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

#2014 - inconsistent behaviour with slicing annotated sequences

Issue - State: closed - Opened by GavinHuttley 27 days ago
Labels: enhancement

#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

#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

#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

#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

#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