Gctree

What's Changed
* Update installation docs by willdumm in https://github.com/matsengrp/gctree/pull/80
* add potential Dockerfile + test.sh by psathyrella in https://github.com/matsengrp/gctree/pull/81
* Address Duncan's suggestions by willdumm in https://github.com/matsengrp/gctree/pull/85
* Fix multiple tree nodes with same name by willdumm in https://github.com/matsengrp/gctree/pull/86

New Contributors
* psathyrella made their first contribution in https://github.com/matsengrp/gctree/pull/81

**Full Changelog**: https://github.com/matsengrp/gctree/compare/v4.0.0...v4.0.1

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