repare 0.1.0__tar.gz → 0.1.1__tar.gz

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  1. {repare-0.1.0 → repare-0.1.1}/PKG-INFO +4 -3
  2. {repare-0.1.0 → repare-0.1.1}/README.md +2 -2
  3. {repare-0.1.0 → repare-0.1.1}/pyproject.toml +3 -0
  4. {repare-0.1.0 → repare-0.1.1}/src/repare.egg-info/PKG-INFO +4 -3
  5. {repare-0.1.0 → repare-0.1.1}/.gitattributes +0 -0
  6. {repare-0.1.0 → repare-0.1.1}/.gitignore +0 -0
  7. {repare-0.1.0 → repare-0.1.1}/.pre-commit-config.yaml +0 -0
  8. {repare-0.1.0 → repare-0.1.1}/LICENSE +0 -0
  9. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/compare_gurgy_pedigrees.py +0 -0
  10. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/compare_nepluyevsky_pedigrees.py +0 -0
  11. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/gurgy/citation.md +0 -0
  12. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/gurgy/inferred_relations_READv2.csv +0 -0
  13. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/gurgy/nodes.csv +0 -0
  14. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/gurgy/published_exact_relations.csv +0 -0
  15. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/hazleton_north/citation.md +0 -0
  16. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/hazleton_north/inferred_relations_coeffs.csv +0 -0
  17. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/hazleton_north/inferred_relations_custom.csv +0 -0
  18. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/hazleton_north/nodes.csv +0 -0
  19. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/hazleton_north/published_exact_relations.csv +0 -0
  20. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/nepluyevsky/citation.md +0 -0
  21. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/nepluyevsky/inferred_relations_KIN.csv +0 -0
  22. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/nepluyevsky/inferred_relations_custom.csv +0 -0
  23. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/nepluyevsky/nodes.csv +0 -0
  24. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/data/nepluyevsky/published_exact_relations.csv +0 -0
  25. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/evaluator/__init__.py +0 -0
  26. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/evaluator/comparison_utils.py +0 -0
  27. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/evaluator/pedigree_evaluator.py +0 -0
  28. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/gurgy_comparison/inferred_pedigree.svg +0 -0
  29. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/gurgy_comparison/inferred_pedigree_repositioned_cropped.pdf +0 -0
  30. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/gurgy_comparison/inferred_pedigree_repositioned_cropped.svg +0 -0
  31. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/gurgy_comparison/published_pedigree.svg +0 -0
  32. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/gurgy_comparison/published_pedigree_cropped.pdf +0 -0
  33. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/gurgy_comparison/published_pedigree_cropped.svg +0 -0
  34. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/gurgy_comparison/relation_differences.csv +0 -0
  35. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/nepluyevsky_comparison/inferred_pedigree.svg +0 -0
  36. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/nepluyevsky_comparison/inferred_pedigree_cropped.pdf +0 -0
  37. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/nepluyevsky_comparison/inferred_pedigree_cropped.svg +0 -0
  38. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/nepluyevsky_comparison/published_pedigree.svg +0 -0
  39. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/nepluyevsky_comparison/published_pedigree_cropped.pdf +0 -0
  40. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/nepluyevsky_comparison/published_pedigree_cropped.svg +0 -0
  41. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/nepluyevsky_comparison/relation_differences.csv +0 -0
  42. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/results/results.csv +0 -0
  43. {repare-0.1.0 → repare-0.1.1}/benchmarks/published/run_evaluations.py +0 -0
  44. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/plot_parameter_data.py +0 -0
  45. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/plot_sampling_data.py +0 -0
  46. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.0_error_rate_scale=0.0.csv +0 -0
  47. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.0_error_rate_scale=0.5.csv +0 -0
  48. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.0_error_rate_scale=1.0.csv +0 -0
  49. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.0_error_rate_scale=2.0.csv +0 -0
  50. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.2_error_rate_scale=0.0.csv +0 -0
  51. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.2_error_rate_scale=0.5.csv +0 -0
  52. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.2_error_rate_scale=1.0.csv +0 -0
  53. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.2_error_rate_scale=2.0.csv +0 -0
  54. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.4_error_rate_scale=0.0.csv +0 -0
  55. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.4_error_rate_scale=0.5.csv +0 -0
  56. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.4_error_rate_scale=1.0.csv +0 -0
  57. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.4_error_rate_scale=2.0.csv +0 -0
  58. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.6_error_rate_scale=0.0.csv +0 -0
  59. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.6_error_rate_scale=0.5.csv +0 -0
  60. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.6_error_rate_scale=1.0.csv +0 -0
  61. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.6_error_rate_scale=2.0.csv +0 -0
  62. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/plots/degree_f1_heatmap.pdf +0 -0
  63. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/plots/pedigree_summary_statistics.pdf +0 -0
  64. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/parameter_experiment/plots/relation_f1_heatmap.pdf +0 -0
  65. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10000_epsilon=0.0.csv +0 -0
  66. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10000_epsilon=0.2.csv +0 -0
  67. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10000_epsilon=0.4.csv +0 -0
  68. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=1000_epsilon=0.0.csv +0 -0
  69. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=1000_epsilon=0.2.csv +0 -0
  70. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=1000_epsilon=0.4.csv +0 -0
  71. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=100_epsilon=0.0.csv +0 -0
  72. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=100_epsilon=0.2.csv +0 -0
  73. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=100_epsilon=0.4.csv +0 -0
  74. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10_epsilon=0.0.csv +0 -0
  75. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10_epsilon=0.2.csv +0 -0
  76. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10_epsilon=0.4.csv +0 -0
  77. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/plots/degree_f1_heatmap.pdf +0 -0
  78. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/results/sampling_experiment/plots/relation_f1_heatmap.pdf +0 -0
  79. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/run_parameter_experiment.py +0 -0
  80. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/run_sampling_experiment.py +0 -0
  81. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/simulator/__init__.py +0 -0
  82. {repare-0.1.0 → repare-0.1.1}/benchmarks/simulations/simulator/simulated_pedigree.py +0 -0
  83. {repare-0.1.0 → repare-0.1.1}/examples/algorithm_diagram.svg +0 -0
  84. {repare-0.1.0 → repare-0.1.1}/examples/nodes.csv +0 -0
  85. {repare-0.1.0 → repare-0.1.1}/examples/outputs/corrected_input_relations.csv +0 -0
  86. {repare-0.1.0 → repare-0.1.1}/examples/outputs/reconstructed_exact_relations.csv +0 -0
  87. {repare-0.1.0 → repare-0.1.1}/examples/outputs/reconstructed_pedigree.pdf +0 -0
  88. {repare-0.1.0 → repare-0.1.1}/examples/relations.csv +0 -0
  89. {repare-0.1.0 → repare-0.1.1}/examples/repare.sh +0 -0
  90. {repare-0.1.0 → repare-0.1.1}/pixi.lock +0 -0
  91. {repare-0.1.0 → repare-0.1.1}/setup.cfg +0 -0
  92. {repare-0.1.0 → repare-0.1.1}/src/repare/__init__.py +0 -0
  93. {repare-0.1.0 → repare-0.1.1}/src/repare/main.py +0 -0
  94. {repare-0.1.0 → repare-0.1.1}/src/repare/pedigree.py +0 -0
  95. {repare-0.1.0 → repare-0.1.1}/src/repare/pedigree_reconstructor.py +0 -0
  96. {repare-0.1.0 → repare-0.1.1}/src/repare.egg-info/SOURCES.txt +0 -0
  97. {repare-0.1.0 → repare-0.1.1}/src/repare.egg-info/dependency_links.txt +0 -0
  98. {repare-0.1.0 → repare-0.1.1}/src/repare.egg-info/entry_points.txt +0 -0
  99. {repare-0.1.0 → repare-0.1.1}/src/repare.egg-info/requires.txt +0 -0
  100. {repare-0.1.0 → repare-0.1.1}/src/repare.egg-info/top_level.txt +0 -0
{repare-0.1.0 → repare-0.1.1}/PKG-INFO RENAMED
@@ -1,9 +1,10 @@
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  Metadata-Version: 2.4
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  Name: repare
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- Version: 0.1.0
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+ Version: 0.1.1
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  Summary: Reconstruct (ancient) pedigrees from pairwise kinship relations.
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  Author-email: Edward Huang <edwardhuangc@gmail.com>
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  License-Expression: MIT
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+ Project-URL: Source, https://github.com/ehuangc/repare
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  Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
@@ -18,7 +19,7 @@ Provides-Extra: plot
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  Requires-Dist: pygraphviz; extra == "plot"
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  Dynamic: license-file
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- :evergreen_tree: **repare** is a Python package for (ancient) pedigree reconstruction.
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+ 🌲 **repare** is a Python package for (ancient) pedigree reconstruction.
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  ## Installation
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@@ -99,7 +100,7 @@ repare -n NODES -r RELATIONS [-o OUTPUT] [-m MAX_CANDIDATE_PEDIGREES] [-e EPSILO
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  **Verbose** (-v) (*flag*): If set, enable verbose output (INFO-level logging).
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  <p align="center">
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- <img src="examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" width="600" />
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+ <img src="https://raw.githubusercontent.com/ehuangc/repare/main/examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" />
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  <br>
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  <em>Diagram of repare's pedigree reconstruction process</em>
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  </p>
{repare-0.1.0 → repare-0.1.1}/README.md RENAMED
@@ -1,4 +1,4 @@
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- :evergreen_tree: **repare** is a Python package for (ancient) pedigree reconstruction.
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+ 🌲 **repare** is a Python package for (ancient) pedigree reconstruction.
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  ## Installation
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  **Verbose** (-v) (*flag*): If set, enable verbose output (INFO-level logging).
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  <p align="center">
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- <img src="examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" width="600" />
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+ <img src="https://raw.githubusercontent.com/ehuangc/repare/main/examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" />
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  <br>
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  <em>Diagram of repare's pedigree reconstruction process</em>
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  </p>
{repare-0.1.0 → repare-0.1.1}/pyproject.toml RENAMED
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  license = "MIT"
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  license-files = ["LICENSE"]
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+ [project.urls]
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+ Source = "https://github.com/ehuangc/repare"
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  [project.optional-dependencies]
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  benchmark = ["scikit-learn", "seaborn"]
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  plot = ["pygraphviz"]
{repare-0.1.0 → repare-0.1.1}/src/repare.egg-info/PKG-INFO RENAMED
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  Metadata-Version: 2.4
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  Name: repare
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- Version: 0.1.0
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+ Version: 0.1.1
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  Summary: Reconstruct (ancient) pedigrees from pairwise kinship relations.
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  Author-email: Edward Huang <edwardhuangc@gmail.com>
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  License-Expression: MIT
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+ Project-URL: Source, https://github.com/ehuangc/repare
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  Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: pygraphviz; extra == "plot"
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  Dynamic: license-file
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- :evergreen_tree: **repare** is a Python package for (ancient) pedigree reconstruction.
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+ 🌲 **repare** is a Python package for (ancient) pedigree reconstruction.
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  ## Installation
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  **Verbose** (-v) (*flag*): If set, enable verbose output (INFO-level logging).
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  <p align="center">
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- <img src="examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" width="600" />
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+ <img src="https://raw.githubusercontent.com/ehuangc/repare/main/examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" />
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  <br>
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  <em>Diagram of repare's pedigree reconstruction process</em>
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  </p>
{repare-0.1.0 → repare-0.1.1}/.gitattributes RENAMED
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