Update cogent3 requirement from >=2026.4.13a0 to >=2026.6.9a0

[dependabot]

Updates the requirements on cogent3 to permit the latest version.

Changelog

Sourced from cogent3's changelog.

Changes in release "2026.6.9a0"

A minor enhancement release.

API

• Added PhyloNode.get_newick(with_support) argument, controlling whether to include support measures in the newick string.

Contributors

• @​GavinHuttley

Enhancements

• Now write out bootstrap support measures in newick format.

Documentation

• Document using PhyloNode.get_newick(with_support) argument.

Changes in release "2026.6.2a0"

A bug fix and minor enhancement release.

Contributors

• @​GavinHuttley
• @​sanvila reported a bug and proposed a fix 🚀

Enhancements

• Added iter_fastq_records to cogent3.parse.fastq for streaming fastq records as (label, sequence, quality) tuples with optional bytes converters.
• Added make_qual_converter and PhredEncoding to cogent3.core.alphabet for mapping Phred+33 / Phred+64 quality ASCII into numpy.uint8 score arrays.
• Added limit keyword argument to all methods that select annotations. Propagated through to the AnnotationDb.get_(features|records)_matching() methods. Applied in aggregate across all tables.

Bug fixes

• load_annotations() now correctly uses format_name. For cases where the file name suffix did not match a known format, format_name argument was having no effect. This is now fixed.
• the coevolution_matrix() function now correctly caps max_workers, thanks to @​sanvila for reporting and proposing the fix!

Documentation

... (truncated)

Commits

• 40f7ef7 Merge pull request #2658 from GavinHuttley/develop
• 68e206b DEV: updated changelog
• 9c61df3 Merge pull request #2657 from GavinHuttley/develop
• 4dfc6ed Merge pull request #2656 from cogent3/dependabot/github_actions/astral-sh/set...
• 9549d60 DEV: bump version to 2026.6.9a0
• d3b7e9a Merge branch 'develop' into dependabot/github_actions/astral-sh/setup-uv-8.1.0
• 801386a Merge pull request #2655 from cogent3/dependabot/pip/ruff-0.15.15
• 332a5a2 Bump astral-sh/setup-uv from 7 to 8.1.0
• d0979b0 Bump ruff from 0.15.14 to 0.15.15
• 7ee5cbc Merge pull request #2651 from cogent3/dependabot/pip/ruff-0.15.14
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[codacy-production]

Up to standards ✅

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