Pachyderm

Added

- New YAML module to create YAML objects, register classes + modules for reading and writing, and additional
helper functions. It generally encapsulate much of the basic YAML functionality. See: `e8009517`.
- Pre-commit hooks configuration to the repository based on `pre-commit`. This should generally improve the
quality of commits. Currently includes `flake8`, `mypy`, `yamllint`, and some additional minor python
checks. See: `586c1549` and `0510a0ba`.
- YAML linting via `yamllint`. Little is done with this yet, but more files should filter in, so it's useful
to have . See: `a6bc250f`.

Fixed

- Fixed breaking change made by `ruamel.yaml` upstream related to base python types receiving anchor support.
It is a good start, but still needs some time to mature for our purposes. Also expanded the tests to check
for such issues. See: `9aa7f4b7` (the commit message has far more information).
- Minor test improvements for `generic_config`. See: `d723bbcb`.

Fixed

- Mixin approach for enum values to/from YAML causes problems with pickling (which is implicitly called while
copying). Revised the approach to be unbound functions, which doesn't have this same problem. See:
`89159dc9`.

Added

- Enumeration YAML read and write mixins. They utilize the `__name__` of the enumeration (not the value!).
See: `3f987afb`.

Changed

- Allow for classes to be registered and constructed via YAML. See: `b877a09e`
- Allows for set of iterable values to be specified in a configuration file. Often used in conjunction
with creating objects in YAML. See: `7cab0476`.

Changed

- Convert each argument via `str()` in the generic_config instead of `obj.str()` which is less portable and
pythonic. Precipitated by changes in the definition of enumeration classes in the jet-hadron package. See:
`595ef2a8`.

Added

- Include `--ignore-missing-includes` when running `mypy` automatically. See: `0ac7d0bd`.
- Full type annotations for the package. See: `a83372b1`.

Changed

- Fully updated API naming scheme to follow python conventions. See: `cd097f3b`, `c7bedc6b`, `68048970`, and
`7d8b1ca9`.
- Remove `pkgconfig` workaround introduced in `4a3c6216` since `python-lz4` merged in an alternative
[approach](https://github.com/python-lz4/python-lz4/pull/160) to workaround the issue. See: `755c276a`.

Added

- Added `mypy` to Travis CI checks. See: `2c6f7dc0`.

Changed

- Reworked iteration over analysis dictionaries. See: `0ead6db8`.
- Updated overwatch-base python version. See: `39fede7e`.

Fixed

- Existing typing issues identified by `mypy`.