Historydag

What's Changed
* Docs improvements by willdumm in https://github.com/matsengrp/historydag/pull/83
* Binary tree resolutions and fast sampling by willdumm in https://github.com/matsengrp/historydag/pull/84


**Full Changelog**: https://github.com/matsengrp/historydag/compare/v1.2.0...v1.3.0

Summary
This release was motivated by updated support for protobufs, in the style of mutation annotated dag protobuf format produced by our related tool `larch`. The previous style of DAG protobuf is no longer supported by `larch` or `historydag` (although the protobuf format has not changed, only its interpretation).

The other notable change is expanded implementation of RF distance computations on the DAG, including all combinations of standard or one-sided RF distance in both the rooted and unrooted sense. Options specifying these variants have been added to all RF distance methods.

What's Changed (automatically generated)
* Adjusted node probabilities by willdumm and williamhowardsnyder in https://github.com/matsengrp/historydag/pull/78
* graphviz dot file output improvements by willdumm in https://github.com/matsengrp/historydag/pull/79
* One Sided RF distances by willdumm in https://github.com/matsengrp/historydag/pull/80
* IntState vs FloatState fix for RF distances by willdumm in https://github.com/matsengrp/historydag/pull/81
* Ambiguous Protobuf Support by willdumm in https://github.com/matsengrp/historydag/pull/82


**Full Changelog**: https://github.com/matsengrp/historydag/compare/v1.1.0...v1.2.0

What's Changed
This release moves some infrastructure to `historydag.parsimony_utils`, and adds classes for defining data according to arbitrary character sets, with support for representing ambiguities, indicating the possibility of any subset of available bases. There are also many small improvements and feature additions below

Here follows the automatically generated list of changes:

* make `trim_optimal_weight` update parents by willdumm in https://github.com/matsengrp/historydag/pull/24
* Consistent Clade Ordering by willdumm in https://github.com/matsengrp/historydag/pull/25
* implemented node counting alg + added small tests by williamhowardsnyder in https://github.com/matsengrp/historydag/pull/19
* Node support annotation squashed by willdumm in https://github.com/matsengrp/historydag/pull/30
* squashed commits from node-utils branch by willdumm in https://github.com/matsengrp/historydag/pull/31
* 21 Fix Names by willdumm in https://github.com/matsengrp/historydag/pull/23
* Sankoff filtering cleanup by marybarker in https://github.com/matsengrp/historydag/pull/32
* working tests and implementation by willdumm in https://github.com/matsengrp/historydag/pull/34
* adding new sequences to a pre-existing DAG (no relabeling) by marybarker in https://github.com/matsengrp/historydag/pull/35
* Trimming weight range by clarisw in https://github.com/matsengrp/historydag/pull/36
* MADAG protobuf support by willdumm in https://github.com/matsengrp/historydag/pull/37
* Various bug fixes by willdumm in https://github.com/matsengrp/historydag/pull/40
* Quickstart suggestions by matsen in https://github.com/matsengrp/historydag/pull/44
* Wd general leaf path dag by willdumm in https://github.com/matsengrp/historydag/pull/46
* docs improvements by willdumm in https://github.com/matsengrp/historydag/pull/49
* Create subclass for ambiguous samples by willdumm in https://github.com/matsengrp/historydag/pull/47
* Expand Quickstart by willdumm in https://github.com/matsengrp/historydag/pull/50
* Implement Sum RF Distances by clarisw in https://github.com/matsengrp/historydag/pull/41
* Add HistoryDagFilter Object by willdumm in https://github.com/matsengrp/historydag/pull/51
* Add average pairwise RF distance method by willdumm in https://github.com/matsengrp/historydag/pull/53
* altered average_pairwise_rf_distance to avoid divide-by-zero in the c… by marybarker in https://github.com/matsengrp/historydag/pull/54
* Count optimal histories by willdumm in https://github.com/matsengrp/historydag/pull/56
* initial commit for adding alternate field name option by marybarker in https://github.com/matsengrp/historydag/pull/57
* fix compact genome mutation and add label change by willdumm in https://github.com/matsengrp/historydag/pull/59
* Implemented Estimate for RF Diameter by clarisw in https://github.com/matsengrp/historydag/pull/61
* Add beast tree loader by willdumm in https://github.com/matsengrp/historydag/pull/63
* HistoryDag subclass defaults by willdumm in https://github.com/matsengrp/historydag/pull/64
* Generalized node support by willdumm in https://github.com/matsengrp/historydag/pull/65
* reorganize dag.py by willdumm in https://github.com/matsengrp/historydag/pull/66
* reorganize dag.py by willdumm in https://github.com/matsengrp/historydag/pull/68
* Updating docstrings by marybarker in https://github.com/matsengrp/historydag/pull/69
* fix bug with parsimony for ambiguous leaf sequences by willdumm in https://github.com/matsengrp/historydag/pull/72
* updating sankoff to accommodate non-singleton-base transition models by marybarker in https://github.com/matsengrp/historydag/pull/71
* Jukes cantor likelihood by willdumm in https://github.com/matsengrp/historydag/pull/73
* minor improvements in parsimony_utils.py by harryrichman in https://github.com/matsengrp/historydag/pull/75
* add a few more tests for recent changes by willdumm in https://github.com/matsengrp/historydag/pull/74

New Contributors
* marybarker made their first contribution in https://github.com/matsengrp/historydag/pull/32
* matsen made their first contribution in https://github.com/matsengrp/historydag/pull/44
* harryrichman made their first contribution in https://github.com/matsengrp/historydag/pull/75

**Full Changelog**: https://github.com/matsengrp/historydag/compare/v1.0.1...v1.1.0

What's Changed
* Tools for DAG topology exploration by willdumm in https://github.com/matsengrp/historydag/pull/20 (Adds methods `unlabel` and `count_topologies_fast` which allow internal labels to be removed from the DAG, essentially converting a history DAG to a multifurcating subsplit DAG)
* Wd-determinism by willdumm in https://github.com/matsengrp/historydag/pull/22 (Fixes an issue where node child clades were stored in an unordered container during pickling and copying, resulting in nondeterministic node ordering)


**Full Changelog**: https://github.com/matsengrp/historydag/compare/v1.0.0...v1.0.1

What's Changed
* 8 more efficient merging by williamhowardsnyder in https://github.com/matsengrp/historydag/pull/10 (Merging of many DAGs is now much more efficient)
* Indexing Histories by clarisw in https://github.com/matsengrp/historydag/pull/14 (history DAGs are now indexable, iterable containers, which support the `|` union operator (equivalent to `merge` method))
* Supertrees by willdumm in https://github.com/matsengrp/historydag/pull/12 (A history DAG may now be constructed from trees with different leaf label sets, as of #12. However, each tree's leaves must still be labeled uniquely)

New Contributors
* williamhowardsnyder made their first contribution in https://github.com/matsengrp/historydag/pull/10
* clarisw made their first contribution in https://github.com/matsengrp/historydag/pull/14

**Full Changelog**: https://github.com/matsengrp/historydag/compare/v0.1.3...v1.0.0

Minor fix to `utils.addFuncDict` tests, and instantiation of `utils.hamming_distance_countfuncs` which caused the readme demo to fail