lmaurits/phyltr issues and pull requests

#37 - Something is physhy in the consensus trees

Issue - State: open - Opened by Anaphory over 3 years ago - 6 comments

#36 - Current sink absorbs internal node names

Issue - State: open - Opened by Anaphory over 4 years ago - 1 comment

#35 - Add two commands

Pull Request - State: open - Opened by Anaphory over 4 years ago - 3 comments

#34 - Newick Networks

Pull Request - State: open - Opened by Anaphory over 5 years ago - 1 comment

#33 - Command line usage results in "unrecognized arguments", followed by the .nex file

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

#32 - Fixes import error

Pull Request - State: closed - Opened by tresoldi over 5 years ago - 2 comments

#31 - pep8 + refactoring mean/median/HPD computation

Pull Request - State: closed - Opened by xrotwang over 5 years ago - 2 comments

#30 - should phyltr be pluggable?

Issue - State: open - Opened by xrotwang over 5 years ago - 1 comment

#29 - `clades` command should output a CSV file, for overall consistency

Issue - State: open - Opened by lmaurits over 5 years ago

#28 - Remove omnipresent files argument

Pull Request - State: closed - Opened by xrotwang over 5 years ago - 5 comments

#27 - first stab at phyltr 1.0

Pull Request - State: closed - Opened by xrotwang over 5 years ago - 4 comments

#26 - phyltr.main._COMMANDS lists non-existing commands

Issue - State: open - Opened by xrotwang over 5 years ago

#25 - Inconsistent CLI syntax for taxa

Issue - State: closed - Opened by xrotwang over 5 years ago - 13 comments

#24 - Another reason to drop py2 support: statistics!

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

#23 - Rename main.py to main.py

Issue - State: closed - Opened by xrotwang over 5 years ago

#22 - Replace optparse with argparse

Issue - State: open - Opened by xrotwang over 5 years ago

#21 - More flexible rename map

Issue - State: open - Opened by xrotwang over 5 years ago - 11 comments

#20 - phyltr cat does not read NEXUS translate block correctly

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

#19 - Consensus tree calculation pretends to run on mixed trees

Issue - State: open - Opened by Anaphory almost 6 years ago - 5 comments

#18 - specify release process

Issue - State: open - Opened by xrotwang almost 6 years ago - 1 comment

#17 - Refactored classmethods, more tests and better custom Nexus support

Pull Request - State: closed - Opened by xrotwang almost 6 years ago - 3 comments

#16 - unsupported nexus format

Issue - State: closed - Opened by xrotwang almost 6 years ago - 8 comments

#15 - refactored test suite, using pytest fixtures to remove boilerplate

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

#14 - Fix clades command for edge case of single taxon tree

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

#13 - IndexError in save_clade_report

Issue - State: closed - Opened by xrotwang almost 6 years ago - 2 comments

#12 - Phyltr-generated treestreams are not guaranteed to have a fixed taxon set, but some commands assume they will

Issue - State: open - Opened by lmaurits almost 6 years ago

#11 - all tests pass on py3.5

Pull Request - State: closed - Opened by xrotwang almost 6 years ago - 9 comments

#10 - port to py3

Issue - State: open - Opened by xrotwang almost 6 years ago - 1 comment

#9 - Cat seems to not work in chunks

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

#8 - Somewhere in phyltr, all tips are aligned

Issue - State: open - Opened by Anaphory almost 7 years ago - 6 comments

#7 - Import of main should be relative

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

#6 - Implement --no-annotations

Issue - State: closed - Opened by Anaphory almost 7 years ago - 6 comments

#5 - See if funky argument handling can be made more elegant

Issue - State: open - Opened by lmaurits about 7 years ago

#4 - Implement siblings command

Issue - State: closed - Opened by lmaurits about 7 years ago

#3 - Implement grep command