bella-companion 0.0.8__tar.gz → 0.0.9__tar.gz

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  1. {bella_companion-0.0.8 → bella_companion-0.0.9}/PKG-INFO +1 -1
  2. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/run_beast.py +6 -6
  3. {bella_companion-0.0.8 → bella_companion-0.0.9}/pyproject.toml +1 -1
  4. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/__init__.py +0 -0
  5. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/cli.py +0 -0
  6. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/__init__.py +0 -0
  7. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/__pycache__/run_beast.cpython-311.pyc +0 -0
  8. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/__pycache__/run_mlp.cpython-311.pyc +0 -0
  9. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/__pycache__/run_nonparametric.cpython-311.pyc +0 -0
  10. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/__pycache__/summarize_logs.cpython-311.pyc +0 -0
  11. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/data/body_mass.csv +0 -0
  12. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/data/change_times.csv +0 -0
  13. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/data/sampling_change_times.csv +0 -0
  14. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/data/trees.nwk +0 -0
  15. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/notbooks.ipynb +0 -0
  16. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/summarize_logs.py +0 -0
  17. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/__init__.py +0 -0
  18. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/__pycache__/__init__.cpython-310.pyc +0 -0
  19. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/__pycache__/__init__.cpython-311.pyc +0 -0
  20. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/__pycache__/features.cpython-310.pyc +0 -0
  21. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/__pycache__/features.cpython-311.pyc +0 -0
  22. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/__pycache__/generate_data.cpython-310.pyc +0 -0
  23. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/__pycache__/generate_data.cpython-311.pyc +0 -0
  24. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/__pycache__/run_beast.cpython-311.pyc +0 -0
  25. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/__pycache__/summarize_logs.cpython-311.pyc +0 -0
  26. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/features.py +0 -0
  27. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__init__.py +0 -0
  28. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/__init__.cpython-311.pyc +0 -0
  29. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/epi_explainations.cpython-311.pyc +0 -0
  30. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/epi_predictions.cpython-311.pyc +0 -0
  31. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/epi_simulations.cpython-311.pyc +0 -0
  32. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/fbd_explainations.cpython-311.pyc +0 -0
  33. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/fbd_predictions.cpython-311.pyc +0 -0
  34. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/fbd_simulations.cpython-311.pyc +0 -0
  35. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/figure1.cpython-311.pyc +0 -0
  36. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/plot.cpython-311.pyc +0 -0
  37. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/scenarios.cpython-311.pyc +0 -0
  38. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/__pycache__/utils.cpython-311.pyc +0 -0
  39. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/epi_multitype_results.py +0 -0
  40. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/epi_skyline_results.py +0 -0
  41. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/explain/__init__.py +0 -0
  42. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/explain/pdp.py +0 -0
  43. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/explain/shap.py +0 -0
  44. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/fbd_2traits_results.py +0 -0
  45. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/fbd_no_traits_results.py +0 -0
  46. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/scenarios.py +0 -0
  47. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/figures/utils.py +0 -0
  48. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/generate_data.py +0 -0
  49. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/generate_figures.py +0 -0
  50. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/metrics.py +0 -0
  51. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/run_beast.py +0 -0
  52. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__init__.py +0 -0
  53. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/__init__.cpython-310.pyc +0 -0
  54. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/__init__.cpython-311.pyc +0 -0
  55. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/common.cpython-310.pyc +0 -0
  56. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/common.cpython-311.pyc +0 -0
  57. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-310.pyc +0 -0
  58. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-311.pyc +0 -0
  59. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-310.pyc +0 -0
  60. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-311.pyc +0 -0
  61. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-310.pyc +0 -0
  62. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-311.pyc +0 -0
  63. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-310.pyc +0 -0
  64. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-311.pyc +0 -0
  65. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/scenario.cpython-310.pyc +0 -0
  66. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/scenario.cpython-311.pyc +0 -0
  67. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/__pycache__/utils.cpython-311.pyc +0 -0
  68. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/common.py +0 -0
  69. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/epi_multitype.py +0 -0
  70. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/epi_skyline.py +0 -0
  71. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/fbd_2traits.py +0 -0
  72. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/fbd_no_traits.py +0 -0
  73. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/scenarios/scenario.py +0 -0
  74. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/simulations/summarize_logs.py +0 -0
  75. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/utils/__init__.py +0 -0
  76. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/utils/beast.py +0 -0
  77. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/utils/explain.py +0 -0
  78. {bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/utils/slurm.py +0 -0
{bella_companion-0.0.8 → bella_companion-0.0.9}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: bella-companion
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- Version: 0.0.8
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+ Version: 0.0.9
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  Summary:
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  Author: gabriele-marino
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  Author-email: gabmarino.8601@gmail.com
{bella_companion-0.0.8 → bella_companion-0.0.9}/bella_companion/fbd_empirical/run_beast.py RENAMED
@@ -38,12 +38,12 @@ def run_beast():
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  os.environ["BELLA_RUN_BEAST_CMD"],
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  f"-D types=0,1,2,3",
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  f'-D startTypePriorProbs="0.25 0.25 0.25 0.25"',
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- f"-D birthRateUpper=10",
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- f"-D deathRateUpper=10",
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- f"-D samplingRateUpper=10",
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- f'-D samplingRateInit="5 5 5 5 5 5 5"',
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- f"-D migrationRateUpper=10",
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- f'-D migrationRateInit="5 0 0 5 5 0 0 5 5 0 0 5"',
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+ f"-D birthRateUpper=5",
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+ f"-D deathRateUpper=5",
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+ f"-D samplingRateUpper=5",
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+ f'-D samplingRateInit="2.5 2.5 2.5 2.5 2.5 2.5 2.5"',
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+ f"-D migrationRateUpper=5",
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+ f'-D migrationRateInit="2.5 0 0 2.5 2.5 0 0 2.5 2.5 0 0 2.5"',
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  f'-D nodes="16 8"',
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  f'-D layersRange="0,1,2"',
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  f"-D treeFile={tree_file}",
{bella_companion-0.0.8 → bella_companion-0.0.9}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "bella-companion"
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- version = "0.0.8"
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+ version = "0.0.9"
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  description = ""
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  authors = ["gabriele-marino <gabmarino.8601@gmail.com>"]
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