bella-companion 0.0.42__py3-none-any.whl → 0.0.44__py3-none-any.whl

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Files changed (16) hide show
  1. bella_companion/BELLA.jar +0 -0
  2. bella_companion/cli.py +12 -0
  3. bella_companion/simulations/figures/__init__.py +4 -12
  4. bella_companion/simulations/figures/{epi_skyline_results.py → epi_skyline.py} +6 -7
  5. bella_companion/simulations/figures/explain/shap.py +13 -7
  6. bella_companion/simulations/figures/{fbd_no_traits_results.py → fbd_no_traits.py} +5 -5
  7. bella_companion/simulations/metrics.py +3 -2
  8. bella_companion/simulations/scenarios/fbd_2traits.py +1 -1
  9. bella_companion/version.xml +13 -0
  10. {bella_companion-0.0.42.dist-info → bella_companion-0.0.44.dist-info}/METADATA +1 -1
  11. {bella_companion-0.0.42.dist-info → bella_companion-0.0.44.dist-info}/RECORD +16 -14
  12. /bella_companion/simulations/figures/{epi_multitype_results.py → epi_multitype.py} +0 -0
  13. /bella_companion/simulations/figures/{fbd_2traits_results.py → fbd_2traits.py} +0 -0
  14. {bella_companion-0.0.42.dist-info → bella_companion-0.0.44.dist-info}/WHEEL +0 -0
  15. {bella_companion-0.0.42.dist-info → bella_companion-0.0.44.dist-info}/entry_points.txt +0 -0
  16. {bella_companion-0.0.42.dist-info → bella_companion-0.0.44.dist-info}/top_level.txt +0 -0
bella_companion/BELLA.jar ADDED
Binary file
bella_companion/cli.py CHANGED
@@ -15,6 +15,18 @@ from bella_companion.simulations import summarize_logs as summarize_simulations
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15
 
16
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  def main():
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  load_dotenv(Path(os.getcwd()) / ".env")
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+ os.environ["BELLA_RUN_BEAST_CMD"] = " ".join(
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+ [
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+ "java",
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+ os.getenv("JAVA_OPTIONS", ""),
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+ f"-jar {Path(__file__).parent / 'BELLA.jar'}",
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+ f"-version_file {Path(__file__).parent / 'version.xml'}",
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+ "-seed 42",
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+ "-overwrite",
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+ "-statefile /tmp/state",
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+ "-DFout /dev/null",
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+ ]
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+ )
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  parser = argparse.ArgumentParser(
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  prog="bella",
bella_companion/simulations/figures/__init__.py CHANGED
@@ -1,15 +1,7 @@
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- from bella_companion.simulations.figures.epi_multitype_results import (
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- plot_epi_multitype_results,
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- )
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- from bella_companion.simulations.figures.epi_skyline_results import (
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- plot_epi_skyline_results,
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- )
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- from bella_companion.simulations.figures.fbd_2traits_results import (
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- plot_fbd_2traits_results,
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- )
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- from bella_companion.simulations.figures.fbd_no_traits_results import (
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- plot_fbd_no_traits_results,
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- )
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+ from bella_companion.simulations.figures.epi_multitype import plot_epi_multitype_results
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+ from bella_companion.simulations.figures.epi_skyline import plot_epi_skyline_results
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+ from bella_companion.simulations.figures.fbd_2traits import plot_fbd_2traits_results
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+ from bella_companion.simulations.figures.fbd_no_traits import plot_fbd_no_traits_results
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  from bella_companion.simulations.figures.scenarios import plot_scenarios
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6
 
15
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  __all__ = [
bella_companion/simulations/figures/{epi_skyline_results.py → epi_skyline.py} RENAMED
@@ -14,8 +14,7 @@ from bella_companion.simulations.scenarios.epi_skyline import REPRODUCTION_NUMBE
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14
 
15
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  def plot_epi_skyline_results():
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- output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "epi-skyline-results"
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- os.makedirs(output_dir, exist_ok=True)
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+ base_output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "epi-skyline"
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18
 
20
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  for i, reproduction_number in enumerate(REPRODUCTION_NUMBERS, start=1):
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  summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"]) / f"epi-skyline_{i}"
@@ -26,6 +25,8 @@ def plot_epi_skyline_results():
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  }
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  true_values = {"reproductionNumberSP": reproduction_number}
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27
 
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+ output_dir = base_output_dir / str(i)
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+ os.makedirs(output_dir, exist_ok=True)
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  for log_summary in logs_summaries.values():
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  step(
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  [
@@ -35,12 +36,10 @@ def plot_epi_skyline_results():
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  )
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  step(reproduction_number, color="k", linestyle="--")
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  plt.ylabel("Reproduction number") # pyright: ignore
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- plt.savefig(output_dir / f"predictions-{i}.svg") # pyright: ignore
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+ plt.savefig(output_dir / "predictions.svg") # pyright: ignore
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  plt.close()
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41
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  plot_coverage_per_time_bin(
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- logs_summaries, true_values, output_dir / f"coverage-{i}.svg"
43
- )
44
- plot_maes_per_time_bin(
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- logs_summaries, true_values, output_dir / f"maes-{i}.svg"
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+ logs_summaries, true_values, output_dir / "coverage.svg"
46
44
  )
45
+ plot_maes_per_time_bin(logs_summaries, true_values, output_dir / "maes.svg")
bella_companion/simulations/figures/explain/shap.py CHANGED
@@ -1,6 +1,7 @@
1
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  from functools import partial
2
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  from itertools import product
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  from pathlib import Path
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+ from typing import Callable
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  import matplotlib.pyplot as plt
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  import numpy as np
@@ -43,13 +44,18 @@ def plot_shap_features_importance(
43
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  ) # shape: (n_runs, n_features)
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  features_importances /= features_importances.sum(axis=1, keepdims=True)
45
46
 
46
- for i, (feature_name, feature) in enumerate(features.items()):
47
- sns.violinplot(
48
- y=features_importances[:, i],
49
- x=[feature_name] * len(features_importances),
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- cut=0,
51
- color="#E74C3C" if feature.is_relevant else "gray",
52
- )
47
+ def _plot_violins(group_check: Callable[[Feature], bool]):
48
+ for i, (feature_name, feature) in enumerate(features.items()):
49
+ if group_check(feature):
50
+ sns.violinplot(
51
+ y=features_importances[:, i],
52
+ x=[feature_name] * len(features_importances),
53
+ cut=0,
54
+ color="#E74C3C" if feature.is_relevant else "gray",
55
+ )
56
+
57
+ _plot_violins(lambda f: not f.is_binary)
58
+ _plot_violins(lambda f: f.is_binary)
53
59
  plt.xlabel("Feature") # pyright: ignore
54
60
  plt.ylabel("Importance") # pyright: ignore
55
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  plt.savefig(output_file) # pyright: ignore
bella_companion/simulations/figures/{fbd_no_traits_results.py → fbd_no_traits.py} RENAMED
@@ -14,8 +14,7 @@ from bella_companion.simulations.scenarios.fbd_no_traits import RATES
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14
 
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  def plot_fbd_no_traits_results():
17
- output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "fbd-no-traits-predictions"
18
- os.makedirs(output_dir, exist_ok=True)
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+ base_output = Path(os.environ["BELLA_FIGURES_DIR"]) / "fbd-no-traits"
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  for i, rates in enumerate(RATES, start=1):
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  summaries_dir = (
@@ -28,6 +27,7 @@ def plot_fbd_no_traits_results():
28
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  }
29
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  true_values = {"birthRateSP": rates["birth"], "deathRateSP": rates["death"]}
30
29
 
30
+ output_dir = base_output / str(i)
31
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  for id, rate in true_values.items():
32
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  for log_summary in logs_summaries.values():
33
33
  step(
@@ -41,18 +41,18 @@ def plot_fbd_no_traits_results():
41
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  plt.ylabel( # pyright: ignore
42
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  r"$\lambda$" if id == "birthRateSP" else r"$\mu$"
43
43
  )
44
- plt.savefig(output_dir / f"{id}-predictions-{i}-.svg") # pyright: ignore
44
+ plt.savefig(output_dir / f"{id}-predictions.svg") # pyright: ignore
45
45
  plt.close()
46
46
 
47
47
  plot_coverage_per_time_bin(
48
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  logs_summaries,
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  true_values,
50
- output_dir / f"coverage-{i}.svg",
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+ output_dir / "coverage.svg",
51
51
  reverse_xticks=True,
52
52
  )
53
53
  plot_maes_per_time_bin(
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  logs_summaries,
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  true_values,
56
- output_dir / f"maes-{i}.svg",
56
+ output_dir / "maes.svg",
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57
  reverse_xticks=True,
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  )
bella_companion/simulations/metrics.py CHANGED
@@ -36,9 +36,10 @@ def _avg_ci_width(summary: pl.DataFrame, true_values: dict[str, float]) -> float
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36
 
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  def print_metrics():
39
+ base_summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"])
39
40
  metrics = {}
40
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  for name, scenario in SCENARIOS.items():
41
- summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"]) / name
42
+ summaries_dir = base_summaries_dir / name
42
43
  summaries = {
43
44
  Path(log_summary).stem: pl.read_csv(log_summary)
44
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  for log_summary in glob(str(summaries_dir / "*.csv"))
@@ -54,5 +55,5 @@ def print_metrics():
54
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  }
55
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  for target, true_values in scenario.targets.items()
56
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  }
57
- with open("simulation-metrics.json", "w") as f:
58
+ with open(base_summaries_dir / "sim-metrics.json", "w") as f:
58
59
  json.dump(metrics, f)
bella_companion/simulations/scenarios/fbd_2traits.py CHANGED
@@ -89,9 +89,9 @@ SCENARIO = Scenario(
89
89
  features={
90
90
  f"{rate}Rate": {
91
91
  "timePredictor": Feature(is_binary=False, is_relevant=True),
92
- "randomPredictor": Feature(is_binary=False, is_relevant=False),
93
92
  "trait1Predictor": Feature(is_binary=True, is_relevant=True),
94
93
  "trait2Predictor": Feature(is_binary=True, is_relevant=False),
94
+ "randomPredictor": Feature(is_binary=False, is_relevant=False),
95
95
  }
96
96
  for rate in RATES
97
97
  },
bella_companion/version.xml ADDED
@@ -0,0 +1,13 @@
1
+ <addon name='BELLA' version='0.0.1'>
2
+ <depends on="BEAST.base" atleast="2.7.0" atmost="2.7.9"/>
3
+ <depends on="BEAST.app" atleast="2.7.0" atmost="2.7.9"/>
4
+
5
+ <service type="beast.base.core.BEASTInterface">
6
+ <provider classname="bella.BayesMLP"/>
7
+ <provider classname="bella.ReLu"/>
8
+ <provider classname="bella.SoftPlus"/>
9
+ <provider classname="bella.Sigmoid"/>
10
+ <provider classname="bella.Tanh"/>
11
+ <provider classname="bella.SkylineNodeTreeLogger"/>
12
+ </service>
13
+ </addon>
{bella_companion-0.0.42.dist-info → bella_companion-0.0.44.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
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2
  Name: bella-companion
3
- Version: 0.0.42
3
+ Version: 0.0.44
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  Summary: Add your description here
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  Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
{bella_companion-0.0.42.dist-info → bella_companion-0.0.44.dist-info}/RECORD RENAMED
@@ -1,5 +1,7 @@
1
+ bella_companion/BELLA.jar,sha256=4mKDzPfz263rTqA9KS2f4Mc-UWGMuj8G48ZDonKSqVw,67408597
1
2
  bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
2
- bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
3
+ bella_companion/cli.py,sha256=2Xa49zHn85UfgsJ-hxsVfacfZDMTQZG0JatEtkFBO6k,2796
4
+ bella_companion/version.xml,sha256=Gr3nsYqFhVNP0Mszl_IfilxefsPN8ZpQlGlB8OJSwnE,522
3
5
  bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
4
6
  bella_companion/eucovid/run_beast.py,sha256=etaD_4SVdy_Pmz5s4jvDLzp2K_QV8leEY8Pe3xySBsk,3443
5
7
  bella_companion/eucovid/beast_configs/GLM.xml,sha256=b5rAeKVEam3u2AGSJsm7EHB6LcC0l9bp1SyZT2QyjpI,10892
@@ -33,7 +35,7 @@ bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZ
33
35
  bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
34
36
  bella_companion/simulations/generate_data.py,sha256=edfhXrs76hl30i_xizup4z6qgzXZyaDzX_PVC62Ytpw,849
35
37
  bella_companion/simulations/generate_figures.py,sha256=layMgoj3Bfl78Ceb1oE7YirAQ8zhjDyD9IrxDRXf6go,657
36
- bella_companion/simulations/metrics.py,sha256=duIkPb8cCXmIzjKA2yk9HLf4Y9eFIB_hRWaH05uIDws,1876
38
+ bella_companion/simulations/metrics.py,sha256=dg85Z5umewEzPXpfhQEEHtbQPCLT7LB0BEIPW8tAQYc,1934
37
39
  bella_companion/simulations/run_beast.py,sha256=qniy326i-vDCeHzzHpQRrSnY2ULqNNrO0z3GEsWx4Mc,3208
38
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  bella_companion/simulations/summarize_logs.py,sha256=Shf3Dx9k4lTbmO__MSLw-aIA8a8kTCXhbctBcV6Izug,1216
39
41
  bella_companion/simulations/beast_configs/epi-multitype/GLM.xml,sha256=VymAYsaZVuB3EPE0DCQSXpKepVq8pPjKaB5yhEpaVkE,4334
@@ -48,29 +50,29 @@ bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml,sha256=e
48
50
  bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml,sha256=Caq7Gxqx-wYAu3_YkMikVqni3DjBv1Wt00sc1Upo1X8,4743
49
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  bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml,sha256=JE_cGh2DW5yPAXyXXr0D3DlovmV-aIbze7qrhENHK3w,4275
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  bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml,sha256=m2xaHZwskCFInvVY1QH1fwQqH6p_fgESlPX2BbBeUhk,2822
51
- bella_companion/simulations/figures/__init__.py,sha256=aBYbJntH4egFmkSSWiVMYDEApXPYxJD7eA3TCPNNegM,658
52
- bella_companion/simulations/figures/epi_multitype_results.py,sha256=j85WgvN5AyAtX-CalMegr2lwlAZBmzyJxkikBPXRjCc,2629
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- bella_companion/simulations/figures/epi_skyline_results.py,sha256=gI5Ha-OIEShcZLmqVuy0W8hJzkrsydQE-Coa65_BFCo,1667
54
- bella_companion/simulations/figures/fbd_2traits_results.py,sha256=JiXrbYkH1HwdJQhTHXj6KhMEXYgQmQ6LmDboAIO1CPA,2728
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- bella_companion/simulations/figures/fbd_no_traits_results.py,sha256=fLsgpV3IbLLtxQEFNOL9K4jEEJrG324ziUM0rxIv7_k,1962
53
+ bella_companion/simulations/figures/__init__.py,sha256=LeHPeBb4vxJo0pxLZi_9s6iRBKvWC32yhAZBByqK2_8,590
54
+ bella_companion/simulations/figures/epi_multitype.py,sha256=j85WgvN5AyAtX-CalMegr2lwlAZBmzyJxkikBPXRjCc,2629
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+ bella_companion/simulations/figures/epi_skyline.py,sha256=5wPGpQujxnSPasetM9lU07Or5ZC5j_h-LfVs6jdDzWc,1677
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+ bella_companion/simulations/figures/fbd_2traits.py,sha256=JiXrbYkH1HwdJQhTHXj6KhMEXYgQmQ6LmDboAIO1CPA,2728
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+ bella_companion/simulations/figures/fbd_no_traits.py,sha256=Hh2wDQFtk5nQTRSgApmtamn5xenWC5XhAlIk_xhOSII,1935
56
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  bella_companion/simulations/figures/scenarios.py,sha256=gbMz1TUxxT2RSIq2kQlFioNdgSHk-gQY2OQuf6-7Fww,2817
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  bella_companion/simulations/figures/utils.py,sha256=0M5OrxaEuqcj9rR2uAc_O7utQvhEceZGH0sKrGRWaWs,3129
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  bella_companion/simulations/figures/explain/__init__.py,sha256=DnmVIWO65nTT5VsWnbS7NyYgKEY_eo4oMCtCY_ML2Vk,260
59
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  bella_companion/simulations/figures/explain/pdp.py,sha256=3n3ssgufW_43pn2hO5V5J_jgcJH3Fpb8stIRtTnlQ8w,3801
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- bella_companion/simulations/figures/explain/shap.py,sha256=qRfOMNwkU-hsBy5MHMTfVFAszaPESVOugCKQTVY8Q4Y,1940
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+ bella_companion/simulations/figures/explain/shap.py,sha256=1PkbCgynbW-PXkkRpIcY7JoBYqOxqmu1OEOif_roFY8,2207
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  bella_companion/simulations/scenarios/__init__.py,sha256=3Kl1lKcFpfb3vLX64DmSW4XCF5kXU1ZoHtstFH-ZIzU,876
62
64
  bella_companion/simulations/scenarios/common.py,sha256=_ddaSuTvEVdttGkXB4HPc2B7IB1F_GBOCW3cVOPZ-ZM,807
63
65
  bella_companion/simulations/scenarios/epi_multitype.py,sha256=fTkFeGHxyV_1f2nX3g_Oyr_e6wkorhXEicJjIAgeZKA,2439
64
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  bella_companion/simulations/scenarios/epi_skyline.py,sha256=JqnOVATECxBUqEbkR5lBlMI2O8k4hO6ipR8k9cHUsm0,2365
65
- bella_companion/simulations/scenarios/fbd_2traits.py,sha256=5UmrDlxdCMWOF0v9_0c1Yh0TyaE_FKEdxhSzHNofwQY,3541
67
+ bella_companion/simulations/scenarios/fbd_2traits.py,sha256=-amB3NX0GsVgYbFuHH71t93FuXUEnRUyhWf2Qpcpia4,3541
66
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  bella_companion/simulations/scenarios/fbd_no_traits.py,sha256=R6CH0fVeQg-Iesl39pq2uY8ICVEO4VZbvUVUCGwauJU,2520
67
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  bella_companion/simulations/scenarios/scenario.py,sha256=_FRWAyOFbw94lAzd3zCD-1ek4TrssoiXfXRQPShLiIA,620
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  bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7UpYw,480
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  bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
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  bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
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  bella_companion/utils/slurm.py,sha256=xEyf-Jxk8fy71t3fko_Ic9WtUFSdLFE3w4tR17gaBPw,1868
72
- bella_companion-0.0.42.dist-info/METADATA,sha256=FY_Ja-RMCMyymPVti1WDLQLOtd5ie4rzWl3Zjj6ZJCg,347
73
- bella_companion-0.0.42.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
74
- bella_companion-0.0.42.dist-info/entry_points.txt,sha256=SVEYDBrkBWPrOGwnEH2aO5TSVIAvfKE37sqm-9ut9jg,51
75
- bella_companion-0.0.42.dist-info/top_level.txt,sha256=q0loZYv4vf3zF_tOATyAJqeyLOEuPyLbObNqIGP7Fmc,16
76
- bella_companion-0.0.42.dist-info/RECORD,,
74
+ bella_companion-0.0.44.dist-info/METADATA,sha256=yLCkFJaRBy303yaBpSoeoOOlzpPanoTybeG7PFr1sf0,347
75
+ bella_companion-0.0.44.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
76
+ bella_companion-0.0.44.dist-info/entry_points.txt,sha256=SVEYDBrkBWPrOGwnEH2aO5TSVIAvfKE37sqm-9ut9jg,51
77
+ bella_companion-0.0.44.dist-info/top_level.txt,sha256=q0loZYv4vf3zF_tOATyAJqeyLOEuPyLbObNqIGP7Fmc,16
78
+ bella_companion-0.0.44.dist-info/RECORD,,