Gctree

Summary
- A major enhancement for parsimony tree search is the use of a [history DAG](https://matsengrp.github.io/historydag/) to expand the set of trees found by dnapars, often by orders of magnitude. h/t willdumm
- Tree ranking can now use a linear combination of branching process likelihood, isotype parsimony, and mutability parsimony (e.g. from a 5mer context model) to score trees.

Backwards-incompatible changes
- The `CollapsedForest` class no longer has a `trees` attribute, as the collection of trees is now represented as a history DAG.
- The gctree CLI can now accept pickled parsimony forests from the current gctree version, but not from older versions.
- Only the unique optimal tree is output by `gctree infer`, if it exists. If more than one tree is optimal, up to 10 will be output arbitrarily, and their numerical rankings will be arbitrary (rather than based on likelihood as before).

Pull requests
* Fit parameters on history DAG by willdumm in https://github.com/matsengrp/gctree/pull/68
* Add ambiguous sequence test and error message by willdumm in https://github.com/matsengrp/gctree/pull/72
* Transplant docs by WSDeWitt in https://github.com/matsengrp/gctree/pull/73
* Transplant patch by WSDeWitt in https://github.com/matsengrp/gctree/pull/74
* Docs fixes by WSDeWitt in https://github.com/matsengrp/gctree/pull/76
* Update README.md by WSDeWitt in https://github.com/matsengrp/gctree/pull/77
* Store isotype data in nodes by willdumm in https://github.com/matsengrp/gctree/pull/75
* Mutability chain split by willdumm in https://github.com/matsengrp/gctree/pull/78
* Prerelease tidying by WSDeWitt in https://github.com/matsengrp/gctree/pull/79


**Full Changelog**: https://github.com/matsengrp/gctree/compare/v3.3.0...v4.0.0

What's Changed
* Add isotype utility by willdumm in https://github.com/matsengrp/gctree/pull/65. See new sections in [API docs](https://matsengrp.github.io/gctree/cli.html#isotype) and [Quickstart](https://matsengrp.github.io/gctree/quickstart.html#isotype).
* A new [docs page](https://matsengrp.github.io/gctree/rendering-demo.html) demoing tree visualization by WSDeWitt in https://github.com/matsengrp/gctree/pull/69
* LB metrics for CollapsedTree with [new method](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedTree.html#gctree.CollapsedTree.local_branching), by WSDeWitt in https://github.com/matsengrp/gctree/pull/69
* [New method](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedTree.html#gctree.CollapsedTree.feature_colormap) for generating a colormap from any numerical node feature in a CollapsedTree, by WSDeWitt in https://github.com/matsengrp/gctree/pull/69
* Sequence-based fitness and seeding with more than one cell for simulation in [`mutation_model.MutationModel`](https://matsengrp.github.io/gctree/stubs/gctree.mutation_model.html#gctree.mutation_model.MutationModel.simulate) by WSDeWitt in https://github.com/matsengrp/gctree/pull/69

**Full Changelog**: https://github.com/matsengrp/gctree/compare/v3.2.1...v3.3.0

Patches a problem with resolution of ambiguous DNA characters in `dnapars` output.

h/t willdumm

New API tree rendering options `scale`, `branch_margin`, and `node_size` described in [docs](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedTree.html#gctree.CollapsedTree.render).

Patches
--
- Fixed a bug in empirical Bayes estimation of branching process parameters for `CollapsedForest`. Previous version v3.1.0 may have resulted in incorrect parsimony tree ranking
- `CollapsedTree.render()` can now be used in a Jupyter notebook for tree visualization
- Parameter checking for more flexible branching process simulations

New features
--
- The CLI program [`gctree infer`](https://matsengrp.github.io/gctree/cli.html#infer) writes a pickled [`CollapsedTree`](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedTree.html) object for each parsimony tree, which can be later loaded and manipulated via the API.
- Updates to [`CollapsedTree.render`](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedTree.html#gctree.CollapsedTree.render) to annotate amino acid substitutions, and associated new parameters in API and CLI. **Note:** these parameters are not supported by the scons pipelines, which are deprecated.
- Classes [`CollapsedTree`](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedTree.html) and [`CollapsedForest`](https://matsengrp.github.io/gctree/stubs/gctree.CollapsedForest.html) are exposed at package level, so they can be imported directly rather than from the [`branching_processes`](https://github.com/matsengrp/gctree/blob/master/gctree/branching_processes.py) module.
- Many improvements in documentation: [matsengrp.github.io/gctree](https://matsengrp.github.io/gctree/)

Developer notes
--
- The [`branching_processes`](https://github.com/matsengrp/gctree/blob/master/gctree/branching_processes.py) module has been refactored to remove illegitimate inheritance
- Better default `p, q` parameters for MLE avoid gradient warnings.