Bump bio from 3.0.0 to 4.0.1

[dependabot]

Bumps bio from 3.0.0 to 4.0.1.

Changelog

Sourced from bio's changelog.

4.0.1 (2026-06-29)

Bug Fixes

• pattern_matching: reject 64-symbol patterns in shift_and and bndm (#675) (49aafac)

Dependencies

• update itertools requirement from >=0.8, <0.15 to >=0.8, <0.16 (#676) (1760c1d)

4.0.0 (2026-06-12)

⚠ BREAKING CHANGES

• Replace anyhow with typed thiserror errors (#674)
• Change Phase conversion methods to use TryFrom for better error handling (#625)
• for pairwise alignment, only apply gap_extend penalty for each extension of a gap beyond length 1, not upon gap opening (#660)

refactor

• Change Phase conversion methods to use TryFrom for better error handling (#625) (c8718fc)
• Replace anyhow with typed thiserror errors (#674) (ae5d31a)

Features

• gff: percent-encode and -decode GFF3 attributes per the spec (#672) (40166d6)
• rank_select: add RankSelect::extend for appending many bits (#671) (3b90bb3)
• rank_select: add RankSelect::push for incremental construction (#670) (aba35b5)

Bug Fixes

• fix compiler warnings (#661) (8c9013a)
• fmindex: avoid usize underflow on backward_search for lex-smallest symbol (#663) (79dc5d1)
• for pairwise alignment, only apply gap_extend penalty for each extension of a gap beyond length 1, not upon gap opening (#660) (51e3d29), closes #656
• import RngExt so tests and benches compile with rand 0.10 (#668) (435d696)
• io: reject non-IUPAC characters in FASTA/FASTQ Record::check (#662) (607960a)
• test: import RngExt for random_range in rank_select test (#667) (ae8d54d)

Miscellaneous

• add keywords and categories to Cargo.toml (#669) (e9f5a84)

Dependencies

... (truncated)

Commits

• 2d70940 chore(master): release 4.0.1 (#678)
• 49aafac fix(pattern_matching): reject 64-symbol patterns in shift_and and bndm (#675)
• 1760c1d deps: update itertools requirement from >=0.8, <0.15 to >=0.8, <0.16 (#676)
• 0500aee chore(master): release 4.0.0 (#665)
• 40166d6 feat(gff): percent-encode and -decode GFF3 attributes per the spec (#672)
• ae5d31a refactor!: Replace anyhow with typed thiserror errors (#674)
• c8718fc refactor!: Change Phase conversion methods to use TryFrom for better error ha...
• 3b90bb3 feat(rank_select): add RankSelect::extend for appending many bits (#671)
• aba35b5 feat(rank_select): add RankSelect::push for incremental construction (#670)
• fed0f4b deps: update strum_macros requirement from >= 0.16, < 0.27 to >= 0.16, < 0.29...
• Additional commits viewable in compare view