Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / 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