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
#131 - Can't set random seed or substitution model in RAxML wrapper
Issue -
State: open - Opened by NoahAmsel over 3 years ago
#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
#105 - Missing space in DIMENSIONS command when writing DataSet to simple NEXUS format
Issue -
State: closed - Opened by jmenglund 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
#102 - suppress_unifurcations=False when computing bipartitions after unrooting is broken
Issue -
State: closed - Opened by thekswenson almost 6 years ago
- 3 comments
#102 - suppress_unifurcations=False when computing bipartitions after unrooting is broken
Issue -
State: closed - Opened by thekswenson almost 6 years ago
- 3 comments
#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
#86 - functions extract_tree_with_taxa and extract_tree_with_taxa_labels have extra parameters in the documentation
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
#37 - Parsing NEXUS trees with undefined taxon labels does not raise error
Issue -
State: open - Opened by jeetsukumaran almost 9 years ago
#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
#13 - Fix Tree.resolve_polytomies() to not fail when a polytomy occurs a the root
Pull Request -
State: closed - Opened by tylershunt over 10 years ago
#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