Update cogent3 requirement from >=2026.6.9a0 to >=2026.7.6a0

[dependabot]

Updates the requirements on cogent3 to permit the latest version.

Changelog

Sourced from cogent3's changelog.

Changes in release "2026.7.6a0"

Feature enhancement release.

API

• phylip parser now accepts a converter for handling sequence conversion. Default is the one used for the fasta parser.

• nexus alignment parser now accepts a converter for handling sequence conversion. Default is the one used for the fasta parser.

Contributors

• @​GavinHuttley

Enhancements

• Generalise the PHYLIP parser for relaxed format. Old PHYLIP was very strict about how long taxa names could be. Relaxed format uses spaces to delineate where taxa names end. We also now use a converter for consistency with other cogent3 parsers. The latter allows the return type to be a string, or a numpy ndarray (for instance). Layout is now auto-detected, can be explicitly controlled using optional interleaved and strict arguments.

• Support parsing phylogenetic "partition" blocks from Nexus files. Partition and PartitionSet data classes added to parse/nexus.py holding resolved charset info for slicing alignments without storing the alignments themselves. Note character ranges are zero-based. Loading the appropriate alignments is up to the user. Users can extract partition data using cogent3.core.parse.nexus.parse_nexus_partitions().

Deprecations

• MinimalPhylipParser is being deprecated for iter_phylip_records, for consistency with other parsers.

• MinimalNexusAlignParser is being deprecated for iter_nexus_align_records, for consistency with other parsers.

Changes in release "2026.6.9a0"

A minor enhancement release.

API

... (truncated)

Commits

• 04274bd Merge pull request #2671 from GavinHuttley/develop
• 1eec677 DEV: bump version to 2026.7.6a0
• 838732f Merge pull request #2670 from GavinHuttley/develop
• 5f1ce24 DEP: removed functions marked for deprecation by 2026.7
• 11b8c46 Merge pull request #2669 from GavinHuttley/develop
• 971eb4c MAINT: convert test_nexus.py NexusParserTests to pytest functions
• 71dc6ad STY: pre-commit linting with ruff
• 0b2383d Merge pull request #2668 from GavinHuttley/develop
• 6df52dc MAINT: use scinexus iter_splitlines more in parse/nexus.py.
• ae9b76d API: deprecate MinimalNexusAlignParser for iter_nexus_align_records
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[codacy-production]

Up to standards ✅

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