Update cogent3 requirement from >=2026.4.13a0 to >=2026.5.25a0

[dependabot]

Updates the requirements on cogent3 to permit the latest version.

Changelog

Sourced from cogent3's changelog.

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 new argument allows redundancy in the input / destination character values. It's being used by the revised parser behaviour to streamline ingesting sequence data from files.

Contributors

• GavinHuttley

Enhancements

• the fasta and genbank iterating sequence format parsers use the new scinexus.io_util.iter_record_chunks streaming parser. This reduces peak RAM while retaining speed.
• improve generality of load_seq for json files, accepts all sequence classes
• alphabet.make_text_to_array_converter() function, returns a bytes_to_array instance that directly transforms sequence text file contents into a numpy.uint8 array. This avoids multiple bytes translation calls, improving speed and reducing peak RAM.

Changes in release "2026.5.14a0"

A bug fix and enhancement release.

Contributors

• GavinHuttley

Enhancements

• Performance of <seq coll>.get_lengths() on the sequence container classes now much more efficient.

... (truncated)

Commits

• c3f6687 Merge pull request #2644 from GavinHuttley/develop
• 4cbf55e EV: bump ruff version and use dependabot cooldown
• 28c3487 DEV: bump version to 2026.5.25a0
• 5c4a295 DOC: fix doc organisation for parsers
• 6f3bcdd DOC: fix docs pertaining to parsers
• db7e477 Merge pull request #2643 from GavinHuttley/develop
• 2046295 API: iterative parser signatures all now positional then keyword only
• 33172a6 Merge pull request #2642 from GavinHuttley/develop
• 68b9237 DOC: fixed grammar
• 35796ad MAINT: style
• Additional commits viewable in compare view

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[codacy-production]

Up to standards ✅

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