tskit 1.0.0b2__tar.gz → 1.0.1__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-1.0.0b2/tskit.egg-info → tskit-1.0.1}/PKG-INFO +8 -8
  2. {tskit-1.0.0b2 → tskit-1.0.1}/_tskitmodule.c +4935 -7889
  3. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/core.c +75 -52
  4. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/core.h +50 -24
  5. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/genotypes.c +231 -8
  6. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/tables.c +47 -4
  7. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/tables.h +15 -1
  8. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/trees.c +333 -245
  9. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/trees.h +54 -5
  10. {tskit-1.0.0b2 → tskit-1.0.1}/pyproject.toml +7 -7
  11. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_balance_metrics.py +1 -1
  12. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_cli.py +1 -3
  13. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_combinatorics.py +5 -0
  14. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_divmat.py +48 -0
  15. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_fileobj.py +3 -0
  16. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_genotypes.py +619 -71
  17. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_highlevel.py +103 -17
  18. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_ibd.py +1 -1
  19. tskit-1.0.1/tests/test_immutable_table_collection.py +717 -0
  20. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_ld_matrix.py +30 -32
  21. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_lowlevel.py +273 -47
  22. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_metadata.py +29 -0
  23. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_phylo_formats.py +2 -6
  24. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_relatedness_vector.py +88 -22
  25. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_tables.py +476 -105
  26. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_threads.py +1 -1
  27. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_topology.py +104 -31
  28. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_wright_fisher.py +2 -2
  29. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/_version.py +1 -1
  30. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/combinatorics.py +6 -0
  31. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/drawing.py +2 -4
  32. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/exceptions.py +8 -0
  33. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/genotypes.py +23 -20
  34. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/metadata.py +105 -1
  35. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/tables.py +1043 -493
  36. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/text_formats.py +4 -0
  37. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/trees.py +440 -261
  38. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/util.py +6 -7
  39. {tskit-1.0.0b2 → tskit-1.0.1/tskit.egg-info}/PKG-INFO +8 -8
  40. {tskit-1.0.0b2 → tskit-1.0.1}/tskit.egg-info/SOURCES.txt +1 -0
  41. {tskit-1.0.0b2 → tskit-1.0.1}/tskit.egg-info/requires.txt +5 -5
  42. {tskit-1.0.0b2 → tskit-1.0.1}/LICENSE +0 -0
  43. {tskit-1.0.0b2 → tskit-1.0.1}/MANIFEST.in +0 -0
  44. {tskit-1.0.0b2 → tskit-1.0.1}/README.rst +0 -0
  45. {tskit-1.0.0b2 → tskit-1.0.1}/lib/subprojects/kastore/kastore.c +0 -0
  46. {tskit-1.0.0b2 → tskit-1.0.1}/lib/subprojects/kastore/kastore.h +0 -0
  47. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/convert.c +0 -0
  48. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/convert.h +0 -0
  49. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/genotypes.h +0 -0
  50. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/haplotype_matching.c +0 -0
  51. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/haplotype_matching.h +0 -0
  52. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/stats.c +0 -0
  53. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit/stats.h +0 -0
  54. {tskit-1.0.0b2 → tskit-1.0.1}/lib/tskit.h +0 -0
  55. {tskit-1.0.0b2 → tskit-1.0.1}/lwt_interface/tskit_lwt_interface.h +0 -0
  56. {tskit-1.0.0b2 → tskit-1.0.1}/setup.cfg +0 -0
  57. {tskit-1.0.0b2 → tskit-1.0.1}/setup.py +0 -0
  58. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_avl_tree.py +0 -0
  59. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_coalrate.py +0 -0
  60. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_dict_encoding.py +0 -0
  61. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_distance_metrics.py +0 -0
  62. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_drawing.py +0 -0
  63. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_extend_haplotypes.py +0 -0
  64. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_file_format.py +0 -0
  65. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_genotype_matching.py +0 -0
  66. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_haplotype_matching.py +0 -0
  67. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_intervals.py +0 -0
  68. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_jit.py +0 -0
  69. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_ms.py +0 -0
  70. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_parsimony.py +0 -0
  71. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_provenance.py +0 -0
  72. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_reference_sequence.py +0 -0
  73. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_stats.py +0 -0
  74. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_table_transforms.py +0 -0
  75. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_text_formats.py +0 -0
  76. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_tree_positioning.py +0 -0
  77. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_tree_stats.py +0 -0
  78. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_util.py +0 -0
  79. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_utilities.py +0 -0
  80. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_vcf.py +0 -0
  81. {tskit-1.0.0b2 → tskit-1.0.1}/tests/test_version.py +0 -0
  82. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/__init__.py +0 -0
  83. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/__main__.py +0 -0
  84. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/cli.py +0 -0
  85. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/intervals.py +0 -0
  86. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/jit/__init__.py +0 -0
  87. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/jit/numba.py +0 -0
  88. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/provenance.py +0 -0
  89. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/provenance.schema.json +0 -0
  90. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/stats.py +0 -0
  91. {tskit-1.0.0b2 → tskit-1.0.1}/tskit/vcf.py +0 -0
  92. {tskit-1.0.0b2 → tskit-1.0.1}/tskit.egg-info/dependency_links.txt +0 -0
  93. {tskit-1.0.0b2 → tskit-1.0.1}/tskit.egg-info/entry_points.txt +0 -0
  94. {tskit-1.0.0b2 → tskit-1.0.1}/tskit.egg-info/top_level.txt +0 -0
{tskit-1.0.0b2/tskit.egg-info → tskit-1.0.1}/PKG-INFO RENAMED
@@ -1,9 +1,9 @@
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  Metadata-Version: 2.4
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  Name: tskit
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- Version: 1.0.0b2
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+ Version: 1.0.1
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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: MIT
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+ License-Expression: MIT
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  Project-URL: Homepage, https://tskit.dev/tskit
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  Project-URL: Documentation, https://tskit.dev/tskit/docs/stable
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  Project-URL: Changelog, https://tskit.dev/tskit/docs/stable/changelogs.html
@@ -17,11 +17,11 @@ Classifier: Programming Language :: Python :: 3.10
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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 :: Only
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  Classifier: Development Status :: 5 - Production/Stable
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  Classifier: Environment :: Other Environment
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  Classifier: Intended Audience :: Science/Research
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- Classifier: License :: OSI Approved :: MIT License
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  Classifier: Operating System :: POSIX
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  Classifier: Operating System :: MacOS :: MacOS X
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  Classifier: Operating System :: Microsoft :: Windows
@@ -39,9 +39,9 @@ Requires-Dist: dendropy==5.0.1; extra == "test"
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  Requires-Dist: kastore==0.3.3; extra == "test"
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  Requires-Dist: lshmm==0.0.8; extra == "test"
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  Requires-Dist: msgpack==1.1.0; extra == "test"
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- Requires-Dist: msprime==1.3.4; extra == "test"
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+ Requires-Dist: msprime==1.4.0b2; extra == "test"
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  Requires-Dist: networkx==3.2.1; extra == "test"
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- Requires-Dist: numba==0.61.2; extra == "test"
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+ Requires-Dist: numba==0.63.1; extra == "test"
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  Requires-Dist: portion==2.6.0; extra == "test"
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  Requires-Dist: pytest==8.3.5; extra == "test"
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  Requires-Dist: pytest-cov==6.0.0; extra == "test"
@@ -57,8 +57,8 @@ Requires-Dist: breathe==4.35.0; extra == "docs"
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  Requires-Dist: sphinx-autodoc-typehints==2.3.0; extra == "docs"
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  Requires-Dist: sphinx-issues==5.0.0; extra == "docs"
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  Requires-Dist: sphinx-argparse==0.5.2; extra == "docs"
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- Requires-Dist: msprime==1.3.3; extra == "docs"
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- Requires-Dist: numba==0.61.2; extra == "docs"
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+ Requires-Dist: msprime==1.4.0b2; extra == "docs"
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+ Requires-Dist: numba==0.63.1; extra == "docs"
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  Requires-Dist: sphinx-book-theme; extra == "docs"
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  Requires-Dist: pandas==2.2.3; extra == "docs"
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  Provides-Extra: dev
@@ -84,7 +84,7 @@ Requires-Dist: tszip; extra == "dev"
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  Requires-Dist: xmlunittest; extra == "dev"
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  Requires-Dist: newick; extra == "dev"
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  Requires-Dist: zarr<3; extra == "dev"
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- Requires-Dist: jupyter-book; extra == "dev"
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+ Requires-Dist: jupyter-book<2; extra == "dev"
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  Requires-Dist: breathe; extra == "dev"
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  Requires-Dist: sphinx-autodoc-typehints; extra == "dev"
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  Requires-Dist: sphinx-issues; extra == "dev"