Merge pull request #70 from datreant/new-awesome-improvment

update to datreant.core changes

.travis.yml

@@ -8,6 +8,8 @@ addons:
 
 python:
   - "2.7"
+  - "3.5"
+  - "3.6"
 
 # whitelist
 branches:
@@ -22,7 +24,7 @@ env:
 
 matrix:
   allow_failures:
-    - env: DATREANT_DEV="true"
+    - env: DATREANT_DEV="false"
 
 # install python dependencies
 install:

docs/api_sims.rst

@@ -22,20 +22,20 @@ The class :class:`mdsynthesis.Sim` is the central object of ``mdsynthesis``.
 
 UniverseDefinition
 ``````````````````
-The class :class:`mdsynthesis.limbs.UniverseDefinition` is the interface used by a Sim to
+The class :class:`mdsynthesis.metadata.UniverseDefinition` is the interface used by a Sim to
 define its :class:`MDAnalysis.Universe`.
 
-.. autoclass:: mdsynthesis.limbs.UniverseDefinition
+.. autoclass:: mdsynthesis.metadata.UniverseDefinition
     :members:
     :inherited-members:
 
 .. _AtomSelections_api:
 
 AtomSelections
 ``````````````
-The class :class:`mdsynthesis.limbs.AtomSelections` is the interface used by Sims to
+The class :class:`mdsynthesis.metadata.AtomSelections` is the interface used by Sims to
 get :class:`MDAnalysis.AtomGroup` objects from stored selection definitions. 
 
-.. autoclass:: mdsynthesis.limbs.AtomSelections
+.. autoclass:: mdsynthesis.metadata.AtomSelections
     :members:
     :inherited-members:

docs/datreant.rst

@@ -6,11 +6,6 @@ exposed in the MDSynthesis namespace.
 
 .. currentmodule:: datreant.core
 
-Functions
-=========
-.. autosummary::
-    discover
-
 Classes
 =======
 .. autosummary::
@@ -19,7 +14,6 @@ Classes
     Leaf
     View
     Bundle
-    Group
 
 Learning more
 =============

docs/sims.rst

@@ -138,7 +138,7 @@ kinase, the protein we simulated. We can store these immediately::
     >>> s.atomselections['core'] = ('resid 1:29', 'resid 60:121', 'resid 160:214')
 
 We can now get new AtomGroups back for each selection at any time with the 
-:meth:`~mdsynthesis.limbs.AtomSelections.create` method::
+:meth:`~mdsynthesis.metadata.AtomSelections.create` method::
 
     >>> s.atomselections.create('lid')
     <AtomGroup with 598 atoms>
@@ -161,7 +161,7 @@ work with many variants of a simulation system without having to micromanage.
           alignments.
 
 Want just the selection strings back? We can use
-:meth:`~mdsynthesis.limbs.AtomSelections.get`::
+:meth:`~mdsynthesis.metadata.AtomSelections.get`::
 
     >>> s.atomselections.get('lid')
     'resid 122:159'
@@ -182,7 +182,7 @@ indices instead of as a selection string? That can be done, too::
 
 Lists/tuples of selection strings or atom indices can be stored in any combination
 as a selection. These are applied in order to yield the AtomGroup when calling the 
-:meth:`~mdsynthesis.limbs.AtomSelections.create` method.
+:meth:`~mdsynthesis.metadata.AtomSelections.create` method.
 
 API Reference: AtomSelections
 -----------------------------

setup.cfg

@@ -1,2 +1,4 @@
-[pytest]
+[tool:pytest]
 pep8ignore = __init__.py E402
+filterwarnings= all
+                 ignore::UserWarning

setup.py

@@ -31,8 +31,6 @@
       long_description=open('README.rst').read(),
       install_requires=[
                 'datreant.core>=0.6.0',
-                'datreant.data>=0.6.0',
-                # TODO: update dependency to 0.16.0 once it's released
-                'MDAnalysis>=0.14.0',
+                'MDAnalysis>=0.16.0',
                 ],
       )

src/mdsynthesis/__init__.py

@@ -8,11 +8,11 @@
 ================================================================
 """
 # Bring some often used objects into the current namespace
-from datreant.core import Treant, Group, Bundle, Tree, Leaf, View
+from datreant.core import Tree, Leaf, View, Bundle
 from datreant.core import discover
 
 from .treants import Sim
-from . import attach
+from .manipulators import discover
 
-__all__ = ['Sim', 'Group', 'Bundle']
+__all__ = ['Sim', 'Bundle', 'discover', 'Tree', 'Leaf', 'View']
 __version__ = "0.6.2-dev"  # NOTE: keep in sync with RELEASE in setup.py