tskit 1.0.3__tar.gz → 1.0.4__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 (94) hide show
  1. {tskit-1.0.3/tskit.egg-info → tskit-1.0.4}/PKG-INFO +3 -3
  2. {tskit-1.0.3 → tskit-1.0.4}/_tskitmodule.c +33 -816
  3. {tskit-1.0.3 → tskit-1.0.4}/lib/subprojects/kastore/kastore.c +23 -7
  4. {tskit-1.0.3 → tskit-1.0.4}/lib/subprojects/kastore/kastore.h +1 -1
  5. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/core.c +0 -16
  6. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/core.h +1 -23
  7. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/tables.c +9 -4
  8. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/trees.c +8 -6
  9. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit.h +0 -1
  10. {tskit-1.0.3 → tskit-1.0.4}/pyproject.toml +6 -6
  11. {tskit-1.0.3 → tskit-1.0.4}/setup.py +0 -1
  12. {tskit-1.0.3 → tskit-1.0.4}/tests/test_cli.py +165 -0
  13. {tskit-1.0.3 → tskit-1.0.4}/tests/test_file_format.py +27 -8
  14. {tskit-1.0.3 → tskit-1.0.4}/tests/test_genotypes.py +1 -1
  15. {tskit-1.0.3 → tskit-1.0.4}/tests/test_highlevel.py +8 -3
  16. {tskit-1.0.3 → tskit-1.0.4}/tests/test_immutable_table_collection.py +1 -0
  17. {tskit-1.0.3 → tskit-1.0.4}/tests/test_metadata.py +114 -0
  18. {tskit-1.0.3 → tskit-1.0.4}/tests/test_python_c.py +16 -181
  19. {tskit-1.0.3 → tskit-1.0.4}/tests/test_table_transforms.py +30 -0
  20. {tskit-1.0.3 → tskit-1.0.4}/tests/test_tables.py +14 -4
  21. {tskit-1.0.3 → tskit-1.0.4}/tests/test_tree_stats.py +10 -0
  22. {tskit-1.0.3 → tskit-1.0.4}/tskit/__init__.py +7 -0
  23. {tskit-1.0.3 → tskit-1.0.4}/tskit/_version.py +1 -1
  24. {tskit-1.0.3 → tskit-1.0.4}/tskit/cli.py +10 -3
  25. {tskit-1.0.3 → tskit-1.0.4}/tskit/genotypes.py +7 -2
  26. {tskit-1.0.3 → tskit-1.0.4}/tskit/metadata.py +19 -0
  27. {tskit-1.0.3 → tskit-1.0.4}/tskit/tables.py +25 -0
  28. {tskit-1.0.3 → tskit-1.0.4}/tskit/trees.py +20 -4
  29. {tskit-1.0.3 → tskit-1.0.4}/tskit/util.py +5 -4
  30. {tskit-1.0.3 → tskit-1.0.4/tskit.egg-info}/PKG-INFO +3 -3
  31. {tskit-1.0.3 → tskit-1.0.4}/tskit.egg-info/SOURCES.txt +0 -4
  32. tskit-1.0.3/lib/tskit/haplotype_matching.c +0 -1770
  33. tskit-1.0.3/lib/tskit/haplotype_matching.h +0 -169
  34. tskit-1.0.3/tests/test_genotype_matching.py +0 -1504
  35. tskit-1.0.3/tests/test_haplotype_matching.py +0 -1327
  36. {tskit-1.0.3 → tskit-1.0.4}/LICENSE +0 -0
  37. {tskit-1.0.3 → tskit-1.0.4}/MANIFEST.in +0 -0
  38. {tskit-1.0.3 → tskit-1.0.4}/README.rst +0 -0
  39. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/convert.c +0 -0
  40. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/convert.h +0 -0
  41. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/genotypes.c +0 -0
  42. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/genotypes.h +0 -0
  43. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/stats.c +0 -0
  44. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/stats.h +0 -0
  45. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/tables.h +0 -0
  46. {tskit-1.0.3 → tskit-1.0.4}/lib/tskit/trees.h +0 -0
  47. {tskit-1.0.3 → tskit-1.0.4}/lwt_interface/tskit_lwt_interface.h +0 -0
  48. {tskit-1.0.3 → tskit-1.0.4}/setup.cfg +0 -0
  49. {tskit-1.0.3 → tskit-1.0.4}/tests/test_avl_tree.py +0 -0
  50. {tskit-1.0.3 → tskit-1.0.4}/tests/test_balance_metrics.py +0 -0
  51. {tskit-1.0.3 → tskit-1.0.4}/tests/test_coalrate.py +0 -0
  52. {tskit-1.0.3 → tskit-1.0.4}/tests/test_combinatorics.py +0 -0
  53. {tskit-1.0.3 → tskit-1.0.4}/tests/test_dict_encoding.py +0 -0
  54. {tskit-1.0.3 → tskit-1.0.4}/tests/test_distance_metrics.py +0 -0
  55. {tskit-1.0.3 → tskit-1.0.4}/tests/test_divmat.py +0 -0
  56. {tskit-1.0.3 → tskit-1.0.4}/tests/test_drawing.py +0 -0
  57. {tskit-1.0.3 → tskit-1.0.4}/tests/test_extend_haplotypes.py +0 -0
  58. {tskit-1.0.3 → tskit-1.0.4}/tests/test_fileobj.py +0 -0
  59. {tskit-1.0.3 → tskit-1.0.4}/tests/test_ibd.py +0 -0
  60. {tskit-1.0.3 → tskit-1.0.4}/tests/test_intervals.py +0 -0
  61. {tskit-1.0.3 → tskit-1.0.4}/tests/test_jit.py +0 -0
  62. {tskit-1.0.3 → tskit-1.0.4}/tests/test_ld_matrix.py +0 -0
  63. {tskit-1.0.3 → tskit-1.0.4}/tests/test_ms.py +0 -0
  64. {tskit-1.0.3 → tskit-1.0.4}/tests/test_parsimony.py +0 -0
  65. {tskit-1.0.3 → tskit-1.0.4}/tests/test_phylo_formats.py +0 -0
  66. {tskit-1.0.3 → tskit-1.0.4}/tests/test_provenance.py +0 -0
  67. {tskit-1.0.3 → tskit-1.0.4}/tests/test_reference_sequence.py +0 -0
  68. {tskit-1.0.3 → tskit-1.0.4}/tests/test_relatedness_vector.py +0 -0
  69. {tskit-1.0.3 → tskit-1.0.4}/tests/test_stats.py +0 -0
  70. {tskit-1.0.3 → tskit-1.0.4}/tests/test_text_formats.py +0 -0
  71. {tskit-1.0.3 → tskit-1.0.4}/tests/test_threads.py +0 -0
  72. {tskit-1.0.3 → tskit-1.0.4}/tests/test_topology.py +0 -0
  73. {tskit-1.0.3 → tskit-1.0.4}/tests/test_tree_positioning.py +0 -0
  74. {tskit-1.0.3 → tskit-1.0.4}/tests/test_util.py +0 -0
  75. {tskit-1.0.3 → tskit-1.0.4}/tests/test_utilities.py +0 -0
  76. {tskit-1.0.3 → tskit-1.0.4}/tests/test_vcf.py +0 -0
  77. {tskit-1.0.3 → tskit-1.0.4}/tests/test_version.py +0 -0
  78. {tskit-1.0.3 → tskit-1.0.4}/tests/test_wright_fisher.py +0 -0
  79. {tskit-1.0.3 → tskit-1.0.4}/tskit/__main__.py +0 -0
  80. {tskit-1.0.3 → tskit-1.0.4}/tskit/combinatorics.py +0 -0
  81. {tskit-1.0.3 → tskit-1.0.4}/tskit/drawing.py +0 -0
  82. {tskit-1.0.3 → tskit-1.0.4}/tskit/exceptions.py +0 -0
  83. {tskit-1.0.3 → tskit-1.0.4}/tskit/intervals.py +0 -0
  84. {tskit-1.0.3 → tskit-1.0.4}/tskit/jit/__init__.py +0 -0
  85. {tskit-1.0.3 → tskit-1.0.4}/tskit/jit/numba.py +0 -0
  86. {tskit-1.0.3 → tskit-1.0.4}/tskit/provenance.py +0 -0
  87. {tskit-1.0.3 → tskit-1.0.4}/tskit/provenance.schema.json +0 -0
  88. {tskit-1.0.3 → tskit-1.0.4}/tskit/stats.py +0 -0
  89. {tskit-1.0.3 → tskit-1.0.4}/tskit/text_formats.py +0 -0
  90. {tskit-1.0.3 → tskit-1.0.4}/tskit/vcf.py +0 -0
  91. {tskit-1.0.3 → tskit-1.0.4}/tskit.egg-info/dependency_links.txt +0 -0
  92. {tskit-1.0.3 → tskit-1.0.4}/tskit.egg-info/entry_points.txt +0 -0
  93. {tskit-1.0.3 → tskit-1.0.4}/tskit.egg-info/requires.txt +0 -0
  94. {tskit-1.0.3 → tskit-1.0.4}/tskit.egg-info/top_level.txt +0 -0
{tskit-1.0.3/tskit.egg-info → tskit-1.0.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: tskit
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- Version: 1.0.3
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+ Version: 1.0.4
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  Summary: The tree sequence toolkit.
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  Author-email: Tskit Developers <admin@tskit.dev>
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  License-Expression: MIT
@@ -13,10 +13,10 @@ Keywords: population genetics,tree sequence,ancestral recombination graph,evolut
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  Classifier: Programming Language :: C
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  Classifier: Programming Language :: Python
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  Classifier: Programming Language :: Python :: 3
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- Classifier: Programming Language :: Python :: 3.11
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  Classifier: Programming Language :: Python :: 3.12
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  Classifier: Programming Language :: Python :: 3.13
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  Classifier: Programming Language :: Python :: 3.14
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+ Classifier: Programming Language :: Python :: 3.15
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  Classifier: Programming Language :: Python :: 3 :: Only
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  Classifier: Development Status :: 5 - Production/Stable
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  Classifier: Environment :: Other Environment
@@ -26,7 +26,7 @@ Classifier: Operating System :: MacOS :: MacOS X
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  Classifier: Operating System :: Microsoft :: Windows
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  Classifier: Topic :: Scientific/Engineering
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  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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- Requires-Python: >=3.11
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+ Requires-Python: >=3.12
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  Description-Content-Type: text/x-rst
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  License-File: LICENSE
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  Requires-Dist: jsonschema>=3.0.0