Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / sgkit-dev/sgkit issues and pull requests
#1264 - Remove VCF support
Pull Request -
State: open - Opened by tomwhite 6 days ago
Labels: documentation, IO
#1263 - Test on Python 3.12
Pull Request -
State: open - Opened by tomwhite 6 days ago
- 1 comment
#1262 - Use sgkit.distarray for gwas_linear_regression
Pull Request -
State: open - Opened by tomwhite 7 days ago
#1261 - Install dask[dataframe] explicitly to fix upstream error
Pull Request -
State: open - Opened by tomwhite 11 days ago
- 1 comment
Labels: upstream
#1259 - Use sgkit.distarray for sample_stats and hardy_weinberg_test
Pull Request -
State: closed - Opened by tomwhite 14 days ago
#1258 - Use vcf2zarr in GWAS tutorial notebook
Pull Request -
State: closed - Opened by tomwhite 14 days ago
- 3 comments
Labels: auto-merge
#1257 - Update GWAS tutorial to use vcf2zarr
Issue -
State: closed - Opened by tomwhite 19 days ago
Labels: documentation, IO
#1256 - Update actions/upload-artifact to v4 in .github/workflows
Pull Request -
State: closed - Opened by tomwhite 19 days ago
Labels: upstream
#1255 - Use sgkit.distarray for count_variant_alleles and variant_stats
Pull Request -
State: closed - Opened by tomwhite 19 days ago
#1254 - Run test_count_call_alleles on Cubed (alternative approach)
Pull Request -
State: closed - Opened by tomwhite 24 days 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] 27 days ago
Labels: dependencies, github_actions
#1252 - Disable validation workflow
Pull Request -
State: closed - Opened by jeromekelleher 27 days ago
- 1 comment
#1251 - Disable validation workflow
Pull Request -
State: closed - Opened by jeromekelleher 27 days ago
- 1 comment
#1249 - Run `test_count_call_alleles` on Cubed
Pull Request -
State: closed - Opened by tomwhite 28 days ago
- 4 comments
#1248 - Pin Dask to fix slow main build
Pull Request -
State: closed - Opened by tomwhite 28 days ago
- 1 comment
#1247 - Main build is very slow and times out
Issue -
State: closed - Opened by tomwhite 28 days ago
Labels: upstream
#1245 - Deprecate VCF write functions
Issue -
State: open - Opened by tomwhite about 1 month ago
- 1 comment
Labels: documentation, IO
#1243 - Unclear how to overwrite a dataset
Issue -
State: open - Opened by hyanwong 2 months ago
- 2 comments
#1242 - No page at https://sgkit-dev.github.io
Issue -
State: open - Opened by hyanwong 2 months ago
#1240 - Displaying alleles when using `sgkit.display_genotypes(ds)`
Issue -
State: open - Opened by hyanwong 2 months ago
#1237 - Numpy 2 testing
Pull Request -
State: closed - Opened by tomwhite 3 months ago
- 1 comment
#1235 - Release 0.9.0
Issue -
State: closed - Opened by tomwhite 3 months ago
- 4 comments
#1234 - Run tests against NumPy 2
Issue -
State: closed - Opened by tomwhite 3 months ago
- 3 comments
Labels: upstream
#1233 - Deprecate functions for reading VCF
Pull Request -
State: closed - Opened by tomwhite 3 months ago
Labels: IO
#1232 - Deprecate functions for reading VCF
Issue -
State: closed - Opened by tomwhite 3 months ago
- 1 comment
Labels: IO
#1231 - Unblock upstream build which now requires Python>=3.10
Pull Request -
State: closed - Opened by tomwhite 3 months ago
Labels: upstream
#1230 - Pin to Zarr < 3
Pull Request -
State: closed - Opened by tomwhite 3 months ago
Labels: upstream
#1229 - Add 'matching' method option to identity_by_state
Pull Request -
State: closed - Opened by timothymillar 3 months ago
- 3 comments
Labels: auto-merge
#1228 - Minor fixes for Numpy 2
Pull Request -
State: closed - Opened by timothymillar 3 months ago
- 5 comments
Labels: auto-merge
#1227 - Option to calculate IBS probabilities via allele matching
Issue -
State: closed - Opened by timothymillar 3 months ago
Labels: enhancement
#1226 - Run tests against Zarr 3
Issue -
State: open - Opened by tomwhite 4 months ago
- 3 comments
Labels: upstream
#1225 - Main build failing with 'RuntimeWarning: overflow encountered in scalar subtract'
Issue -
State: closed - Opened by tomwhite 4 months ago
Labels: bug, upstream
#1223 - Update docs to say "Scalable genetics toolkit"
Issue -
State: open - Opened by jeromekelleher 4 months ago
#1222 - simulate_genotype_call_dataset creates alleles as byte strings
Issue -
State: open - Opened by hyanwong 4 months ago
- 1 comment
Labels: bug
#1221 - simulate_genotype_call_dataset creates duplicate alleles
Issue -
State: open - Opened by hyanwong 4 months ago
Labels: bug
#1220 - ImportError: dlopen[...]: symbol not found in flat namespace '_bcf_float_missing' - sgkit-vcf requirements are not installed
Issue -
State: closed - Opened by simonharnqvist 4 months ago
- 4 comments
#1219 - Genome accessibility/callability
Issue -
State: open - Opened by mufernando 4 months ago
- 4 comments
#1218 - Python 3.11,3.12 conda install fails.
Issue -
State: open - Opened by benjeffery 5 months ago
#1217 - Fix wheel test on macOS
Pull Request -
State: closed - Opened by tomwhite 5 months ago
- 3 comments
#1216 - Release 0.8.0
Issue -
State: closed - Opened by tomwhite 5 months ago
- 2 comments
Labels: process + tools
#1213 - MemoryError: Allocation failed (probably too large) with ped.compute()
Issue -
State: open - Opened by fouerghi 6 months ago
- 7 comments
#1212 - Move docs to sgkit.dev
Issue -
State: open - Opened by hammer 6 months ago
Labels: documentation
#1211 - Update project email address
Pull Request -
State: closed - Opened by hammer 6 months ago
#1210 - `vcf_to_zarr` raises error instead of truncating INFO fields of length `R`
Issue -
State: open - Opened by timothymillar 7 months ago
- 3 comments
Labels: bug, IO
#1209 - read_plink returns bytes for variant_alleles not unicode
Issue -
State: open - Opened by jeromekelleher 7 months ago
Labels: bug
#1208 - Partial changes for VCF Character S->U
Pull Request -
State: open - Opened by jeromekelleher 7 months ago
#1207 - Mixed-ploidy VanRaden GRM
Issue -
State: open - Opened by timothymillar 7 months ago
Labels: enhancement
#1205 - Fix xarray repr in doctests
Pull Request -
State: closed - Opened by tomwhite 7 months ago
- 3 comments
Labels: auto-merge
#1204 - Change in Xarray repr is causing doctest failures
Issue -
State: closed - Opened by tomwhite 7 months ago
Labels: upstream
#1203 - partition_into_regions: tabix index returns illegal region with multiple contigs
Issue -
State: open - Opened by jeromekelleher 7 months ago
Labels: bug
#1202 - partition_into_regions: CSI indexed BCFs return empty regions
Issue -
State: open - Opened by jeromekelleher 7 months ago
Labels: bug
#1201 - partition_into_regions: CSI indexed VCFs have incorrect sequence names
Issue -
State: open - Opened by jeromekelleher 7 months ago
Labels: bug
#1200 - partition_into_regions returns empty region for all contigs in header
Issue -
State: closed - Opened by jeromekelleher 7 months ago
- 5 comments
#1199 - Avoid disabling jit on guvectorised functions
Pull Request -
State: closed - Opened by timothymillar 7 months ago
- 3 comments
Labels: auto-merge
#1197 - Cannot round-trip explicitly set missing INFO values in VCF
Issue -
State: closed - Opened by jeromekelleher 8 months ago
- 3 comments
#1196 - vcf_writer emitting incorrect missing values for INFO fields
Issue -
State: closed - Opened by jeromekelleher 8 months ago
Labels: bug
#1195 - read_scikit_allel_vcfzarr returns string pad values instead of missing for INFO fields
Issue -
State: open - Opened by jeromekelleher 8 months ago
Labels: bug
#1194 - Numba cache masking compile warnings and deprecations
Issue -
State: closed - Opened by jeromekelleher 8 months ago
- 7 comments
Labels: process + tools
#1193 - Irrelavant change for build
Pull Request -
State: closed - Opened by jeromekelleher 8 months ago
- 1 comment
#1192 - VCF parser returning FILL instead of MISSING values
Issue -
State: closed - Opened by jeromekelleher 8 months ago
Labels: bug
#1191 - Turn off numba cache by default
Pull Request -
State: closed - Opened by jeromekelleher 8 months ago
- 3 comments
Labels: auto-merge
#1190 - Errors in missing vs pad values in VCF
Pull Request -
State: closed - Opened by jeromekelleher 8 months ago
- 9 comments
Labels: auto-merge
#1188 - Genealogical relatedness greater than 1
Issue -
State: closed - Opened by fouerghi 8 months ago
- 3 comments
#1186 - Do chunk sizes have to be the same for all variables in a given dimension?
Issue -
State: open - Opened by jeromekelleher 8 months ago
- 1 comment
#1185 - Two-pass non-Dask VCF conversion
Pull Request -
State: closed - Opened by jeromekelleher 8 months ago
- 3 comments
#1184 - Upgrade sphinx to fix build
Pull Request -
State: closed - Opened by tomwhite 8 months ago
- 2 comments
Labels: auto-merge, upstream
#1183 - Sequential VCF parsing
Issue -
State: closed - Opened by hammer 8 months ago
- 2 comments
Labels: IO
#1182 - `sgkit.regenie` review. Work in progress
Pull Request -
State: open - Opened by jdstamp 8 months ago
#1181 - `sgkit.genee` improvements
Pull Request -
State: open - Opened by jdstamp 8 months ago
#1180 - genee review: sgkit implementation limitations
Issue -
State: open - Opened by jdstamp 8 months ago
- 1 comment
#1179 - Howto: join biallelic SNPs into a single record?
Issue -
State: open - Opened by hyanwong 8 months ago
- 1 comment
#1176 - Variant positions less than one?
Issue -
State: open - Opened by hyanwong 8 months ago
- 1 comment
#1175 - Add getting REF to how_do_i
Pull Request -
State: open - Opened by hyanwong 8 months ago
#1174 - FAQ - mask out duplicate positions
Issue -
State: open - Opened by hyanwong 8 months ago
#1173 - Document how to use save_dataset to overwrite existing files
Issue -
State: open - Opened by hyanwong 8 months ago
- 1 comment
#1172 - "missing_pct" misnamed in simulate_genotype_call_dataset
Issue -
State: open - Opened by hyanwong 8 months ago
#1171 - Iterating through variants
Issue -
State: open - Opened by hyanwong 8 months ago
#1170 - How do I identify the REF from a VCF
Issue -
State: open - Opened by hyanwong 8 months ago
- 4 comments
#1169 - `partition_into_regions` fails to partition correctly in when absent contigs are listed in the header.
Issue -
State: closed - Opened by benjeffery 9 months ago
- 9 comments
Labels: bug
#1168 - VCF parsing memory usage
Issue -
State: open - Opened by benjeffery 9 months ago
- 7 comments
#1167 - Change organization and project name expansion
Issue -
State: closed - Opened by hammer 9 months ago
- 18 comments
Labels: documentation, process + tools
#1165 - How do I... additions
Issue -
State: open - Opened by hammer 9 months ago
- 3 comments
Labels: documentation
#1163 - Change `Dataset.dims` to `Dataset.sizes` to address Xarray FutureWarning
Pull Request -
State: closed - Opened by tomwhite 10 months ago
- 1 comment
Labels: auto-merge
#1163 - Change `Dataset.dims` to `Dataset.sizes` to address Xarray FutureWarning
Pull Request -
State: closed - Opened by tomwhite 10 months ago
- 1 comment
Labels: auto-merge
#1162 - Main build is failing
Issue -
State: closed - Opened by tomwhite 10 months ago
Labels: upstream
#1162 - Main build is failing
Issue -
State: closed - Opened by tomwhite 10 months ago
Labels: upstream
#1161 - Fix broken links in the getting started guide
Pull Request -
State: open - Opened by isumitjha 10 months ago
- 2 comments
Labels: auto-merge
#1160 - Broken dask tutorial links in getting started guide
Issue -
State: open - Opened by isumitjha 10 months ago
Labels: documentation
#1160 - Broken dask tutorial links in getting started guide
Issue -
State: open - Opened by isumitjha 10 months ago
Labels: documentation
#1159 - Make copyright year dynamic
Pull Request -
State: open - Opened by isumitjha 10 months ago
Labels: auto-merge
#1158 - Update copyright in the docs
Issue -
State: open - Opened by aktech 10 months ago
#1158 - Update copyright in the docs
Issue -
State: open - Opened by aktech 10 months ago
#1157 - Don't display attributes expanded for dataset
Issue -
State: open - Opened by jeromekelleher 10 months ago
- 5 comments
Labels: enhancement
#1156 - Set SGKIT_DISABLE_NUMBA_CACHE=1 by default
Issue -
State: open - Opened by jeromekelleher 10 months ago
- 3 comments
Labels: bug
#1155 - Writing a subset of a dataset to VCF
Issue -
State: open - Opened by jeromekelleher 10 months ago
#1155 - Writing a subset of a dataset to VCF
Issue -
State: open - Opened by jeromekelleher 10 months ago
#1154 - Parts of work redone when a dask worker dies
Issue -
State: open - Opened by benjeffery 10 months ago
- 2 comments
#1152 - read_plink scalability
Issue -
State: closed - Opened by hammer 10 months ago
- 4 comments
Labels: IO
#1151 - How do I add a new sample or variant data variable from a file?
Issue -
State: open - Opened by hammer 10 months ago
- 1 comment
Labels: documentation
#1151 - How do I add a new sample or variant data variable from a file?
Issue -
State: open - Opened by hammer 10 months ago
- 1 comment
Labels: documentation