Internal updates to build infrastructure

This release does not change the functionality but does upgrade the CI infrastructure to use black rather than yapf for code formatting.

Second major version

Complete rewrite of the templates and subsets, plus a fundamental change to the underlying database. This version correctly handles changing bonds and atoms.

Bugfix for reading mol & gif files

The release fixes a problem reading in mol or cif files. The data in the system was not cleared before reading the structure, leading to strange results.

Adding functionality for setting coordinates and deleting atoms

The release is needed for plug-ins and workflows that set the coordinates -- which is most! -- and for deleting atoms or bonds.

Fixed issue#16, errors setting the cell for periodic system.

Merge pull request #17 from molssi-seamm/issue#16

Issue#16 Problem setting the cell in periodic systems.

Fix for bugs with systems with no bonds.

Merge pull request #15 from molssi-seamm/hotfix

Hotfix for missed code with hydrogen atoms needed for atom typing.

SQLite based system structures

The first version based on SQLite to provide a native file format. Reasonably complete implementation with periodicity, templates and subsets.

Initial, complete version with atoms, bonds and cell.

0.9

Updated to latest version of numpy.