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

#1716 - FIX: empty SeqView absolute/relative position returns 0

Pull Request - State: closed - Opened by GavinHuttley 8 months ago - 1 comment

#1715 - Add `seq_len` attribute to `SeqView` class

Issue - State: closed - Opened by fredjaya 8 months ago - 4 comments

#1714 - Feature querying now works when sequences renamed

Pull Request - State: closed - Opened by GavinHuttley 8 months ago - 1 comment

#1713 - Bump numpy from 1.26.3 to 1.26.4

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#1712 - MAINT: convert some tests to pytest style

Pull Request - State: closed - Opened by GavinHuttley 8 months ago - 1 comment

#1711 - Steps towards simplifying Map

Pull Request - State: closed - Opened by GavinHuttley 8 months ago - 1 comment

#1710 - DEV: Alignment construction embeds seqid in underlying SeqView

Pull Request - State: closed - Opened by KatherineCaley 8 months ago - 1 comment

#1709 - DEV: added seqid arg to SeqView, fixes #1708

Pull Request - State: closed - Opened by KatherineCaley 8 months ago - 3 comments

#1708 - add attribute to `SeqView` to keep track of the original seqid

Issue - State: closed - Opened by KatherineCaley 8 months ago - 1 comment

#1707 - REL: prepping for release

Pull Request - State: closed - Opened by GavinHuttley 8 months ago - 1 comment

#1706 - DOC: added scriv snippets for the changelog

Pull Request - State: closed - Opened by GavinHuttley 8 months ago - 1 comment

#1705 - DEV: update pinned numba version for python3.12

Pull Request - State: closed - Opened by GavinHuttley 8 months ago - 1 comment

#1704 - ENH: added SeqView.copy()

Pull Request - State: closed - Opened by GavinHuttley 8 months ago - 1 comment

#1703 - MAINT: remove old todo

Pull Request - State: closed - Opened by KatherineCaley 8 months ago - 1 comment

#1702 - Bump black from 23.12.1 to 24.1.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 2 comments
Labels: dependencies

#1701 - ENH: new Sequence.parent_coordinates() method

Pull Request - State: closed - Opened by GavinHuttley 8 months ago - 1 comment

#1700 - ENH: added new properties on SeqView

Pull Request - State: closed - Opened by GavinHuttley 8 months ago - 2 comments

#1699 - BUG: fix ArrayAlignment.get_degapped_relative_to

Pull Request - State: closed - Opened by khiron 8 months ago - 1 comment

#1698 - Bump scipy from 1.11.4 to 1.12.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#1697 - Bump psutil from 5.9.7 to 5.9.8

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#1696 - DOC: Add docstring examples for app.sample.omit_gap_pos

Pull Request - State: closed - Opened by fredjaya 9 months ago - 1 comment

#1695 - Docstring examples for app.sample.concat and omit_degenerates.

Pull Request - State: closed - Opened by fredjaya 9 months ago - 1 comment

#1694 - Maintenance

Pull Request - State: closed - Opened by GavinHuttley 9 months ago - 1 comment

#1693 - MAINT: mixture of patches

Pull Request - State: closed - Opened by GavinHuttley 9 months ago - 1 comment

#1692 - DOC: Add `min_length` app docstring, fixes #1681

Pull Request - State: closed - Opened by fredjaya 9 months ago - 1 comment

#1691 - DEV: support doctesting app module and fix errors

Pull Request - State: closed - Opened by GavinHuttley 9 months ago - 2 comments

#1690 - Thoughts on refactor of location.Map

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

#1689 - DEV: prepping for python 3.12

Pull Request - State: closed - Opened by GavinHuttley 9 months ago - 1 comment

#1688 - Bump pillow from 10.1.0 to 10.2.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#1687 - Bump numpy from 1.26.2 to 1.26.3

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#1686 - MAINT: improved handling of sequence creation via MolType

Pull Request - State: closed - Opened by GavinHuttley 9 months ago - 1 comment

#1685 - Maintenance

Pull Request - State: closed - Opened by GavinHuttley 9 months ago - 1 comment

#1684 - Bump black from 23.12.0 to 23.12.1

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#1682 - Add `SequenceCollection.__repr__` and `SequenceCollection._repr_html_`

Issue - State: closed - Opened by GavinHuttley 10 months ago
Labels: enhancement, help wanted

#1681 - Add a code example to the `min_length` app

Issue - State: closed - Opened by GavinHuttley 10 months ago - 4 comments

#1680 - Bump isort from 5.12.0 to 5.13.2

Pull Request - State: open - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#1679 - Bump psutil from 5.9.6 to 5.9.7

Pull Request - State: open - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#1678 - Bump black from 23.9.1 to 23.12.0

Pull Request - State: open - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#1676 - REL: 2023.12.15a1

Pull Request - State: closed - Opened by GavinHuttley 10 months ago

#1675 - Prep for release

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1674 - Major refactor of sequence collection classes

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1673 - DEP: deleted more deprecated functions

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1672 - MAINT: delete deprecated code

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1671 - DOC: docs for using a dotplot to evaluate alignment quality, fixes #1063

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

#1670 - DEP: dropping the CodonArrayAlignment class

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1669 - DEP: Add Table.to_pandas() #1658

Pull Request - State: closed - Opened by fredjaya 10 months ago - 1 comment

#1668 - ENH: add methods to get the max and min pair of a distance matrix, fixes #1626

Pull Request - State: closed - Opened by KatherineCaley 10 months ago - 1 comment

#1667 - Bump isort from 5.12.0 to 5.13.0

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 2 comments
Labels: dependencies

#1666 - API: to_moltype() methods return same object if same moltype

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1665 - Code tidy

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1664 - DEV: add support for more tree distance metrics

Pull Request - State: closed - Opened by rmcar17 10 months ago - 2 comments

#1663 - Partial refactor of _SequenceCollectionBase

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1662 - ENH: enable indexing seqs with numpy int dtypes

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1661 - API: discontinue unused classes in core.location, fixes #1660

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1660 - discontinue location Range, Point, SpansOnly

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

#1659 - DOC: add detail to the docstring of approx_pdist, fixes #1630

Pull Request - State: closed - Opened by KatherineCaley 10 months ago - 3 comments

#1658 - Add Table.to_pandas() method

Issue - State: closed - Opened by GavinHuttley 10 months ago - 4 comments
Labels: help wanted, needs-documentation

#1657 - DOC: updated to using parallel.as_completed, fixes #1611

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1656 - DOC: updated readme and changelog

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1655 - API: Make reverse slicing of Alignment and ArrayAlignment consistent. Fixes #1649

Pull Request - State: closed - Opened by fredjaya 10 months ago - 1 comment

#1654 - DEV: edit pytest config

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1653 - DOC: Add name_filter to available_apps. Fixes #1640

Pull Request - State: closed - Opened by fredjaya 10 months ago - 1 comment

#1652 - MAINT: simplify _SequenceCollectionBase.__init__

Issue - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1648 - DEV: dropped support for python 3.8, fixes #1600

Pull Request - State: closed - Opened by GavinHuttley 10 months ago - 1 comment

#1647 - Add to the wiki how to test a doc

Issue - State: closed - Opened by GavinHuttley 10 months ago - 8 comments
Labels: documentation

#1646 - update project history section in readme

Issue - State: closed - Opened by KatherineCaley 10 months ago
Labels: documentation, trivial

#1645 - Generalise tree infrastructure to handle multifurcating rooted trees

Issue - State: open - Opened by rmcar17 10 months ago - 2 comments
Labels: enhancement, design

#1644 - Add support for more tree distance measures

Issue - State: closed - Opened by rmcar17 10 months ago - 5 comments

#1643 - BUG: Aligned.get_seq() returns SeqView, fixes #1639

Pull Request - State: closed - Opened by KatherineCaley 10 months ago - 2 comments

#1641 - AnnotationDb's should support subsetting

Issue - State: closed - Opened by GavinHuttley 10 months ago
Labels: enhancement, needs-documentation

#1640 - Add use of new name_filter argument to available_apps()

Issue - State: closed - Opened by GavinHuttley 11 months ago
Labels: documentation, help wanted, good first issue

#1639 - Alignment.get_seq() returns the full underlying sequence

Issue - State: closed - Opened by GavinHuttley 11 months ago
Labels: bug

#1638 - MAINT: tweak to new available_apps() change

Pull Request - State: closed - Opened by GavinHuttley 11 months ago - 1 comment

#1637 - Filter available_apps by name

Pull Request - State: closed - Opened by cosmastech 11 months ago - 2 comments

#1636 - cookbook for apps

Issue - State: open - Opened by KatherineCaley 11 months ago - 14 comments
Labels: documentation

#1635 - improve error message for writing to a data store that has already been written to

Issue - State: closed - Opened by KatherineCaley 11 months ago - 4 comments
Labels: enhancement

#1634 - Add accepted format type to load_seq function

Issue - State: open - Opened by cthwe 11 months ago - 2 comments
Labels: documentation, good first issue

#1633 - `available_apps()` should take string to filter on

Issue - State: closed - Opened by KatherineCaley 11 months ago
Labels: enhancement, good first issue

#1632 - improve error message for invalid sequence file format

Issue - State: closed - Opened by GavinHuttley 11 months ago - 10 comments
Labels: enhancement, help wanted, good first issue

#1630 - Add example to `approx_pdist`

Issue - State: closed - Opened by KatherineCaley 11 months ago
Labels: documentation

#1629 - Bump scipy from 1.11.3 to 1.11.4

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#1628 - Avoid hidden file in read only data stores for .zip

Issue - State: closed - Opened by YapengLang 11 months ago - 7 comments
Labels: bug, help wanted, good first issue

#1627 - Document app to keep only the translatable sequences in a collection

Issue - State: open - Opened by KatherineCaley 11 months ago - 1 comment
Labels: documentation

#1626 - `DistantanceMatrix` should have a method to find max_pair

Issue - State: closed - Opened by KatherineCaley 11 months ago - 2 comments
Labels: enhancement, good first issue

#1625 - MAINT: change tree_align gap params to more sensible defaults

Pull Request - State: closed - Opened by KatherineCaley 11 months ago - 1 comment

#1624 - DOC: explain _calc_see algorithm

Pull Request - State: closed - Opened by GavinHuttley 11 months ago - 1 comment

#1623 - MAINT: misc changes

Pull Request - State: closed - Opened by GavinHuttley 11 months ago - 1 comment

#1622 - bug fixes for dotplot and related code, fixes #1619

Pull Request - State: closed - Opened by KatherineCaley 11 months ago - 1 comment

#1621 - pytest config preventing deprecation warnings being converted to errors

Issue - State: open - Opened by GavinHuttley 11 months ago - 2 comments
Labels: help wanted, contributor-experience

#1620 - pytest flag to convert DeprecationWarning into error not working

Issue - State: open - Opened by GavinHuttley 11 months ago - 1 comment

#1619 - dotplot doesn't use argument for kmer size, defualt k is buggy

Issue - State: closed - Opened by KatherineCaley 11 months ago - 11 comments

#1618 - BUG: load_annotations() now raises IOError if no matching paths found

Pull Request - State: closed - Opened by GavinHuttley 11 months ago - 1 comment

#1617 - Bump black from 23.9.1 to 23.11.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#1616 - Bump numpy from 1.26.1 to 1.26.2

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#1615 - DEV: updated the issue templates for deprecated and discontinued

Pull Request - State: closed - Opened by GavinHuttley 11 months ago - 1 comment

#1614 - Bump plotly from 5.17.0 to 5.18.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#1613 - Bump black from 23.9.1 to 23.10.1

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 2 comments
Labels: dependencies