Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / matsengrp/historydag issues and pull requests

#81 - IntState vs FloatState fix for RF distances

Pull Request - State: closed - Opened by willdumm about 1 year ago

#80 - One Sided RF distances

Pull Request - State: closed - Opened by willdumm about 1 year ago - 1 comment

#79 - graphviz dot file output improvements

Pull Request - State: closed - Opened by willdumm over 1 year ago

#78 - Wd adjusted node probs

Pull Request - State: closed - Opened by willdumm over 1 year ago

#76 - One sided RF distance

Pull Request - State: closed - Opened by clarisw almost 2 years ago - 1 comment

#75 - minor improvements in parsimony_utils.py

Pull Request - State: closed - Opened by harryrichman almost 2 years ago

#74 - add a few more tests for recent changes

Pull Request - State: closed - Opened by willdumm almost 2 years ago

#73 - Jukes cantor likelihood

Pull Request - State: closed - Opened by willdumm almost 2 years ago - 2 comments

#72 - fix bug with parsimony for ambiguous leaf sequences

Pull Request - State: closed - Opened by willdumm almost 2 years ago

#71 - updating sankoff to accommodate non-singleton-base transition models

Pull Request - State: closed - Opened by marybarker almost 2 years ago

#70 - weighting edges of the DAG using Jukes-Cantor

Issue - State: open - Opened by matsen almost 2 years ago - 1 comment

#69 - Updating docstrings

Pull Request - State: closed - Opened by marybarker almost 2 years ago

#68 - reorganize dag.py

Pull Request - State: closed - Opened by willdumm almost 2 years ago

#67 - Split dag.py, improved tests, and mean weights

Pull Request - State: closed - Opened by willdumm almost 2 years ago - 1 comment

#66 - reorganize dag.py

Pull Request - State: closed - Opened by willdumm almost 2 years ago

#65 - Generalized node support

Pull Request - State: closed - Opened by willdumm almost 2 years ago - 2 comments

#64 - HistoryDag subclass defaults

Pull Request - State: closed - Opened by willdumm almost 2 years ago - 1 comment

#63 - Add beast tree loader

Pull Request - State: closed - Opened by willdumm almost 2 years ago - 1 comment

#62 - HistoryDag subclass defaults

Pull Request - State: closed - Opened by willdumm about 2 years ago - 1 comment

#61 - Implemented Estimate for RF Diameter

Pull Request - State: closed - Opened by clarisw about 2 years ago

#60 - Beast tree loading

Pull Request - State: closed - Opened by willdumm about 2 years ago - 2 comments

#59 - fix compact genome mutation and add label change

Pull Request - State: closed - Opened by willdumm about 2 years ago

#58 - Estimate RF distance diameter

Issue - State: open - Opened by willdumm about 2 years ago

#57 - initial commit for adding alternate field name option

Pull Request - State: closed - Opened by marybarker about 2 years ago - 1 comment

#56 - Count optimal histories

Pull Request - State: closed - Opened by willdumm about 2 years ago

#55 - Sankoff with multiple criteria

Issue - State: open - Opened by marybarker about 2 years ago - 1 comment

#54 - altered average_pairwise_rf_distance to avoid divide-by-zero in the c…

Pull Request - State: closed - Opened by marybarker about 2 years ago - 1 comment

#53 - Add average pairwise RF distance method

Pull Request - State: closed - Opened by willdumm about 2 years ago

#52 - Implement sum pairwise rf distance

Pull Request - State: closed - Opened by willdumm about 2 years ago

#51 - Add HistoryDagFilter Object

Pull Request - State: closed - Opened by willdumm about 2 years ago - 1 comment

#50 - Expand Quickstart

Pull Request - State: closed - Opened by willdumm about 2 years ago

#49 - docs improvements

Pull Request - State: closed - Opened by willdumm about 2 years ago

#48 - various docs todos from the perspective of a naive user

Issue - State: open - Opened by matsen about 2 years ago - 1 comment

#47 - Create subclass for ambiguous samples

Pull Request - State: closed - Opened by willdumm about 2 years ago

#46 - Wd general leaf path dag

Pull Request - State: closed - Opened by willdumm about 2 years ago

#45 - Method tags aren't parsed correctly in docs

Issue - State: closed - Opened by matsen about 2 years ago

#44 - Quickstart suggestions

Pull Request - State: closed - Opened by matsen about 2 years ago

#43 - does historydag implicitly assume that a tree's sequences are named `sequence`?

Issue - State: closed - Opened by matsen about 2 years ago - 4 comments

#42 - Consider how to load in BEAST trees with compact descriptions of a history

Issue - State: open - Opened by matsen about 2 years ago - 9 comments

#41 - Implement Sum RF Distances

Pull Request - State: closed - Opened by clarisw about 2 years ago - 4 comments

#40 - Various bug fixes

Pull Request - State: closed - Opened by willdumm over 2 years ago

#39 - Implement Sum RF distance

Issue - State: closed - Opened by willdumm over 2 years ago

#38 - Support for leaf labels with ambiguities

Issue - State: open - Opened by marybarker over 2 years ago - 2 comments

#37 - MADAG protobuf support

Pull Request - State: closed - Opened by willdumm over 2 years ago - 1 comment

#36 - Trimming weight range

Pull Request - State: closed - Opened by clarisw over 2 years ago

#35 - adding new sequences to a pre-existing DAG (no relabeling)

Pull Request - State: closed - Opened by marybarker over 2 years ago - 1 comment

#34 - working tests and implementation

Pull Request - State: closed - Opened by willdumm over 2 years ago

#33 - Suboptimal Trimming

Pull Request - State: closed - Opened by willdumm over 2 years ago - 1 comment

#32 - Sankoff filtering cleanup

Pull Request - State: closed - Opened by marybarker over 2 years ago

#31 - squashed commits from node-utils branch

Pull Request - State: closed - Opened by willdumm over 2 years ago

#30 - Node support annotation squashed

Pull Request - State: closed - Opened by willdumm over 2 years ago

#29 - Node support annotation

Pull Request - State: closed - Opened by willdumm over 2 years ago

#28 - Node utils

Pull Request - State: closed - Opened by willdumm over 2 years ago - 1 comment

#27 - Do Sankoff on the history DAG

Issue - State: closed - Opened by willdumm over 2 years ago - 1 comment

#26 - Agg mut staging

Pull Request - State: closed - Opened by williamhowardsnyder over 2 years ago

#25 - Consistent Clade Ordering

Pull Request - State: closed - Opened by willdumm over 2 years ago

#24 - make `trim_optimal_weight` update parents

Pull Request - State: closed - Opened by willdumm over 2 years ago

#23 - 21 Fix Names

Pull Request - State: closed - Opened by willdumm over 2 years ago - 1 comment

#22 - Wd-determinism

Pull Request - State: closed - Opened by willdumm over 2 years ago

#20 - Wd topologies explore

Pull Request - State: closed - Opened by willdumm over 2 years ago

#19 - implemented node counting alg + added small tests

Pull Request - State: closed - Opened by williamhowardsnyder over 2 years ago

#18 - V1 docs changes

Pull Request - State: closed - Opened by willdumm over 2 years ago

#17 - Infrastructure to invite exploration

Issue - State: closed - Opened by matsen almost 3 years ago - 1 comment

#16 - Bound trimming after single edge addition to the history DAG

Issue - State: closed - Opened by matsen almost 3 years ago - 2 comments

#15 - (intern) Trimming within a percentage of the best weight

Issue - State: closed - Opened by matsen almost 3 years ago - 2 comments

#14 - Indexing Histories

Pull Request - State: closed - Opened by clarisw almost 3 years ago - 1 comment

#13 - Update docs and readme for PR #12

Issue - State: open - Opened by willdumm almost 3 years ago - 1 comment

#12 - Supertrees

Pull Request - State: closed - Opened by willdumm almost 3 years ago

#11 - move docs

Pull Request - State: closed - Opened by willdumm almost 3 years ago

#10 - 8 more efficient merging

Pull Request - State: closed - Opened by williamhowardsnyder almost 3 years ago - 1 comment

#9 - fix typo in utils.hamming_distance_countfuncs

Pull Request - State: closed - Opened by willdumm almost 3 years ago

#8 - Faster hDAG construction

Issue - State: open - Opened by willdumm almost 3 years ago - 1 comment
Labels: enhancement

#7 - Characterize variety of histories in the history DAG

Issue - State: open - Opened by willdumm almost 3 years ago - 2 comments
Labels: proposed feature

#6 - In-DAG tree search

Issue - State: open - Opened by willdumm almost 3 years ago
Labels: proposed feature

#5 - Efficient sequence/mutation storage

Issue - State: closed - Opened by willdumm almost 3 years ago
Labels: proposed feature

#4 - Allow histories with different leaf sets in the same DAG

Issue - State: closed - Opened by willdumm almost 3 years ago - 1 comment
Labels: enhancement

#3 - Indexing histories

Issue - State: closed - Opened by willdumm almost 3 years ago - 3 comments
Labels: proposed feature

#2 - Move docs to separate branch

Issue - State: closed - Opened by willdumm almost 3 years ago

#1 - Cleanup

Pull Request - State: closed - Opened by willdumm about 3 years ago