Update cogent3 requirement from >=2026.4.13a0 to >=2026.6.2a0

[dependabot]

Updates the requirements on cogent3 to permit the latest version.

Changelog

Sourced from cogent3's changelog.

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

• Added cookbook sections covering direct fastq parsing with iter_fastq_records and constructing quality-score converters with make_qual_converter.
• Added docs describing the new limit argument.

Changes in release "2026.5.19a0"

This is a feature enhancement release.

API

• added a SequenceParserBase.accepts_converter property. By default, this returns False. The cogent3 iterative parsers (fasta and genbank) are modified so its True. The top level sequence load_* functions use this to conditionally inject a converter into the parser_kw which directly converts plain text into the numpy.uint8 consistent with the moltypes most degenerate alphabet.
• added alphabet.bytes_to_array(dest=None) as an optional keyword argument. This takes the explicit destination bytes. The default behaviour (takes only non-redundant source alphabet characters and maps to ordered characters for conversion to numpy.uint8) is unchanged. This

... (truncated)

Commits

• 599b079 Merge pull request #2649 from GavinHuttley/develop
• 9968725 DEV: bump version to 2026.6.2a0
• a91a008 Merge pull request #2648 from GavinHuttley/develop
• b6b0148 MAINT: fix type-check failure
• 9b07e13 ENH: sample features using optional limit keyword argument
• 1c88995 Merge pull request #2645 from cogent3/dependabot/github_actions/github/codeql...
• e9c5367 Merge pull request #2647 from GavinHuttley/develop
• fd35fe2 BUG: cap max_workers for coevo matrix, fixes #2646
• 356262c Bump github/codeql-action from 4 to 4.35.5
• c3f6687 Merge pull request #2644 from GavinHuttley/develop
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Up to standards ✅

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