v4.0.3

What's Changed

• 71 ambiguous input data by @willdumm in #91
• Local branching metrics fixes by @wsdewitt in #96

Full Changelog: v4.0.2...v4.0.3

v4.0.2

What's Changed

• Simplify abundance logic and remove tuple sequence names by @willdumm in #89
• Fix numpy errors on gctree import by @willdumm in #94

Full Changelog: v4.0.1...v4.0.2

v4.0.1

What's Changed

• Update installation docs by @willdumm in #80
• add potential Dockerfile + test.sh by @psathyrella in #81
• Address Duncan's suggestions by @willdumm in #85
• Fix multiple tree nodes with same name by @willdumm in #86

New Contributors

• @psathyrella made their first contribution in #81

Full Changelog: v4.0.0...v4.0.1

v4.0.0

Summary

• A major enhancement for parsimony tree search is the use of a history DAG 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 #68
• Add ambiguous sequence test and error message by @willdumm in #72
• Transplant docs by @wsdewitt in #73
• Transplant patch by @wsdewitt in #74
• Docs fixes by @wsdewitt in #76
• Update README.md by @wsdewitt in #77
• Store isotype data in nodes by @willdumm in #75
• Mutability chain split by @willdumm in #78
• Prerelease tidying by @wsdewitt in #79

Full Changelog: v3.3.0...v4.0.0

v3.3.0

What's Changed

• Add isotype utility by @willdumm in #65. See new sections in API docs and Quickstart.
• A new docs page demoing tree visualization by @wsdewitt in #69
• LB metrics for CollapsedTree with new method, by @wsdewitt in #69
• New method for generating a colormap from any numerical node feature in a CollapsedTree, by @wsdewitt in #69
• Sequence-based fitness and seeding with more than one cell for simulation in mutation_model.MutationModel by @wsdewitt in #69

Full Changelog: v3.2.1...v3.3.0

v3.2.1: Merge pull request #57 from matsengrp/56-disambiguate-optimally

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

h/t @willdumm

v3.2.0: Merge pull request #55 from matsengrp/render-options

New API tree rendering options scale, branch_margin, and node_size described in docs.

v3.1.1: Merge pull request #54 from matsengrp/mlepatch

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

v3.1.0

New features

• The CLI program gctree infer writes a pickled CollapsedTree object for each parsimony tree, which can be later loaded and manipulated via the API.
• Updates to 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 and CollapsedForest are exposed at package level, so they can be imported directly rather than from the branching_processes module.
• Many improvements in documentation: matsengrp.github.io/gctree

Developer notes

• The branching_processes module has been refactored to remove illegitimate inheritance
• Better default p, q parameters for MLE avoid gradient warnings.

v3.0.2

Patch to set seeds for more repeatable behavior (especially in tests and docs), and better default rooting behavior for gctree infer.