Ecosyste.ms: Issues

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

GitHub / jeetsukumaran/dendropy issues and pull requests

#212 - Further fix up JOSS ISSNs

Pull Request - State: closed - Opened by mmore500 24 days ago

#211 - Fix ISSNs in JOSS bib

Pull Request - State: closed - Opened by mmore500 25 days ago

#210 - Incorporate JOSS editor suggestions

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

#209 - Update JOSS draft

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

#208 - Touchup RE JOSS review

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

#207 - Standardize License to BST 3 Clause

Pull Request - State: closed - Opened by mmore500 about 2 months ago - 1 comment

#206 - Only deploy docs from main branch

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

#205 - Improved docstring for src/dendropy/datamodel/treemodel/_tree.py/reroot_at_edge

Pull Request - State: closed - Opened by terrycojones about 2 months ago - 2 comments

#203 - Bump certifi from 2023.7.22 to 2024.7.4 in /docs

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies

#202 - Bump urllib3 from 2.0.7 to 2.2.2 in /docs

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies

#201 - Fix unnecessary quoting in newick format

Pull Request - State: closed - Opened by mmore500 4 months ago - 1 comment

#200 - Support values written as quoted node labels since >4.6.1

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

#199 - Bump requests from 2.31.0 to 2.32.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago - 1 comment
Labels: dependencies

#198 - JOSS Paper?

Issue - State: closed - Opened by mmore500 4 months ago

#197 - Final Steps for Version 5 Release

Issue - State: closed - Opened by mmore500 4 months ago

#196 - JOSS

Pull Request - State: closed - Opened by mmore500 4 months ago - 1 comment

#195 - Fix readthedocs build

Pull Request - State: closed - Opened by mmore500 4 months ago - 2 comments

#194 - Implement, test polytomize_root

Pull Request - State: open - Opened by mmore500 4 months ago - 1 comment

#193 - Warn on implicit splice operations

Pull Request - State: closed - Opened by mmore500 5 months ago

#192 - Fix escaping of newick strings

Pull Request - State: closed - Opened by mmore500 5 months ago

#191 - Fix newick parser handling of terminating unnamed unifurcations

Pull Request - State: closed - Opened by mmore500 5 months ago

#190 - Fix extant/extinct bug for custom tree birthdeath

Pull Request - State: closed - Opened by mmore500 5 months ago

#189 - Update setup.py

Pull Request - State: closed - Opened by mmore500 5 months ago

#187 - Bump jinja2 from 3.1.3 to 3.1.4 in /docs

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#186 - Option to give leaf nodes in polytomies a default order in Tree.ladderize.

Pull Request - State: closed - Opened by davipatti 5 months ago - 5 comments

#185 - Website dendropy.org is down

Issue - State: closed - Opened by Wytamma 5 months ago - 5 comments

#184 - Add codecov token

Pull Request - State: closed - Opened by mmore500 5 months ago - 1 comment

#183 - Bump idna from 3.4 to 3.7 in /docs

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

#181 - Bump jinja2 from 3.1.2 to 3.1.3 in /docs

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#180 - Multithreaded option fails with no error message - leaf labels issue?

Issue - State: closed - Opened by AthinaGav 10 months ago - 2 comments
Labels: bug

#179 - Create smoke tests

Issue - State: closed - Opened by Nephrain 11 months ago

#179 - Create smoke tests

Issue - State: open - Opened by Nephrain 11 months ago

#178 - Setup deploy CI job

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

#178 - Setup deploy CI job

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

#177 - Documentation Deployment

Issue - State: closed - Opened by mmore500 11 months ago

#176 - Prepare version 5.0 release

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

#175 - Flesh out ongoing development documentation

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

#175 - Flesh out ongoing development documentation

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

#174 - Pin ruff linter version

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

#173 - Switch classmethod, staticmethod to decorator syntax

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

#173 - Switch classmethod, staticmethod to decorator syntax

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

#172 - quote_underscores argument unrecognized

Issue - State: closed - Opened by davidrasm about 1 year ago - 1 comment

#171 - Test packaging

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

#170 - Pass rng in evolve_states

Pull Request - State: closed - Opened by actapia over 1 year ago - 4 comments

#170 - Pass rng in evolve_states

Pull Request - State: closed - Opened by actapia over 1 year ago - 4 comments

#169 - Provide public interface for `_convert_node_to_root_polytomy`

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

#168 - `paup_estimate_tree_nj` example experiences intermittent failure

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

#167 - Fix invalid escape sequences

Pull Request - State: closed - Opened by mmore500 over 1 year ago - 3 comments

#166 - Chore: fix `distutils` deprecation warning

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

#166 - Chore: fix `distutils` deprecation warning

Issue - State: open - Opened by mmore500 over 1 year ago

#165 - Chore: Fix `ResourceWarning`s from tests

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

#165 - Chore: Fix `ResourceWarning`s from tests

Issue - State: open - Opened by mmore500 over 1 year ago

#164 - Add coverage to CI

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

#163 - Update PyPi project url

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

#163 - Update PyPi project url

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

#162 - Track PyPi URL change for project homepage

Issue - State: open - Opened by mmore500 over 1 year ago

#162 - Track PyPi URL change for project homepage

Issue - State: closed - Opened by mmore500 over 1 year ago

#161 - Add developer documentation

Issue - State: closed - Opened by mmore500 over 1 year ago

#160 - Some examples in `/docs/source/examples` are broken

Issue - State: open - Opened by mmore500 over 1 year ago
Labels: enhancement, infrastructure

#159 - Keep supporting Python2.7?

Issue - State: closed - Opened by mmore500 over 1 year ago - 3 comments

#159 - Keep supporting Python2.7?

Issue - State: open - Opened by mmore500 over 1 year ago - 2 comments

#158 - Fix broken tests, miscellaneous lint

Pull Request - State: closed - Opened by mmore500 over 1 year ago - 3 comments

#158 - Fix broken tests, miscellaneous lint

Pull Request - State: closed - Opened by mmore500 over 1 year ago - 3 comments

#157 - Setup CI

Pull Request - State: closed - Opened by mmore500 over 1 year ago - 3 comments

#156 - WIP Setup CI

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

#156 - WIP Setup CI

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

#155 - Remove deprecated `random.sample` from `Tree.shuffle_taxa()`

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

#155 - Remove deprecated `random.sample` from `Tree.shuffle_taxa()`

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

#154 - `shuffle_taxa` raises `DeprecationWarning`

Issue - State: closed - Opened by mmore500 over 1 year ago

#153 - Fix unexpected rooting side effects of `Tree.mrca()`

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

#152 - `Tree.mrca` has side effect of changing rooting state

Issue - State: closed - Opened by mmore500 over 1 year ago - 6 comments
Labels: enhancement

#151 - Corrected step number calculation for unrooted trees

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

#151 - Corrected step number calculation for unrooted trees

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

#150 - API docs

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

#150 - API docs

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

#149 - Fix minor copy/paste pre/post-order typos in docs

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

#149 - Fix minor copy/paste pre/post-order typos in docs

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

#148 - Bugfix: Tree mrca method does not account for internal unifurcation

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

#148 - Bugfix: Tree mrca method does not account for internal unifurcation

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

#147 - Fixup docstring code block

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

#146 - Underscores appear to be removed in tree taxonnamespace

Issue - State: closed - Opened by Mahim1997 over 1 year ago - 1 comment

#146 - Underscores appear to be removed in tree taxonnamespace

Issue - State: closed - Opened by Mahim1997 over 1 year ago - 1 comment

#145 - Correctly load newick node annotations containing nested lists

Issue - State: open - Opened by willdumm almost 2 years ago
Labels: enhancement

#144 - Special characters in input tree tip labels causes unpredictable renaming

Issue - State: open - Opened by AlesBucek about 2 years ago - 5 comments

#144 - Special characters in input tree tip labels causes unpredictable renaming

Issue - State: closed - Opened by AlesBucek about 2 years ago - 6 comments
Labels: bug

#143 - Should `Node.extract_subtree` return Tree, not seed node, & copy annotations?

Issue - State: open - Opened by MordorianGuy about 2 years ago
Labels: enhancement

#142 - multiprocess :: mp.cpu_count() instead of len(os.sched_getaffinity(0))

Issue - State: open - Opened by EricDeveaud about 2 years ago
Labels: enhancement

#141 - Calling tab complete on a tree surpresses unifurcations in Python 3.7.3

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

#140 - Documentation appears to be down

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

#140 - Documentation appears to be down

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

#139 - Help catching exception?

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

#139 - Help catching exception?

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

#138 - Creating new tree from seed node removes node from original tree

Issue - State: closed - Opened by Adam-Gleave almost 3 years ago - 1 comment
Labels: bug

#137 - please create a release

Issue - State: closed - Opened by joelb123 almost 3 years ago - 6 comments