Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nextstrain/augur issues and pull requests

#1744 - Add default geolocation rules

Pull Request - State: open - Opened by joverlee521 3 days ago - 1 comment

#1742 - 28.0.0 release

Issue - State: closed - Opened by victorlin 8 days ago

#1741 - apply-geolocation-rules: Add `--case-sensitive` flag

Pull Request - State: closed - Opened by joverlee521 10 days ago - 1 comment

#1740 - curate apply-geolocation-rules: Use case-insensitive matching

Pull Request - State: closed - Opened by joverlee521 10 days ago - 1 comment

#1739 - error from Treetime

Issue - State: closed - Opened by alfredobrunoc 10 days ago - 1 comment
Labels: source: discussion forum

#1738 - apply-geolocation-rules: Rule matching should be case-insensitive

Issue - State: closed - Opened by joverlee521 11 days ago - 1 comment
Labels: enhancement

#1737 - align: trim down print statements for insertions

Issue - State: open - Opened by joverlee521 16 days ago - 1 comment
Labels: proposal

#1736 - Ignore gnu.org link

Pull Request - State: closed - Opened by victorlin 16 days ago

#1734 - Sync pandas-stubs and pandas dependency versions

Pull Request - State: closed - Opened by victorlin 17 days ago

#1733 - 27.2.0 release

Issue - State: closed - Opened by victorlin 17 days ago

#1732 - Temporarily disable failing test

Pull Request - State: closed - Opened by victorlin 17 days ago - 1 comment

#1731 - Use custom values to define sequence format

Pull Request - State: closed - Opened by victorlin 21 days ago - 2 comments
Labels: breaking

#1730 - Centralize sequence read operations

Pull Request - State: closed - Opened by victorlin 21 days ago - 1 comment

#1729 - Hide BiopythonDeprecationWarnings when reading certain sequence files

Pull Request - State: closed - Opened by victorlin 21 days ago - 3 comments

#1728 - Add changelog entry for Auspice dataset warning support

Pull Request - State: closed - Opened by victorlin 22 days ago

#1727 - CI failing with new BioPython deprecation warning

Issue - State: closed - Opened by victorlin 22 days ago - 5 comments

#1726 - export: Add `--warning`, update schema

Pull Request - State: closed - Opened by victorlin 22 days ago

#1725 - Update schema descriptions

Pull Request - State: closed - Opened by victorlin 24 days ago

#1724 - 27.1.0 release

Issue - State: closed - Opened by victorlin 24 days ago

#1723 - tree: automatically remove intermediate files with option to disable clean up

Issue - State: open - Opened by joverlee521 24 days ago - 1 comment
Labels: enhancement

#1722 - `export`: Add warning text to output JSON and schema

Issue - State: closed - Opened by victorlin 24 days ago
Labels: enhancement

#1721 - Skip CI for PRs on Markdown changes

Pull Request - State: closed - Opened by huddlej 24 days ago - 1 comment

#1720 - Help text indentation renders differently in rendered docs vs. `--help` output

Issue - State: open - Opened by victorlin 24 days ago - 1 comment
Labels: documentation

#1719 - Add instructions on adding subcommands

Issue - State: open - Opened by victorlin 25 days ago
Labels: documentation

#1716 - Bump minimum pandas version to 1.4.0

Pull Request - State: closed - Opened by victorlin 28 days ago

#1715 - export: Clarify behavior of `--lat-longs`

Pull Request - State: closed - Opened by victorlin 28 days ago - 1 comment
Labels: documentation

#1715 - export: Clarify behavior of `--lat-longs`

Pull Request - State: closed - Opened by victorlin 28 days ago - 1 comment
Labels: documentation

#1714 - export: Clarify behavior of `--lat-longs`

Issue - State: closed - Opened by victorlin 29 days ago - 1 comment
Labels: documentation

#1714 - export: Clarify behavior of `--lat-longs`

Issue - State: closed - Opened by victorlin 29 days ago - 1 comment
Labels: documentation

#1713 - Speed up CI run times

Issue - State: open - Opened by victorlin 30 days ago

#1712 - Fix silent parse bug

Pull Request - State: closed - Opened by huddlej about 1 month ago - 1 comment

#1711 - augur clades should assign clades hierarchically and parsimonously

Issue - State: open - Opened by huddlej about 1 month ago
Labels: bug

#1710 - Update mypy ignore comments

Pull Request - State: closed - Opened by victorlin about 1 month ago - 2 comments

#1709 - Use `ExtendOverwriteDefault` for all multi-value options

Pull Request - State: closed - Opened by victorlin about 1 month ago - 4 comments

#1708 - CI failing on mypy step

Issue - State: closed - Opened by victorlin about 1 month ago
Labels: bug

#1707 - curate format-dates : `--expected-date-formats` builtins cannot be overridden

Issue - State: open - Opened by victorlin about 1 month ago - 2 comments
Labels: bug

#1706 - Help text injected by `CustomHelpFormatter` is not included in rendered docs

Issue - State: closed - Opened by victorlin about 1 month ago
Labels: documentation

#1705 - Add help text to clarify extend actions

Pull Request - State: closed - Opened by victorlin about 1 month ago - 2 comments

#1704 - CI: Add new pathogens to `pathogen-repo-ci`

Pull Request - State: closed - Opened by joverlee521 about 2 months ago - 1 comment

#1703 - CI: Add new core pathogens to pathogen-repo-ci

Issue - State: open - Opened by joverlee521 about 2 months ago - 3 comments

#1702 - Remove unsupported pylint `no-space-check` option

Pull Request - State: closed - Opened by huddlej about 2 months ago - 5 comments

#1701 - .readthedocs.yml: explicit Sphinx configuration

Pull Request - State: closed - Opened by joverlee521 about 2 months ago

#1700 - Add CITATION.cff file

Pull Request - State: closed - Opened by victorlin 2 months ago - 5 comments
Labels: documentation

#1699 - Add note on quoting behavior

Pull Request - State: closed - Opened by victorlin 2 months ago - 1 comment

#1698 - Fix release job condition

Pull Request - State: closed - Opened by victorlin 2 months ago

#1697 - Ignore TreeTime citation link for linkcheck

Pull Request - State: closed - Opened by victorlin 2 months ago
Labels: documentation

#1697 - Ignore TreeTime citation link for linkcheck

Pull Request - State: closed - Opened by victorlin 2 months ago
Labels: documentation

#1696 - Tidy changelog

Pull Request - State: closed - Opened by victorlin 2 months ago

#1696 - Tidy changelog

Pull Request - State: closed - Opened by victorlin 2 months ago

#1695 - 27.0.0 release

Issue - State: closed - Opened by victorlin 2 months ago

#1695 - 27.0.0 release

Issue - State: closed - Opened by victorlin 2 months ago

#1694 - merge: Quoting behavior

Issue - State: closed - Opened by victorlin 2 months ago - 1 comment

#1693 - Drop Python 3.8 support

Pull Request - State: closed - Opened by victorlin 2 months ago
Labels: breaking

#1693 - Drop Python 3.8 support

Pull Request - State: closed - Opened by victorlin 2 months ago
Labels: breaking

#1692 - Drop support for xopen v1

Pull Request - State: closed - Opened by victorlin 2 months ago - 1 comment
Labels: breaking

#1692 - Drop support for xopen v1

Pull Request - State: closed - Opened by victorlin 2 months ago - 1 comment
Labels: breaking

#1691 - Use jsonschema ≥4.18.0 and new referencing library

Pull Request - State: closed - Opened by victorlin 2 months ago - 2 comments
Labels: breaking

#1691 - Use jsonschema ≥4.18.0 and new referencing library

Pull Request - State: closed - Opened by victorlin 2 months ago - 2 comments
Labels: breaking

#1690 - fix: explicitly specify how the root and ambiguous states are handled…

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

#1689 - Inconsistency of lengths and mutations assigned to branches that are children of the root.

Issue - State: open - Opened by rneher 2 months ago - 3 comments
Labels: bug

#1689 - Inconsistency of lengths and mutations assigned to branches that are children of the root.

Issue - State: closed - Opened by rneher 2 months ago - 3 comments
Labels: bug

#1688 - Fix type errors in titer models

Pull Request - State: closed - Opened by huddlej 3 months ago - 1 comment

#1688 - Fix type error in titer model cross-validation

Pull Request - State: open - Opened by huddlej 3 months ago - 1 comment

#1687 - DEV_DOCS: Remove hardcoded default branch names

Pull Request - State: closed - Opened by victorlin 3 months ago

#1686 - Rename `master` to `main`

Issue - State: open - Opened by victorlin 3 months ago

#1686 - Rename `master` to `main`

Issue - State: open - Opened by victorlin 3 months ago

#1685 - Remove `authors` hard-coding in `augur export`

Issue - State: open - Opened by genehack 3 months ago - 1 comment
Labels: enhancement

#1685 - Remove `authors` hard-coding in `augur export`

Issue - State: open - Opened by genehack 3 months ago - 1 comment
Labels: enhancement

#1684 - 26.2.0 release

Issue - State: closed - Opened by victorlin 3 months ago

#1683 - Update changelog

Pull Request - State: closed - Opened by victorlin 3 months ago - 1 comment

#1683 - Update changelog

Pull Request - State: closed - Opened by victorlin 3 months ago - 1 comment

#1682 - Bump codecov/codecov-action from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies

#1680 - Remove Python 3.8 support

Issue - State: closed - Opened by corneliusroemer 3 months ago
Labels: enhancement, breaking

#1680 - Remove Python 3.8 support

Issue - State: closed - Opened by corneliusroemer 3 months ago
Labels: enhancement, breaking

#1679 - Support Python 3.13

Issue - State: open - Opened by corneliusroemer 3 months ago
Labels: enhancement, blocked

#1679 - Support Python 3.13

Issue - State: open - Opened by corneliusroemer 3 months ago
Labels: enhancement, blocked

#1678 - Support Python 3.12 and test in CI

Pull Request - State: closed - Opened by corneliusroemer 3 months ago

#1678 - Support Python 3.12 and test in CI

Pull Request - State: closed - Opened by corneliusroemer 3 months ago

#1676 - Pass secrets to release job

Pull Request - State: closed - Opened by victorlin 3 months ago - 1 comment

#1676 - Pass secrets to release job

Pull Request - State: closed - Opened by victorlin 3 months ago - 1 comment

#1675 - release: Remove condition on event_name

Pull Request - State: closed - Opened by victorlin 3 months ago

#1674 - Bug in release workflow: it doesn't actually release anymore

Issue - State: closed - Opened by corneliusroemer 3 months ago - 5 comments
Labels: bug

#1673 - Add internal changes to changelog to improve visibility for developers and give credit

Issue - State: open - Opened by corneliusroemer 3 months ago - 4 comments
Labels: proposal

#1673 - Add internal changes to changelog to improve visibility for developers and give credit

Issue - State: open - Opened by corneliusroemer 3 months ago - 4 comments
Labels: proposal

#1671 - Support pandas v2

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

#1671 - Support pandas v2

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