matsengrp/gctree issues and pull requests

#132 - 131 Fix rendering hang when parent directory of output file doesn't exist

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

#131 - tree rendering hangs when write directory doesn't exist.

Issue - State: closed - Opened by jgallowa07 about 2 months ago - 1 comment

#130 - Add filtering by reversions to naive sequence, generalize ranking strategy

Pull Request - State: closed - Opened by willdumm 3 months ago - 4 comments

#129 - Handle truncated dnapars `outfile`s correctly

Pull Request - State: closed - Opened by willdumm 5 months ago

#128 - Fix single ranking criterion bug

Pull Request - State: closed - Opened by willdumm 6 months ago

#127 - Qt platform plugin could be initialized

Issue - State: closed - Opened by NSchwanPhy 6 months ago - 2 comments

#125 - Fix ufunc attribute error from numpy.log

Pull Request - State: closed - Opened by willdumm 7 months ago

#124 - Extreme Runtime

Issue - State: open - Opened by lejecrs 7 months ago - 5 comments

#123 - Phylip Installaion

Issue - State: closed - Opened by vivekruhela 8 months ago - 4 comments

#122 - Dependency and warning fix and compatibility with Scipy 1.12

Pull Request - State: closed - Opened by willdumm 9 months ago - 1 comment

#121 - update historydag version requirement

Issue - State: closed - Opened by jgallowa07 9 months ago - 1 comment

#120 - Disagreement in node coloring for (some) identical sequences

Issue - State: closed - Opened by victor-ramos 10 months ago - 6 comments

#119 - Tree visualization without the number text

Issue - State: closed - Opened by markutz556 about 1 year ago - 2 comments

#118 - fix gap character ambiguity bug

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

#117 - Tree inference taking very long time - advice needed

Issue - State: closed - Opened by fabio-t about 1 year ago - 11 comments

#116 - Rethink isotype inference

Issue - State: open - Opened by willdumm over 1 year ago

#115 - Python 3.10, and macOS integration testing

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

#114 - GitHub action runner OS not set

Issue - State: closed - Opened by WSDeWitt over 1 year ago

#113 - Incorrect dnapars outfile parsing

Issue - State: closed - Opened by willdumm almost 2 years ago
Labels: bug

#112 - rename master to main

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

#111 - swap master --> main

Issue - State: closed - Opened by psathyrella almost 2 years ago - 1 comment

#110 - Remove `S5F` contents and mark experimental features

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

#109 - Allow all ranking stats to be computed on individual `CollapsedTree`s

Issue - State: open - Opened by willdumm almost 2 years ago - 1 comment
Labels: Next Release

#108 - to support amino acids sequences

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

#107 - Add option to recover all top-ranked trees instead of sampling from topology classes

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

#106 - gctree infer with --tree-stats argument does not write pickled tree outputs

Issue - State: open - Opened by willdumm about 2 years ago - 1 comment
Labels: Next Release

#105 - ValueError: Zero likelihood event

Issue - State: closed - Opened by chaoszhang about 2 years ago - 7 comments
Labels: Next Release

#104 - interface with SAMM or bypass Galton branching

Issue - State: open - Opened by Lan-h about 2 years ago - 7 comments

#103 - jumble parameter in `mkconfig`

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

#102 - Colormap enhancements

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

#101 - Jumble parameter for tree space search should be user configurable

Issue - State: open - Opened by WSDeWitt over 2 years ago - 6 comments

#100 - Make gctree deterministic when ranking is degenerate

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

#99 - local branching metric harmonization

Issue - State: open - Opened by WSDeWitt over 2 years ago

#98 - Rename master branch to main

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

#97 - Add full inference test and remove mutation model ignore_ualabel call

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

#96 - Local branching metrics fixes

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

#95 - Errors installing PyQt5 dependency on ARM Mac using pip

Issue - State: open - Opened by WSDeWitt over 2 years ago

#94 - Fix numpy errors on gctree import

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

#93 - CLI to calculate parsimony scores

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

#92 - `import gctree` causes `FloatingPointError` in independent matplotlib/numpy calls

Issue - State: closed - Opened by WSDeWitt over 2 years ago - 2 comments
Labels: bug

#91 - 71 ambiguous input data

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

#90 - Ability to count reversions

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

#89 - Simplify abundance logic and remove tuple sequence names

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

#88 - Avoid tuple root node name

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

#87 - stringified tuple sequence name

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

#86 - Fix multiple tree nodes with same name

Pull Request - State: closed - Opened by willdumm over 2 years ago - 3 comments

#85 - Address Duncan's suggestions

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

#84 - Various comments/suggestions

Issue - State: closed - Opened by psathyrella over 2 years ago - 3 comments

#83 - add isotype to mutation model simulation

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

#82 - Support for Python 3.10

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

#81 - add potential Dockerfile + test.sh

Pull Request - State: closed - Opened by psathyrella over 2 years ago - 8 comments

#80 - Update installation docs

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

#79 - Prerelease tidying

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

#78 - Mutability chain split

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

#77 - Update README.md

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

#76 - Docs fixes

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

#75 - Store isotype data in nodes

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

#74 - Transplant patch

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

#73 - Transplant docs

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

#72 - Add ambiguous sequence test and error message

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

#71 - accommodate ambiguous observed sequences

Issue - State: closed - Opened by willdumm over 2 years ago - 7 comments

#70 - Fix underflow errors on some machines by avoiding calling np.exp(-np.inf) in ll.

Pull Request - State: closed - Opened by willdumm over 2 years ago - 3 comments

#69 - LB metrics for CollapsedTree and sequence-based fitness for simulation

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

#68 - Fit parameters on history DAG

Pull Request - State: closed - Opened by willdumm almost 3 years ago - 11 comments

#67 - Consistent Numpy underflow error on some machines

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

#66 - Any parallel or accelerated parameters?

Issue - State: closed - Opened by liyi522 almost 3 years ago - 1 comment

#65 - Add isotype utility

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

#64 - restrict tuple-valued node names to bootstrap trees

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

#63 - obey isotype switching order

Issue - State: closed - Opened by willdumm almost 3 years ago - 4 comments

#62 - Use history DAG to find more maximum parsimony trees

Pull Request - State: closed - Opened by willdumm almost 3 years ago - 5 comments

#61 - Disambiguate with mutability

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

#60 - Uniqueness of IDs not necessary

Pull Request - State: closed - Opened by fabio-t about 3 years ago - 1 comment

#59 - Default help menu missing

Issue - State: closed - Opened by fabio-t about 3 years ago - 1 comment

#58 - Problem with Sequence IDs

Issue - State: closed - Opened by fabio-t about 3 years ago - 10 comments

#57 - Disambiguate trees using Sankoff Algorithm

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

#56 - Phylip_parse.disambiguate sometimes chooses non-optimal tree

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

#55 - a few tree rendering options

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

#54 - Mlepatch

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

#53 - find identical mamaras in the tree

Issue - State: closed - Opened by matsen about 3 years ago - 10 comments

#52 - update README (and potentially web link) with reference for full paper

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

#51 - Plot annotations

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

#50 - Packagify

Pull Request - State: closed - Opened by WSDeWitt over 3 years ago

#49 - Plot are not generated due to a problem with Qt

Issue - State: closed - Opened by Aurelien-Pelissier over 3 years ago - 3 comments

#48 - 46 biopython upgrade

Pull Request - State: closed - Opened by WSDeWitt over 3 years ago

#47 - colors in hex

Issue - State: closed - Opened by cstrlln over 3 years ago - 2 comments

#46 - Error: Biopython

Issue - State: closed - Opened by jonoave over 3 years ago - 1 comment

#45 - Error: scons: *** No SConstruct file found.

Issue - State: closed - Opened by jonoave over 3 years ago - 3 comments

#44 - Data inconsistency between simulation and inference

Issue - State: closed - Opened by NikaAb almost 4 years ago - 3 comments

#43 - About the output file when using the --bootstrap option

Issue - State: closed - Opened by xvtyzn over 4 years ago - 2 comments

#42 - It is possible parallel processing in step python -u bin/gctree.py

Issue - State: closed - Opened by Chuang1118 over 4 years ago - 5 comments

#41 - --idlabel not working?

Issue - State: closed - Opened by cstrlln over 4 years ago - 2 comments

#40 - use of color argument

Issue - State: closed - Opened by cstrlln about 5 years ago - 3 comments

#39 - Limit of abundance for each sequence

Issue - State: closed - Opened by NikaAb over 5 years ago - 5 comments

#38 - Fasta file with variable sequence length

Issue - State: closed - Opened by NikaAb over 5 years ago - 2 comments

#37 - Dockerfile, and a release

Issue - State: closed - Opened by matsen over 6 years ago

#36 - Installation or user idiocy problem

Issue - State: closed - Opened by vnminin over 6 years ago - 6 comments

#35 - Output the best tree as newick

Issue - State: closed - Opened by krdav almost 7 years ago

#34 - cleaning repo for submission

Issue - State: closed - Opened by WSDeWitt about 7 years ago - 2 comments

#33 - Multiple t

Pull Request - State: closed - Opened by krdav about 7 years ago

#32 - Multiple t

Pull Request - State: closed - Opened by krdav about 7 years ago

GitHub / matsengrp/gctree issues and pull requests