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
#1817 - Refactor of map
Pull Request -
State: closed - Opened by GavinHuttley 5 months ago
- 1 comment
#1816 - Pull features from dynamic-plugin_loading into plugin-support branch
Pull Request -
State: closed - Opened by khiron 5 months ago
#1815 - MAINT: SQL where clause function now handles numpy ints for start, stop
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
- 1 comment
#1814 - Bump black from 23.12.1 to 24.4.0
Pull Request -
State: closed - Opened by dependabot[bot] 6 months ago
- 2 comments
Labels: dependencies, python
#1813 - Bump nox from 2024.3.2 to 2024.4.15
Pull Request -
State: closed - Opened by dependabot[bot] 6 months ago
- 1 comment
Labels: dependencies, python
#1812 - DEV: plugin metadata classifiers
Issue -
State: open - Opened by GavinHuttley 6 months ago
- 1 comment
#1811 - MAINT: reduce max_workers if too large
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
- 1 comment
#1810 - BUG: Alignment.quick_tree() defaults to pdist calculator
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
- 1 comment
#1809 - Bump scipy from 1.12.0 to 1.13.0
Pull Request -
State: closed - Opened by dependabot[bot] 6 months ago
- 1 comment
Labels: dependencies, python
#1808 - MAINT: merged changes on develop branch into map refactor
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
- 1 comment
#1807 - DEV: acknowledge Lizhaozhe123's contribution to docs
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
#1806 - MAINT: app writers as_completed() no longer requires .md5 attribute
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
#1805 - Validate composable app WRITER types return a DataMemberABC instance.
Issue -
State: closed - Opened by GavinHuttley 6 months ago
- 1 comment
#1804 - DOC: Docstring examples for cogent3.app.sample.trim_stop_codons
Pull Request -
State: closed - Opened by fredjaya 6 months ago
- 1 comment
#1803 - Dynamic plugin loading
Pull Request -
State: closed - Opened by khiron 6 months ago
- 2 comments
#1802 - Bug: Replace pkg_resources with import_lib
Issue -
State: closed - Opened by khiron 6 months ago
#1801 - App namespace resolution #1789
Pull Request -
State: closed - Opened by khiron 6 months ago
- 3 comments
#1800 - Merging plug-in functionality into branch plugin-support
Pull Request -
State: closed - Opened by khiron 6 months ago
- 1 comment
#1799 - Bump pillow from 10.2.0 to 10.3.0
Pull Request -
State: closed - Opened by dependabot[bot] 6 months ago
- 1 comment
Labels: dependencies, python
#1798 - MAINT: explicit attribution for Von Bing Yap integration algorithm
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
- 1 comment
#1797 - ENH: improve accessibility of ENS statistic from likelihood functions
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
- 2 comments
#1796 - DOC: fixed incorrect docstring
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
- 1 comment
#1795 - seqcoll.to_fasta should support specifying block_size
Issue -
State: closed - Opened by GavinHuttley 6 months ago
Labels: enhancement
#1794 - MAINT: refactor sqlite array type handling
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
- 3 comments
#1793 - DEV: added contributors to changelog
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
- 1 comment
#1792 - Enh: Add bibliography to define_app
Issue -
State: open - Opened by khiron 6 months ago
- 3 comments
#1791 - STY: fix code style and delete unused imports from recent contributions
Pull Request -
State: closed - Opened by GavinHuttley 6 months ago
#1790 - ENH: use gap characters in <seqs>.get_identical_seqs()
Issue -
State: open - Opened by GavinHuttley 6 months ago
Labels: enhancement
#1789 - Enh: allow apps to be referenced by scope to avoid namespace collisions
Issue -
State: open - Opened by khiron 7 months ago
- 1 comment
#1788 - TST: add tests for update_file_format
Pull Request -
State: closed - Opened by rmcar17 7 months ago
- 1 comment
#1787 - MAINT: DeprecationWarning->UserWarning addresses comment in #1777
Pull Request -
State: closed - Opened by rmcar17 7 months ago
- 1 comment
#1785 - DOC: tweaked docstring for take_codon_positions
Pull Request -
State: closed - Opened by GavinHuttley 7 months ago
- 1 comment
#1784 - Bump plotly from 5.19.0 to 5.20.0
Pull Request -
State: closed - Opened by dependabot[bot] 7 months ago
- 1 comment
Labels: dependencies, python
#1783 - Bump black from 23.12.1 to 24.3.0
Pull Request -
State: closed - Opened by dependabot[bot] 7 months ago
- 2 comments
Labels: dependencies, python
#1782 - DEP: remove the erf() and erfc function fixes #1738
Pull Request -
State: closed - Opened by ShunyiYang 7 months ago
- 3 comments
#1781 - Enh: Allow the construction of "on-the-fly" apps
Issue -
State: closed - Opened by khiron 7 months ago
- 1 comment
#1780 - Refactor AnnotationDb to not use SQL keywords for column names, fixes #1750
Pull Request -
State: closed - Opened by rmcar17 7 months ago
- 2 comments
#1779 - Cogent3 plugin
Pull Request -
State: closed - Opened by khiron 7 months ago
- 3 comments
#1778 - DEP: remove the erf() and erfc() function, fixes #1738
Pull Request -
State: closed - Opened by ShunyiYang 7 months ago
- 2 comments
#1777 - BUG: fix representation of numpy arrays in sqlite databases
Pull Request -
State: open - Opened by rmcar17 7 months ago
- 3 comments
#1776 - BUG: GenbankAnnotationDb and GffAnnotationDb files are not OS independent
Issue -
State: closed - Opened by rmcar17 7 months ago
- 3 comments
#1775 - DOC: app.sample.take_codon_positions docstring example
Pull Request -
State: closed - Opened by fredjaya 7 months ago
- 1 comment
#1774 - DEV: added better message when deprecating a class
Pull Request -
State: closed - Opened by GavinHuttley 7 months ago
#1773 - Feature/issue 1738
Pull Request -
State: closed - Opened by ShunyiYang 7 months ago
#1772 - Feature/issue 1738
Pull Request -
State: closed - Opened by ShunyiYang 7 months ago
#1771 - Feature/issue #1738
Pull Request -
State: closed - Opened by ShunyiYang 7 months ago
#1770 - DEP: remove the function erf() and erfc()
Pull Request -
State: closed - Opened by ShunyiYang 7 months ago
#1769 - feature/issue 1734
Pull Request -
State: closed - Opened by Tesla686 7 months ago
- 3 comments
#1768 - Feature/issue 1733
Pull Request -
State: closed - Opened by Zongjing-Han 7 months ago
- 1 comment
#1767 - feature/issue 1754
Pull Request -
State: closed - Opened by Lizhaozhe123 7 months ago
- 2 comments
#1766 - feature/issue 1733
Pull Request -
State: closed - Opened by Zongjing-Han 7 months ago
#1765 - feature/issue 1752
Pull Request -
State: closed - Opened by Ruizhe-wang 7 months ago
- 4 comments
#1764 - feature/issue-1628
Pull Request -
State: closed - Opened by GaoPeizhong 7 months ago
- 1 comment
#1763 - Feature/issue 1733
Pull Request -
State: closed - Opened by Zongjing-Han 7 months ago
- 1 comment
#1762 - Feature/issue 1737
Pull Request -
State: closed - Opened by Firimp 7 months ago
- 3 comments
#1761 - Feature/issue 1739
Pull Request -
State: closed - Opened by YouzhiHuang 7 months ago
#1760 - Feature/issue #1739
Pull Request -
State: closed - Opened by YouzhiHuang 7 months ago
#1759 - feature/ issue #1740
Pull Request -
State: closed - Opened by sharonli126 7 months ago
- 1 comment
#1758 - feature/issue 1739
Pull Request -
State: closed - Opened by YouzhiHuang 7 months ago
#1757 - feature/issue 1632
Pull Request -
State: closed - Opened by KyleSu12 7 months ago
- 1 comment
#1756 - feature/issue 1632
Pull Request -
State: closed - Opened by KyleSu12 7 months ago
#1755 - feature/issue 1732
Pull Request -
State: closed - Opened by Yutong-Shao 7 months ago
- 1 comment
#1754 - Add code example snippet to cogent3.app.sample.trim_stop_codons
Issue -
State: closed - Opened by GavinHuttley 7 months ago
- 2 comments
Labels: help wanted, good first issue
#1753 - feature/issue 1731
Pull Request -
State: closed - Opened by ChangsenJiang 7 months ago
- 4 comments
#1752 - Add code example snippet to cogent3.app.sample.omit_duplicated
Issue -
State: closed - Opened by GavinHuttley 7 months ago
- 1 comment
Labels: help wanted, good first issue
#1751 - Feature/issue 1736
Pull Request -
State: open - Opened by yantonglu 7 months ago
- 3 comments
#1750 - Refactor AnnotationDb to not use SQL keywords for column names
Issue -
State: closed - Opened by GavinHuttley 7 months ago
#1749 - ENH: write a db wrapper class for handling annotations etc...
Issue -
State: open - Opened by GavinHuttley 7 months ago
- 5 comments
#1748 - ENH: Prep for plugin infrastructure
Issue -
State: open - Opened by GavinHuttley 7 months ago
- 4 comments
#1747 - Explore using DuckDb as the backend for AnnotationDb classes
Issue -
State: open - Opened by GavinHuttley 7 months ago
- 2 comments
Labels: task, proposal
#1746 - Simplifying FeatureMap
Pull Request -
State: closed - Opened by GavinHuttley 7 months ago
- 1 comment
#1745 - MAINT: override CharAlphabet character / int conversion methods
Pull Request -
State: closed - Opened by GavinHuttley 7 months ago
- 1 comment
#1744 - Bump nox from 2023.4.22 to 2024.3.2
Pull Request -
State: closed - Opened by dependabot[bot] 7 months ago
- 1 comment
Labels: dependencies, python
#1743 - MAINT: deleted dead comment
Pull Request -
State: closed - Opened by GavinHuttley 7 months ago
- 1 comment
#1742 - DEV: fix linting action repo owner and isort command
Pull Request -
State: closed - Opened by rmcar17 7 months ago
- 1 comment
#1741 - DEV: added ignore patterns for Docker
Pull Request -
State: closed - Opened by GavinHuttley 7 months ago
- 1 comment
#1740 - mark identity() function for removal
Issue -
State: open - Opened by GavinHuttley 7 months ago
- 3 comments
Labels: help wanted, good first issue
#1739 - mark tprob() function for removal
Issue -
State: open - Opened by GavinHuttley 7 months ago
- 1 comment
Labels: help wanted, good first issue
#1738 - mark erf(), erfc(), functions for removal
Issue -
State: closed - Opened by GavinHuttley 7 months ago
- 2 comments
Labels: help wanted, good first issue
#1737 - mark combinations(), combinations_exact(), ln_combinations() functions for removal
Issue -
State: closed - Opened by GavinHuttley 7 months ago
- 1 comment
Labels: help wanted, good first issue
#1736 - mark permutations(), permutations_exact(), ln_permutations() functions for removal
Issue -
State: open - Opened by GavinHuttley 7 months ago
- 10 comments
Labels: help wanted, good first issue
#1735 - DEV: simplify text around indicating code removal date
Pull Request -
State: closed - Opened by GavinHuttley 7 months ago
#1734 - mark poisson_exact() function for removal
Issue -
State: open - Opened by GavinHuttley 7 months ago
- 1 comment
Labels: help wanted, good first issue
#1733 - mark poisson_low() function for removal
Issue -
State: open - Opened by GavinHuttley 7 months ago
- 1 comment
Labels: help wanted, good first issue
#1732 - mark poisson_high() function for removal
Issue -
State: closed - Opened by GavinHuttley 7 months ago
- 2 comments
Labels: help wanted, good first issue
#1731 - mark binomial_exact() function for removal
Issue -
State: open - Opened by GavinHuttley 7 months ago
- 1 comment
Labels: help wanted, good first issue
#1730 - Migrate develop branch changes to refactor-of-map branch
Pull Request -
State: closed - Opened by GavinHuttley 7 months ago
#1729 - DOC: add Python 3.12 classifier
Pull Request -
State: closed - Opened by rmcar17 7 months ago
- 2 comments
#1728 - MAINT: fix issue caught by codacy
Pull Request -
State: closed - Opened by GavinHuttley 8 months ago
- 1 comment
#1727 - Progress towards refactor of map
Pull Request -
State: closed - Opened by GavinHuttley 8 months ago
- 1 comment
#1726 - Split core.location.Map with specialist classes
Issue -
State: closed - Opened by GavinHuttley 8 months ago
#1725 - API: Add `seq_len` attribute to `SeqView`
Pull Request -
State: closed - Opened by fredjaya 8 months ago
- 1 comment
#1724 - DEV: Fix coveralls job reporting
Pull Request -
State: closed - Opened by rmcar17 8 months ago
- 1 comment
#1723 - Bump plotly from 5.18.0 to 5.19.0
Pull Request -
State: closed - Opened by dependabot[bot] 8 months ago
- 1 comment
Labels: dependencies, python
#1722 - Bump black from 23.12.1 to 24.2.0
Pull Request -
State: closed - Opened by dependabot[bot] 8 months ago
- 2 comments
Labels: dependencies, python
#1721 - DEV: configure dependabot to also update github-actions
Pull Request -
State: closed - Opened by rmcar17 8 months ago
- 1 comment
#1720 - DEV: changelog snippet about Robert's patches
Pull Request -
State: closed - Opened by GavinHuttley 8 months ago
- 1 comment
#1719 - DEV: Coverage only runs when arguments passed through nox command, fixes #1718
Pull Request -
State: closed - Opened by rmcar17 8 months ago
- 1 comment
#1718 - amend noxfile to take pytest args from command line
Issue -
State: closed - Opened by GavinHuttley 8 months ago
- 2 comments
#1717 - DEV: Update GitHub Actions and Fix Coveralls
Pull Request -
State: closed - Opened by rmcar17 8 months ago
- 1 comment