openpathsampling · jhprinz · Nov 19, 2015 · Nov 19, 2015 · Nov 26, 2015 · Dec 2, 2015
diff --git a/docs/Makefile b/docs/Makefile
@@ -2,7 +2,6 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build
@@ -46,6 +45,9 @@ help:
 	@echo "  linkcheck  to check all external links for integrity"
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
 
+rmapi:
+	rm -rf api/
+
 clean:
 	rm -rf $(BUILDDIR)/*
 

diff --git a/docs/api.rst b/docs/api.rst
@@ -68,3 +68,11 @@ Snapshot
 
 .. automodule:: snapshot
 	:members:
+
+**********
+Trajectory
+**********
+
+.. automodule:: trajectory
+	:members:
+
diff --git a/docs/collectivevariable.rst b/docs/collectivevariable.rst
@@ -4,8 +4,7 @@
 
 CollectiveVariable Functions
 ============================
-
-:class:`openpathsampling.CollectiveVariables`
+:class:`openpathsampling.CollectiveVariable`
 
     >>> import openpathsampling as paths
     >>> mover = paths.CollectiveVariable()
@@ -31,9 +30,11 @@ mdtraj orderparamters
 .. autosummary::
     :toctree: api/generated/
 
-    CV_MD_Function
+    CV_MDTraj_Function
 
 msmbuilder3 collectivevariables
 -------------------------------
+.. autosummary::
+    :toctree: api/generated/
 
-    CV_Featurizer
+    CV_MSMB_Featurizer
diff --git a/docs/conf.py b/docs/conf.py
@@ -42,24 +42,25 @@
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
     'sphinx.ext.ifconfig',
-    'IPython.sphinxext.ipython_console_highlighting',
-    'IPython.sphinxext.ipython_directive',
-    'matplotlib.sphinxext.plot_directive',
-    'numpydoc'
-#    ,'sphinxcontrib.napoleon'
+#    'IPython.sphinxext.ipython_console_highlighting',
+#    'IPython.sphinxext.ipython_directive',
+#    'matplotlib.sphinxext.plot_directive',
+#    'numpydoc'
+#     'sphinxcontrib.napoleon'
+    'sphinx.ext.napoleon'
 ]
 
 # Napoleon settings
-#napoleon_google_docstring = False
-#napoleon_numpy_docstring = True
-#napoleon_include_private_with_doc = False
-#napoleon_include_special_with_doc = False
-#napoleon_use_admonition_for_examples = False
-#napoleon_use_admonition_for_notes = True
-#napoleon_use_admonition_for_references = False
-#napoleon_use_ivar = False
-#napoleon_use_param = True
-#napoleon_use_rtype = True
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
 
 # add pandoc directives
 pandoc_from = ['markdown', 'mediawiki']

diff --git a/docs/engine.rst b/docs/engine.rst
@@ -13,7 +13,7 @@ engine basic
 .. autosummary::
     :toctree: api/generated/
 
-	DynamicsEngine
+    DynamicsEngine
 
 .. currentmodule:: openpathsampling.openmm_engine
 

diff --git a/docs/ensemble.rst b/docs/ensemble.rst
@@ -19,32 +19,86 @@ where you choose the right kind of ensemble and give it the right
 initialization parameters. What's more, ensembles can be combined using the
 logical infix operators `&` (and) and `|` (or).
 
+Abstract class
+--------------
+
+.. autosummary::
+    :toctree: api/generated/
+
+    Ensemble
+
+Basic Ensembles
+---------------
+.. autosummary::
+    :toctree: api/generated/
+
+        EmptyEnsemble
+        FullEnsemble
+
 Volume Ensembles
 ----------------
 .. autosummary::
     :toctree: api/generated/
 
-	VolumeEnsemble
-	AllInXEnsemble
-	AllOutXEnsemble
+        VolumeEnsemble
+        AllInXEnsemble
+        AllOutXEnsemble
         PartInXEnsemble
-	PartOutXEnsemble
-
+        PartOutXEnsemble
+        EntersXEnsemble
+        ExitsXEnsemble
+
 Set-based Ensemble combinations
 -------------------------------
 .. autosummary::
     :toctree: api/generated/
 
-        IntersectionEnsemble
-        UnionEnsemble
-        SymmetricDifferenceEnsemble
-        RelativeComplementEnsemble
-        EnsembleCombination
-
-length Ensembles
+    IntersectionEnsemble
+    UnionEnsemble
+    SymmetricDifferenceEnsemble
+    RelativeComplementEnsemble
+    EnsembleCombination
+    NegatedEnsemble
+
+
+Length specific Ensembles
+-------------------------
+.. autosummary::
+    :toctree: api/generated/
+
+    LengthEnsemble
+    SingleFrameEnsemble
+    OptionalEnsemble
+
+Trajectory Altering Ensembles
 -----------------------------
+
+.. autosummary::
+    :toctree: api/generated/
+
+    ReversedTrajectoryEnsemble
+    SuffixTrajectoryEnsemble
+    PrefixTrajectoryEnsemble
+    WrappedEnsemble
+
+Sequential Ensembles
+--------------------
+.. autosummary::
+    :toctree: api/generated/
+
+    SequentialEnsemble
+
+TIS-specific Ensembles
+----------------------
+.. autosummary::
+    :toctree: api/generated/
+
+    TISEnsemble
+    MinusInterfaceEnsemble
+
+Ensemble Functions
+------------------
 .. autosummary::
     :toctree: api/generated/
 
-        LengthEnsemble
-
+    join_ensembles
diff --git a/docs/examples/index.rst b/docs/examples/index.rst
@@ -23,7 +23,6 @@ examples and the notebooks are available in the top level
    :maxdepth: 3
    :glob:
 
-   introduction
    *
 
 Let us know if you would like to contribute other example notebooks, or have

diff --git a/docs/getting_started.rst b/docs/getting_started.rst
@@ -19,7 +19,7 @@ We recommend using `conda` to install OpenPathSampling.  `conda
 scientific python. Unlike ``easy_install`` or ``pip``, it handles binaries
 and binary dependencies, which are critical for most scientific workflows.
 If you're a ``conda`` user, you can install OpenPathSampling by adding the
-omnia channel. ::
+omnia channel.
 
 To install the most recent release of OpenPathSampling with conda, use the
 following commands ::

diff --git a/docs/absolute_beginners.md → docs/guides/absolute_beginners.md b/docs/absolute_beginners.md → docs/guides/absolute_beginners.md
diff --git a/...mbles_apply_to_trajectories_not_frames.md → ...mbles_apply_to_trajectories_not_frames.md b/...mbles_apply_to_trajectories_not_frames.md → ...mbles_apply_to_trajectories_not_frames.md
diff --git a/docs/guides/index.rst b/docs/guides/index.rst
@@ -0,0 +1,31 @@
+.. _guides:
+
+Guides to OpenPathSampling
+==========================
+
+This section contains larger texts that discuss more detailed the works of OpenPathSampling.
+
+.. markdown:: docs/guides/user_levels.md
+
+
+For Beginners
+-------------
+
+.. markdown:: docs/guides/absolute_beginners.md
+
+
+For advanced users
+------------------
+
+.. markdown:: docs/guides/power_users.md
+
+
+Topics
+======
+
+This part covers discussions about various topics.
+
+
+Ensembles vs Volumes
+--------------------
+
diff --git a/docs/power_users.md → docs/guides/power_users.md b/docs/power_users.md → docs/guides/power_users.md
diff --git a/docs/user_levels.md → docs/guides/user_levels.md b/docs/user_levels.md → docs/guides/user_levels.md
diff --git a/docs/index.rst b/docs/index.rst
@@ -13,46 +13,48 @@ Documentation
 -------------
 
 .. toctree::
-   :maxdepth: 2
+    :maxdepth: 2
 
-   getting_started
-   examples/index
-   whatsnew
-   faq
-   Discussion Forums <http://discourse.openpathsampling.org>
+    getting_started
+    examples/index
+    guides/index
+    whatsnew
+    faq
+    Discussion Forums <http://discourse.openpathsampling.org>
 
 API Reference
 -------------
 
 .. toctree::
-   :maxdepth: 1
-
-   core
-   collectivevariable
-   volume
-   ensemble
-   shooting
-   pathmover
-   pathsimulator
-   engine
-   storage
+    :maxdepth: 1
+
+    collectivevariable
+    volume
+    ensemble
+    shooting
+    pathmover
+    pathsimulator
+    engine
+    storage
+    treemixin
+    trajectory
 
 Developing
 ----------
 
 .. toctree::
-   :maxdepth: 1
+    :maxdepth: 1
 
-   netcdf_format
-   api
+    netcdfplus/index
+    api
 
 README
 ------
 
 .. toctree::
-   :maxdepth: 1
+    :maxdepth: 1
 
-   readme
+    readme
 
 --------------------------------------------------------------------------------
 

diff --git a/docs/netcdf_format.rst b/docs/netcdf_format.rst
diff --git a/docs/netcdfplus/base.rst b/docs/netcdfplus/base.rst
@@ -0,0 +1,17 @@
+.. _base:
+
+.. currentmodule:: openpathsampling.netcdfplus.base
+
+Base Functions
+==============
+
+
+mixins for storable objects
+---------------------------
+
+.. autosummary::
+    :toctree: api/generated/
+
+    StorableObject
+    StorableNamedObject
+
diff --git a/docs/netcdfplus/cache.rst b/docs/netcdfplus/cache.rst
@@ -0,0 +1,17 @@
+.. _cache:
+
+.. currentmodule:: openpathsampling.netcdfplus.cache
+
+Caching Functions
+=================
+
+.. autosummary::
+    :toctree: api/generated/
+
+    WeakKeyCache
+    WeakLRUCache
+    WeakValueCache
+    MaxCache
+    NoCache
+    Cache
+    LRUCache
diff --git a/docs/netcdfplus/dictify.rst b/docs/netcdfplus/dictify.rst
@@ -0,0 +1,12 @@
+.. _dictify:
+
+.. currentmodule:: openpathsampling.netcdfplus.dictify
+
+JSON Serialization Functions
+============================
+
+.. autosummary::
+    :toctree: api/generated/
+
+    ObjectJSON
+    StorableObjectJSON