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Issues list

ImportError: cannot import name 'vcf2zarr' from 'bio2zarr' bug Something isn't working upstream Used when our build breaks due to upstream changes
#1308 by tomwhite was closed Apr 14, 2025
2
2
Wheels always have 0.0.0 version number bug Something isn't working process + tools
#1306 by tomwhite was closed Apr 7, 2025
1
Release 0.10.0
#1304 by tomwhite was closed Apr 8, 2025
2
Wheels build is broken github_actions Pull requests that update GitHub Actions code good first issue Good for newcomers help wanted Extra attention is needed process + tools
#1302 by tomwhite was closed Apr 7, 2025
1
Unit test failures under Zarr Python 3.0.2 IO Issues related to reading and writing common third-party file formats upstream Used when our build breaks due to upstream changes
#1290 by tomwhite was closed Feb 25, 2025
1
Unit tests failures under Cubed bug Something isn't working
#1284 by tomwhite was closed Feb 10, 2025
1
1
Fix CI for Zarr Python v3 upstream Used when our build breaks due to upstream changes
#1283 by tomwhite was closed Jan 14, 2025
1
Chunked pedigree kinship
#1280 by timothymillar was closed Jan 13, 2025
1
@timothymillar
GPU build is failing process + tools
#1270 by tomwhite was closed Oct 14, 2024
1
Benchmarking Numba vs JAX performance
#1266 by tomwhite was closed Feb 10, 2025
4
Update GWAS tutorial to use vcf2zarr documentation Improvements or additions to documentation IO Issues related to reading and writing common third-party file formats
#1257 by tomwhite was closed Sep 17, 2024
1
Main build is very slow and times out upstream Used when our build breaks due to upstream changes
#1247 by tomwhite was closed Sep 2, 2024
1
Deprecate VCF write functions documentation Improvements or additions to documentation IO Issues related to reading and writing common third-party file formats
#1245 by tomwhite was closed Oct 11, 2024
2
Release 0.9.0
#1235 by tomwhite was closed Jul 1, 2024
4
Run tests against NumPy 2 upstream Used when our build breaks due to upstream changes
#1234 by tomwhite was closed Sep 2, 2024
1
3
Deprecate functions for reading VCF IO Issues related to reading and writing common third-party file formats
#1232 by tomwhite was closed Jun 27, 2024
1
1
Option to calculate IBS probabilities via allele matching enhancement New feature or request
#1227 by timothymillar was closed Jul 4, 2024
1
Run tests against Zarr 3 upstream Used when our build breaks due to upstream changes
#1226 by tomwhite was closed Nov 5, 2024
1
4
Main build failing with 'RuntimeWarning: overflow encountered in scalar subtract' bug Something isn't working upstream Used when our build breaks due to upstream changes
#1225 by tomwhite was closed Jun 19, 2024
1
@timothymillar
ImportError: dlopen[...]: symbol not found in flat namespace '_bcf_float_missing' - sgkit-vcf requirements are not installed
#1220 by simonharnqvist was closed May 23, 2024
4
Release 0.8.0 process + tools
#1216 by tomwhite was closed May 7, 2024
2
MemoryError: Allocation failed (probably too large) with ped.compute()
#1213 by fouerghi was closed Jan 13, 2025
1
8
vcf_to_zarr raises error instead of truncating INFO fields of length R bug Something isn't working IO Issues related to reading and writing common third-party file formats
#1210 by timothymillar was closed May 7, 2025
5
Change in Xarray repr is causing doctest failures upstream Used when our build breaks due to upstream changes
#1204 by tomwhite was closed Mar 4, 2024
1
partition_into_regions: tabix index returns illegal region with multiple contigs bug Something isn't working
#1203 by jeromekelleher was closed May 7, 2025 0.9.1
1
ProTip! Updated in the last three days: updated:>2025-05-31.