Piqtree2

ENH

- Add support for Lie Markov Models.
- Base frequencies default to None (specified by model).

BUG

- `piqtree2` apps are now pickleable (they can now be run with `parallel=True` in the cogent3 app infrastructure)

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Contributors

- rmcar17 Added new classes to enhance model specification when calling `build_tree` and `fit_tree`.
- thomaskf fixed a bug in IQ-TREE resulting in segmentation faults on some invalid arguments.

ENH

- `build_tree` and `fit_tree` now allow specifying base frequencies, invariable sites and rate heterogeneity options.

BUG

- Fixed a segmentation fault on repetitive calls to IQ-TREE with particular arguments.

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Contributors

- Richard Morris
- Robert McArthur

ENH

- `build_tree` and `fit_tree` now use enums for the substitution model.

BUG

- Fixed an issue where calling `build_tree` or `fit_tree` twice, then another function with invalid input resulted in a segmentation fault.

DOC

- Implement scriv as a tool to manage collection of changes, and automated collation into the changelog