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
#1897 - some app.typing union types not working when importing annotations from future
Issue -
State: closed - Opened by GavinHuttley 4 months ago
- 7 comments
#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
#1889 - Monomer alphabets to_bytes() method simplifies building alphabet inter converters
Pull Request -
State: closed - Opened by GavinHuttley 4 months ago
- 1 comment
#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
#1863 - Add big announcement about plugins to readme etc...
Issue -
State: closed - Opened by GavinHuttley 5 months ago
#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
#1844 - `doctest-modules` doesn't recognise docstring examples in decorated functions
Issue -
State: open - Opened by fredjaya 5 months ago
#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