Foyer

Breaking Changes
* Officially drop Python 2.7 (257)

Features

* Add workaround function for applying nbfixes (268)
* Store atomtyping results in a dict instead of the topology (249)
* Add `overrides` term to `xml_writer` (254)
* Remove undefined atom types from SMARTS string in `xml_writer` (255)

Bug fix

* Change `OS` oxygen atoms in silica.mol2 file to `O` (260)

Maintenance

* Use vector graphics for gitter badge on the README.md (248)
* Update links for COMMAT paper (251)
* Enforce deletion of temporary XML files (252)
* Update links in README.md (253)
* Improve documentation of various Foyer classes and functions (261, 263, 266)
* Remove duplicate docs files (270)
* Add some pytest skips for `has_mbuild = False` (272)

Breaking Changes

Foyer now officially supports Python 3.7. Python 3.5 is no longer packaged or used in development testing. (247)

Features

* Foyer can now write a Foyer XML from a parametrized ParmEd structure (161, 241)
* Foyer now supports CHARMM-style periodic torsions (165)

Maintenance

* A conftest.py file as added to delete temporary files generated while testing writers (245)
* A compatibility issue with OpenMM 7.3+ has been resolved (246 or see commits by ahy3nz in 247)

paper_COMMAT_2019
Foyer software and examples associated with our year 2019 publication in Computational Materials Science. This paper is also available on arXiv.

Bugfixes

This is a bugfix release, fixing an issue in the conda recipe not caught until packaging the previous release ( 23ba645d75830e53e3352a1589ad2f1dd790bbc3)

Features
* SMARTS strings are now parsed with `lark` instead of `plyplus`, which is no longer being developed. `lark` is more modern and appears to be more performant. (224)
* The whitelists and blacklists used in resolving atom types now use built-in sets.
* Python 3.6 is now supported (204)

Maintenance
* A number of dependencies have been dropped (`MDTraj`: 4c0020a, `plyplus`: 224, `oset`: 231)
* `networkx` is now pinned to v2.0+ to avoid using previous versions that are no longer compatible.
* A contributor's guide has been added (214)
* Some issue and PR templates for GitHub have been added (215)
* Codecov is now used as part of the CI routine (227)
* Conda builds are once again done with `noarch` (218)
* Python 2.7 is not tested on Appveyor, though it is still being tested in Travis CI and is still officially supported.

Bugfixes
* An incorrect mass in `oplsaa.xml` has been fixed (236)

Features
* Similar to previous checks on angle and dihedral parameters (155), sanity checks can now (optionally) be done on the existence of bond parameters. (199)
* An error is now thrown when trying to atom-type using a force field that has no atom types defined (i.e. an empty force field). (194)

Maintenance
* mBuild is now an optional ("dev") dependency. The core features of Foyer do not rely on mbuild, but some tests do. Atom-typing mBuild compounds to `Forcefield.apply()` is unchanged. (207)
* The .gitignore file has been updated for compatability with VSCode. (197)

Documentation
* A link to our preprint was added to the README. (202)

Bug Fixes
OpenMM is pinned to versions before 7.3 (190)
MDTraj is now a dependency as a temporary fix to a dependency loop with mBuild (190)