Merge branch 'master' into ray_documentation

.gitignore

@@ -86,3 +86,13 @@ Icon
 Network Trash Folder
 Temporary Items
 .apdisk
+
+# GROMACS files
+*.cpt
+*.edr
+*.xtc
+*.trr
+*.tpr
+
+# LAMMPS files
+*.lammpstrj

README.md

@@ -1 +1,3 @@
-## Topology: Flexible storage of chemical topology for molecular simulation
+## GMSO: General Molecular Simulation Object
+
+Flexible storage of chemical topology for molecular simulation

azure-pipelines.yml

@@ -30,7 +30,7 @@ jobs:
 
       - bash: |
           source activate test-environment
-          python -m pytest -v topology
+          python -m pytest -v gmso/tests/ 
         displayName: Run Tests
 
 

docs/conf.py

@@ -17,7 +17,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'topology'
+project = 'gmso'
 copyright = '2020, mosdef-hub, Vanderbilt University'
 author = 'Matt Thompson, Alex Yang, Ray Matsumoto, Parashara Shamaprasad, Umesh Timalsina, Co Quach, Ryan S. DeFever, Justin Gilmer'
 

docs/contributing.rst

@@ -1,3 +1,56 @@
 Contributing
-------------
-plz help
+============
+Contributions are welcomed via `pull requests on GitHub <https://github.com/mattwthompson/topology/pulls>`_. Developers and/or
+users will review requested changes and make comments. The rest of this file will serve as a set of general guidelines
+for contributors.
+
+Features
+--------
+Implement functionality in a general and flexible fashion
+*********************************************************
+GMSO is designed to be general and flexible, not limited to single chemistries, file formats, simulation engines, or
+simulation methods. Additions to core features should attempt to provide something that is applicable to a variety of
+use-cases and not targeted at only the focus area of your research. However, some specific features targeted toward
+a limited use case may be appropriate. Speak to the developers before writing your code and they will help you make design
+choices that allow flexibility.
+
+Version control
+---------------
+
+We currently use the "standard" Pull Request model. Contributions should be implemented on feature branches of forks.
+Please try to keep the `master` branch of your fork up-to-date with the `master` branch of the main repository.
+
+Propose a single set of related changes
+****************************************
+
+Small changes are preferred over large changes. A major contribution can often be broken down into smaller PRs. Large PRs that
+affect many parts of the codebase can be harder to review and are more likely to cause merge conflicts.
+
+Source code
+-----------
+Use a consistent style
+*************************
+It is important to have a consistent style throughout the source code. The following criteria are desired:
+
+* Lines wrapped to 80 characters
+* Lines are indented with spaces
+* Lines do not end with whitespace
+* For other details, refer to `PEP8 <https://www.python.org/dev/peps/pep-0008>`_
+
+To help with the above, there are tools such as `flake8 <https://pypi.org/project/flake8/>`_ and `Black <https://github.com/psf/black>`_.
+
+Document code with comments
+****************************
+All public-facing functions should have docstrings using the numpy style. This includes concise paragraph-style description
+of what the class or function does, relevant limitations and known issues, and descriptions of arguments. Internal functions
+can have simple one-liner docstrings.
+
+
+Tests
+-----
+Write unit tests
+****************
+All new functionality in GMSO should be tested with automatic unit tests that execute in a few seconds. These tests
+should attempt to cover all options that the user can select. All or most of the added lines of source code should be
+covered by unit test(s). We currently use `pytest <https://docs.pytest.org/en/latest/>`_, which can be executed simply by calling
+`pytest` from the root directory of the package.

docs/data_structures.rst

@@ -1,53 +1,53 @@
-Data Structures in topology
+Data Structures in GMSO 
 ---------------------------
-Following data structures are available within topology, which are generally referred to  `CoreMembers` and `CoreTypes`.
+Following data structures are available within GMSO, which are generally referred to  `CoreMembers` and `CoreTypes`.
 
 Core Members
 =============
 
 Site
 ****
-    .. autoclass:: topology.Site
+    .. autoclass:: gmso.Site
         :members:
 
 Bond
 ****
-    .. autoclass:: topology.Bond
+    .. autoclass:: gmso.Bond
         :members:
 
 Angle
 *****
-    .. autoclass:: topology.Angle
+    .. autoclass:: gmso.Angle
         :members:
 
 Dihedral
 ********
-    .. autoclass:: topology.Dihedral
+    .. autoclass:: gmso.Dihedral
         :members:
 
 Potential Classes(CoreTypes)
 ============================
-    .. autoclass:: topology.Potential
+    .. autoclass:: gmso.Potential
         :members:
 
 AtomType
 ********
-    .. autoclass:: topology.AtomType
+    .. autoclass:: gmso.AtomType
         :members:
 
 BondType
 ********
-    .. autoclass:: topology.BondType
+    .. autoclass:: gmso.BondType
         :members:
 
 AngleType
 **********
-    .. autoclass:: topology.AngleType
+    .. autoclass:: gmso.AngleType
         :members:
 
 DihedralType
 ************
-    .. autoclass:: topology.DihedralType
+    .. autoclass:: gmso.DihedralType
         :members:
 
 

docs/design_principles.rst

@@ -2,16 +2,16 @@
 Design Principles
 =================
 
-Scope and Features of ``Topology``
+Scope and Features of ``GMSO``
 ----------------------------------
 
-``Topology`` is designed to enable the flexible, general representation of
+``GMSO`` is designed to enable the flexible, general representation of
 chemical topologies for molecular simulation. Efforts are made to enable
 lossless, bias-free storage of data, without assuming particular chemistries,
 models, or using any particular engine's ecosystem as a starting point. The
 scope is generally restrained to the preparation, manipulation, and conversion
 of and of input files for molecular simulation, i.e. before engines are called
-to execute the simulations themselves. ``Topology`` currently does not support
+to execute the simulations themselves. ``GMSO`` currently does not support
 conversions between trajectory file formats for analysis codes. In the scope of
 molecular simulation, we loosely define a chemical topology as everything
 needed to reproducibly prepare a chemical system for simulation. This includes
@@ -20,7 +20,7 @@ particle coordinates and connectivity, box information, force field data
 some optional information that may not apply to all systems (i.e. specification
 of elements with each particle).
 
-``Topology`` enables the following features:
+``GMSO`` enables the following features:
 
 * Supporting a variety of models in the molecular simulation/computational
   chemistry community: No assumptions are made about an interaciton site
@@ -40,7 +40,7 @@ of elements with each particle).
 
 
 * Compatibility with existing community tools: No single molecular simulation
-  tool will be a silver bullet, so ``Topology`` includes functions to convert
+  tool will be a silver bullet, so ``GMSO`` includes functions to convert
   objects. These can be used in their own right to convert between objects in
   memory and also to support conversion to file formats not natively support at
   any given time. Currently supported conversions include ``ParmEd``,
@@ -52,10 +52,10 @@ of elements with each particle).
   libraries, for many more!
 
 
-Structure of ``Topology``
+Structure of ``GMSO``
 -------------------------
 There are three main modules within the Python package:
 
-* ``topology.core`` stores the classes that constitute the core data structures.
-* ``topology.formats`` stores readers and writers for (on-disk) file formats.
-* ``topology.external`` includes functions that convert core data structures between external libraries and their internal representation.
+* ``gmso.core`` stores the classes that constitute the core data structures.
+* ``gmso.formats`` stores readers and writers for (on-disk) file formats.
+* ``gmso.external`` includes functions that convert core data structures between external libraries and their internal representation.

docs/forcefield.rst

@@ -1,7 +1,7 @@
 ForceField
 ==========
-A force field class implemented for topology core objects
+A force field class implemented for GMSO core objects
 
-.. autoclass:: topology.ForceField
+.. autoclass:: gmso.ForceField
     :members:
 

docs/index.rst

@@ -1,10 +1,10 @@
-.. topology documentation master file, created by
+.. GMSO documentation master file, created by
    sphinx-quickstart on Mon Feb 24 11:46:58 2020.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Topology: Flexible storage of chemical topology for molecular simulation
-========================================================================
+GMSO: Flexible storage of chemical topology for molecular simulation
+====================================================================
 
 .. toctree::
    :hidden:

docs/installation.rst

@@ -5,7 +5,7 @@ Installation
 Installing dependencies with `conda <http://continuum.io/downloads>`_
 ---------------------------------------------------------------------
 
-Dependencies of ``Topology`` are listed in the file ``requirements.txt``. They
+Dependencies of ``GMSO`` are listed in the file ``requirements.txt``. They
 can be installed in one line:
 ::
 
@@ -40,7 +40,7 @@ Installing dependencies with `pip <https://pypi.org/project/pip/>`_
 Install an editable version from source
 ---------------------------------------
 
-Once all dependencies are installed, the ``Topology`` itself can be installed.
+Once all dependencies are installed, the ``GMSO`` itself can be installed.
 It is currently only available through its source code. It will be available
 through ``pip`` and ``conda`` in the future.
 ::
@@ -62,7 +62,7 @@ is made to support Python 2 because it is considered obsolete as of early 2020.
 Testing your installation
 -------------------------
 
-``Topology`` uses ``py.test`` to execute its unit tests. To run them, first install some extra depdencies:
+``GMSO`` uses ``py.test`` to execute its unit tests. To run them, first install some extra depdencies:
 ::
     $ conda install --file requirements-test.txt
 

examples/argon/argon.ipynb

@@ -14,7 +14,7 @@
    "metadata": {},
    "source": [
     "This example requires GROMACS. You can install it from source or conda via `conda install -c bioconda gromacs`.\n",
-    "You also need to `pip install -e` the topology package after February 14, 2020, when PR #121 was merged."
+    "You also need to `pip install -e` the topology or GMSO package after February 14, 2020, when PR #121 was merged."
    ]
   },
   {
@@ -27,10 +27,10 @@
     "warnings.filterwarnings('ignore')\n",
     "\n",
     "import mbuild as mb\n",
-    "import topology as topo\n",
-    "from topology.external.convert_mbuild import from_mbuild\n",
-    "from topology.formats.gro import write_gro\n",
-    "from topology.formats.top import write_top"
+    "import gmso\n",
+    "from gmso.external.convert_mbuild import from_mbuild\n",
+    "from gmso.formats.gro import write_gro\n",
+    "from gmso.formats.top import write_top"
    ]
   },
   {
@@ -72,7 +72,7 @@
     "top = from_mbuild(packed_system)\n",
     "\n",
     "# Load force field from XML\n",
-    "ff = topo.ForceField('ar.xml')\n",
+    "ff = gmso.ForceField('ar.xml')\n",
     "ar_type = ff.atom_types['Ar']\n",
     "\n",
     "# Manually set types, bypassing foyer or any atomtyping engine\n",

topology/core/angle.py → gmso/core/angle.py

@@ -1,20 +1,25 @@
 import warnings
 
-from topology.core.connection import Connection
-from topology.core.angle_type import AngleType
-from topology.exceptions import TopologyError
+from gmso.core.connection import Connection
+from gmso.core.angle_type import AngleType
+from gmso.exceptions import GMSOError
 
 
 class Angle(Connection):
     """A 3-partner connection between sites.
 
-    Partners
-    --------
-    connection_members: list of topology.Site
-        Should be length 3
-    connection_type : topology.AngleType
-    name : name of the angle
-        inherits the name attribute from Connection
+    This is a subclass of the gmso.Connection superclass.
+    This class has strictly 3 members in its connection members.
+    The connection_type in this class corresponds to gmso.AngleType.
+
+    Parameters
+    ----------
+    connection_members: list of gmso.Site
+        3 sites of an angle.
+    connection_type : gmso.AngleType, optional, default=None
+        AngleType of this angle.
+    name : str, optional, default="Angle"
+        Name of the angle. 
 
     Notes
     -----
@@ -33,8 +38,9 @@ def __init__(self, connection_members=[], connection_type=None, name="Angle"):
 
 def _validate_three_partners(connection_members):
     """Ensure 3 partners are involved in Angle"""
+    assert connection_members is not None, "connection_members is not given"
     if len(connection_members) != 3:
-        raise TopologyError("Trying to create an Angle "
+        raise GMSOError("Trying to create an Angle "
                 "with {} connection members". format(len(connection_members)))
 
     return connection_members
@@ -45,5 +51,5 @@ def _validate_angletype(contype):
     if contype is None:
         warnings.warn("Non-parametrized Angle detected")
     elif not isinstance(contype, AngleType):
-        raise TopologyError("Supplied non-AngleType {}".format(contype))
+        raise GMSOError("Supplied non-AngleType {}".format(contype))
     return contype