Mbuild

Features
- Add `wrap_coords` function for wrapping particles into a box (643)

Bug Fixes
- Don't populate empty lists for hoomd snapshot (647)

Maintenance
- Add `nbval` as requirement for tests in conda recpe (656)
- Remove `six` and some Python 2 legacy code (641)
- Remove examples (from this repository) (658)
- Fix travis by not installing md5sha1sum (660)
- Add CHANGELOG (632)

Features
- Add Cassandra MCF writer (636)
- Add HOOMD snapshot converter (622)
- Generate `mb.Compound` from Parmed or MDTraj residues (526)
- Add `**kwargs` for `write_gsd` (653)

Bug Fixes
- Fix unique naming problem in `to_networkx` (583)
- Default the mBuild PAR-writer to use `IMPROPER` (648)
- Fix ghost ports attached to removed compound (593)
- Remove duplicate NP particles in TNP example (625)
- Only import MCF writer if `networkx` is installed (654)

Maintenance
- Add LGTM (616)
- Add Azure CI testing (615, 617, 618, 630, 637, 638)
- Update Travis CI (649)
- Update conda recipe to include nbval (611, 656)
- Pin `nglview` to 2.7+ (651, 655)
- Reduce length of some unit tests (621)
- Rename `AmorphousSilica` to be more descriptive (630)

This is a bugfix release to resolve a potential issue with a foyer dependency with mBuild 0.10.0.

Bugfixes
* Remove a `foyer` import that was producing a circular dependency (610)

Breaking Change
- Officially drop Python 2.7 (573)

Features
- Load mBuild compounds from existing ParmEd and MDTraj objects (561)
- Convert mBuild compound to and from JSON format (581)
- Include testing of notebooks in CI (590)
- Add NGLView tooltip (600)
- Initialize mBuild Compounds from SMILES strings (598)
- Write out parameterized structures to a CHARMM `.par` file (508)
- Add method to convert to and from Pybel (555)
- Add POSCAR file writer in an effort to incorporate VASP into mBuild (468)

Bug Fixes
- Remove unnecessary Pybel import statement in `mb.load` (604)
- Change how proxy compounds are named so that `MOL2` files are in the correct format (605)
- Rename atom names in silica interface example to be compatible with recent mBuild release (594)
- Improve error handling for Box class (576)
- Add a `with open` block to manage file open (585)
- Add `_clone()` function to the Proxy class to properly clone an instance of Proxy (592)

Miscellaneous
- Add `compound_pb2.py` file generated from `protoc` compiler to gitignore (602)
- Improve documentation of various mBuild classes and functions (577, 578, 579, 580)
- Add additional testing for `foyer_kwargs` (428)

Breaking Changes
* This is the last release supporting Python 2.7

Features
* A more descriptive exception is raised when attempting to access a non-existent Port (544)
* Element capitalization is better enforced in ParmEd conversions (550)
* The XYZ reader can now act on a passed compound (567)
* The LAMMPS writer now accurately prints residue IDs (569)

Bugfixes
* Visualizing compounds in notebooks no longer returns a duplicate widget (545)
* Names of custom elements are no longer clobbered during visualization (563)

Maintenance
* The image in our gitter link has been updated (543)
* Some links in tutorials have been corrected (548)
* Installation documentation has been updated to reflect changes in conda configurations (558)
* Some other documentation has been refreshed (560)
* The GSD version is pinned to 1.7 in order to continue Python 2.7 support (572)

Breaking Changes
* Python 3.5 is no longer officially supported or tested on as part of the development process.

Features
* mBuild is now tested and packaged on Python 3.7 (542)

Maintenance
* MDTraj is no longer pinned to an old version (542)
* Coveralls is dropped; we have been using codecov for a few months (542)