BEEflow API
**************************

BEEflow
===========================
.. automodule:: beeflow.client.bee_client
   :members:

BEEflow Core
===========================
.. automodule:: beeflow.client.core
   :members:

Builder (Container)
===========================

Build Interfaces
---------------------------
.. automodule:: beeflow.common.build_interfaces
   :members:

Build Driver
---------------------------
.. automodule:: beeflow.common.build.build_driver
   :members:

Build Container Drivers
--------------------------
.. automodule:: beeflow.common.build.container_drivers
   :members:

Database
===========================
Task Manager Database
---------------------
.. automodule:: beeflow.common.db.tm_db
   :members:

Scheduler Database
------------------
.. automodule:: beeflow.common.db.sched_db
   :members:

Configuration
===========================
Configuration Driver
---------------------------
.. automodule:: beeflow.common.config_driver
   :members:

Configuration Validator
---------------------------
.. automodule:: beeflow.common.config_validator
   :members:

Connection Communication
===========================
.. automodule:: beeflow.common.connection
   :members:

.. automodule:: beeflow.common.cli_connection
   :members:

Container Runtime
===========================

Container Runtime Driver
---------------------------
.. automodule:: beeflow.common.crt.crt_driver
   :members:

Charliecloud Driver
-------------------
.. automodule:: beeflow.common.crt.charliecloud_driver
   :members:

Singularity Driver
---------------------------
.. automodule:: beeflow.common.crt.singularity_driver
   :members:

Container Path
---------------------------
.. automodule:: beeflow.common.container_path
   :members:

Container Runtime Interface
---------------------------
.. automodule:: beeflow.common.crt_interface
   :members:

Graph Database
===========================

Evaluate CWL expressions
---------------------------
.. automodule:: beeflow.common.expr
   :members:

Graph Database Driver
---------------------------
.. automodule:: beeflow.common.gdb.gdb_driver
   :members:

Graph Database Interface
---------------------------
.. automodule:: beeflow.common.gdb_interface
   :members:

Neo4j Cypher Module
---------------------------
.. automodule:: beeflow.common.gdb.neo4j_cypher
   :members:

Neo4j Driver
---------------------------
.. automodule:: beeflow.common.gdb.neo4j_driver
   :members:

Logging
========================
.. automodule:: beeflow.common.log
   :members:

Parser (CWL)
========================
.. automodule:: beeflow.common.parser.parser
   :members:

Worker
===========================
.. automodule:: beeflow.common.worker.worker
   :members:

LSF Worker
---------------------------
.. automodule:: beeflow.common.worker.lsf_worker
   :members:

Simple Worker
---------------------------
.. automodule:: beeflow.common.worker.simple_worker
   :members:

Slurm Worker
---------------------------
.. automodule:: beeflow.common.worker.slurm_worker
   :members:

Task Manager
---------------------------
.. automodule:: beeflow.task_manager
   :members:


Worker Interface
---------------------------
.. automodule:: beeflow.common.worker_interface
   :members:

Workflow Data Structures
========================
.. automodule:: beeflow.common.wf_data
   :members:
   :special-members:

Workflow Interface
==================
.. automodule:: beeflow.common.wf_interface
   :members:

Workflow Manager
===========================
.. automodule:: beeflow.wf_manager.wf_manager
   :members:

Workflow Manager Resources
---------------------------
.. automodule:: beeflow.wf_manager.resources.wf_actions
   :members:
.. automodule:: beeflow.wf_manager.resources.wf_list
   :members:
.. automodule:: beeflow.wf_manager.resources.wf_metadata
   :members:
.. automodule:: beeflow.wf_manager.resources.wf_update
   :members:
.. automodule:: beeflow.wf_manager.resources.wf_utils
   :members:

Workflow Manager Dependency Manager
------------------------------------
.. automodule:: beeflow.wf_manager.common.dep_manager
   :members:

Workflow Profiler
------------------------------------
.. automodule:: beeflow.common.wf_profiler
   :members: