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thempel · Mar 28, 2017 · d7799c6 · d7799c6
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diff --git a/adaptivemd/__init__.py b/adaptivemd/__init__.py
@@ -29,9 +29,13 @@
 from brain import Brain
 from event import StopEvent, Event, TasksFinished, FunctionalEvent
 from condition import Condition, Now, Never
-from file import File, Copy, Link, Move, Remove, Transfer, Directory, AddPathAction, Location, \
-    JSONFile
-from bundle import Bundle, SortedBundle, ViewBundle
+from file import File, Copy, Link, Move, Remove, \
+    Transfer, Directory, AddPathAction, Location, \
+    JSONFile, Action, FileTransaction, FileAction, Touch, \
+    MakeDir
+from bundle import Bundle, SortedBundle, ViewBundle, AndBundle, \
+    BaseBundle, BundleDelegator, FunctionDelegator, LogicBundle, \
+    OrBundle, StoredBundle
 from resource import AllegroCluster, LocalResource
 from task import Task, PythonTask, DummyTask
 from project import Project
@@ -40,8 +44,9 @@
 from generator import TaskGenerator
 from worker import WorkerScheduler, Worker
 from logentry import LogEntry
-from reducer import ActionParser, BashParser, ChainedParser, DictFilterParser, \
-    PrefixParser, StageParser, StrFilterParser, StageInParser
+from reducer import ActionParser, BashParser, ChainedParser, \
+    DictFilterParser, PrefixParser, StageParser, StrFilterParser, \
+    StageInParser
 
 from engine import Engine, Trajectory, Frame, \
     TrajectoryGenerationTask, TrajectoryExtensionTask

diff --git a/docs/Makefile b/docs/Makefile
@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -j8
 SPHINXBUILD   = sphinx-build
 SPHINXPROJ    = AdaptiveMD
 SOURCEDIR     = .

diff --git a/docs/action.rst b/docs/action.rst
@@ -1,8 +1,8 @@
 .. _action:
 
-.. currentmodule:: adaptivemd.file
+.. currentmodule:: adaptivemd
 
-Engine Functions
+Action Functions
 ================
 
 .. autosummary::

diff --git a/docs/bundle.rst b/docs/bundle.rst
@@ -1,20 +1,11 @@
 .. _bundle:
 
-.. currentmodule:: adaptivemd.bundle
+.. currentmodule:: adaptivemd
 
-Bundle Functions
-================
+Bundles
+-------
 
-.. autosummary::
-    :toctree: api/generated/
-
-    BaseBundle
-    Bundle
-    StoredBundle
-    ViewBundle
-    SortedBundle
-    LogicBundle
-    AndBundle
-    OrBundle
-    BundleDelegator
-    FunctionDelegator
+.. automodule:: adaptivemd.bundle
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/condition.rst b/docs/condition.rst
@@ -0,0 +1,11 @@
+.. _condition:
+
+.. currentmodule:: adaptivemd
+
+Conditions
+----------
+
+.. automodule:: adaptivemd.condition
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/conf.py b/docs/conf.py
@@ -45,8 +45,9 @@
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
     'sphinx.ext.githubpages',
-    'sphinx.ext.autosummary',
-    'sphinxcontrib.issuetracker']
+    'sphinx.ext.autosummary'
+    # ,'sphinxcontrib.issuetracker'
+]
 
 
 issuetracker = 'github'
@@ -195,7 +196,7 @@
 autosummary_generate = True
 autodoc_default_flags = ['members', 'inherited-members']
 
-numpydoc_class_members_toctree = False
+numpydoc_class_members_toctree = True
 
 
 # spell checking
@@ -207,10 +208,11 @@
 # Napoleon settings
 napoleon_google_docstring = False
 napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = True
 napoleon_include_private_with_doc = False
 napoleon_include_special_with_doc = False
 napoleon_use_admonition_for_examples = False
-napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_notes = True
 napoleon_use_admonition_for_references = False
 napoleon_use_ivar = True
 napoleon_use_param = True

diff --git a/docs/engine.rst b/docs/engine.rst
@@ -1,12 +1,12 @@
 .. _engine:
 
-.. currentmodule:: adaptivemd.engine
+.. currentmodule:: adaptivemd
 
 Engine Functions
 ================
 
 .. autosummary::
     :toctree: api/generated/
 
-    ~Engine
-    ~openmm.OpenMMEngine
+    Engine
+    OpenMMEngine
diff --git a/docs/event.rst b/docs/event.rst
@@ -0,0 +1,11 @@
+.. _event:
+
+.. currentmodule:: adaptivemd
+
+Events
+------
+
+.. automodule:: adaptivemd.event
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/file.rst b/docs/file.rst
@@ -8,7 +8,9 @@ File Functions
 .. autosummary::
     :toctree: api/generated/
 
-    ~file.Location
-    ~file.File
-    ~engine.Trajectory
-    ~engine.Frame
+    Location
+    File
+    Trajectory
+    Frame
+    JSONFile
+    ~mongodb.DataDict
diff --git a/docs/index.rst b/docs/index.rst
@@ -9,7 +9,7 @@ Documentation
 =============
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    install
    examples
@@ -23,6 +23,7 @@ Documentation
    scheduler
    worker
    adaptivemd
+   logentry
    subpackages
    api/index
 

diff --git a/docs/logentry.rst b/docs/logentry.rst
@@ -0,0 +1,11 @@
+.. _logentry:
+
+.. currentmodule:: adaptivemd
+
+LogEntry Functions
+==================
+
+.. autosummary::
+    :toctree: api/generated/
+
+    LogEntry
diff --git a/docs/project.rst b/docs/project.rst
@@ -1,11 +1,10 @@
 .. _project:
 
-.. currentmodule:: adaptivemd.project
+.. currentmodule:: adaptivemd
 
 Project Functions
 =================
 
-
 .. autosummary::
     :toctree: api/generated/
 

diff --git a/docs/resource.rst b/docs/resource.rst
@@ -1,6 +1,6 @@
 .. _resource:
 
-.. currentmodule:: adaptivemd.resource
+.. currentmodule:: adaptivemd
 
 Resource Functions
 ==================

diff --git a/docs/scheduler.rst b/docs/scheduler.rst
@@ -1,6 +1,6 @@
 .. _scheduler:
 
-.. currentmodule:: adaptivemd.worker
+.. currentmodule:: adaptivemd
 
 Scheduler Functions
 ===================

diff --git a/docs/task.rst b/docs/task.rst
@@ -1,11 +1,10 @@
 .. _task:
 
-.. currentmodule:: adaptivemd.task
+.. currentmodule:: adaptivemd
 
 Task Functions
 ==============
 
-
 .. autosummary::
     :toctree: api/generated/
 

diff --git a/docs/worker.rst b/docs/worker.rst
@@ -1,6 +1,6 @@
 .. _worker:
 
-.. currentmodule:: adaptivemd.worker
+.. currentmodule:: adaptivemd
 
 Worker Functions
 ================