bed-reader 1.0.1b2__tar.gz → 1.0.2__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 (179) hide show
  1. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/CHANGELOG.md +1 -1
  2. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/Cargo.lock +307 -481
  3. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/Cargo.toml +13 -37
  4. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/PKG-INFO +1 -1
  5. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/README-rust.md +7 -11
  6. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/_open_bed.py +17 -23
  7. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/test_open_bed_cloud.py +1 -1
  8. bed_reader-1.0.2/examples/cloud.rs +34 -0
  9. bed_reader-1.0.2/examples/no_cloud.rs +19 -0
  10. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/requirements-dev.txt +3 -3
  11. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/src/bed_cloud.rs +546 -848
  12. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/src/lib.rs +142 -182
  13. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/src/python_module.rs +18 -29
  14. bed_reader-1.0.2/src/supplemental_documents/cloud_urls_etc.md +195 -0
  15. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/src/supplemental_documents/options_etc.md +5 -5
  16. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/src/tests.rs +1 -46
  17. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/tests/tests_api_cloud.rs +237 -367
  18. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/useful.md +21 -0
  19. bed_reader-1.0.1b2/.cargo/config.toml +0 -2
  20. bed_reader-1.0.1b2/_static/css/badge_only.css +0 -1
  21. bed_reader-1.0.1b2/_static/css/fonts/Roboto-Slab-Bold.woff +0 -0
  22. bed_reader-1.0.1b2/_static/css/fonts/Roboto-Slab-Bold.woff2 +0 -0
  23. bed_reader-1.0.1b2/_static/css/fonts/Roboto-Slab-Regular.woff +0 -0
  24. bed_reader-1.0.1b2/_static/css/fonts/Roboto-Slab-Regular.woff2 +0 -0
  25. bed_reader-1.0.1b2/_static/css/fonts/fontawesome-webfont.eot +0 -0
  26. bed_reader-1.0.1b2/_static/css/fonts/fontawesome-webfont.svg +0 -2671
  27. bed_reader-1.0.1b2/_static/css/fonts/fontawesome-webfont.ttf +0 -0
  28. bed_reader-1.0.1b2/_static/css/fonts/fontawesome-webfont.woff +0 -0
  29. bed_reader-1.0.1b2/_static/css/fonts/fontawesome-webfont.woff2 +0 -0
  30. bed_reader-1.0.1b2/_static/css/fonts/lato-bold-italic.woff +0 -0
  31. bed_reader-1.0.1b2/_static/css/fonts/lato-bold-italic.woff2 +0 -0
  32. bed_reader-1.0.1b2/_static/css/fonts/lato-bold.woff +0 -0
  33. bed_reader-1.0.1b2/_static/css/fonts/lato-bold.woff2 +0 -0
  34. bed_reader-1.0.1b2/_static/css/fonts/lato-normal-italic.woff +0 -0
  35. bed_reader-1.0.1b2/_static/css/fonts/lato-normal-italic.woff2 +0 -0
  36. bed_reader-1.0.1b2/_static/css/fonts/lato-normal.woff +0 -0
  37. bed_reader-1.0.1b2/_static/css/fonts/lato-normal.woff2 +0 -0
  38. bed_reader-1.0.1b2/_static/css/theme.css +0 -4
  39. bed_reader-1.0.1b2/_static/fonts/FontAwesome.otf +0 -0
  40. bed_reader-1.0.1b2/_static/fonts/Inconsolata-Bold.ttf +0 -0
  41. bed_reader-1.0.1b2/_static/fonts/Inconsolata-Regular.ttf +0 -0
  42. bed_reader-1.0.1b2/_static/fonts/Inconsolata.ttf +0 -0
  43. bed_reader-1.0.1b2/_static/fonts/Lato/lato-bold.eot +0 -0
  44. bed_reader-1.0.1b2/_static/fonts/Lato/lato-bold.ttf +0 -0
  45. bed_reader-1.0.1b2/_static/fonts/Lato/lato-bold.woff +0 -0
  46. bed_reader-1.0.1b2/_static/fonts/Lato/lato-bold.woff2 +0 -0
  47. bed_reader-1.0.1b2/_static/fonts/Lato/lato-bolditalic.eot +0 -0
  48. bed_reader-1.0.1b2/_static/fonts/Lato/lato-bolditalic.ttf +0 -0
  49. bed_reader-1.0.1b2/_static/fonts/Lato/lato-bolditalic.woff +0 -0
  50. bed_reader-1.0.1b2/_static/fonts/Lato/lato-bolditalic.woff2 +0 -0
  51. bed_reader-1.0.1b2/_static/fonts/Lato/lato-italic.eot +0 -0
  52. bed_reader-1.0.1b2/_static/fonts/Lato/lato-italic.ttf +0 -0
  53. bed_reader-1.0.1b2/_static/fonts/Lato/lato-italic.woff +0 -0
  54. bed_reader-1.0.1b2/_static/fonts/Lato/lato-italic.woff2 +0 -0
  55. bed_reader-1.0.1b2/_static/fonts/Lato/lato-regular.eot +0 -0
  56. bed_reader-1.0.1b2/_static/fonts/Lato/lato-regular.ttf +0 -0
  57. bed_reader-1.0.1b2/_static/fonts/Lato/lato-regular.woff +0 -0
  58. bed_reader-1.0.1b2/_static/fonts/Lato/lato-regular.woff2 +0 -0
  59. bed_reader-1.0.1b2/_static/fonts/Lato-Bold.ttf +0 -0
  60. bed_reader-1.0.1b2/_static/fonts/Lato-Regular.ttf +0 -0
  61. bed_reader-1.0.1b2/_static/fonts/Roboto-Slab-Bold.woff +0 -0
  62. bed_reader-1.0.1b2/_static/fonts/Roboto-Slab-Bold.woff2 +0 -0
  63. bed_reader-1.0.1b2/_static/fonts/Roboto-Slab-Light.woff +0 -0
  64. bed_reader-1.0.1b2/_static/fonts/Roboto-Slab-Light.woff2 +0 -0
  65. bed_reader-1.0.1b2/_static/fonts/Roboto-Slab-Regular.woff +0 -0
  66. bed_reader-1.0.1b2/_static/fonts/Roboto-Slab-Regular.woff2 +0 -0
  67. bed_reader-1.0.1b2/_static/fonts/Roboto-Slab-Thin.woff +0 -0
  68. bed_reader-1.0.1b2/_static/fonts/Roboto-Slab-Thin.woff2 +0 -0
  69. bed_reader-1.0.1b2/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot +0 -0
  70. bed_reader-1.0.1b2/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf +0 -0
  71. bed_reader-1.0.1b2/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff +0 -0
  72. bed_reader-1.0.1b2/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2 +0 -0
  73. bed_reader-1.0.1b2/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot +0 -0
  74. bed_reader-1.0.1b2/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf +0 -0
  75. bed_reader-1.0.1b2/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff +0 -0
  76. bed_reader-1.0.1b2/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2 +0 -0
  77. bed_reader-1.0.1b2/_static/fonts/RobotoSlab-Bold.ttf +0 -0
  78. bed_reader-1.0.1b2/_static/fonts/RobotoSlab-Regular.ttf +0 -0
  79. bed_reader-1.0.1b2/_static/fonts/fontawesome-webfont.eot +0 -0
  80. bed_reader-1.0.1b2/_static/fonts/fontawesome-webfont.svg +0 -2671
  81. bed_reader-1.0.1b2/_static/fonts/fontawesome-webfont.ttf +0 -0
  82. bed_reader-1.0.1b2/_static/fonts/fontawesome-webfont.woff +0 -0
  83. bed_reader-1.0.1b2/_static/fonts/fontawesome-webfont.woff2 +0 -0
  84. bed_reader-1.0.1b2/_static/fonts/lato-bold-italic.woff +0 -0
  85. bed_reader-1.0.1b2/_static/fonts/lato-bold-italic.woff2 +0 -0
  86. bed_reader-1.0.1b2/_static/fonts/lato-bold.woff +0 -0
  87. bed_reader-1.0.1b2/_static/fonts/lato-bold.woff2 +0 -0
  88. bed_reader-1.0.1b2/_static/fonts/lato-normal-italic.woff +0 -0
  89. bed_reader-1.0.1b2/_static/fonts/lato-normal-italic.woff2 +0 -0
  90. bed_reader-1.0.1b2/_static/fonts/lato-normal.woff +0 -0
  91. bed_reader-1.0.1b2/_static/fonts/lato-normal.woff2 +0 -0
  92. bed_reader-1.0.1b2/bed_reader/_open_bed_cloud.py +0 -1583
  93. bed_reader-1.0.1b2/src/supplemental_documents/cloud_urls_etc.md +0 -333
  94. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/.flake8 +0 -0
  95. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/.github/workflows/ci.yml +0 -0
  96. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/.gitignore +0 -0
  97. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/.isort.cfg +0 -0
  98. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/AUTHORS.txt +0 -0
  99. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/LICENSE.md +0 -0
  100. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/README.md +0 -0
  101. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/_sphinx_javascript_frameworks_compat.js +0 -0
  102. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/basic.css +0 -0
  103. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/doctools.js +0 -0
  104. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/documentation_options.js +0 -0
  105. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/file.png +0 -0
  106. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/jquery-3.4.1.js +0 -0
  107. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/jquery-3.5.1.js +0 -0
  108. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/jquery-3.6.0.js +0 -0
  109. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/jquery.js +0 -0
  110. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/js/badge_only.js +0 -0
  111. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/js/html5shiv-printshiv.min.js +0 -0
  112. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/js/html5shiv.min.js +0 -0
  113. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/js/modernizr.min.js +0 -0
  114. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/js/theme.js +0 -0
  115. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/language_data.js +0 -0
  116. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/minus.png +0 -0
  117. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/plus.png +0 -0
  118. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/pygments.css +0 -0
  119. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/searchtools.js +0 -0
  120. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/sphinx_highlight.js +0 -0
  121. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/underscore-1.12.0.js +0 -0
  122. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/underscore-1.13.1.js +0 -0
  123. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/underscore-1.3.1.js +0 -0
  124. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/_static/underscore.js +0 -0
  125. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/__init__.py +0 -0
  126. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/_sample_data.py +0 -0
  127. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/_to_bed.py +0 -0
  128. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/__init__.py +0 -0
  129. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/benchmark/benchmark.py +0 -0
  130. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/500x400_o640_array.memmap +0 -0
  131. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/badfile.bed +0 -0
  132. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/empty.bed +0 -0
  133. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/plink_sim_10s_100v_10pmiss.bed +0 -0
  134. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/plink_sim_10s_100v_10pmiss.bim +0 -0
  135. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/plink_sim_10s_100v_10pmiss.fam +0 -0
  136. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small.bad_bim +0 -0
  137. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small.bed +0 -0
  138. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small.bim +0 -0
  139. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small.bim_bad_positions.bim +0 -0
  140. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small.deb +0 -0
  141. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small.fam +0 -0
  142. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small.fam_bad +0 -0
  143. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small.maf +0 -0
  144. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small.mib +0 -0
  145. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small2_array.memmap +0 -0
  146. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small_array.memmap +0 -0
  147. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small_no_bim.bed +0 -0
  148. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small_no_bim.fam +0 -0
  149. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small_no_fam.bed +0 -0
  150. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small_no_fam.bim +0 -0
  151. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small_too_short.bed +0 -0
  152. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small_too_short.bim +0 -0
  153. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/small_too_short.fam +0 -0
  154. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/smallmode0.bed +0 -0
  155. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/smallmode0.bim +0 -0
  156. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/smallmode0.fam +0 -0
  157. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/smallmodebad.bed +0 -0
  158. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/some_missing.bed +0 -0
  159. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/some_missing.bim +0 -0
  160. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/some_missing.fam +0 -0
  161. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/some_missing.properties.npz +0 -0
  162. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/some_missing.val.npy +0 -0
  163. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/sparse.bed +0 -0
  164. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/sparse.bim +0 -0
  165. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/sparse.fam +0 -0
  166. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/toydata.5chrom.bed +0 -0
  167. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/toydata.5chrom.bim +0 -0
  168. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/data/toydata.5chrom.fam +0 -0
  169. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/registry.txt +0 -0
  170. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/test_file_dot.py +0 -0
  171. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/test_open_bed.py +0 -0
  172. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/bed_reader/tests/test_opt_dep.py +0 -0
  173. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/build.rs +0 -0
  174. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/pyproject.toml +0 -0
  175. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/pytest.ini +0 -0
  176. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/requirements-min-dev.txt +0 -0
  177. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/requirements.txt +0 -0
  178. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/setpath.bat +0 -0
  179. {bed_reader-1.0.1b2 → bed_reader-1.0.2}/tests/tests_api.rs +0 -0
{bed_reader-1.0.1b2 → bed_reader-1.0.2}/CHANGELOG.md RENAMED
@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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  ## [1.0.1] - 2024-4-16
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+ - Add support for cloud files to both Rust and Python.
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  ## [1.0.0] - 2023-11-5
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