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

#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

#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

#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

#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