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
#204 - Remove preserve_underscores as an argument in docstring example usages of datamodel.basemodel.Serializable.write
Pull Request -
State: closed - Opened by terrycojones 2 months ago
- 3 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 4 months ago
#192 - Fix escaping of newick strings
Pull Request -
State: closed - Opened by mmore500 4 months ago
#191 - Fix newick parser handling of terminating unnamed unifurcations
Pull Request -
State: closed - Opened by mmore500 4 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
#188 - treesim.birth_death_tree() raises division by zero error when used to extend an existing tree
Issue -
State: closed - Opened by Androstane 5 months ago
- 4 comments
#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
#182 - Error runnig picrust due to cannot import name '_convert_node_to_root_polytomy'
Issue -
State: closed - Opened by Zathzk 8 months ago
- 2 comments
#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 9 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
#168 - `paup_estimate_tree_nj` example experiences intermittent failure
Issue -
State: open - Opened by mmore500 over 1 year ago
#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
#142 - multiprocess :: mp.cpu_count() instead of len(os.sched_getaffinity(0))
Issue -
State: open - Opened by EricDeveaud about 2 years ago
#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
#138 - Creating new tree from seed node removes node from original tree
Issue -
State: open - Opened by Adam-Gleave almost 3 years ago
#137 - please create a release
Issue -
State: closed - Opened by joelb123 almost 3 years ago
- 6 comments