chore(main): release 6.5.3

[github-actions]

🤖 I have created a release beep boop

6.5.3 (2026-03-03)

⚠ BREAKING CHANGES

• appris/mane: this change also fixes gencode.v41 to use the correct source (e107 now instead of e103).
• vcfbin: VCFTable.GT_HETEROZYGOUS is replaced with VCFTable.GT_HETEROZYGOUS_UNPHASED

Features

• add appris data (#132) (6914b05)
• add gencode.v46 (#181) (8fdbc33)
• add gencode.v47 adjacent annos + appris (#143) (34b94df), closes #134
• add mouse annos and appris (#137) (3e2b148), closes #129
• compatibility with python 3.10 (#28) (1d51397)
• deprecate py38, support py11 py12 (#101) (cd94123)
• gtrack: inplace output (#73) (17838b7)
• gtrack: interval iteration (#71) (1e2b672)
• list available genome configs (#549) (#19) (fb9776c)
• modernize usage of setuptools (#176) (412a00d)
• publish pip wheels for linux+mac (#163) (100cc81)
• read/write files for refg name hash lookups (#62) (8074701)
• S3 data manager (#121) (85f1cbd)
• support gencode v47 (#131) (210ec32)
• support gencode vM31 appris (#197) (f0c6222)
• support MANE Select and Clinical Plus transcripts (#127) (98d0757)
• support refseq anno GCF_000001405.40-RS_2024_08 (#125) (b8e1ca3), closes #124
• use new dedicated requester-pays public bucket (#33) (e4fb7a1)
• vcfbin: support phased VCF (#92) (a1f0b2a)
• wheel distribution for linux on python 3.9-3.12 (#150) (6faecce)
• wheel distribution for linux on python 3.9-3.12, arm architecture (#156) (4a3ed58)

Bug Fixes

• add condition for prepending chr to variant chromosome (#195) (8abe006)
• allow local-only files to be loaded (#38) (a56a5dc), closes #37
• allow VariantGenome to be serialized (#161) (18f3253)
• appris/mane: allow data source to determine availability (#157) (41c1fbe)
• assert that appris transcripts match the requested gene (#70) (fd93609)
• avoid accessing released memory (#63) (1ab7456)
• avoid errors when blob metadata is None (#54) (e850c54)
• avoid user confusion when loading annotation (#53) (e556030)
• broken installation on osx-arm64 (#65) (6bd68c2)
• build all supported MANE annotations (#185) (e369690)
• build anno relies on utr/cds ordering (#142) (e28678b), closes #135
• check genome.dna(Interval) arg type (#68) (f7b6e5c), closes #67
• data: exception raising was dependent on an envvar before (#99) (3d461c1)
• dna: consistent allow_outside_chromosome defaults (#98) (611970d)
• ensure correctness of signed/unsigned comparisons (#55) (23c1d03)
• handle anchor within deletions (#140) (3c8aabb)
• intersect() with mismtached chrom (#191) (8c59110), closes #189
• missing mock for dna boundary (#25) (b058b53)
• propagate errors when datamanager fails to resolve paths for a refg (#172) (00d61c7)
• provide a better hint in case of permissions error (#42) (cb21280)
• track: check inplace dtype (#79) (5a2cb38)
• track: handle res>1 for track interval interrogation (#84) (246a6dc)
• track: OOB issue with negative strands on u1 tracks (#104) (53ae2f5)
• track: segfault when decoding large dims (#75) (6f5c29e)
• track: sparse encoding broken (#88) (c8f6732)
• track: strided decoding (#77) (1fc1b37)

Documentation

• acknowledge past contributors (#43) (d0dcfd5)
• clarify how to get a list of all genomes (#182) (912b201)
• more standard cmake instructions (#21) (55a73d8)
• prepare required documentation for AWS Open Data (#116) (364d723)
• provide a data starter script (#39) (a257da1)
• restore and document link to versionized docs (#51) (cc22955), closes #50
• show project description on https://pypi.org/project/genomekit/ (#164) (f13ed06)
• simplify strandedness instructions for bedgraph/wig (#118) (60c44dd)
• starter_build script download (#96) (1245558)

Miscellaneous Chores

• avoid CI failure on conda-forge (#3) (468272e)
• avoid compile error on mac (#5) (1f9d59e)
• avoid import on Windows (#15) (0aef946)
• avoid some tests on windows (#7) (7359a45)
• fix windows build (#106) (e1754c7)
• move releases to conda-forge (#1) (c2ddf93)
• reenable tests on windows (#13) (fb90358)
• release 5.0.0 (#36) (cc939ef)
• release 6.0.3 (e3ff39e)
• release 6.0.3 (#110) (f8a1062)
• release 6.1.1 (#119) (e081b55)
• release 6.5.3 (#152) (49633a8)
• replace libfmt with std::format (#148) (ae7100a)
• revert the windows test change (#11) (879adb5)
• skip bioconda-dependant tests on conda-forge (#17) (cad0584)
• skip gcs-dependent tests on conda-forge (#23) (1595cba)
• skip windows tests correctly (#9) (ce7f1b3)

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