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
#1651 - API: no longer raise ValueError if input data already processed or empty, fixes #1635
Pull Request -
State: closed - Opened by GavinHuttley 10 months ago
- 1 comment
#1650 - ENH: AnnotationDb.subset returns a subset of rows matching condition, fixes #1641
Pull Request -
State: closed - Opened by GavinHuttley 10 months ago
- 1 comment
#1649 - Alignment slicing behaviour inconsistent with sequence and string slicing
Issue -
State: closed - Opened by GavinHuttley 10 months ago
Labels: bug
#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