bella-companion 0.0.0__tar.gz
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- bella_companion-0.0.0/PKG-INFO +13 -0
- bella_companion-0.0.0/bella_companion/__init__.py +0 -0
- bella_companion-0.0.0/bella_companion/cli.py +24 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/__pycache__/run_beast.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/__pycache__/run_mlp.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/__pycache__/run_nonparametric.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/__pycache__/summarize_logs.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/data/body_mass.csv +1378 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/data/change_times.csv +22 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/data/sampling_change_times.csv +6 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/data/trees.nwk +100 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/figure.py +37 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/notbooks.ipynb +359 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/params.json +11 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/run_beast.py +54 -0
- bella_companion-0.0.0/bella_companion/fbd_empirical/summarize_logs.py +50 -0
- bella_companion-0.0.0/bella_companion/simulations/__init__.py +0 -0
- bella_companion-0.0.0/bella_companion/simulations/__pycache__/__init__.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/__pycache__/features.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/__pycache__/generate_data.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/__pycache__/run_beast.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/__pycache__/summarize_logs.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/features.py +7 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__init__.py +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/__init__.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/epi_explainations.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/epi_predictions.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/epi_simulations.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/fbd_explainations.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/fbd_predictions.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/fbd_simulations.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/figure1.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/plot.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/scenarios.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/__pycache__/utils.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/epi_explainations.py +101 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/epi_predictions.py +58 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/fbd_explainations.py +99 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/fbd_predictions.py +66 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/scenarios.py +87 -0
- bella_companion-0.0.0/bella_companion/simulations/figures/utils.py +250 -0
- bella_companion-0.0.0/bella_companion/simulations/generate_data.py +25 -0
- bella_companion-0.0.0/bella_companion/simulations/run_beast.py +92 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/__init__.py +20 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/__pycache__/__init__.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/__pycache__/common.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/__pycache__/scenario.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/__pycache__/utils.cpython-311.pyc +0 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/common.py +29 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/epi_multitype.py +68 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/epi_skyline.py +65 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/fbd_2traits.py +101 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/fbd_no_traits.py +71 -0
- bella_companion-0.0.0/bella_companion/simulations/scenarios/scenario.py +26 -0
- bella_companion-0.0.0/bella_companion/simulations/summarize_logs.py +39 -0
- bella_companion-0.0.0/bella_companion/utils.py +164 -0
- bella_companion-0.0.0/pyproject.toml +18 -0
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Metadata-Version: 2.1
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Name: bella-companion
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Version: 0.0.0
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Summary:
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Author: gabriele-marino
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Author-email: gabmarino.8601@gmail.com
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Requires-Python: >=3.10,<4.0
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Requires-Dist: dotenv (>=0.9.9,<0.10.0)
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Requires-Dist: phylogenie (>=2.1.21,<3.0.0)
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import argparse
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from dotenv import load_dotenv
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def main():
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load_dotenv()
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parser = argparse.ArgumentParser(prog="bella")
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subparsers = parser.add_subparsers(dest="command")
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gen_sim_data_parser = subparsers.add_parser("generate-simulations-data")
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generate_simulations_data_parser.set_defaults(func=generate_simulations_data)
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args = parser.parse_args()
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if hasattr(args, "func"):
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args.func(args)
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else:
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parser.print_help()
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def generate_simulations_data(args):
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print("Generating simulations data...")
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# your logic here
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