Ecosyste.ms: Issues

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GitHub / jjmccollum/teiphy issues and pull requests

#85 - Add support for time-dependent substitution models with EpochSubstitutionModel in BEAST outputs

Issue - State: closed - Opened by jjmccollum 5 months ago - 2 comments
Labels: enhancement

#78 - Change CSV outputs to include BOM

Issue - State: closed - Opened by jjmccollum 9 months ago - 1 comment
Labels: bug

#77 - Add support for NEXUS-style CSV/Excel output

Issue - State: closed - Opened by jjmccollum 9 months ago - 1 comment
Labels: enhancement

#73 - Relative path to chron file for stemma output

Issue - State: closed - Opened by rbturnbull about 1 year ago - 2 comments

#72 - Create directory for output if needed

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

#71 - Update README.rst

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

#70 - Merged beast-xml branch

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

#69 - add tip date sampling for beast

Issue - State: closed - Opened by rbturnbull over 1 year ago - 5 comments

#68 - Substantive units

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

#67 - Listwit validation

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

#66 - Add support for BEAST XML output

Issue - State: closed - Opened by jjmccollum over 1 year ago - 73 comments
Labels: enhancement

#65 - Should teiphy convert all variation units, including trivial ones?

Issue - State: closed - Opened by jjmccollum over 1 year ago
Labels: enhancement, question

#64 - Failure with no user-oriented error message

Issue - State: closed - Opened by cmsmcq almost 2 years ago - 10 comments

#63 - Patch 1

Pull Request - State: closed - Opened by danielskatz almost 2 years ago - 1 comment

#62 - Bump certifi from 2022.9.24 to 2022.12.7

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#61 - Iqtree fix

Pull Request - State: closed - Opened by rbturnbull almost 2 years ago

#60 - Fix github actions workflow for iqtree

Issue - State: closed - Opened by rbturnbull almost 2 years ago - 1 comment

#59 - Code revisions from second review

Pull Request - State: closed - Opened by jjmccollum almost 2 years ago

#58 - Add `--long-table` option for tabular output

Issue - State: closed - Opened by jjmccollum almost 2 years ago

#57 - Incorporate latest feedback on paper

Issue - State: closed - Opened by jjmccollum almost 2 years ago

#56 - Add support for `--ascertainment` option

Issue - State: closed - Opened by jjmccollum almost 2 years ago - 4 comments

#55 - Make `--states-present` default option for NEXUS output

Issue - State: closed - Opened by jjmccollum almost 2 years ago

#53 - :abc: Did a pass at revising paper (#52)

Pull Request - State: closed - Opened by jjmccollum almost 2 years ago

#52 - Revise paper

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

#51 - Updated readme and advanced usage documentation (#50)

Pull Request - State: closed - Opened by jjmccollum almost 2 years ago

#50 - Update documentation

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

#49 - App --version command and PHYLIP and FASTA support

Pull Request - State: closed - Opened by jjmccollum almost 2 years ago

#48 - Add support for PHYLIP and FASTA formats

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

#47 - Add --version argument to app

Issue - State: closed - Opened by jjmccollum almost 2 years ago - 10 comments

#46 - Exampledocs

Pull Request - State: closed - Opened by jjmccollum about 2 years ago

#45 - Example in docs

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

#44 - logo/banner

Issue - State: closed - Opened by rbturnbull about 2 years ago - 12 comments

#43 - cicd

Pull Request - State: closed - Opened by jjmccollum about 2 years ago

#42 - docs for command line flags

Issue - State: closed - Opened by rbturnbull about 2 years ago - 6 comments

#41 - CHARSTATELABELS block?

Issue - State: closed - Opened by rbturnbull about 2 years ago - 4 comments

#40 - example with fewer witnesses and add into paper

Issue - State: closed - Opened by rbturnbull about 2 years ago - 8 comments

#39 - clean up XML file

Issue - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#38 - system tests in CI

Issue - State: closed - Opened by rbturnbull about 2 years ago - 8 comments

#37 - :zap: using rich to enhance help output

Pull Request - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#36 - adding help text for input and output in main.py

Issue - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#35 - Pyproject

Pull Request - State: closed - Opened by rbturnbull about 2 years ago

#34 - :abc: a few edits to the paper

Pull Request - State: closed - Opened by rbturnbull about 2 years ago - 3 comments

#33 - Black

Pull Request - State: closed - Opened by rbturnbull about 2 years ago - 2 comments

#32 - Docscli

Pull Request - State: closed - Opened by rbturnbull about 2 years ago

#31 - :abc: refactoring docs and reusing information from readme in the doc…

Pull Request - State: closed - Opened by rbturnbull about 2 years ago

#30 - start writing JOSS paper

Issue - State: closed - Opened by rbturnbull about 2 years ago - 8 comments

#29 - :abc: adding in api reference to docs. (issue #27)

Pull Request - State: closed - Opened by rbturnbull about 2 years ago

#28 - testing coverage to 100%

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

#27 - autogenerate docs from classes

Issue - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#26 - Simplecli

Pull Request - State: closed - Opened by rbturnbull about 2 years ago

#25 - Testing

Pull Request - State: closed - Opened by rbturnbull about 2 years ago

#24 - simplify CLI to one command

Issue - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#23 - refactor into separate files

Issue - State: closed - Opened by rbturnbull about 2 years ago - 6 comments

#22 - Testing

Pull Request - State: closed - Opened by rbturnbull about 2 years ago

#21 - changing the name of the py directory

Issue - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#20 - add testing coverage to github actions and have a badge in the readme and docs

Issue - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#19 - think about name?

Issue - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#18 - add docstrings with consistent format

Issue - State: closed - Opened by rbturnbull about 2 years ago

#17 - :tv: adding lxml to dependencies in a pyproject.toml. Addresses issue #5

Pull Request - State: closed - Opened by rbturnbull about 2 years ago

#16 - add code of conduct and contributing info

Issue - State: closed - Opened by rbturnbull about 2 years ago - 4 comments

#15 - decide on licence

Issue - State: closed - Opened by rbturnbull about 2 years ago - 3 comments

#14 - refactor for calling directly in python rather than from the command line

Issue - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#13 - make class names start with capital letters

Issue - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#12 - release to PyPI

Issue - State: closed - Opened by rbturnbull about 2 years ago

#11 - deploy docs with github actions

Issue - State: closed - Opened by rbturnbull about 2 years ago - 4 comments

#10 - add sphinx docs and move info from readme there

Issue - State: closed - Opened by rbturnbull about 2 years ago - 6 comments

#9 - convert from argparse to typer

Issue - State: closed - Opened by rbturnbull about 2 years ago - 3 comments

#8 - add github actions for unit tests

Issue - State: closed - Opened by rbturnbull about 2 years ago - 1 comment

#7 - add unit tests

Issue - State: closed - Opened by rbturnbull about 2 years ago - 4 comments

#6 - add black pre-commit hook

Issue - State: closed - Opened by rbturnbull about 2 years ago - 4 comments

#5 - convert to using pyproject.toml/poetry

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

#4 - Add export methods for other output formats

Issue - State: closed - Opened by jjmccollum about 2 years ago - 14 comments

#3 - Support StatesFormat=Frequency for NEXUS

Issue - State: closed - Opened by jjmccollum about 2 years ago - 1 comment

#2 - Support filling corrector text based on previous witness's text

Issue - State: closed - Opened by jjmccollum about 2 years ago - 1 comment

#1 - Anticipate encoding of ambiguous readings using `witDetail`

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