Ecosyste.ms: Issues

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

GitHub / eaton-lab/toytree issues and pull requests

#105 - initial blomberg K code

Pull Request - State: closed - Opened by natetrux 17 days ago

#104 - fixed type in traversal notebook

Pull Request - State: closed - Opened by natetrux 29 days ago - 1 comment

#103 - `scalebar` error

Issue - State: closed - Opened by POMulhair about 1 month ago - 1 comment

#102 - Network Restructuring without Hidden Files

Pull Request - State: closed - Opened by natetrux 3 months ago

#101 - Admix annotate

Pull Request - State: closed - Opened by natetrux 3 months ago - 2 comments

#100 - no 'node_scale_root_height' (and other documentation issues)

Issue - State: closed - Opened by luka-sato 3 months ago - 3 comments

#99 - Network changes

Pull Request - State: closed - Opened by natetrux 4 months ago

#98 - lift numpy version ceiling?

Issue - State: closed - Opened by ryneches 4 months ago - 1 comment

#97 - annotation documentation

Pull Request - State: closed - Opened by natetrux 5 months ago - 1 comment

#96 - Annotate subpackage fixes

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

#95 - Starting .annotate fixes & docs

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

#94 - Distance Metrics Documentation

Pull Request - State: closed - Opened by natetrux 6 months ago - 1 comment

#93 - Cookbook and Draw Options

Pull Request - State: closed - Opened by natetrux 6 months ago - 1 comment

#92 - Copying old docs over

Pull Request - State: closed - Opened by natetrux 6 months ago - 1 comment

#91 - new submodule for RED & related functions

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

#89 - restructured, simple tests for quadripartitions

Pull Request - State: closed - Opened by natetrux 7 months ago - 1 comment

#88 - topology mod documentation intro and node level mods

Pull Request - State: closed - Opened by natetrux 7 months ago - 1 comment

#87 - simple documentation for quartet method added

Pull Request - State: closed - Opened by natetrux 7 months ago - 1 comment

#86 - "Added documentation for bipartition methods"

Pull Request - State: closed - Opened by natetrux 7 months ago - 1 comment

#85 - Enum tests

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

#84 - limit mtree grid plotting to size of tree list, bypass div by zero error

Pull Request - State: closed - Opened by ryneches 8 months ago - 2 comments

#83 - testing commit

Pull Request - State: closed - Opened by natetrux 8 months ago - 1 comment

#82 - added pandas import

Pull Request - State: closed - Opened by eaton-lab 8 months ago - 1 comment

#81 - 'ToyTree' object has no attribute 'drop_tips'

Issue - State: closed - Opened by isgilman 9 months ago - 2 comments

#80 - allow missing tips in draw_cloud_tree()?

Issue - State: open - Opened by ryneches 9 months ago - 3 comments

#78 - Update pip release

Issue - State: closed - Opened by Gizzio 12 months ago - 2 comments

#77 - Long labels partially displayed

Issue - State: closed - Opened by chtate over 1 year ago - 2 comments

#76 - Fixed bug for visualizations using layout 'd'

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

#75 - Shape mismatch using .draw() function

Issue - State: open - Opened by MauriAndresMU1313 over 1 year ago

#74 - Fan (limited angle circular) tree layout

Issue - State: open - Opened by ilevantis over 1 year ago - 1 comment

#73 - invalid mode when loading tree in Python 3.11.*

Issue - State: closed - Opened by dmnfarrell over 1 year ago - 1 comment

#72 - Drawing cloud trees

Issue - State: open - Opened by mrmrwinter over 1 year ago - 1 comment

#71 - Adding support to directly parse BEAST format trees

Issue - State: open - Opened by tongqiu-jia almost 2 years ago

#70 - fix ValueError if there is no support value for a node (e.g. the root)

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

#69 - Fix np bool

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

#68 - New toy3 distance module updates

Pull Request - State: closed - Opened by smau8 almost 2 years ago - 1 comment

#67 - Fix circular trees in v3

Issue - State: closed - Opened by eaton-lab about 2 years ago - 1 comment
Labels: bug

#65 - fix style dict font size use in MultiTree drawings

Issue - State: open - Opened by eaton-lab about 2 years ago
Labels: bug

#64 - Styling individual tip labels

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

#63 - Drawing is very slow when layout='c'

Issue - State: closed - Opened by aleferna12 over 2 years ago - 2 comments

#62 - remove rU as it's deprecated

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

#61 - Node sizes/color set to only zero

Issue - State: open - Opened by MauriAndresMU1313 over 2 years ago - 2 comments

#60 - Set svg tree plot without transparency

Issue - State: closed - Opened by MauriAndresMU1313 over 2 years ago - 1 comment

#59 - recursion depth on copy for large trees

Issue - State: open - Opened by eaton-lab over 2 years ago

#58 - Toy3

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

#57 - Toy3

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

#56 - nni with subfunction to get all nearest neighbors

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

#55 - Setting node "dist"

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

#54 - distance RF and quartets functions

Pull Request - State: closed - Opened by smau8 about 3 years ago - 1 comment

#53 - removed error message for prune function

Pull Request - State: closed - Opened by pmckenz1 over 3 years ago

#52 - cannot generate italic labels

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

#50 - Node coloring issue

Issue - State: closed - Opened by johnpatramanis almost 4 years ago - 2 comments

#49 - ts='p' plotting bug

Issue - State: closed - Opened by pmckenz1 about 4 years ago - 1 comment

#48 - Network parsing bug

Issue - State: open - Opened by pmckenz1 about 4 years ago

#47 - Added custom root option for parsing networks

Pull Request - State: closed - Opened by pmckenz1 about 4 years ago

#46 - Legend

Issue - State: open - Opened by codemeleon about 4 years ago

#45 - `draw()` arguments`fixed_order` and `tip_labels_colors` are mutually exclusive

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

#44 - Fixed misspellings in tutorial

Pull Request - State: closed - Opened by Rahim16 about 4 years ago - 1 comment

#43 - Unrooting does not preserve distances

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

#42 - Question about inner node labels position

Issue - State: closed - Opened by Tdanis over 4 years ago - 1 comment

#41 - coloring external tips by feature and internal tips by support

Issue - State: closed - Opened by dezordi over 4 years ago

#40 - Issue 26

Pull Request - State: closed - Opened by aalsabag over 4 years ago

#39 - Randomtree `random_names` isn't working

Issue - State: closed - Opened by isaacovercast over 4 years ago - 1 comment

#38 - Improvements to bdtree

Pull Request - State: closed - Opened by isaacovercast over 4 years ago

#37 - Have consensus function record blen info

Issue - State: open - Opened by eaton-lab over 4 years ago

#36 - fixed_order should be a draw setting, not tree setting.

Issue - State: closed - Opened by eaton-lab over 4 years ago - 1 comment

#35 - Get API in rtfd

Issue - State: open - Opened by isaacovercast over 4 years ago - 1 comment

#34 - `set_tip_labels` should cast to str() imho

Issue - State: closed - Opened by isaacovercast almost 5 years ago - 1 comment

#33 - add bdtree to Randmtree

Pull Request - State: closed - Opened by isaacovercast almost 5 years ago

#32 - treenode.add_sister should set sister.up imho

Issue - State: closed - Opened by isaacovercast almost 5 years ago - 1 comment

#31 - Coords.py NameError -> ToyTreeError

Issue - State: closed - Opened by isaacovercast almost 5 years ago - 1 comment

#30 - Toytree.prune()

Issue - State: closed - Opened by isaacovercast almost 5 years ago - 2 comments

#29 - unrecognized arguments skipped: ['layout']

Issue - State: closed - Opened by Markkunitomi about 5 years ago - 1 comment

#28 - bug fix! (and added vcv function)

Pull Request - State: closed - Opened by pmckenz1 about 5 years ago

#27 - add matrix to tree view

Issue - State: closed - Opened by phiweger about 5 years ago - 2 comments

#26 - Please add an easy way of labelling clades

Issue - State: closed - Opened by SimonGreenhill about 5 years ago - 6 comments

#25 - change __getattribute__ and __setattribute__ to getattr() and setattr()

Pull Request - State: closed - Opened by pmckenz1 about 6 years ago

#24 - exporting trees from Toytree

Issue - State: closed - Opened by Hazelhuangup over 6 years ago - 1 comment

#23 - scalebar extra ticks

Issue - State: closed - Opened by eaton-lab over 6 years ago - 1 comment

#22 - Documentation at https://toytree.readthedocs.io/ is broken

Issue - State: closed - Opened by cndewey over 6 years ago - 1 comment

#21 - xrange error - Python3

Issue - State: closed - Opened by sokrypton over 6 years ago - 1 comment

#20 - [styleclass branch] make core attributes like height available by tab-completion

Issue - State: closed - Opened by eaton-lab over 6 years ago - 1 comment
Labels: enhancement

#19 - [styleclass branch] node idx is jumbled.

Issue - State: closed - Opened by eaton-lab over 6 years ago - 1 comment
Labels: bug

#18 - help wanted: edge_label

Issue - State: closed - Opened by zhh210 over 6 years ago - 1 comment

#17 - Example in the doc does not work (format problem)

Issue - State: closed - Opened by mapio over 6 years ago - 3 comments

#16 - Inconsistent tip color behavior

Issue - State: closed - Opened by isgilman almost 7 years ago - 3 comments
Labels: bug

#15 - long tip labels are cut off

Issue - State: closed - Opened by eaton-lab about 7 years ago - 1 comment
Labels: bug, help wanted

#14 - Py3 is not ordering node labels correctly

Issue - State: closed - Opened by eaton-lab about 7 years ago
Labels: bug, help wanted

#12 - Fix relative imports.

Pull Request - State: closed - Opened by Zsailer about 7 years ago - 2 comments

#11 - toytree error

Issue - State: closed - Opened by tangerzhang over 7 years ago - 1 comment

#10 - Python 3 fix

Pull Request - State: closed - Opened by Zsailer over 7 years ago

#9 - fixing issue-8, bad variable

Pull Request - State: closed - Opened by Zsailer over 7 years ago - 1 comment

#8 - NameError: global name 'ns' is not defined

Issue - State: closed - Opened by AlexMikhalev over 7 years ago

#7 - fix importing errors in python 3

Pull Request - State: closed - Opened by Zsailer over 7 years ago - 2 comments

#6 - custom Tree object

Issue - State: closed - Opened by eaton-lab over 7 years ago - 1 comment
Labels: enhancement

#5 - make compatible with new toyplot release and update conda recipe

Issue - State: closed - Opened by dereneaton over 7 years ago - 1 comment

#4 - can't set self as root

Issue - State: closed - Opened by dereneaton over 7 years ago - 1 comment

#3 - implement text markers for nodes

Issue - State: closed - Opened by dereneaton over 7 years ago
Labels: enhancement