bella-companion 0.0.22__tar.gz → 0.0.24__tar.gz

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  1. {bella_companion-0.0.22 → bella_companion-0.0.24}/PKG-INFO +1 -1
  2. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/beast_configs/MLP.xml +0 -4
  3. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/run_beast.py +5 -5
  4. {bella_companion-0.0.22 → bella_companion-0.0.24}/pyproject.toml +1 -1
  5. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/__init__.py +0 -0
  6. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/cli.py +0 -0
  7. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/__init__.py +0 -0
  8. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/beast_configs/GLM.xml +0 -0
  9. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/beast_configs/Nonparametric.xml +0 -0
  10. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/case_data.tsv +0 -0
  11. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/change_dates.tsv +0 -0
  12. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/msa.fasta +0 -0
  13. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/osi.tsv +0 -0
  14. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/all/closedborders_7e_nt.tsv +0 -0
  15. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/all/dist_7e_ls.tsv +0 -0
  16. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/all/flight_7e_ls.tsv +0 -0
  17. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/all/flight_pop_x_7e_ls.tsv +0 -0
  18. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/all/osi_x_7e_ls.tsv +0 -0
  19. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/all/osi_y_7e_ls.tsv +0 -0
  20. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/all/pop_x_7e_ls.tsv +0 -0
  21. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/all/pop_y_7e_ls.tsv +0 -0
  22. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv +0 -0
  23. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv +0 -0
  24. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv +0 -0
  25. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv +0 -0
  26. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/platyrrhine/__init__.py +0 -0
  27. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/platyrrhine/beast_config.xml +0 -0
  28. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/platyrrhine/data/change_times.csv +0 -0
  29. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/platyrrhine/data/traits.csv +0 -0
  30. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/platyrrhine/data/trees.nwk +0 -0
  31. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/platyrrhine/results.py +0 -0
  32. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/platyrrhine/run_beast.py +0 -0
  33. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/platyrrhine/summarize_logs.py +0 -0
  34. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/__init__.py +0 -0
  35. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/__pycache__/__init__.cpython-310.pyc +0 -0
  36. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/__pycache__/__init__.cpython-311.pyc +0 -0
  37. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/__pycache__/features.cpython-310.pyc +0 -0
  38. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/__pycache__/features.cpython-311.pyc +0 -0
  39. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/__pycache__/generate_data.cpython-310.pyc +0 -0
  40. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/__pycache__/generate_data.cpython-311.pyc +0 -0
  41. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/__pycache__/run_beast.cpython-311.pyc +0 -0
  42. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/__pycache__/summarize_logs.cpython-311.pyc +0 -0
  43. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/epi-multitype/GLM.xml +0 -0
  44. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/epi-multitype/MLP.xml +0 -0
  45. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml +0 -0
  46. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/epi-skyline/GLM.xml +0 -0
  47. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/epi-skyline/MLP.xml +0 -0
  48. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml +0 -0
  49. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml +0 -0
  50. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml +0 -0
  51. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml +0 -0
  52. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml +0 -0
  53. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml +0 -0
  54. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml +0 -0
  55. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/features.py +0 -0
  56. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__init__.py +0 -0
  57. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/__init__.cpython-311.pyc +0 -0
  58. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/epi_explainations.cpython-311.pyc +0 -0
  59. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/epi_predictions.cpython-311.pyc +0 -0
  60. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/epi_simulations.cpython-311.pyc +0 -0
  61. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/fbd_explainations.cpython-311.pyc +0 -0
  62. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/fbd_predictions.cpython-311.pyc +0 -0
  63. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/fbd_simulations.cpython-311.pyc +0 -0
  64. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/figure1.cpython-311.pyc +0 -0
  65. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/plot.cpython-311.pyc +0 -0
  66. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/scenarios.cpython-311.pyc +0 -0
  67. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/__pycache__/utils.cpython-311.pyc +0 -0
  68. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/epi_multitype_results.py +0 -0
  69. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/epi_skyline_results.py +0 -0
  70. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/explain/__init__.py +0 -0
  71. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/explain/pdp.py +0 -0
  72. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/explain/shap.py +0 -0
  73. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/fbd_2traits_results.py +0 -0
  74. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/fbd_no_traits_results.py +0 -0
  75. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/scenarios.py +0 -0
  76. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/figures/utils.py +0 -0
  77. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/generate_data.py +0 -0
  78. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/generate_figures.py +0 -0
  79. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/metrics.py +0 -0
  80. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/run_beast.py +0 -0
  81. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__init__.py +0 -0
  82. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/__init__.cpython-310.pyc +0 -0
  83. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/__init__.cpython-311.pyc +0 -0
  84. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/common.cpython-310.pyc +0 -0
  85. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/common.cpython-311.pyc +0 -0
  86. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-310.pyc +0 -0
  87. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-311.pyc +0 -0
  88. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-310.pyc +0 -0
  89. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-311.pyc +0 -0
  90. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-310.pyc +0 -0
  91. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-311.pyc +0 -0
  92. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-310.pyc +0 -0
  93. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-311.pyc +0 -0
  94. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/scenario.cpython-310.pyc +0 -0
  95. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/scenario.cpython-311.pyc +0 -0
  96. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/__pycache__/utils.cpython-311.pyc +0 -0
  97. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/common.py +0 -0
  98. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/epi_multitype.py +0 -0
  99. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/epi_skyline.py +0 -0
  100. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/fbd_2traits.py +0 -0
  101. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/fbd_no_traits.py +0 -0
  102. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/scenarios/scenario.py +0 -0
  103. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/simulations/summarize_logs.py +0 -0
  104. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/utils/__init__.py +0 -0
  105. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/utils/beast.py +0 -0
  106. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/utils/explain.py +0 -0
  107. {bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/utils/slurm.py +0 -0
{bella_companion-0.0.22 → bella_companion-0.0.24}/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: 0.0.22
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+ Version: 0.0.24
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  Summary:
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  Author: gabriele-marino
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  Author-email: gabmarino.8601@gmail.com
{bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/beast_configs/MLP.xml RENAMED
@@ -175,10 +175,6 @@
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  <log idref="samplingProportionSP"/>
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  <log idref="migrationRateSP"/>
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  <log idref="migrationRate"/>
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- <plate var="n" range="$(layersRange)">
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- <log idref="migrationW$(n)"/>
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- </plate>
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-
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  <log spec="TypedTreeStatsLogger" includeRootEdge="true" typeLabel="type" typeSet="@typeSet">
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  <typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
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  </log>
{bella_companion-0.0.22 → bella_companion-0.0.24}/bella_companion/eucovid/run_beast.py RENAMED
@@ -47,7 +47,7 @@ def run_beast():
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  ]
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  ),
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  base_log_dir / "Nonparametric",
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- mem_per_cpu="12000",
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+ mem_per_cpu="64000",
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  )
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  os.makedirs(output_dir / "all-predictors-GLM", exist_ok=True)
@@ -62,7 +62,7 @@ def run_beast():
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  ]
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  ),
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  base_log_dir / "all-predictors-GLM",
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- mem_per_cpu="12000",
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+ mem_per_cpu="64000",
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  )
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  os.makedirs(output_dir / "flights-GLM", exist_ok=True)
@@ -77,7 +77,7 @@ def run_beast():
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  ]
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  ),
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  base_log_dir / "flights-GLM",
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+ mem_per_cpu="64000",
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  )
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  os.makedirs(output_dir / "all-predictors-MLP", exist_ok=True)
@@ -93,7 +93,7 @@ def run_beast():
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  ),
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  base_log_dir / "all-predictors-MLP",
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- mem_per_cpu="12000",
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+ mem_per_cpu="64000",
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  )
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  os.makedirs(output_dir / "flights-MLP", exist_ok=True)
@@ -109,7 +109,7 @@ def run_beast():
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  ),
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  base_log_dir / "flights-MLP",
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- mem_per_cpu="12000",
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+ mem_per_cpu="64000",
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  )
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  with open(base_output_dir / "eucovid_job_ids.json", "w") as f:
{bella_companion-0.0.22 → bella_companion-0.0.24}/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 = "0.0.22"
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+ version = "0.0.24"
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  description = ""
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  authors = ["gabriele-marino <gabmarino.8601@gmail.com>"]
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