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

#1917 - can we remove tinydb dependency?

Issue - State: closed - Opened by GavinHuttley 3 months ago - 1 comment

#1916 - ENH: implement serialisation methods on new_alphabet classes

Pull Request - State: closed - Opened by GavinHuttley 3 months ago - 1 comment

#1915 - new_sequence.Sequence.__str__ method should complement the sequence

Issue - State: closed - Opened by GavinHuttley 3 months ago - 1 comment

#1914 - Bump psutil from 5.9.8 to 6.0.0

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies, python

#1913 - TST: port seqview slicing test

Pull Request - State: closed - Opened by fredjaya 3 months ago - 1 comment

#1912 - refactor seqs.get_translation and add method to rename seqs in a collection

Pull Request - State: closed - Opened by KatherineCaley 3 months ago - 2 comments

#1911 - Merged changes from develop

Pull Request - State: closed - Opened by GavinHuttley 3 months ago - 1 comment

#1910 - MAINT: now support numpy 2.0

Pull Request - State: closed - Opened by GavinHuttley 3 months ago - 1 comment

#1909 - Amendments to improve genetic code translate

Pull Request - State: closed - Opened by GavinHuttley 3 months ago - 3 comments

#1908 - MAINT: type hinting

Pull Request - State: closed - Opened by KatherineCaley 3 months ago - 1 comment

#1907 - TST: xfailing sequence tests

Pull Request - State: closed - Opened by fredjaya 3 months ago - 2 comments

#1906 - BUG: updating a db with the same db causes the code to hang

Issue - State: closed - Opened by KatherineCaley 4 months ago - 2 comments

#1905 - TST: Port some seqview and serialisation tests

Pull Request - State: closed - Opened by fredjaya 4 months ago - 2 comments

#1904 - TST: unmark passing xfails

Pull Request - State: closed - Opened by fredjaya 4 months ago - 1 comment

#1903 - Mods to alphabets to incorporate missing characters

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 2 comments

#1902 - Bump numpy from 1.26.4 to 2.0.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago - 1 comment
Labels: dependencies, python

#1901 - Define a SeqViewABC

Issue - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1900 - DEV: `SeqViewABC` and methods for translation on `SequenceCollection`, #1901

Pull Request - State: closed - Opened by KatherineCaley 4 months ago - 10 comments

#1899 - ENH: DataStoreDirectory.write now handles compression

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1898 - MAINT: code tidy and splification

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1896 - Seq collections refactor

Pull Request - State: closed - Opened by KatherineCaley 4 months ago - 7 comments

#1895 - DEV: Porting sequence tests (trim_stop_codon) and new module methods

Pull Request - State: closed - Opened by fredjaya 4 months ago - 11 comments

#1894 - Seq collections refactor

Pull Request - State: closed - Opened by KatherineCaley 4 months ago - 2 comments

#1893 - MAINT: remove profiling comment, seq_to_kmer_indices is faster with numba

Pull Request - State: closed - Opened by rmcar17 4 months ago - 1 comment

#1892 - ENH: new get_code() handles GeneticCode instance as a value

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1891 - Enhancing alphabet and moltype

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1890 - SequenceCollection refactor - general and annotation db methods

Pull Request - State: closed - Opened by KatherineCaley 4 months ago - 5 comments

#1888 - MAINT: refactor new_alphabet converter classes

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 2 comments

#1887 - ENH: new_moltype.Moltype supports is_gapped and is_degenerate

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1886 - DEV: more refactoring of SequenceCollection

Pull Request - State: closed - Opened by KatherineCaley 4 months ago - 2 comments

#1885 - API: added refactor of genetic code

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1884 - TST: Port `SeqView` tests and ruff fixes

Pull Request - State: closed - Opened by fredjaya 4 months ago - 1 comment

#1883 - API: MonomerAlphabetABC.get_kmer_alphabet instead of get_word_alphabet

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1882 - Additions to new alphabet

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1881 - Start on SequenceCollections refactor

Pull Request - State: closed - Opened by KatherineCaley 4 months ago - 1 comment

#1880 - Start on new alphabets, moltypes and sequences

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1879 - Merging in develop branch changes

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1878 - ENH: Improvements to the GFF parser

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1877 - Bump scipy from 1.13.0 to 1.13.1

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago - 1 comment
Labels: dependencies, python

#1876 - DEV: Update `SeqDataView` with `SliceRecordsABC`

Pull Request - State: closed - Opened by fredjaya 4 months ago - 1 comment

#1875 - Revert "Merge branch 'seq-collections-refactor' into develop"

Pull Request - State: closed - Opened by KatherineCaley 4 months ago - 1 comment

#1874 - Merging changes on develop

Pull Request - State: closed - Opened by GavinHuttley 4 months ago - 1 comment

#1873 - DOC: Add IndelMap param docstring

Pull Request - State: closed - Opened by fredjaya 4 months ago - 1 comment

#1872 - `MolType.make_seq()` incompatible with `SeqDataView`

Issue - State: closed - Opened by fredjaya 4 months ago

#1871 - refactor alphabet

Issue - State: open - Opened by GavinHuttley 5 months ago

#1870 - NEW: abstract base class for views, fixes #1865

Pull Request - State: closed - Opened by KatherineCaley 5 months ago - 2 comments

#1869 - Improve performance of annotation db creation, querying

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1868 - DOC: Add IndelMap parameter docstring

Pull Request - State: closed - Opened by fredjaya 5 months ago - 2 comments

#1867 - begin new_alignment.SequenceCollection

Issue - State: closed - Opened by GavinHuttley 5 months ago - 3 comments

#1866 - modify SeqData

Issue - State: closed - Opened by GavinHuttley 5 months ago - 10 comments

#1865 - The New SeqView foundation

Issue - State: closed - Opened by GavinHuttley 5 months ago - 9 comments

#1864 - Mixture of patches

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 2 comments

#1862 - `seq-collections-refactor` branch

Pull Request - State: closed - Opened by fredjaya 5 months ago - 1 comment

#1861 - Refactor of sequence collections and alignments

Issue - State: open - Opened by GavinHuttley 5 months ago - 2 comments

#1860 - Create new branch with sequence collections backend prototypes

Issue - State: closed - Opened by GavinHuttley 5 months ago - 2 comments
Labels: enhancement, design

#1859 - REL: 2024.5.7a1

Pull Request - State: closed - Opened by GavinHuttley 5 months ago

#1858 - DEV: tidy

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1857 - REL: final steps before Q1 release

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1856 - DEV: acknowledge contributors to project

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1855 - Bump plotly from 5.21.0 to 5.22.0

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#1854 - DOC: added sample apps to cookbook

Pull Request - State: closed - Opened by KatherineCaley 5 months ago - 1 comment

#1853 - MAINT: mishmash of commits -- whoops!

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1852 - cookbook for io apps

Pull Request - State: closed - Opened by KatherineCaley 5 months ago - 1 comment

#1851 - DOC: Docstring examples for `app.model` and `app.tabulate_stats`

Pull Request - State: closed - Opened by YapengLang 5 months ago - 2 comments

#1850 - Fix `__repr__` handling of limit in Alignment/SeqCol related objects

Pull Request - State: closed - Opened by rmcar17 5 months ago - 1 comment

#1849 - DEP: deleted code marked for deprecation in upcoming release, fixes #1840

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1848 - TST: improve testing of the IndelMap.nucleic_reversed() method

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1847 - add test to check for #1844

Pull Request - State: closed - Opened by khiron 5 months ago - 1 comment

#1846 - Address code review comments

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1845 - MAINT: tidy __repr__ methods in Alignment classes

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1843 - ENH: apps now work as intended for the `|` union syntax

Pull Request - State: closed - Opened by rmcar17 5 months ago - 2 comments

#1842 - DOC: Docstring examples for `app.translate`, `app.align`, and `app.dist`

Pull Request - State: closed - Opened by fredjaya 5 months ago - 1 comment

#1841 - MAINT: remove some plugins from toml file, relates to #1636

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1840 - remove code marked for deprecation

Issue - State: closed - Opened by GavinHuttley 5 months ago

#1839 - MAINT: responses to first batch of code-review comments

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1838 - Add `__repr__` and `_repr_html_` to `SequenceCollection`

Pull Request - State: closed - Opened by rmcar17 5 months ago - 1 comment

#1837 - MAINT: type hints and docstring mods for dotplot code

Pull Request - State: closed - Opened by GavinHuttley 5 months ago

#1836 - Bump black from 23.12.1 to 24.4.2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, python

#1835 - app.sample docstring examples

Pull Request - State: closed - Opened by fredjaya 5 months ago - 1 comment

#1834 - DEV: doctest_rsts tests are broken when run in parallel

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1833 - DEV: upgrade macos back to latest

Pull Request - State: closed - Opened by rmcar17 5 months ago - 1 comment

#1832 - Address issues from the code review of plugin-support

Pull Request - State: closed - Opened by khiron 5 months ago - 1 comment

#1831 - DEV: added changelog comments about Map refactor

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1830 - MAINT: yet more codacy issues

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1829 - MAINT: addresses additional issues identified by codacy

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1828 - MAINT: address some issues identified by codacy

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1827 - API: refactor of map into IndelMap and FeatureMap, fixes #1726

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 2 comments

#1826 - MAINT: improves testing of edge cases

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1825 - Address edge cases in dotplot code

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 2 comments

#1824 - MAINT: use IndelMap for dotplotting

Pull Request - State: closed - Opened by GavinHuttley 5 months ago - 1 comment

#1823 - DEV: downgrade macos from latest to 13

Pull Request - State: closed - Opened by rmcar17 5 months ago - 1 comment

#1822 - ENH: seqcoll.to_fasta supports block_size

Pull Request - State: closed - Opened by rmcar17 5 months ago - 4 comments

#1821 - Bump plotly from 5.20.0 to 5.21.0

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies, python

#1820 - Plugin support address codacy/coverage issues

Pull Request - State: closed - Opened by khiron 5 months ago

#1819 - Plugin support test coverage

Pull Request - State: closed - Opened by khiron 5 months ago - 1 comment

#1818 - Plugin support

Pull Request - State: closed - Opened by khiron 5 months ago - 1 comment