scikit-allel2 2.0.0rc1__tar.gz → 2.1.0rc1__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (192) hide show
  1. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/.github/workflows/deploy.yml +1 -0
  2. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/.github/workflows/test.yml +3 -0
  3. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/.readthedocs.yaml +2 -0
  4. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/MANIFEST.in +4 -0
  5. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/PKG-INFO +1 -1
  6. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/io/vcf_read.py +339 -30
  7. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/opt/io_vcf_read.pyx +4 -2
  8. scikit_allel2-2.1.0rc1/allel2/test/data/region.vcf +24 -0
  9. scikit_allel2-2.1.0rc1/allel2/test/data/region.vcf.gz +0 -0
  10. scikit_allel2-2.1.0rc1/allel2/test/data/region.vcf.gz.tbi +0 -0
  11. scikit_allel2-2.1.0rc1/allel2/test/data/region_csi.vcf.gz +0 -0
  12. scikit_allel2-2.1.0rc1/allel2/test/data/region_csi.vcf.gz.csi +0 -0
  13. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/io/test_vcf_read.py +28 -3
  14. scikit_allel2-2.1.0rc1/allel2/test/io/test_vcf_read_backends.py +900 -0
  15. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/version.py +3 -3
  16. scikit_allel2-2.1.0rc1/bench/vcf_rust.py +131 -0
  17. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/ci/smoke_wheel.py +13 -1
  18. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/index.rst +6 -2
  19. scikit_allel2-2.1.0rc1/docs/io.rst +71 -0
  20. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/release.rst +69 -0
  21. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/pyproject.toml +4 -0
  22. scikit_allel2-2.1.0rc1/rust/io_vcf_read/Cargo.lock +558 -0
  23. scikit_allel2-2.1.0rc1/rust/io_vcf_read/Cargo.toml +28 -0
  24. scikit_allel2-2.1.0rc1/rust/io_vcf_read/src/lib.rs +1704 -0
  25. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/scikit_allel2.egg-info/PKG-INFO +1 -1
  26. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/scikit_allel2.egg-info/SOURCES.txt +10 -0
  27. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/scikit_allel2.egg-info/scm_file_list.json +10 -0
  28. scikit_allel2-2.1.0rc1/scikit_allel2.egg-info/scm_version.json +8 -0
  29. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/setup.py +9 -0
  30. scikit_allel2-2.0.0rc1/docs/io.rst +0 -29
  31. scikit_allel2-2.0.0rc1/scikit_allel2.egg-info/scm_version.json +0 -8
  32. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/.gitattributes +0 -0
  33. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/.gitignore +0 -0
  34. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/.pep8speaks.yml +0 -0
  35. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/LICENSE +0 -0
  36. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/README.rst +0 -0
  37. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/RELEASING.md +0 -0
  38. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/__init__.py +0 -0
  39. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/abc.py +0 -0
  40. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/chunked/__init__.py +0 -0
  41. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/chunked/core.py +0 -0
  42. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/chunked/storage_hdf5.py +0 -0
  43. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/chunked/storage_zarr.py +0 -0
  44. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/chunked/util.py +0 -0
  45. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/compat.py +0 -0
  46. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/conftest.py +0 -0
  47. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/constants.py +0 -0
  48. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/io/__init__.py +0 -0
  49. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/io/fasta.py +0 -0
  50. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/io/gff.py +0 -0
  51. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/io/util.py +0 -0
  52. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/io/vcf_write.py +0 -0
  53. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/model/__init__.py +0 -0
  54. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/model/chunked.py +0 -0
  55. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/model/dask.py +0 -0
  56. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/model/generic.py +0 -0
  57. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/model/ndarray.py +0 -0
  58. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/model/util.py +0 -0
  59. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/opt/__init__.py +0 -0
  60. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/opt/model.pyx +0 -0
  61. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/opt/stats.pyx +0 -0
  62. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/plot.py +0 -0
  63. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/__init__.py +0 -0
  64. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/admixture.py +0 -0
  65. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/decomposition.py +0 -0
  66. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/distance.py +0 -0
  67. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/diversity.py +0 -0
  68. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/fst.py +0 -0
  69. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/hw.py +0 -0
  70. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/ld.py +0 -0
  71. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/mendel.py +0 -0
  72. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/misc.py +0 -0
  73. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/preprocessing.py +0 -0
  74. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/roh.py +0 -0
  75. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/selection.py +0 -0
  76. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/sf.py +0 -0
  77. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/stats/window.py +0 -0
  78. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/__init__.py +0 -0
  79. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/__init__.py +0 -0
  80. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/altlen.vcf +0 -0
  81. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/ann.vcf +0 -0
  82. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/eff.vcf +0 -0
  83. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/empty.vcf +0 -0
  84. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/sample.gff +0 -0
  85. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/sample.scikit-allel-1.3.13.zarr.zip +0 -0
  86. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/sample.sorted.gff.gz +0 -0
  87. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/sample.sorted.gff.gz.tbi +0 -0
  88. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/sample.utf8.vcf +0 -0
  89. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/sample.vcf +0 -0
  90. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/sample.vcf.gz +0 -0
  91. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/sample.vcf.gz.tbi +0 -0
  92. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test1.vcf +0 -0
  93. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test14.vcf +0 -0
  94. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test16.vcf +0 -0
  95. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test176.vcf +0 -0
  96. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test32.vcf +0 -0
  97. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test4.vcf +0 -0
  98. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test48a.vcf +0 -0
  99. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test48b.vcf +0 -0
  100. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test54.vcf.gz +0 -0
  101. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test54.vcf.gz.tbi +0 -0
  102. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/test63.vcf +0 -0
  103. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/data/unsorted.vcf +0 -0
  104. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/io/__init__.py +0 -0
  105. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/io/test_gff_read.py +0 -0
  106. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/model/__init__.py +0 -0
  107. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/model/ndarray/__init__.py +0 -0
  108. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/model/ndarray/test_arrays.py +0 -0
  109. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/model/ndarray/test_indexes.py +0 -0
  110. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/model/ndarray/test_tables.py +0 -0
  111. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/model/test_api.py +0 -0
  112. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/model/test_chunked.py +0 -0
  113. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/model/test_dask.py +0 -0
  114. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/stats/__init__.py +0 -0
  115. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/stats/test_mendel.py +0 -0
  116. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/stats/test_selection.py +0 -0
  117. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/stats/test_sf.py +0 -0
  118. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/test_api.py +0 -0
  119. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/test_stats.py +0 -0
  120. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/test_util.py +0 -0
  121. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/test/tools.py +0 -0
  122. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/allel2/util.py +0 -0
  123. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/ci/check_dist.py +0 -0
  124. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/ci/test_check_dist.py +0 -0
  125. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/Makefile +0 -0
  126. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/_static/EXISTS +0 -0
  127. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/_static/copybutton.js +0 -0
  128. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/adr/0001-stringdtype-par-defaut-pour-les-lectures-vcf.md +0 -0
  129. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/adr/0002-zarr-v3-par-defaut-pour-vcf-to-zarr.md +0 -0
  130. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/adr/0003-pas-d-alias-allel.md +0 -0
  131. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/adr/0004-parseur-vcf-rust-avec-repli-cython.md +0 -0
  132. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/chunked.rst +0 -0
  133. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/conf.py +0 -0
  134. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/migrating.rst +0 -0
  135. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/migrating_chunked.rst +0 -0
  136. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/model/chunked.rst +0 -0
  137. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/model/dask.rst +0 -0
  138. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/model/ndarray.rst +0 -0
  139. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/model/util.rst +0 -0
  140. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/model.rst +0 -0
  141. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/admixture.rst +0 -0
  142. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/decomposition.rst +0 -0
  143. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/distance.rst +0 -0
  144. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/diversity.rst +0 -0
  145. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/fst.rst +0 -0
  146. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/hw.rst +0 -0
  147. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/ld.rst +0 -0
  148. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/mendel.rst +0 -0
  149. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/misc.rst +0 -0
  150. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/preprocessing.rst +0 -0
  151. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/roh.rst +0 -0
  152. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/selection.rst +0 -0
  153. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/sf.rst +0 -0
  154. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats/window.rst +0 -0
  155. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/stats.rst +0 -0
  156. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/docs/util.rst +0 -0
  157. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/chunked.ipynb +0 -0
  158. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/diversity_divergence.ipynb +0 -0
  159. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/fst.ipynb +0 -0
  160. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/gff3.ipynb +0 -0
  161. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/ihs.ipynb +0 -0
  162. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/ihs_standardization.ipynb +0 -0
  163. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/io_vcf.ipynb +0 -0
  164. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/ld.ipynb +0 -0
  165. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/misc_plotting.ipynb +0 -0
  166. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/model.ipynb +0 -0
  167. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/nsl.ipynb +0 -0
  168. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/pairwise_distance.ipynb +0 -0
  169. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/sfs.ipynb +0 -0
  170. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/spike.vcf.gz +0 -0
  171. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/tables.ipynb +0 -0
  172. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/tajima_d.ipynb +0 -0
  173. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/window_utils.ipynb +0 -0
  174. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/xpehh.ipynb +0 -0
  175. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/profiling/xpnsl.ipynb +0 -0
  176. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/repr_html.ipynb +0 -0
  177. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/sandbox/chunked_repr.ipynb +0 -0
  178. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/sandbox/dask_bcolz.ipynb +0 -0
  179. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/sandbox/dask_count_alleles_mask.ipynb +0 -0
  180. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/sandbox/dask_map_alleles.ipynb +0 -0
  181. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/sandbox/dask_profiling.ipynb +0 -0
  182. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/sandbox/dask_subset.ipynb +0 -0
  183. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/sandbox/issue_77.ipynb +0 -0
  184. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/sandbox/phase_by_transmission.ipynb +0 -0
  185. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/notebooks/sandbox/roh_mhmm.ipynb +0 -0
  186. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/profiling/read_vcf.py +0 -0
  187. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/pytest.ini +0 -0
  188. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/scikit_allel2.egg-info/dependency_links.txt +0 -0
  189. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/scikit_allel2.egg-info/not-zip-safe +0 -0
  190. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/scikit_allel2.egg-info/requires.txt +0 -0
  191. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/scikit_allel2.egg-info/top_level.txt +0 -0
  192. {scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/setup.cfg +0 -0
{scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/.github/workflows/deploy.yml RENAMED
@@ -17,6 +17,7 @@ on:
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  - pyproject.toml
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  - setup.py
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  - MANIFEST.in
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+ - rust/**
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  jobs:
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  build_wheels:
{scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/.github/workflows/test.yml RENAMED
@@ -40,6 +40,9 @@ jobs:
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  with:
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  python-version: ${{ matrix.python-version }}
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+ - name: Set up Rust
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+ uses: dtolnay/rust-toolchain@stable
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+
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  - name: Prerequisites (Linux)
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  if: runner.os == 'Linux'
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  run: |
{scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/.readthedocs.yaml RENAMED
@@ -6,6 +6,8 @@ build:
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  os: ubuntu-24.04
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  tools:
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  python: "3.13"
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+ # the package includes a Rust extension
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+ rust: "latest"
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  jobs:
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  post_checkout:
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  # setuptools-scm needs the history to compute the version
{scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/MANIFEST.in RENAMED
@@ -8,6 +8,10 @@ prune docs/_build
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  graft allel2
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+ include rust/io_vcf_read/Cargo.toml
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+ include rust/io_vcf_read/Cargo.lock
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+ graft rust/io_vcf_read/src
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+
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  global-exclude *.so
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  global-exclude *.pyd
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  global-exclude *.pyc
{scikit_allel2-2.0.0rc1 → scikit_allel2-2.1.0rc1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: scikit-allel2
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- Version: 2.0.0rc1
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+ Version: 2.1.0rc1
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  Summary: A Python package for exploring and analysing genetic variation data.
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  Author-email: Alistair Miles <alistair.miles@sanger.ac.uk>
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  Maintainer-email: Loïc Talignani <loic.talignani@ird.fr>