emilydolson/phylotrackpy issues and pull requests

#110 - Try free-threaded support

Pull Request - State: closed - Opened by emilydolson 2 months ago - 1 comment

#109 - Update ci.yml

Pull Request - State: closed - Opened by emilydolson 2 months ago - 1 comment

#108 - No prebuilt wheels with Python3.13

Issue - State: closed - Opened by vivaansinghvi07 3 months ago - 3 comments
Labels: bug

#107 - Track count of coalescence events

Issue - State: open - Opened by emilydolson 5 months ago
Labels: enhancement

#106 - Update citations in manuscript

Pull Request - State: closed - Opened by mmore500 6 months ago - 1 comment

#105 - Consolidate to single composite figure

Pull Request - State: closed - Opened by mmore500 6 months ago - 1 comment

#104 - Bump the pip group across 1 directory with 2 updates

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies, python

#103 - Implement collapse unifurcations feature

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

#102 - Add submission materials

Pull Request - State: closed - Opened by mmore500 6 months ago - 2 comments

#101 - Bump zipp from 2.2.1 to 3.19.1 in the pip group across 1 directory

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 2 comments
Labels: dependencies, python

#100 - Fix various small bugs

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

#99 - Add test recommended in #81

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

#98 - Try adding more mac tests

Pull Request - State: closed - Opened by emilydolson 7 months ago - 2 comments

#97 - Installation failure on macOS

Issue - State: closed - Opened by amlalejini 7 months ago - 1 comment
Labels: bug

#96 - Add citing info to README.md

Pull Request - State: closed - Opened by mmore500 8 months ago

#95 - Revise manuscript

Pull Request - State: closed - Opened by mmore500 8 months ago - 3 comments

#94 - Fix number formatting

Pull Request - State: closed - Opened by mmore500 8 months ago - 1 comment

#93 - Fix citations in manuscript

Pull Request - State: closed - Opened by mmore500 8 months ago

#92 - Fix typo in README

Pull Request - State: closed - Opened by mmore500 8 months ago - 1 comment

#91 - Mysterious interaction with Jupyter/IPython causes deserialization to hang

Issue - State: open - Opened by mmore500 9 months ago - 2 comments
Labels: bug

#90 - Bump pillow from 10.2.0 to 10.3.0 in /profile

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies, python

#89 - Bump Empirical from `a0b6ecc` to `9e7165a`

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies, submodules

#88 - Add Zenodo badge

Pull Request - State: closed - Opened by mmore500 10 months ago - 1 comment

#87 - `get_mean_pairwise_distance` hangs (>10 min) on deserialized tree

Issue - State: closed - Opened by mmore500 10 months ago - 7 comments
Labels: bug

#86 - Loading from bad path crashes Python interpreter

Issue - State: closed - Opened by mmore500 10 months ago - 1 comment
Labels: bug

#85 - Requested feature: `GetNumTips()`

Issue - State: open - Opened by mmore500 10 months ago
Labels: enhancement

#84 - Docs improvements

Pull Request - State: closed - Opened by emilydolson 10 months ago - 1 comment

#83 - `colless_like_index` crashes for empty tree

Issue - State: closed - Opened by mmore500 10 months ago - 1 comment
Labels: bug

#82 - Remove leftover debugging cruft

Pull Request - State: closed - Opened by mmore500 10 months ago

#81 - Packaging: wheel not available, build from source fails

Issue - State: closed - Opened by mmore500 10 months ago - 4 comments
Labels: bug

#80 - Quickstart test

Pull Request - State: open - Opened by Sanaz11-3 10 months ago - 1 comment

#79 - Remove under construction warning from API docs

Pull Request - State: closed - Opened by mmore500 11 months ago - 1 comment

#78 - Add example usage using nbshinx

Pull Request - State: closed - Opened by mmore500 11 months ago - 1 comment

#77 - Rename `sys` variables to avoid shadowing `sys` module

Pull Request - State: closed - Opened by mmore500 11 months ago - 2 comments

#76 - Remove taxon constructor

Pull Request - State: closed - Opened by emilydolson 11 months ago - 1 comment

#75 - Bump checkout action

Pull Request - State: closed - Opened by emilydolson 11 months ago - 1 comment

#74 - Bump wheels to latest versions

Pull Request - State: closed - Opened by emilydolson 11 months ago - 1 comment

#73 - Fix no-longer in press citation

Pull Request - State: closed - Opened by emilydolson 11 months ago - 1 comment

#72 - Final touchups on JOSS manuscript

Pull Request - State: closed - Opened by mmore500 11 months ago - 1 comment

#71 - Bump pillow from 10.1.0 to 10.2.0 in /profile

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies, python

#70 - Bump version: 0.1.18 → 0.2.0

Pull Request - State: closed - Opened by mmore500 11 months ago

#69 - Bump cibuildwheel pin

Pull Request - State: closed - Opened by mmore500 11 months ago

#68 - Fix CI wheel build on windows

Pull Request - State: closed - Opened by mmore500 11 months ago

#67 - Impl, test sum branch distance binding

Pull Request - State: closed - Opened by mmore500 11 months ago - 2 comments

#66 - Write blurb for alife newsletter

Issue - State: open - Opened by mmore500 12 months ago
Labels: enhancement

#65 - Crossref hstrat and phylotrackpy with each other

Pull Request - State: closed - Opened by mmore500 12 months ago - 1 comment

#64 - Try adding test coverage

Pull Request - State: closed - Opened by emilydolson about 1 year ago - 3 comments

#63 - Update docs

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

#62 - Fix segfault in load

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

#61 - Clearer error on comparison between unsupported taxon_info types

Issue - State: open - Opened by emilydolson about 1 year ago
Labels: enhancement

#60 - Avoid storing eq operator for every taxon_info object

Issue - State: open - Opened by emilydolson about 1 year ago
Labels: enhancement

#59 - Fix citation syntax

Pull Request - State: closed - Opened by mmore500 about 1 year ago

#58 - Add get pairwise distance

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

#57 - Demonstrate and fix string bug

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

#56 - Bump Empirical from `ed27152` to `58c6d81`

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 3 comments
Labels: dependencies, submodules

#55 - Fix windows build

Pull Request - State: closed - Opened by emilydolson about 1 year ago - 6 comments

#54 - Tests fail on wheels for windows

Issue - State: closed - Opened by mmore500 about 1 year ago - 1 comment
Labels: bug

#53 - Add instructions for github, local installs RE #32

Pull Request - State: closed - Opened by mmore500 about 1 year ago - 1 comment

#52 - Fixup dev experience, RE #33

Pull Request - State: closed - Opened by mmore500 about 1 year ago - 1 comment

#51 - Column key `"info"` defaulted in `load_from_file` isn't included by default when calling `snapshot`

Issue - State: open - Opened by mmore500 about 1 year ago - 1 comment
Labels: enhancement

#50 - Fix broken docs links in README

Pull Request - State: closed - Opened by mmore500 about 1 year ago

#49 - `load_from_file` segfaults if root is extant

Issue - State: closed - Opened by mmore500 about 1 year ago
Labels: bug

#48 - Creating a taxon manually can cause invalid snapshot files

Issue - State: closed - Opened by mmore500 about 1 year ago - 2 comments
Labels: enhancement

#47 - Implement, test py::object as taxon type

Pull Request - State: closed - Opened by mmore500 about 1 year ago - 16 comments

#46 - Drop unnecessary lambda

Pull Request - State: closed - Opened by mmore500 about 1 year ago

#45 - Add profiling section

Pull Request - State: closed - Opened by mmore500 about 1 year ago - 2 comments

#44 - Line edits RE #35

Pull Request - State: closed - Opened by mmore500 about 1 year ago - 1 comment

#43 - Add alifedata-phyloinformatics-convert info

Pull Request - State: closed - Opened by mmore500 about 1 year ago - 4 comments

#42 - Bump version: 0.1.16 → 0.1.17

Pull Request - State: closed - Opened by mmore500 about 1 year ago

#41 - Test over Python3.12 and deploy wheels for it

Pull Request - State: closed - Opened by mmore500 about 1 year ago - 2 comments

#40 - Bump urllib3 from 1.26.14 to 1.26.18

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies, python

#39 - Bump certifi from 2022.12.7 to 2023.7.22

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies, python

#38 - Document project organization

Pull Request - State: closed - Opened by mmore500 over 1 year ago - 1 comment

#37 - JOSS review - exporting data

Issue - State: closed - Opened by RussellGarwood over 1 year ago - 1 comment
Labels: enhancement

#36 - JOSS Review: Input data format conversion

Issue - State: closed - Opened by CFGrote over 1 year ago - 1 comment
Labels: enhancement

#35 - JOSS Review: Paper

Issue - State: closed - Opened by CFGrote over 1 year ago - 3 comments

#34 - JOSS Review: Functionality, documentation

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

#33 - JOSS Review: Documentation hosting and building

Issue - State: closed - Opened by CFGrote over 1 year ago - 3 comments

#32 - JOSS Review: Installation

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

#31 - Document use of data nodes

Issue - State: open - Opened by emilydolson over 1 year ago - 1 comment
Labels: documentation

#30 - Bump Empirical from `f11e64a` to `1578787`

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, submodules

#29 - Document the funky stuff I just did with deep copies of taxon objects

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

#28 - Bump pygments from 2.14.0 to 2.15.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#27 - Bump requests from 2.28.2 to 2.31.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#26 - Third argument to add_snapshot_fun should be optional

Issue - State: closed - Opened by emilydolson over 1 year ago - 1 comment
Labels: bug

#25 - Enable deepcopy

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

#24 - Add support for tool tips and bibliography

Pull Request - State: closed - Opened by rodsan0 over 1 year ago - 1 comment

#23 - Implement more phylogeny metrics

Issue - State: open - Opened by emilydolson over 1 year ago
Labels: enhancement, good first issue

#22 - Outstanding API documentation changes

Issue - State: closed - Opened by rodsan0 over 1 year ago - 2 comments
Labels: enhancement

#21 - Add JOSS badge to readme

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

#20 - Add missing DOIs

Pull Request - State: closed - Opened by mmore500 over 1 year ago - 1 comment

#19 - Allow real-time collapsing of unifurcations to save space

Issue - State: closed - Opened by emilydolson over 1 year ago - 1 comment
Labels: enhancement, good first issue

#18 - Bioinformatics compatability tools

Issue - State: open - Opened by emilydolson over 1 year ago - 2 comments
Labels: enhancement

#17 - [WIP] Add API docs

Pull Request - State: closed - Opened by rodsan0 over 1 year ago - 11 comments

#16 - Bump Empirical from `96717aa` to `1578787`

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#15 - Implement Robust Universal Balance Index

Issue - State: open - Opened by emilydolson over 1 year ago
Labels: enhancement, good first issue

#14 - Add tests

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

#13 - Add API documentation

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

#12 - More JOSS revisions

Pull Request - State: closed - Opened by mmore500 over 1 year ago - 1 comment

#11 - WIP mmore500 Joss edits

Pull Request - State: closed - Opened by mmore500 over 1 year ago - 2 comments

GitHub / emilydolson/phylotrackpy issues and pull requests