Ecosyste.ms: Issues

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GitHub / sgkit-dev/sgkit issues and pull requests

#1287 - Use sgkit.distarray for windowing

Pull Request - State: open - Opened by tomwhite 10 days ago

#1285 - Fix CI for Zarr Python v3

Pull Request - State: closed - Opened by tomwhite 18 days ago - 1 comment

#1284 - Unit tests failures under Cubed

Issue - State: open - Opened by tomwhite 18 days ago - 1 comment
Labels: bug

#1283 - Fix CI for Zarr Python v3

Issue - State: closed - Opened by tomwhite 18 days ago
Labels: upstream

#1282 - Simple chunked pedigree kinship

Pull Request - State: closed - Opened by timothymillar 25 days ago - 4 comments
Labels: auto-merge

#1281 - Use sgkit.distarray for popgen and windowing

Pull Request - State: open - Opened by tomwhite about 1 month ago

#1280 - Chunked pedigree kinship

Issue - State: closed - Opened by timothymillar about 2 months ago

#1279 - Add separate function for Watterson's theta

Issue - State: open - Opened by percyfal about 2 months ago - 2 comments

#1278 - Diversity calculations on windowed datasets generate lots of unmanaged memory

Issue - State: open - Opened by percyfal about 2 months ago - 8 comments

#1277 - Run tests using Zarr Python v3

Pull Request - State: closed - Opened by tomwhite 3 months ago - 1 comment

#1276 - Drop Python 3.9

Pull Request - State: closed - Opened by tomwhite 3 months ago

#1275 - Don't use local functions to wrap numba functions

Pull Request - State: closed - Opened by tomwhite 3 months ago
Labels: upstream

#1274 - Use sgkit.distarray for PCA

Pull Request - State: closed - Opened by tomwhite 3 months ago - 1 comment

#1271 - Disable failing GPU build

Pull Request - State: closed - Opened by tomwhite 4 months ago

#1270 - GPU build is failing

Issue - State: closed - Opened by tomwhite 4 months ago
Labels: process + tools

#1269 - Fix windows wheels test

Pull Request - State: closed - Opened by tomwhite 4 months ago
Labels: bug

#1268 - Windowing fails for datasets where contigs lack variant sites

Issue - State: open - Opened by percyfal 4 months ago - 5 comments
Labels: bug

#1267 - Dask 2024.8.1 and later is very slow

Issue - State: open - Opened by tomwhite 4 months ago - 8 comments
Labels: performance, upstream

#1266 - Benchmarking Numba vs JAX

Issue - State: open - Opened by tomwhite 4 months ago - 4 comments
Labels: performance

#1264 - Remove VCF support

Pull Request - State: closed - Opened by tomwhite 4 months ago - 1 comment
Labels: documentation, IO

#1263 - Test on Python 3.12

Pull Request - State: closed - Opened by tomwhite 4 months ago - 5 comments

#1262 - Use sgkit.distarray for gwas_linear_regression

Pull Request - State: closed - Opened by tomwhite 4 months ago

#1261 - Install dask[dataframe] explicitly to fix upstream error

Pull Request - State: open - Opened by tomwhite 4 months ago - 2 comments
Labels: upstream

#1259 - Use sgkit.distarray for sample_stats and hardy_weinberg_test

Pull Request - State: closed - Opened by tomwhite 5 months ago

#1258 - Use vcf2zarr in GWAS tutorial notebook

Pull Request - State: closed - Opened by tomwhite 5 months ago - 3 comments
Labels: auto-merge

#1257 - Update GWAS tutorial to use vcf2zarr

Issue - State: closed - Opened by tomwhite 5 months ago
Labels: documentation, IO

#1256 - Update actions/upload-artifact to v4 in .github/workflows

Pull Request - State: closed - Opened by tomwhite 5 months ago
Labels: upstream

#1255 - Use sgkit.distarray for count_variant_alleles and variant_stats

Pull Request - State: closed - Opened by tomwhite 5 months ago

#1254 - Run test_count_call_alleles on Cubed (alternative approach)

Pull Request - State: closed - Opened by tomwhite 5 months ago - 5 comments
Labels: auto-merge

#1253 - Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies, github_actions

#1252 - Disable validation workflow

Pull Request - State: closed - Opened by jeromekelleher 5 months ago - 1 comment

#1251 - Disable validation workflow

Pull Request - State: closed - Opened by jeromekelleher 5 months ago - 1 comment

#1249 - Run `test_count_call_alleles` on Cubed

Pull Request - State: closed - Opened by tomwhite 5 months ago - 4 comments

#1248 - Pin Dask to fix slow main build

Pull Request - State: closed - Opened by tomwhite 5 months ago - 1 comment

#1247 - Main build is very slow and times out

Issue - State: closed - Opened by tomwhite 5 months ago
Labels: upstream

#1245 - Deprecate VCF write functions

Issue - State: closed - Opened by tomwhite 6 months ago - 2 comments
Labels: documentation, IO

#1243 - Unclear how to overwrite a dataset

Issue - State: open - Opened by hyanwong 6 months ago - 2 comments

#1242 - No page at https://sgkit-dev.github.io

Issue - State: open - Opened by hyanwong 6 months ago

#1237 - Numpy 2 testing

Pull Request - State: closed - Opened by tomwhite 7 months ago - 1 comment

#1235 - Release 0.9.0

Issue - State: closed - Opened by tomwhite 7 months ago - 4 comments

#1234 - Run tests against NumPy 2

Issue - State: closed - Opened by tomwhite 7 months ago - 3 comments
Labels: upstream

#1233 - Deprecate functions for reading VCF

Pull Request - State: closed - Opened by tomwhite 7 months ago
Labels: IO

#1232 - Deprecate functions for reading VCF

Issue - State: closed - Opened by tomwhite 7 months ago - 1 comment
Labels: IO

#1231 - Unblock upstream build which now requires Python>=3.10

Pull Request - State: closed - Opened by tomwhite 7 months ago
Labels: upstream

#1230 - Pin to Zarr < 3

Pull Request - State: closed - Opened by tomwhite 7 months ago
Labels: upstream

#1229 - Add 'matching' method option to identity_by_state

Pull Request - State: closed - Opened by timothymillar 8 months ago - 3 comments
Labels: auto-merge

#1228 - Minor fixes for Numpy 2

Pull Request - State: closed - Opened by timothymillar 8 months ago - 5 comments
Labels: auto-merge

#1227 - Option to calculate IBS probabilities via allele matching

Issue - State: closed - Opened by timothymillar 8 months ago
Labels: enhancement

#1226 - Run tests against Zarr 3

Issue - State: closed - Opened by tomwhite 8 months ago - 4 comments
Labels: upstream

#1225 - Main build failing with 'RuntimeWarning: overflow encountered in scalar subtract'

Issue - State: closed - Opened by tomwhite 8 months ago
Labels: bug, upstream

#1222 - simulate_genotype_call_dataset creates alleles as byte strings

Issue - State: open - Opened by hyanwong 8 months ago - 1 comment
Labels: bug

#1221 - simulate_genotype_call_dataset creates duplicate alleles

Issue - State: open - Opened by hyanwong 8 months ago
Labels: bug

#1219 - Genome accessibility/callability

Issue - State: open - Opened by mufernando 8 months ago - 4 comments

#1218 - Python 3.11,3.12 conda install fails.

Issue - State: open - Opened by benjeffery 9 months ago

#1217 - Fix wheel test on macOS

Pull Request - State: closed - Opened by tomwhite 9 months ago - 3 comments

#1216 - Release 0.8.0

Issue - State: closed - Opened by tomwhite 9 months ago - 2 comments
Labels: process + tools

#1213 - MemoryError: Allocation failed (probably too large) with ped.compute()

Issue - State: closed - Opened by fouerghi 10 months ago - 8 comments

#1212 - Move docs to sgkit.dev

Issue - State: open - Opened by hammer 10 months ago
Labels: documentation

#1211 - Update project email address

Pull Request - State: closed - Opened by hammer 10 months ago

#1210 - `vcf_to_zarr` raises error instead of truncating INFO fields of length `R`

Issue - State: open - Opened by timothymillar 11 months ago - 3 comments
Labels: bug, IO

#1209 - read_plink returns bytes for variant_alleles not unicode

Issue - State: open - Opened by jeromekelleher 11 months ago
Labels: bug

#1208 - Partial changes for VCF Character S->U

Pull Request - State: open - Opened by jeromekelleher 11 months ago

#1207 - Mixed-ploidy VanRaden GRM

Issue - State: open - Opened by timothymillar 11 months ago
Labels: enhancement

#1205 - Fix xarray repr in doctests

Pull Request - State: closed - Opened by tomwhite 11 months ago - 3 comments
Labels: auto-merge

#1204 - Change in Xarray repr is causing doctest failures

Issue - State: closed - Opened by tomwhite 11 months ago
Labels: upstream

#1202 - partition_into_regions: CSI indexed BCFs return empty regions

Issue - State: open - Opened by jeromekelleher 11 months ago
Labels: bug

#1200 - partition_into_regions returns empty region for all contigs in header

Issue - State: closed - Opened by jeromekelleher 11 months ago - 5 comments

#1199 - Avoid disabling jit on guvectorised functions

Pull Request - State: closed - Opened by timothymillar 11 months ago - 3 comments
Labels: auto-merge

#1197 - Cannot round-trip explicitly set missing INFO values in VCF

Issue - State: closed - Opened by jeromekelleher 12 months ago - 3 comments

#1196 - vcf_writer emitting incorrect missing values for INFO fields

Issue - State: closed - Opened by jeromekelleher 12 months ago
Labels: bug

#1194 - Numba cache masking compile warnings and deprecations

Issue - State: closed - Opened by jeromekelleher 12 months ago - 7 comments
Labels: process + tools

#1193 - Irrelavant change for build

Pull Request - State: closed - Opened by jeromekelleher 12 months ago - 1 comment

#1192 - VCF parser returning FILL instead of MISSING values

Issue - State: closed - Opened by jeromekelleher 12 months ago
Labels: bug

#1191 - Turn off numba cache by default

Pull Request - State: closed - Opened by jeromekelleher 12 months ago - 3 comments
Labels: auto-merge

#1190 - Errors in missing vs pad values in VCF

Pull Request - State: closed - Opened by jeromekelleher 12 months ago - 9 comments
Labels: auto-merge

#1188 - Genealogical relatedness greater than 1

Issue - State: closed - Opened by fouerghi 12 months ago - 3 comments

#1185 - Two-pass non-Dask VCF conversion

Pull Request - State: closed - Opened by jeromekelleher 12 months ago - 3 comments

#1184 - Upgrade sphinx to fix build

Pull Request - State: closed - Opened by tomwhite 12 months ago - 2 comments
Labels: auto-merge, upstream

#1183 - Sequential VCF parsing

Issue - State: closed - Opened by hammer 12 months ago - 2 comments
Labels: IO

#1182 - `sgkit.regenie` review. Work in progress

Pull Request - State: open - Opened by jdstamp about 1 year ago

#1181 - `sgkit.genee` improvements

Pull Request - State: open - Opened by jdstamp about 1 year ago

#1180 - genee review: sgkit implementation limitations

Issue - State: open - Opened by jdstamp about 1 year ago - 1 comment

#1179 - Howto: join biallelic SNPs into a single record?

Issue - State: open - Opened by hyanwong about 1 year ago - 1 comment

#1176 - Variant positions less than one?

Issue - State: open - Opened by hyanwong about 1 year ago - 1 comment

#1175 - Add getting REF to how_do_i

Pull Request - State: open - Opened by hyanwong about 1 year ago

#1174 - FAQ - mask out duplicate positions

Issue - State: open - Opened by hyanwong about 1 year ago

#1173 - Document how to use save_dataset to overwrite existing files

Issue - State: open - Opened by hyanwong about 1 year ago - 1 comment

#1172 - "missing_pct" misnamed in simulate_genotype_call_dataset

Issue - State: open - Opened by hyanwong about 1 year ago

#1171 - Iterating through variants

Issue - State: open - Opened by hyanwong about 1 year ago

#1170 - How do I identify the REF from a VCF

Issue - State: open - Opened by hyanwong about 1 year ago - 4 comments

#1168 - VCF parsing memory usage

Issue - State: open - Opened by benjeffery about 1 year ago - 7 comments