bed-reader 1.0.4b2__tar.gz → 1.0.5b1__tar.gz

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Files changed (105) hide show
  1. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/.isort.cfg +1 -1
  2. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/CHANGELOG.md +4 -0
  3. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/Cargo.lock +386 -314
  4. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/Cargo.toml +11 -11
  5. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/PKG-INFO +1 -1
  6. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/_open_bed.py +17 -41
  7. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/test_open_bed.py +1 -1
  8. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/test_open_bed_cloud.py +1 -1
  9. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/test_opt_dep.py +3 -3
  10. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/requirements-dev.txt +2 -1
  11. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/src/lib.rs +17 -20
  12. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/src/python_module.rs +72 -62
  13. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/src/tests.rs +6 -46
  14. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/useful.md +2 -1
  15. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/.flake8 +0 -0
  16. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/.github/workflows/ci.yml +0 -0
  17. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/.gitignore +0 -0
  18. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/AUTHORS.txt +0 -0
  19. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/LICENSE.md +0 -0
  20. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/README-rust.md +0 -0
  21. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/README.md +0 -0
  22. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/_sphinx_javascript_frameworks_compat.js +0 -0
  23. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/basic.css +0 -0
  24. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/doctools.js +0 -0
  25. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/documentation_options.js +0 -0
  26. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/file.png +0 -0
  27. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/jquery-3.4.1.js +0 -0
  28. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/jquery-3.5.1.js +0 -0
  29. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/jquery-3.6.0.js +0 -0
  30. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/jquery.js +0 -0
  31. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/js/badge_only.js +0 -0
  32. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/js/html5shiv-printshiv.min.js +0 -0
  33. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/js/html5shiv.min.js +0 -0
  34. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/js/modernizr.min.js +0 -0
  35. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/js/theme.js +0 -0
  36. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/language_data.js +0 -0
  37. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/minus.png +0 -0
  38. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/plus.png +0 -0
  39. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/pygments.css +0 -0
  40. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/searchtools.js +0 -0
  41. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/sphinx_highlight.js +0 -0
  42. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/underscore-1.12.0.js +0 -0
  43. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/underscore-1.13.1.js +0 -0
  44. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/underscore-1.3.1.js +0 -0
  45. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/_static/underscore.js +0 -0
  46. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/__init__.py +0 -0
  47. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/_sample_data.py +0 -0
  48. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/_to_bed.py +0 -0
  49. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/__init__.py +0 -0
  50. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/benchmark/bench2.ipynb +0 -0
  51. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/benchmark/benchmark.py +0 -0
  52. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/500x400_o640_array.memmap +0 -0
  53. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/badfile.bed +0 -0
  54. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/empty.bed +0 -0
  55. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/plink_sim_10s_100v_10pmiss.bed +0 -0
  56. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/plink_sim_10s_100v_10pmiss.bim +0 -0
  57. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/plink_sim_10s_100v_10pmiss.fam +0 -0
  58. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small.bad_bim +0 -0
  59. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small.bed +0 -0
  60. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small.bim +0 -0
  61. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small.bim_bad_positions.bim +0 -0
  62. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small.deb +0 -0
  63. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small.fam +0 -0
  64. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small.fam_bad +0 -0
  65. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small.maf +0 -0
  66. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small.mib +0 -0
  67. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small2_array.memmap +0 -0
  68. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small_array.memmap +0 -0
  69. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small_no_bim.bed +0 -0
  70. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small_no_bim.fam +0 -0
  71. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small_no_fam.bed +0 -0
  72. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small_no_fam.bim +0 -0
  73. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small_too_short.bed +0 -0
  74. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small_too_short.bim +0 -0
  75. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/small_too_short.fam +0 -0
  76. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/smallmode0.bed +0 -0
  77. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/smallmode0.bim +0 -0
  78. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/smallmode0.fam +0 -0
  79. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/smallmodebad.bed +0 -0
  80. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/some_missing.bed +0 -0
  81. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/some_missing.bim +0 -0
  82. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/some_missing.fam +0 -0
  83. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/some_missing.properties.npz +0 -0
  84. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/some_missing.val.npy +0 -0
  85. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/sparse.bed +0 -0
  86. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/sparse.bim +0 -0
  87. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/sparse.fam +0 -0
  88. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/toydata.5chrom.bed +0 -0
  89. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/toydata.5chrom.bim +0 -0
  90. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/data/toydata.5chrom.fam +0 -0
  91. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/registry.txt +0 -0
  92. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/bed_reader/tests/test_file_dot.py +0 -0
  93. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/build.rs +0 -0
  94. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/examples/cloud.rs +0 -0
  95. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/examples/no_cloud.rs +0 -0
  96. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/pyproject.toml +0 -0
  97. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/pytest.ini +0 -0
  98. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/requirements-min-dev.txt +0 -0
  99. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/requirements.txt +0 -0
  100. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/setpath.bat +0 -0
  101. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/src/bed_cloud.rs +0 -0
  102. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/src/supplemental_documents/cloud_urls_etc.md +0 -0
  103. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/src/supplemental_documents/options_etc.md +0 -0
  104. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/tests/tests_api.rs +0 -0
  105. {bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/tests/tests_api_cloud.rs +0 -0
{bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/.isort.cfg RENAMED
@@ -1,5 +1,5 @@
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  [settings]
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- skip=.conda
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+ # skip=.conda
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  profile=black
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  multi_line_output = 3
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  include_trailing_comma = true
{bed_reader-1.0.4b2 → bed_reader-1.0.5b1}/CHANGELOG.md RENAMED
@@ -5,6 +5,10 @@ All notable changes to this project will be documented in this file.
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  The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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  and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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+ ## [1.05] - 2024-7-1
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+
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+ - Add support for Python's Numpy 2
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+
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  ## [1.0.4] - 2024-4-24
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  - Fix a minor bug in helper functions used by PySnpTools.