Catkit

- Final release for code utilized in the manuscript

- Minor corrections to the surface generator module when performing cleaves with 0 in miller index.

- Linked adsorbate construction to the molecule 3D generator module.

- Bug fix in the conversion between standard and primitive unit cell basis
- Change of the default settings in slab generation to help people using the SlabGenerator class directly
- Periodically constrained orthogonalization of the bulk unit cell to help with numerical problems of surface atom identification.

1. Heavy reconfiguration of the slab generation algorithm. First stable release for complete functionality set.
- Matrix notation for surface sizing and an algorithm for orthogonalized cell search.
- Bulk primitive unit cell first.
- All cells are standardized by default. Miller indices are taken with respect to the standard cell.
- Proper handling of the connectivity graph
- The process is broken into 3 stages of various symmetry conservation.


2. 3D molecule generation algorithm
- RDKit testing and functionality removed.

3. Cathub module added.
- Catalysis-hub.org CLI

4. Misc
- Testing databases removed and packaged reduced to below 2MB.
- Requirements significantly relaxed, RDKit testing removed, scipy>=0.19.

- catkit.build module added to easy access to most commonly used generation features.
- First attempt at documentation on ReadTheDocs
- Last version which will use individual modules. Future versions will have all modules call from catkit...
- PawPrint module added for lightweight fingerprint designing.
- Catflow module added (will be moved to catkit.flow in the next release)

Refactoring of CatKit into the general modules (Gratoms) and the generator functionality, CatGen.

1. The first implementation of the Builder class (not tests)
- Need to include a more flexible enumeration of non-symmetric sites.

2. Molecule generation module to assist the user in creation of topological structures of small molecules.

**Additions:**
- Gratoms: atoms object with integrated graph
- Molecule and pathway enumerations made compatible with gratoms
- Fingerprint database

**Development:**
- Integration of slab and site enumeration with gratoms