bella-companion 0.1.2__tar.gz → 0.1.4__tar.gz

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  1. {bella_companion-0.1.2 → bella_companion-0.1.4}/PKG-INFO +1 -1
  2. {bella_companion-0.1.2 → bella_companion-0.1.4}/pyproject.toml +1 -1
  3. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/eucovid/beast_configs/GLM.xml +7 -7
  4. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/eucovid/run_beast.py +1 -1
  5. {bella_companion-0.1.2 → bella_companion-0.1.4}/README.md +0 -0
  6. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/BELLA.jar +0 -0
  7. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/__init__.py +0 -0
  8. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/cli.py +0 -0
  9. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/eucovid/__init__.py +0 -0
  10. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/eucovid/beast_configs/MLP.xml +0 -0
  11. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/eucovid/data/changetimes.csv +0 -0
  12. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/eucovid/data/flights.csv +0 -0
  13. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/eucovid/data/msa.fasta +0 -0
  14. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/features.py +0 -0
  15. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/platyrrhine/__init__.py +0 -0
  16. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/platyrrhine/beast_config.xml +0 -0
  17. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/platyrrhine/data/change_times.csv +0 -0
  18. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/platyrrhine/data/traits.csv +0 -0
  19. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/platyrrhine/data/trees.nwk +0 -0
  20. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/platyrrhine/results.py +0 -0
  21. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/platyrrhine/run_beast.py +0 -0
  22. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/platyrrhine/summarize.py +0 -0
  23. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/__init__.py +0 -0
  24. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/epi-multitype/GLM.xml +0 -0
  25. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/epi-multitype/MLP.xml +0 -0
  26. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml +0 -0
  27. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/epi-skyline/GLM.xml +0 -0
  28. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/epi-skyline/MLP.xml +0 -0
  29. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml +0 -0
  30. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml +0 -0
  31. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml +0 -0
  32. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml +0 -0
  33. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml +0 -0
  34. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml +0 -0
  35. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml +0 -0
  36. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/figures/__init__.py +0 -0
  37. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/figures/epi_multitype.py +0 -0
  38. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/figures/epi_skyline.py +0 -0
  39. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/figures/fbd_2traits.py +0 -0
  40. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/figures/fbd_no_traits.py +0 -0
  41. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/figures/scenarios.py +0 -0
  42. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/figures/utils.py +0 -0
  43. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/generate_data.py +0 -0
  44. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/generate_figures.py +0 -0
  45. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/metrics.py +0 -0
  46. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/run_beast.py +0 -0
  47. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/scenarios/__init__.py +0 -0
  48. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/scenarios/common.py +0 -0
  49. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/scenarios/epi_multitype.py +0 -0
  50. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/scenarios/epi_skyline.py +0 -0
  51. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/scenarios/fbd_2traits.py +0 -0
  52. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/scenarios/fbd_no_traits.py +0 -0
  53. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/scenarios/scenario.py +0 -0
  54. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/simulations/summarize.py +0 -0
  55. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/utils/__init__.py +0 -0
  56. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/utils/beast.py +0 -0
  57. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/utils/explain/__init__.py +0 -0
  58. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/utils/explain/pdp.py +0 -0
  59. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/utils/explain/shap.py +0 -0
  60. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/utils/explain/typeguards.py +0 -0
  61. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/utils/slurm.py +0 -0
  62. {bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/version.xml +0 -0
{bella_companion-0.1.2 → bella_companion-0.1.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: bella-companion
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- Version: 0.1.2
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+ Version: 0.1.4
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  Summary: Bayesian Evolutionary Layered Learning Architectures (BELLA) companion
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  Author: gabriele-marino
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  Author-email: gabriele-marino <gabmarino.8601@gmail.com>
{bella_companion-0.1.2 → bella_companion-0.1.4}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "bella-companion"
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- version = "0.1.2"
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+ version = "0.1.4"
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  description = "Bayesian Evolutionary Layered Learning Architectures (BELLA) companion"
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  readme = "README.md"
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  authors = [
{bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/eucovid/beast_configs/GLM.xml RENAMED
@@ -94,27 +94,27 @@
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  </distribution>
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  <!-- Sampling proportion in China -->
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- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.1E-4 1.2E-4 1.3E-4 1.4E-4 1.5E-4">
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+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-4 1.2E-4 1.3E-4 1.4E-4 1.5E-4">
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  <Uniform name="distr" upper="0.024714828897338403"/>
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  </distribution>
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  <!-- Sampling proportion in China -->
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- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.11E-4 1.2E-4 1.3E-4 1.4E-4 1.5E-4">
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- <Uniform name="distr" upper="$1.8682742128337982e-4"/>
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+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.11E-4 1.2E-4 1.3E-4 1.4E-4 1.5E-4">
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+ <Uniform name="distr" upper="1.8682742128337982e-4"/>
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  </distribution>
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  <!-- Sampling proportion in France -->
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- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.1E-4 1.11E-4 1.3E-4 1.4E-4 1.5E-4">
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+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-4 1.11E-4 1.3E-4 1.4E-4 1.5E-4">
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  <Uniform name="distr" upper="0.09217877094972067"/>
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  </distribution>
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  <!-- Sampling proportion in Germany -->
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- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.1E-4 1.11E-4 1.2E-4 1.4E-4 1.5E-4">
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+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-4 1.11E-4 1.2E-4 1.4E-4 1.5E-4">
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  <Uniform name="distr" upper="0.01770956316410862"/>
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  </distribution>
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  <!-- Sampling proportion in Germany -->
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- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.1E-4 1.11E-4 1.2E-4 1.3E-4 1.5E-4">
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+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-4 1.11E-4 1.2E-4 1.3E-4 1.5E-4">
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  <Uniform name="distr" upper="0.002209756926738059"/>
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  </distribution>
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  <!-- Sampling proportion in EU -->
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- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportionValues" classesToExclude="1.1E-4 1.11E-4 1.2E-4 1.3E-4 1.4E-4">
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+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-4 1.11E-4 1.2E-4 1.3E-4 1.4E-4">
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  <Uniform name="distr" lower="0" upper="0.012770137524557957"/>
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  </distribution>
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{bella_companion-0.1.2 → bella_companion-0.1.4}/src/bella_companion/eucovid/run_beast.py RENAMED
@@ -14,7 +14,7 @@ def run_beast():
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  data_dir = Path(__file__).parent / "data"
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  beast_configs_dir = Path(__file__).parent / "beast_configs"
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- for seed, model in product(range(3), ["GLM", "MLP"]):
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+ for seed, model in product(range(1, 4), ["GLM", "MLP"]):
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  extra_data = '-D layersRange="0,1,2",nodes="16 8"' if model == "MLP" else ""
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  os.makedirs(output_dir / model, exist_ok=True)
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  submit_job(