Py2sambvca

- citation updated
- added type hints to constructor
- small python style/security changes
- 100% (!!) code coverage and a pull request coverage verification action/branch protection

What's Changed
* `py2sambvca` v1.3.1 by JacksonBurns in https://github.com/JacksonBurns/py2sambvca/pull/18


**Full Changelog**: https://github.com/JacksonBurns/py2sambvca/compare/v1.3.0...v1.3.1

This release to `py2sambvca` adds a new optional argument to specify a 'working directory', in which all input and output files will be placed. Thanks to GwydionJon for opening the PR!

__v1.3.0__ maintains backwards compatibility with all __v1.*__ releases of `py2sambvca`.

What's Changed
* Added ability to set working directory by GwydionJon in https://github.com/JacksonBurns/py2sambvca/pull/7

New Contributors
* GwydionJon made their first contribution in https://github.com/JacksonBurns/py2sambvca/pull/7

**Full Changelog**: https://github.com/JacksonBurns/py2sambvca/compare/v1.2.0...v1.3.0

What's Changed
This update to `py2sambvca` includes _significant_ quality of life improvements for the codebase, as well as a complete backend re-write to enable the addition of a multitude of useful functions:
- README now contains better examples
- All functions interfacing with the output of `py2sambvca` now use a single internal `get_regex` function
- Tests now cover __96%__ of the codebase
- `import` has been dramatically simplified
- All results from _SambVca_ are readily accessible through getters and class attributes.

This minor version maintains complete backwards compatibility with previous versions of `py2sambvca`.

New Functions
Running is now simple with the single line `run()` function.

All values for the total complex, quadrants, and octants are available through getters:

Total Values:
- `get_free_volume()`
- `get_buried_volume()`
- `get_exact_volume()`
- `get_total_volume()`
- `get_percent_buried_volume()`
- `get_percent_free_volume()`
- `get_percent_total_volume()`

Quadrant Values:
- `get_quadrant_free_volume()`
- `get_quadrant_buried_volume()`
- `get_quadrant_total_volume()`
- `get_quadrant_percent_buried_volume()`
- `get_quadrant_percent_free_volume()`

Octant Values:
- `get_octant_free_volume()`
- `get_octant_buried_volume()`
- `get_octant_total_volume()`
- `get_octant_percent_buried_volume()`
- `get_octant_percent_free_volume()`

Results can also be accessed through a general getter method: `get()`, `get_quadrant_result()`, and `get_octant_result()`.

All results can also be directly accessed through dictionaries, returned from a call to `run()` or `parse_output()` and available through `p2s.total_results`, `p2s.quadrant_results`, and `p2s.octant_results`.

In case there is something else you are looking for, you can use a general purpose `get_regex()` function to return the line containing a pattern.

PR's and Changelog
* Quality of Life Improvements for `py2sambvca` by JacksonBurns in https://github.com/JacksonBurns/py2sambvca/pull/2
* get version from __init__ by JacksonBurns in https://github.com/JacksonBurns/py2sambvca/pull/3

**Full Changelog**: https://github.com/JacksonBurns/py2sambvca/compare/v1.1.0...v1.2.0

Added method 'parse_output()' to retrieve more values from the output file.

v1.1.0 also contains some general repository cleanup -- removal of .pyc, dist files, etc.

py2sambvca
Simple thin client to interface python scripts with SambVca catalytic pocket Fortran calculator.

Installation
`py2sambvca` is available on PyPi and can be installed like so:
python
pip install py2sambvca


Usage
After installation, `py2sambvca` can be added to a Python script via `import` and instantiated:
python
import the class and give it a simpler alias
from py2sambvca.py2sambvca import py2sambvca as p2s

buried_vol = p2s(r'myxyzfiles\ligand_4.xyz',...)
buried_vol.write_input()
buried_vol.calc()

retrieve the buried volume and assign it
ligand_4_buried_volume = buried_vol.get_buried_vol()
...
clean up input and output files
buried_vol.clean_files()


License
`py2sambvca` is available under the GNU GPLv3 in accordance with the base Fortran code which is available under the same license and can be retreieved here: https://www.molnac.unisa.it/OMtools/sambvca2.1/download/download.html

Updates
Version 1.0.0 is the initial release of `py2sambvca`.