Ecosyste.ms: Issues

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GitHub / nextstrain/augur issues and pull requests

#1667 - tests: add cram wrapper parallel_cram.sh that runs cram tests in parallel

Pull Request - State: open - Opened by corneliusroemer 3 months ago - 5 comments

#1666 - fix(tests): Fix false negative cram tests

Pull Request - State: open - Opened by corneliusroemer 3 months ago - 2 comments

#1666 - fix(tests): Fix false negative cram tests

Pull Request - State: open - Opened by corneliusroemer 3 months ago - 2 comments

#1664 - feat(ancestral): Add optional Nextclade GFF3 compatibility mode

Pull Request - State: open - Opened by corneliusroemer 3 months ago - 5 comments

#1664 - feat(ancestral): Add optional Nextclade GFF3 compatibility mode

Pull Request - State: open - Opened by corneliusroemer 3 months ago - 5 comments

#1663 - Layering Auspice config files

Issue - State: closed - Opened by genehack 3 months ago - 4 comments
Labels: enhancement

#1663 - Layering Auspice config files

Issue - State: closed - Opened by genehack 3 months ago - 4 comments
Labels: enhancement

#1662 - chore(ancestral): more informative AugurError message

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

#1662 - chore(ancestral): more informative AugurError message

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

#1661 - Validation regex pattern for `branch_label` display default values in Auspice config JSON is too strict

Issue - State: open - Opened by huddlej 3 months ago - 3 comments
Labels: bug, please take this issue

#1660 - docs: Ignore FastTree link for linkcheck

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

#1660 - docs: Ignore FastTree link for linkcheck

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

#1659 - pyright: Use basic ruleset explicitly

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

#1659 - pyright: Use basic ruleset explicitly

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

#1656 - Centralize --validation-mode and --skip-validation

Pull Request - State: closed - Opened by victorlin 4 months ago - 1 comment

#1655 - Gff3 file: differences between nextclade datasets and augur ancestral

Issue - State: open - Opened by anna-parker 4 months ago - 3 comments
Labels: documentation

#1654 - Improve help text of CLI options that use `extend` and `ExtendOverwriteDefault` actions

Issue - State: closed - Opened by joverlee521 4 months ago - 6 comments
Labels: documentation

#1653 - Update docs for `curate format-dates`

Pull Request - State: closed - Opened by joverlee521 4 months ago - 2 comments

#1653 - Update docs for `curate format-dates`

Pull Request - State: closed - Opened by joverlee521 4 months ago - 2 comments

#1651 - Update help docs for augur curate format-dates

Issue - State: closed - Opened by anna-parker 4 months ago - 7 comments
Labels: documentation

#1651 - Update help docs for augur curate format-dates

Issue - State: closed - Opened by anna-parker 4 months ago - 7 comments
Labels: documentation

#1650 - docs: Allow BUILDDIR to be set from environment

Pull Request - State: closed - Opened by victorlin 4 months ago - 1 comment

#1650 - docs: Allow BUILDDIR to be set from environment

Pull Request - State: closed - Opened by victorlin 4 months ago - 1 comment

#1648 - curate apply-geolocation-rules: Allow rule overrides

Issue - State: open - Opened by joverlee521 4 months ago - 2 comments
Labels: enhancement

#1647 - Update cram tests

Pull Request - State: closed - Opened by victorlin 4 months ago - 1 comment

#1646 - index: Allow FileNotFoundError to be handled at the top level

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

#1642 - Improve rendering of CLI documentation

Issue - State: open - Opened by victorlin 5 months ago

#1641 - CLI: Use raw descriptions

Pull Request - State: open - Opened by victorlin 5 months ago

#1641 - CLI: Use raw descriptions

Pull Request - State: open - Opened by victorlin 5 months ago

#1640 - Register subparsers recursively

Pull Request - State: open - Opened by victorlin 5 months ago - 1 comment

#1640 - Register subparsers recursively

Pull Request - State: open - Opened by victorlin 5 months ago - 1 comment

#1634 - Run release from CI workflow

Pull Request - State: closed - Opened by victorlin 5 months ago - 1 comment

#1634 - Run release from CI workflow

Pull Request - State: closed - Opened by victorlin 5 months ago - 1 comment

#1632 - merge: Omit generated source columns by default

Pull Request - State: closed - Opened by tsibley 5 months ago - 3 comments
Labels: breaking

#1631 - merge: Support sequences without cross-checking

Pull Request - State: open - Opened by victorlin 5 months ago - 3 comments

#1629 - parse: Prefer `strain` over `name` as sequence ID field

Pull Request - State: closed - Opened by victorlin 5 months ago - 1 comment
Labels: breaking

#1624 - Fix tests for `augur merge`

Pull Request - State: closed - Opened by tsibley 5 months ago

#1618 - Properly upload coverage file with upload-artifact v4.4.0

Pull Request - State: closed - Opened by victorlin 5 months ago - 4 comments

#1618 - Properly upload coverage file with upload-artifact v4.4.0

Pull Request - State: closed - Opened by victorlin 5 months ago - 4 comments

#1616 - CI: codecov artifact download failing

Issue - State: open - Opened by victorlin 5 months ago
Labels: bug

#1615 - Allow spaces in BEAST annotations mk2

Pull Request - State: closed - Opened by jameshadfield 5 months ago - 1 comment

#1614 - Align fractional sequences per group conversion methods

Issue - State: open - Opened by victorlin 5 months ago
Labels: proposal

#1613 - filter: Error on sequence duplicates

Pull Request - State: closed - Opened by victorlin 5 months ago - 4 comments
Labels: breaking

#1611 - Legacy editable installs are deprecated

Issue - State: open - Opened by genehack 5 months ago - 1 comment
Labels: bug

#1610 - Allow spaces in BEAST annotations

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

#1609 - Spaces in BEAST annotations cause error

Issue - State: closed - Opened by watronfire 5 months ago - 1 comment
Labels: bug

#1608 - merge: Ignore the user's ~/.sqliterc file, if any

Pull Request - State: closed - Opened by tsibley 5 months ago - 1 comment

#1607 - filter: Prefer "output sequences" over "output"?

Issue - State: open - Opened by victorlin 5 months ago - 1 comment
Labels: proposal

#1606 - Pin deepdif <8.0.0

Pull Request - State: closed - Opened by victorlin 5 months ago - 1 comment

#1605 - CI failing on JSON diff

Issue - State: closed - Opened by victorlin 5 months ago
Labels: bug

#1604 - Clarify missing column messages

Pull Request - State: closed - Opened by victorlin 5 months ago - 1 comment

#1603 - merge: Uncaught error with user-defined `.sqliterc`

Issue - State: closed - Opened by victorlin 5 months ago - 1 comment
Labels: bug

#1602 - filter: `--output-sequences` silently allows duplicates

Issue - State: open - Opened by victorlin 5 months ago
Labels: bug

#1601 - merge: Support sequences with cross-checking

Pull Request - State: closed - Opened by victorlin 5 months ago - 3 comments

#1600 - augur ancestral - IndexError when using wrong (shorter) reference

Issue - State: open - Opened by ammaraziz 5 months ago
Labels: bug

#1599 - Use exact fractional sequences per group

Pull Request - State: open - Opened by victorlin 6 months ago - 5 comments

#1598 - Subsample has uncaught assertion in ncov

Issue - State: open - Opened by corneliusroemer 6 months ago - 3 comments
Labels: bug

#1597 - Use identical help text for shared options

Issue - State: open - Opened by victorlin 6 months ago
Labels: documentation

#1596 - Use ngettext to handle plurality

Pull Request - State: closed - Opened by victorlin 6 months ago - 1 comment

#1595 - Update changelog entry for weighted sampling

Pull Request - State: closed - Opened by victorlin 6 months ago

#1594 - merge: Support table-specific id columns and delimiters

Pull Request - State: closed - Opened by tsibley 6 months ago - 4 comments

#1593 - merge: Avoid overwriting the output id column with non-id columns

Pull Request - State: closed - Opened by tsibley 6 months ago - 2 comments

#1592 - filter: Confusing warning and error combination when query contains a missing column

Issue - State: closed - Opened by victorlin 6 months ago - 2 comments
Labels: bug

#1591 - merge: polish

Pull Request - State: closed - Opened by tsibley 6 months ago - 3 comments

#1590 - filter: Make under-sampling more apparent

Issue - State: open - Opened by victorlin 6 months ago
Labels: enhancement

#1589 - Test new CI workflow

Pull Request - State: closed - Opened by genehack 6 months ago - 1 comment

#1588 - Simplify probabilistic sampling calculation

Issue - State: open - Opened by victorlin 6 months ago - 2 comments
Labels: proposal

#1587 - `AUGUR_DEBUG` documentation

Pull Request - State: closed - Opened by tsibley 6 months ago

#1586 - augur curate format-host

Issue - State: open - Opened by joverlee521 6 months ago - 2 comments
Labels: enhancement

#1585 - CLI docs have incorrect default values for options using `store_false` action

Issue - State: open - Opened by victorlin 6 months ago - 2 comments
Labels: bug, documentation

#1584 - Missing trait literals are converted to lower case in augur export stderr output

Issue - State: open - Opened by corneliusroemer 6 months ago - 1 comment
Labels: bug

#1583 - Write blog post about new features in Augur v25 releases

Issue - State: open - Opened by genehack 6 months ago
Labels: documentation

#1582 - Update language around snakemake install

Issue - State: open - Opened by genehack 6 months ago
Labels: documentation

#1581 - merge: polish

Pull Request - State: closed - Opened by tsibley 6 months ago - 2 comments

#1580 - Uncaught error when root not in tree.

Issue - State: open - Opened by vanessazubach 6 months ago - 10 comments
Labels: bug

#1579 - merge: Support sequences

Issue - State: open - Opened by tsibley 6 months ago - 23 comments
Labels: enhancement

#1578 - Should `parse-genbank-location` automatically fix region/locality mix ups?

Issue - State: open - Opened by joverlee521 6 months ago - 2 comments
Labels: enhancement, proposal

#1577 - Add a debugging mode controlled by AUGUR_DEBUG

Pull Request - State: closed - Opened by tsibley 6 months ago - 5 comments

#1576 - Command descriptions mangled in `--help` output

Issue - State: closed - Opened by tsibley 6 months ago - 2 comments

#1575 - Speed up augur filter

Issue - State: open - Opened by victorlin 6 months ago
Labels: enhancement

#1574 - Speed up augur filter by replacing Pandas

Issue - State: open - Opened by victorlin 6 months ago - 1 comment
Labels: enhancement

#1573 - Speed up augur filter without replacing Pandas

Issue - State: open - Opened by victorlin 6 months ago - 1 comment
Labels: enhancement

#1572 - Poorly formatted metadata TSV leads to KeyError

Issue - State: closed - Opened by joverlee521 6 months ago - 1 comment
Labels: duplicate

#1571 - Simplify Python version config for mypy/pyright

Pull Request - State: closed - Opened by victorlin 6 months ago

#1570 - Fix broken links [#1569]

Pull Request - State: closed - Opened by genehack 6 months ago - 3 comments

#1569 - Fix broken links in docs

Issue - State: closed - Opened by genehack 6 months ago
Labels: documentation

#1568 - Fix broken links [nextstrain/docs.nextstrain.org#14]

Pull Request - State: closed - Opened by genehack 6 months ago - 2 comments

#1566 - Pick a meaning of TSV and use it consistently

Issue - State: open - Opened by tsibley 6 months ago - 12 comments

#1565 - Fix curate internal quotes take 2

Pull Request - State: closed - Opened by joverlee521 6 months ago - 7 comments

#1564 - Fix newline handling when reading CSV/TSV

Pull Request - State: closed - Opened by tsibley 6 months ago - 2 comments

#1563 - augur merge

Pull Request - State: closed - Opened by tsibley 6 months ago - 11 comments

#1562 - augur {read,write}-file

Pull Request - State: closed - Opened by tsibley 6 months ago - 3 comments

#1561 - io.metadata: Fix newline handling when reading CSV/TSV

Pull Request - State: closed - Opened by tsibley 6 months ago

#1559 - tree: Update Cram tests

Pull Request - State: closed - Opened by victorlin 7 months ago