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

#136 - Use `case_sensitive_taxon_labels` in kwargs to set TaxonNamespace is_case_sensitive

Pull Request - State: closed - Opened by crosenth over 3 years ago - 1 comment

#136 - Use `case_sensitive_taxon_labels` in kwargs to set TaxonNamespace is_case_sensitive

Pull Request - State: closed - Opened by crosenth over 3 years ago - 1 comment

#135 - ValueError: Attempting case sensitive read with case insensitive TaxonNamespace

Issue - State: closed - Opened by crosenth over 3 years ago - 1 comment

#135 - ValueError: Attempting case sensitive read with case insensitive TaxonNamespace

Issue - State: closed - Opened by crosenth over 3 years ago - 1 comment

#134 - Typo in PhylogeneticIndependentContrasts class

Issue - State: closed - Opened by Puumanamana over 3 years ago - 1 comment

#133 - Re-enable secure SSL in setup.py

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

#132 - raxml set rand seed

Pull Request - State: closed - Opened by NoahAmsel over 3 years ago - 1 comment

#132 - raxml set rand seed

Pull Request - State: closed - Opened by NoahAmsel over 3 years ago - 1 comment

#131 - Can't set random seed or substitution model in RAxML wrapper

Issue - State: closed - Opened by NoahAmsel over 3 years ago - 1 comment
Labels: enhancement

#130 - Dendropy web page with documentation is not working

Issue - State: closed - Opened by fpichardom over 3 years ago - 1 comment

#130 - Dendropy web page with documentation is not working

Issue - State: closed - Opened by fpichardom over 3 years ago - 1 comment

#129 - Add label lookup to improve nexusreader speed

Pull Request - State: closed - Opened by SamStudio8 over 3 years ago - 7 comments

#129 - Add label lookup to improve nexusreader speed

Pull Request - State: closed - Opened by SamStudio8 over 3 years ago - 7 comments

#128 - added faster tree generation

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

#128 - added faster tree generation

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

#127 - PhylogeneticDistanceMatrix.distances: return symmetric distances

Issue - State: closed - Opened by nick-youngblut almost 4 years ago - 4 comments

#127 - PhylogeneticDistanceMatrix.distances: return symmetric distances

Issue - State: open - Opened by nick-youngblut almost 4 years ago - 4 comments

#126 - resolve_polytomies could return number of polytomies resolved

Issue - State: open - Opened by hyanwong almost 4 years ago
Labels: enhancement

#125 - Please tag a new release that contains 972d12fe2be3241c33fb2a969e5f0271158a24fc

Issue - State: closed - Opened by jonchang about 4 years ago - 6 comments

#124 - Add Bandelt Encoding

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

#124 - Add Bandelt Encoding

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

#123 - Bipartition.edge

Issue - State: closed - Opened by jtfield over 4 years ago - 5 comments

#123 - Bipartition.edge

Issue - State: closed - Opened by jtfield over 4 years ago - 5 comments

#122 - Test suite vanished from download tarball

Issue - State: open - Opened by tillea almost 5 years ago - 4 comments
Labels: enhancement, infrastructure

#122 - Test suite vanished from download tarball

Issue - State: open - Opened by tillea almost 5 years ago - 4 comments

#121 - dendropy.utility.error.UltrametricityError

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

#121 - dendropy.utility.error.UltrametricityError

Issue - State: open - Opened by nick-youngblut about 5 years ago - 2 comments
Labels: enhancement

#120 - accuracy of gene tree simlation

Issue - State: open - Opened by zzbbf123 about 5 years ago
Labels: question

#119 - Calling the Paup tree estimate method returns an error

Issue - State: closed - Opened by mlalith2006 about 5 years ago - 1 comment

#118 - Unexpected unifurcation suppression in reroot_at_node()

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

#117 - Best way to add a long branch above root

Issue - State: closed - Opened by psathyrella over 5 years ago - 2 comments

#116 - Fixing bug in contained_coalescent_tree function.

Pull Request - State: closed - Opened by joaks1 over 5 years ago - 1 comment

#116 - Fixing bug in contained_coalescent_tree function.

Pull Request - State: closed - Opened by joaks1 over 5 years ago - 1 comment

#115 - Bug in dendropy.model.coalescent.contained_coalescent_tree

Issue - State: closed - Opened by joaks1 over 5 years ago - 2 comments

#114 - phylogenetic distances with gigantic tree

Issue - State: closed - Opened by b-tierney over 5 years ago - 4 comments

#114 - phylogenetic distances with gigantic tree

Issue - State: closed - Opened by b-tierney over 5 years ago - 4 comments

#113 - TaxonNamespace partition() not working

Issue - State: closed - Opened by sojovictor over 5 years ago - 4 comments

#113 - TaxonNamespace partition() not working

Issue - State: closed - Opened by sojovictor over 5 years ago - 4 comments

#112 - Preserve_underscores

Issue - State: open - Opened by wrightaprilm over 5 years ago - 2 comments

#112 - Preserve_underscores

Issue - State: open - Opened by wrightaprilm over 5 years ago - 2 comments
Labels: enhancement

#111 - Use dictionary.items instead of iteritems for Python3 Compatibility

Pull Request - State: closed - Opened by petercombs over 5 years ago - 1 comment

#111 - Use dictionary.items instead of iteritems for Python3 Compatibility

Pull Request - State: closed - Opened by petercombs over 5 years ago - 1 comment

#110 - Seg Fault when deepcopy-ing large tree

Issue - State: closed - Opened by MGNute over 5 years ago - 4 comments

#109 - Bipartition comparison depends on rootedness

Issue - State: closed - Opened by benjaminwilson over 5 years ago - 5 comments

#109 - Bipartition comparison depends on rootedness

Issue - State: closed - Opened by benjaminwilson over 5 years ago - 5 comments

#108 - RNG seed doesn't determine result of `treesim.birth_death_tree`

Issue - State: closed - Opened by benjaminwilson over 5 years ago - 4 comments

#107 - NewickReaderMalformedStatementError: NewickReaderMalformedStatementError

Issue - State: closed - Opened by snowflake01986 over 5 years ago - 1 comment

#107 - NewickReaderMalformedStatementError: NewickReaderMalformedStatementError

Issue - State: closed - Opened by snowflake01986 over 5 years ago - 1 comment

#106 - Typo in treemeasure.py

Issue - State: closed - Opened by ArtPoon over 5 years ago - 1 comment

#104 - fix typos in primer/treemanips.rst

Pull Request - State: closed - Opened by wosnat almost 6 years ago - 1 comment

#104 - fix typos in primer/treemanips.rst

Pull Request - State: closed - Opened by wosnat almost 6 years ago - 1 comment

#103 - single / to double //, with a single slash url is interpreted as rel…

Pull Request - State: closed - Opened by Carreau almost 6 years ago - 1 comment

#103 - single / to double //, with a single slash url is interpreted as rel…

Pull Request - State: closed - Opened by Carreau almost 6 years ago - 1 comment

#101 - keep_sequences() issue

Issue - State: closed - Opened by wrightaprilm about 6 years ago - 4 comments

#101 - keep_sequences() issue

Issue - State: closed - Opened by wrightaprilm about 6 years ago - 4 comments

#100 - Bipartition is mutable: hash is unstable

Issue - State: closed - Opened by any333 about 6 years ago - 3 comments

#99 - MRCA algorithm can be faster

Issue - State: open - Opened by niemasd about 6 years ago - 1 comment
Labels: enhancement

#98 - as_ascii_plot() kwargs not showing up in docs

Issue - State: closed - Opened by psathyrella about 6 years ago - 1 comment

#97 - documentation: viewing and displaying Newick tree needs semi-colon

Issue - State: closed - Opened by thekswenson about 6 years ago - 1 comment

#97 - documentation: viewing and displaying Newick tree needs semi-colon

Issue - State: closed - Opened by thekswenson about 6 years ago - 1 comment

#95 - extract_tree_with_taxa + str() produces malformed tree

Issue - State: closed - Opened by niemasd over 6 years ago - 5 comments

#95 - extract_tree_with_taxa + str() produces malformed tree

Issue - State: open - Opened by niemasd over 6 years ago - 4 comments

#89 - `split_distribution` crashes with `TypeError`

Issue - State: closed - Opened by mjr129 over 6 years ago - 2 comments

#88 - random seed reproducibility of treesim.birth_death_tree when using numpy.save

Issue - State: closed - Opened by idavydov almost 7 years ago - 1 comment

#83 - Is there a summarization demo of the DendroPy/

Issue - State: closed - Opened by JafferWilson about 7 years ago - 1 comment

#81 - Dedropy mistakenly looking for DNA alphabet in ProteinCharacterMatrix.get

Issue - State: closed - Opened by tauanajc over 7 years ago - 2 comments

#81 - Dedropy mistakenly looking for DNA alphabet in ProteinCharacterMatrix.get

Issue - State: open - Opened by tauanajc over 7 years ago - 1 comment

#76 - Dendropy incorrectly reads terminating unnamed unifurcations

Issue - State: closed - Opened by hyanwong over 7 years ago - 3 comments
Labels: bug

#74 - test failure on ubuntu with python 2.7.11+

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

#63 - Floating point error accumulation in contained coalescent trees

Issue - State: open - Opened by yasuiniko about 8 years ago
Labels: enhancement

#57 - Documentation for newick output possibly wrong

Issue - State: closed - Opened by hyanwong over 8 years ago - 2 comments

#54 - possible enhancement: retain edge identity when rerooting

Issue - State: open - Opened by mtholder over 8 years ago - 1 comment
Labels: enhancement

#52 - Maximum recursion depth error

Issue - State: open - Opened by ericmjl over 8 years ago - 8 comments
Labels: enhancement

#46 - Feature request: Writing to JSON schema

Issue - State: open - Opened by Zsailer over 8 years ago - 14 comments

#46 - Feature request: Writing to JSON schema

Issue - State: open - Opened by Zsailer over 8 years ago - 14 comments
Labels: enhancement

#44 - Add support for PhyML interoperability

Pull Request - State: closed - Opened by jmenglund over 8 years ago - 2 comments

#40 - Add support for interleaved PHYLIP writing

Pull Request - State: closed - Opened by pranjalv123 over 8 years ago - 1 comment

#37 - Parsing NEXUS trees with undefined taxon labels does not raise error

Issue - State: open - Opened by jeetsukumaran almost 9 years ago
Labels: enhancement

#32 - Common Ancestors age strategy for --set-edges

Issue - State: open - Opened by nitishnarula about 9 years ago
Labels: enhancement

#30 - reroot_at_edge() causes trifurcation and incorrect branch lengths

Issue - State: closed - Opened by donovan-h-parks about 9 years ago - 4 comments

#30 - reroot_at_edge() causes trifurcation and incorrect branch lengths

Issue - State: closed - Opened by donovan-h-parks about 9 years ago - 4 comments

#25 - Ordered Parsimony

Issue - State: open - Opened by mccannj9 about 9 years ago - 1 comment
Labels: enhancement

#23 - scm is not supported in Dendropy 4.0.2

Issue - State: closed - Opened by Kajori about 9 years ago - 2 comments

#18 - Is there a recommended way to run the tests in parallel?

Issue - State: closed - Opened by mtholder over 9 years ago - 5 comments
Labels: question

#18 - Is there a recommended way to run the tests in parallel?

Issue - State: closed - Opened by mtholder over 9 years ago - 5 comments
Labels: question

#11 - trprobs memory crash causes truncated consensus tree

Issue - State: closed - Opened by willgearty over 10 years ago - 1 comment

#11 - trprobs memory crash causes truncated consensus tree

Issue - State: closed - Opened by willgearty over 10 years ago - 1 comment

#9 - Added missing "check_ultrametricity_prec" parameter

Pull Request - State: closed - Opened by ngcrawford about 11 years ago

#9 - Added missing "check_ultrametricity_prec" parameter

Pull Request - State: closed - Opened by ngcrawford about 11 years ago

#7 - The trprobs file built by sumtrees.py contains unrooted duplicates when run with rooted trees

Issue - State: closed - Opened by Boussau over 11 years ago - 1 comment
Labels: question

#6 - Added reading of label for NeXML characters.

Pull Request - State: closed - Opened by balhoff almost 12 years ago

#6 - Added reading of label for NeXML characters.

Pull Request - State: closed - Opened by balhoff almost 12 years ago

#5 - Apply node_label_compose_function to taxlabels in nexus format

Pull Request - State: closed - Opened by evoling almost 12 years ago