Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / cogent3/cogent3 issues and pull requests
#2018 - REL: bump version to 2024.7.19a6
Pull Request -
State: closed - Opened by GavinHuttley 27 days ago
- 1 comment
#2017 - MAINT: bug fix and minor edits
Pull Request -
State: closed - Opened by GavinHuttley 27 days ago
- 1 comment
#2016 - Fix a regression
Pull Request -
State: closed - Opened by GavinHuttley 27 days ago
- 1 comment
#2015 - ENH: add set_repr_policy() method to Sequence class
Issue -
State: open - Opened by GavinHuttley 27 days ago
#2014 - inconsistent behaviour with slicing annotated sequences
Issue -
State: closed - Opened by GavinHuttley 27 days ago
Labels: enhancement
#2013 - ENH: add support for reversing and strides when indexing IndelMaps and Alignments, fixes #1967
Pull Request -
State: open - Opened by KatherineCaley 29 days ago
- 2 comments
#2012 - DOC: update docs related to parallel computing
Pull Request -
State: closed - Opened by GavinHuttley 29 days ago
- 1 comment
#2011 - ENH: use loky for multiprocess parallel
Pull Request -
State: closed - Opened by GavinHuttley 30 days ago
- 1 comment
#2010 - Bump plotly from 5.23.0 to 5.24.0
Pull Request -
State: open - Opened by dependabot[bot] about 1 month ago
- 1 comment
Labels: dependencies, python
#2009 - Bump ruff from 0.5.7 to 0.6.3
Pull Request -
State: open - Opened by dependabot[bot] about 1 month ago
- 1 comment
Labels: dependencies, python
#2008 - ENH: improve performance of pycompare.find_matched_paths
Pull Request -
State: closed - Opened by GavinHuttley about 1 month ago
- 1 comment
#2007 - ENH: explore joblib for supporting jupyter notebook parallelisation
Issue -
State: closed - Opened by GavinHuttley about 1 month ago
- 1 comment
Labels: enhancement
#2006 - BUG: dotplot alignment path is funky
Issue -
State: open - Opened by GavinHuttley about 1 month ago
- 1 comment
Labels: bug, help wanted
#2005 - ENH: add a SequenceCollection.count_ambiguous_per_seq method
Issue -
State: open - Opened by GavinHuttley about 1 month ago
Labels: help wanted
#2004 - improve app docstring generation for decorated functions
Issue -
State: open - Opened by GavinHuttley about 1 month ago
#2003 - ENH: support slicing of Alignment/Aligned
Pull Request -
State: closed - Opened by KatherineCaley about 1 month ago
- 2 comments
#2002 - Bugfix
Pull Request -
State: closed - Opened by GavinHuttley about 1 month ago
- 1 comment
#2001 - Bump ruff from 0.5.7 to 0.6.2
Pull Request -
State: closed - Opened by dependabot[bot] about 1 month ago
- 2 comments
Labels: dependencies, python
#2000 - Bump stevedore from 5.2.0 to 5.3.0
Pull Request -
State: closed - Opened by dependabot[bot] about 1 month ago
- 1 comment
Labels: dependencies, python
#1999 - Bump scipy from 1.14.0 to 1.14.1
Pull Request -
State: closed - Opened by dependabot[bot] about 1 month ago
- 1 comment
Labels: dependencies, python
#1998 - MAINT: final changes pre-release
Pull Request -
State: closed - Opened by GavinHuttley about 1 month ago
- 1 comment
#1997 - BUG: fixed bug preventing using an integer to set dendrogram tip_font size
Pull Request -
State: closed - Opened by GavinHuttley about 1 month ago
- 1 comment
#1996 - ENH: improve type-hint stripping in app_help()
Pull Request -
State: closed - Opened by GavinHuttley about 1 month ago
- 1 comment
#1995 - ENH: changes to app_help(), fixes #1994
Pull Request -
State: closed - Opened by GavinHuttley about 1 month ago
- 1 comment
#1994 - DOC: app_help() display has issues
Issue -
State: closed - Opened by GavinHuttley about 1 month ago
#1993 - Bump numpy from 2.0.1 to 2.1.0
Pull Request -
State: open - Opened by dependabot[bot] about 1 month ago
- 1 comment
Labels: dependencies, python
#1992 - Bump ruff from 0.5.7 to 0.6.1
Pull Request -
State: closed - Opened by dependabot[bot] about 1 month ago
- 2 comments
Labels: dependencies, python
#1991 - ENH: add suuport for slicing an `IndelMap` with a step > 1
Pull Request -
State: closed - Opened by KatherineCaley about 2 months ago
- 2 comments
#1990 - STY: tweak ruff linting of imports
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
- 1 comment
#1989 - ENH: faster sequence format parsers
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
- 1 comment
#1988 - REL: 2024.7.19a4
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
#1987 - DEV: minor edits before bug-fix release
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
- 1 comment
#1986 - Bump ruff from 0.5.5 to 0.5.7
Pull Request -
State: closed - Opened by dependabot[bot] about 2 months ago
- 1 comment
Labels: dependencies, python
#1985 - MAINT: revert `charset-normalizer` dependency to `chardet`
Pull Request -
State: closed - Opened by rmcar17 about 2 months ago
#1984 - `load_tree` doesn't work on specific file input
Issue -
State: closed - Opened by rmcar17 about 2 months ago
- 1 comment
#1983 - REL: 2024.7.19a3
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
#1982 - REL: bump release minor _version
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
#1981 - DEV: fix release docbuild action
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
#1980 - REL: minor version increment for bug fix release
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
- 1 comment
#1979 - DEV: replace pip with uv in release docbuild step
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
#1978 - DEV: add a full build of the docs to release GHA
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
#1977 - DEV: further GHA tweaks
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
#1976 - MAINT: edits to releasing github related settings
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
- 1 comment
#1975 - DEV: edits in toml and release action
Pull Request -
State: closed - Opened by GavinHuttley about 2 months ago
- 1 comment
#1974 - DEV: add release workflow
Pull Request -
State: closed - Opened by rmcar17 about 2 months ago
- 1 comment
#1973 - Bump ruff from 0.5.5 to 0.5.6
Pull Request -
State: closed - Opened by dependabot[bot] about 2 months ago
- 3 comments
Labels: dependencies, python
#1972 - TST: added a test for the recent regression on loading sequence files
Pull Request -
State: closed - Opened by GavinHuttley 2 months ago
- 1 comment
#1971 - REL get github actions for doing a release
Issue -
State: closed - Opened by GavinHuttley 2 months ago
- 1 comment
#1970 - ENH: select_translatable frame argument
Pull Request -
State: closed - Opened by GavinHuttley 2 months ago
- 2 comments
#1969 - Maintenance
Pull Request -
State: closed - Opened by GavinHuttley 2 months ago
- 1 comment
#1968 - BUG: fixed regression in parsing sequence files
Pull Request -
State: closed - Opened by GavinHuttley 2 months ago
- 1 comment
#1967 - ENH: implement support for strides in IndelMap
Issue -
State: open - Opened by GavinHuttley 2 months ago
- 3 comments
#1966 - Bump plotly from 5.22.0 to 5.23.0
Pull Request -
State: closed - Opened by dependabot[bot] 2 months ago
- 1 comment
Labels: dependencies, python
#1965 - Bump ruff from 0.5.4 to 0.5.5
Pull Request -
State: closed - Opened by dependabot[bot] 2 months ago
- 1 comment
Labels: dependencies, python
#1964 - DOC: fixed language
Pull Request -
State: closed - Opened by GavinHuttley 2 months ago
- 1 comment
#1962 - Updated docs
Pull Request -
State: closed - Opened by GavinHuttley 2 months ago
- 1 comment
#1961 - ENH: begin Alignment refactor
Pull Request -
State: closed - Opened by KatherineCaley 2 months ago
- 3 comments
#1960 - Rebasing branch
Pull Request -
State: closed - Opened by GavinHuttley 2 months ago
- 1 comment
#1959 - Bump numpy from 2.0.0 to 2.0.1
Pull Request -
State: closed - Opened by dependabot[bot] 2 months ago
- 1 comment
Labels: dependencies, python
#1958 - Use ruff for linting
Pull Request -
State: closed - Opened by GavinHuttley 2 months ago
- 1 comment
#1957 - Added tag 2024.7.19a1 for changeset 67f6cf3a5666
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment
#1956 - REL: final steps to release
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment
#1955 - MAINT: fixed regression and address deprecation warning
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment
#1954 - DOC: announce new features in README
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment
#1953 - Merging sequence collection refactor into develop
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
#1952 - Merging develop into seq-collection-refactor
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment
#1951 - DEV: new moltype method and some documentation
Pull Request -
State: closed - Opened by KatherineCaley 3 months ago
- 1 comment
#1950 - DEV: preps and documentation of new_type
Pull Request -
State: closed - Opened by KatherineCaley 3 months ago
- 1 comment
#1949 - `test_find_matched_paths_moltype` fails for bytes when using new `MolType`
Issue -
State: open - Opened by KatherineCaley 3 months ago
#1948 - ENH: implement `new_moltype.MolType.degenerate_from_seq`
Issue -
State: closed - Opened by KatherineCaley 3 months ago
- 1 comment
#1947 - MAINT: refactoring sequence parsing
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment
#1946 - DOC: Add app docstring examples #1636
Pull Request -
State: closed - Opened by fredjaya 3 months ago
- 1 comment
#1945 - ENH: added CodonAlphabet
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment
#1944 - ENH: sequence refactor
Pull Request -
State: closed - Opened by KatherineCaley 3 months ago
- 1 comment
#1943 - BUG: fixed bug in composable apply_to and as_completed methods
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment
#1942 - TST: Port Sequence unittest classes
Pull Request -
State: closed - Opened by fredjaya 3 months ago
- 3 comments
#1941 - Decide on porting (or not porting) `Sequence` methods
Issue -
State: closed - Opened by KatherineCaley 3 months ago
- 1 comment
#1940 - DEV: added changelog snippet
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment
#1939 - ENH: porting `Moltype` methods
Issue -
State: closed - Opened by KatherineCaley 3 months ago
- 1 comment
#1938 - ENH: add counting methods to `Moltype`
Issue -
State: closed - Opened by KatherineCaley 3 months ago
- 1 comment
#1937 - ENH: overwrite the bounds in `lf` to be consistent with the arguments specified in the `model`
Pull Request -
State: closed - Opened by YapengLang 3 months ago
- 1 comment
#1936 - DOC: array representation of sequences should always be created with `most_degen_alphabet`
Issue -
State: open - Opened by KatherineCaley 3 months ago
#1935 - ENH: add strip methods to moltype
Pull Request -
State: closed - Opened by KatherineCaley 3 months ago
- 5 comments
#1934 - Bump pillow from 10.3.0 to 10.4.0
Pull Request -
State: closed - Opened by dependabot[bot] 3 months ago
- 1 comment
Labels: dependencies, python
#1933 - Bump scipy from 1.13.1 to 1.14.0
Pull Request -
State: closed - Opened by dependabot[bot] 3 months ago
- 1 comment
Labels: dependencies, python
#1932 - MolType methods to port
Issue -
State: closed - Opened by GavinHuttley 3 months ago
- 2 comments
#1931 - DEV: raise not implemented error on top level stringified type hint
Pull Request -
State: closed - Opened by rmcar17 3 months ago
- 3 comments
#1930 - The upper/lower bounds cannot be successfully imposed on a model app
Issue -
State: closed - Opened by YapengLang 3 months ago
- 4 comments
#1929 - ENH: deserialisation of `SequenceCollection` and `SeqsData`, fixes #1924
Pull Request -
State: closed - Opened by KatherineCaley 3 months ago
- 3 comments
#1928 - ENH: add new_type arguments for top-level function, fixes #1923
Pull Request -
State: closed - Opened by KatherineCaley 3 months ago
- 2 comments
#1927 - TST: port seqview tests
Pull Request -
State: closed - Opened by fredjaya 3 months ago
- 7 comments
#1926 - ENH: add reversed field to SeqsData
Pull Request -
State: closed - Opened by KatherineCaley 3 months ago
- 2 comments
#1925 - Cannot get tree with lengths as ENS for a rate heterogeneous model
Issue -
State: open - Opened by GavinHuttley 3 months ago
#1924 - ENH: deserialise function for SequenceCollection
Issue -
State: closed - Opened by KatherineCaley 3 months ago
- 4 comments
#1923 - ENH: `new_type` arguments for top-level function
Issue -
State: closed - Opened by KatherineCaley 3 months ago
- 1 comment
#1922 - ENH: SequenceCollection serialisation
Pull Request -
State: closed - Opened by KatherineCaley 3 months ago
- 3 comments
#1921 - Sequence and SeqView classes should not be used to replace characters
Issue -
State: closed - Opened by GavinHuttley 3 months ago
- 2 comments
#1920 - DEV: delete matplotlib as a dependency
Pull Request -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment
#1919 - TST: Port SeqView tests and #1915
Pull Request -
State: closed - Opened by fredjaya 3 months ago
- 2 comments
#1918 - modify all tests to using new style sequence collections
Issue -
State: closed - Opened by GavinHuttley 3 months ago
- 1 comment