Mbuild

Breaking Changes
This is the last release including official support for Python 3.5. It will likely work for some time but mBuild will not be tested on Python 3.5 during development.

Features
* Residue names can optionally be inferred from compound names in conversion to ParmEd (475)
* Custom cross-interactions (NBFIXES in ParmEd jargon) can now be written to LAMMPS data files (456)
* The LAMMPS writer now prints helpful comments to more verbosely describe which atom types are associated with each potential (535)

Maintenance
* Some stylistic changes were made as suggested by various linters (522)
* Appveyor now tests on Python 3.6 (520)

Documentation
* Installation docs were updated to explicitly list supported Python versions (532)
* A comment pointing to the `glozter` Anaconda channel has been updated to point to `conda-forge` (534)

Miscellaneous
* Some tests depending on `foyer` are now properly skipped when it it not installed (521)
* Some examples were updated in accordance with their new structure as internal recipes (536, 538)

Features
* A plugin or "recipe" architecture has been added to allow external modules to be imported inside of mBuild (501)
* Python 3.6 is now explicitly supported and tested (518)

Maintenance
* A contributor's guide (500) and `.github` issue & pull request templates (498) have been added
* A redundant and unused block of code was removed (515)
* The `glotzer` and `bioconda` channels, which are now obsolete in this scope, have been dropped (516)

Breaking Changes
* When writing hoomdxml files, units will now be in kJ/mol & nm instead of kcal/mol & ang, so particle positions will differ by a factor of 10.

Features
* A `to_networkx` function was added to convert the hierarchy of a compound to a graph (484)
* Packing functions now use XYZ files while running PACKMOL, bypassing some issues with PDB files (422)
* When saving hoomdxml files, `auto_scale=True` will scale reference units from max forcefield parameters. (488)

Maintenance
* Switched to codecov for code coverage testing (485)
* Some dependencies accidentally missing in earlier PRs were cleaned up (493)

Bugfixes
* `update_coordinates` now behaves well when passed an XYZ file or operating on simple hierarchies (496)
* Internal conversion from ParmEd structures to HOOMDXML files was improved (463, see above)

Features
* Special Pair Support (1-4 pair information) to GSD writers (473)
* GSD files now include 1-4 special pairs for use in OPLS

Misc and Bugfixes
* Dependency requirements have been updated (457)
* A dependency loop between `Foyer` and `mBuild` has been resolved
* Fixed a bug that prevented Appveyor builds from running (477)
* Temporary PDB files left behind by packing functions are now properly removed (471)
* Packing.py uses temporary files which were previously never closed. This sometimes caused the program to reach the limit of open files for a process set by the OS
* `pytest-ignore-flaky` has been replaced in favor of `xfail` (471)
* Additonal fixes for PACKMOL input files (474)
* Input files are now closed by `mBuild` in order to ensure it can be read by PACKMOL
* Error reporting is now caught when the subprocess returns an error code
* Microsoft VSCode extraneous files are now ignored by git (478)

Features
* Packing functions can optionally constrain the rotation of `Compounds` when using `fill_box` (407)
* Additional lammps datafile support (412)
* Add functionality for `atomic`, `charge`, and `molecular` atom_styles
* Fix `atomic` and `molecular` atom-styles
* Add optional `atom-style` argument to `save` function
* Add tests to check for correct `Atoms` format
* A `Compound` can be generated from a SMILES string if the user has [Open Babel](http://openbabel.org/wiki/Main_Page) installed (430)
* The [website](https://mosdef-hub.github.io/mbuild/) was updated with details how to properly cite mBuild (421)
* OpenMM can now be used for energy minimization (416)
* A simple xyz file reader was added (423)
* Defaults in `Compound.visualize` have been improved (438)
* mBuild boxes can now store angles (448)
* mBuild boxes can now be passed to various writers (448)
* A changelog is now included in the root directory (454)

Misc and Bugfixes
* Switched from OpenMM to MDTraj to check for element existence (408)
* Changed bilayer notebook to use `Compound` methods for object manipulation (406)
* Added test to ensure that users can provide a custom forcefield XML file when applying a forcefield to a `Compound` (431)
* An error is now generated if the miniconda MD5 sum does not match when performing tests (409)
* LAMMPS box values are now written appropriately in Angstroms (459)
* Coordinates in HOOMDXML and GSD files are now correctly written in the range [L /2 to L] (452)
* A bug in the ordering of some Bravais angles in non-rectangular lattices has been fixed (450)

Features
* Improved packing API
* `fill_box` method now supports user-specified densities (372)
* Support for non-cubic boxes (385)
* Added edge buffer for pseudo-support of periodic boundaries (385)
* Allow users to access PACKMOL raw output (385)
* Improve documentation and removed repetitious code (385)
* Proper support for triclinic lattices (386)
* More intuitive `Port` behavior when adding/removing bonds
* `Ports` are now added along the bond vector when bonds are removed
* `Ports` are removed when using `force_overlap` when attribute `add_bond` is `True` (390)
Misc and Bugfixes
* Increased precision of PACKMOL overlap tolerance (367)
* Increased robustness for `packing.py` argument types (368)
* Continuous Integration (CI) fixes (369, 375, 392, 402, 405)
* Documentation updates (371)
* Combining rules for non-bonded interactions can now be specified when saving compounds (377)
* Remove ambigious data types for `Box` attributes (384)
* Fixed changing of basis for non-cubic lattices (386)
* Fixed issue where `Ports` were not aligned properly along user-specified direction (390)
* Add support for controlling `Foyer` warning verbosity when saving `Compounds` (391)
* Added more information to `Port.__repr__` (396)
* Fixed bug in unit conversion for periodicity in `Compound.from_parmed()` (401)
* Rounding `Lattice.lattice_point` positions to 0. when below a certain threshold (404)