Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / jjmccollum/teiphy issues and pull requests
#90 - :bug: Added rootFrequencies attribute (and, for convenience, value at…
Pull Request -
State: closed - Opened by jjmccollum 17 days ago
#89 - Update BEAST ancestral state/sequence logger template to reference rootFrequencies
Issue -
State: closed - Opened by jjmccollum 17 days ago
#88 - Use letters for states greater than 9 in STEMMA outputs
Issue -
State: open - Opened by jjmccollum 18 days ago
#87 - 85 add support for time dependent substitution models with epochsubstitutionmodel in beast outputs
Pull Request -
State: closed - Opened by jjmccollum 5 months ago
#86 - 84 add option for choice of ancestralsequencelogger or ancestralstatelogger for beast outputs
Pull Request -
State: closed - Opened by jjmccollum 5 months ago
#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
#84 - Add option for choice of AncestralSequenceLogger or AncestralStateLogger for BEAST outputs
Issue -
State: closed - Opened by jjmccollum 5 months ago
Labels: enhancement
#83 - 82 change ancestralstatelogger to ancestralsequencelogger in beast output
Pull Request -
State: closed - Opened by jjmccollum 7 months ago
#82 - Change AncestralStateLogger to AncestralSequenceLogger in BEAST output
Issue -
State: closed - Opened by jjmccollum 7 months ago
#81 - :bug: Fixed beast_template.xml to include/exclude BDSKY origin distri…
Pull Request -
State: closed - Opened by jjmccollum 7 months ago
#80 - Use fixed origin for BEAST BDSKY model if tradition has a fixed composition date
Issue -
State: closed - Opened by jjmccollum 7 months ago
Labels: bug
#79 - :zap: Updated tabular output options; :zap: added support for creatin…
Pull Request -
State: closed - Opened by jjmccollum 9 months ago
#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
#76 - :zap: Added support for --seed option, changed transcriptional rate b…
Pull Request -
State: closed - Opened by jjmccollum about 1 year ago
#75 - Assignment of random starting rate parameter values, new prior distributions, and support for `--seed` option
Issue -
State: closed - Opened by jjmccollum about 1 year ago
#74 - :zap: Updated collation.to_stemma to write relative path to chron fil…
Pull Request -
State: closed - Opened by jjmccollum about 1 year ago
#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
#54 - Added support for taxon date calibration with MrBayes and BEAST2 NEXUS output
Pull Request -
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