflow.workflow_common import WorkflowError
-from lie_workflow.workflow_task_types import task_types, WORKFLOW_ORM
+from mdstudio_workflow import __version__
+from mdstudio_workflow.workflow_common import WorkflowError
+from mdstudio_workflow.workflow_task_types import task_types, WORKFLOW_ORM
 
 # Path to default workflow JSON schema part of the module
-workflow_metadata_template = pkg_resources.resource_filename('lie_workflow',
+workflow_metadata_template = pkg_resources.resource_filename('mdstudio_workflow',
                                                              '/schemas/resources/workflow_metadata_template.json')
 
 
@@ -35,7 +35,7 @@ class WorkflowSpec(object):
     tasks and the edges the connections between them. The Workflow class
     acts as manager collecting output from tasks and forwarding it to other
     tasks along the edges (push execution).
-    The `lie_workflow` DAG follows the workflow principles as described by the
+    The `mdstudio_workflow` DAG follows the workflow principles as described by the
     Workflow Patterns initiative supporting many but not all of the described
     patterns (http://www.workflowpatterns.com).
 

lie_workflow/workflow_task_types/task_base_type.py → mdstudio_workflow/workflow_task_types/task_base_type.py

@@ -17,7 +17,7 @@
 from graphit.graph_py2to3 import prepaire_data_dict, PY_STRING
 from graphit.graph_io.io_jsonschema_format import read_json_schema
 
-from lie_workflow.workflow_common import WorkflowError, collect_data, concat_dict
+from mdstudio_workflow.workflow_common import WorkflowError, collect_data, concat_dict
 
 # Set twisted logger
 from twisted.logger import Logger
@@ -42,7 +42,7 @@ def load_task_schema(schema_name):
     # Set 'directed' to True to import JSON schema as directed graph
     template_graph = GraphAxis(directed=True)
 
-    task_schema = pkg_resources.resource_filename('lie_workflow', '/schemas/endpoints/{0}'.format(schema_name))
+    task_schema = pkg_resources.resource_filename('mdstudio_workflow', '/schemas/endpoints/{0}'.format(schema_name))
     task_template = read_json_schema(task_schema, graph=template_graph,
                                      exclude_args=['title', 'description', 'schema_label'])
     task_node = task_template.query_nodes(key='task')
@@ -259,7 +259,7 @@ def get_input(self, **kwargs):
         connected to it. The latter may be post-processed selecting and
         transforming data based on edge definitions.
 
-        lie_workflows are dynamic and therefore the `get_input` and `get_output`
+        mdstudio_workflows are dynamic and therefore the `get_input` and `get_output`
         methods are always called even if input/output was previously stored
         locally.
 

lie_workflow/workflow_task_types/task_loop_type.py → mdstudio_workflow/workflow_task_types/task_loop_type.py

@@ -8,7 +8,7 @@
 
 from graphit.graph_utils.graph_utilities import edges_parent_to_subgraph
 from graphit.graph_combinatorial.graph_split_join_operations import graph_join
-from lie_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema, edge_select_transform
+from mdstudio_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema, edge_select_transform
 
 # Set twisted logger
 from twisted.logger import Logger

lie_workflow/workflow_task_types/task_python_type.py → mdstudio_workflow/workflow_task_types/task_python_type.py

@@ -11,7 +11,7 @@
 
 from graphit.graph_mixin import NodeTools
 from graphit.graph_combinatorial.graph_split_join_operations import graph_join
-from lie_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema
+from mdstudio_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema
 
 # Set twisted logger
 from twisted.logger import Logger

lie_workflow/workflow_task_types/task_wamp_type.py → mdstudio_workflow/workflow_task_types/task_wamp_type.py

@@ -22,8 +22,8 @@
 from graphit.graph_io.io_jsonschema_format import read_json_schema
 from graphit.graph_io.io_pydata_format import write_pydata
 
-from lie_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema
-from lie_workflow.workflow_common import is_file, WorkflowError
+from mdstudio_workflow.workflow_task_types.task_base_type import TaskBase, load_task_schema
+from mdstudio_workflow.workflow_common import is_file, WorkflowError
 
 # Set twisted logger
 logging = Logger()
@@ -469,7 +469,7 @@ def get_input(self, **kwargs):
         param_dict = write_pydata(request)
 
         # Remove all 'value' parameters with value None.
-        # TODO: These are left overs from lie_graph.
+        # TODO: These are left overs from graphit.
         def recursive_remove_none(d):
 
             for k, v in d.items():