v1.3.0

What's Changed

• Docs improvements by @willdumm in #83
• Binary tree resolutions and fast sampling by @willdumm in #84

Full Changelog: v1.2.0...v1.3.0

v1.2.0

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 #78
• graphviz dot file output improvements by @willdumm in #79
• One Sided RF distances by @willdumm in #80
• IntState vs FloatState fix for RF distances by @willdumm in #81
• Ambiguous Protobuf Support by @willdumm in #82

Full Changelog: v1.1.0...v1.2.0

v1.1.0

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

New Contributors

• @marybarker made their first contribution in #32
• @matsen made their first contribution in #44
• @harryrichman made their first contribution in #75

Full Changelog: v1.0.1...v1.1.0

v1.0.1 Deterministic node ordering

What's Changed

• Tools for DAG topology exploration by @willdumm in #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 #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: v1.0.0...v1.0.1

v1.0.0 Unequal leaf sets, indexing, and more!

What's Changed

• 8 more efficient merging by @williamhowardsnyder in #10 (Merging of many DAGs is now much more efficient)
• Indexing Histories by @clarisw in #14 (history DAGs are now indexable, iterable containers, which support the | union operator (equivalent to merge method))
• Supertrees by @willdumm in #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 #10
• @clarisw made their first contribution in #14

Full Changelog: v0.1.3...v1.0.0

v0.1.3

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

HistoryDAG v0.1.2

Minor changes to version management and init.py import structure

v0.1.1

Initial release for gctree integration