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