bella-companion 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

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Files changed (7) hide show
  1. bella_companion/eucovid/beast_configs/GLM.xml +6 -6
  2. bella_companion/eucovid/run_beast.py +2 -2
  3. {bella_companion-0.1.1.dist-info → bella_companion-0.1.3.dist-info}/METADATA +1 -1
  4. {bella_companion-0.1.1.dist-info → bella_companion-0.1.3.dist-info}/RECORD +6 -7
  5. bella_companion/.DS_Store +0 -0
  6. {bella_companion-0.1.1.dist-info → bella_companion-0.1.3.dist-info}/WHEEL +0 -0
  7. {bella_companion-0.1.1.dist-info → bella_companion-0.1.3.dist-info}/entry_points.txt +0 -0
bella_companion/eucovid/beast_configs/GLM.xml CHANGED
@@ -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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+ <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/eucovid/run_beast.py CHANGED
@@ -14,13 +14,13 @@ 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(
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  " ".join(
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  [
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- *os.environ["BELLA_RUN_BEAST_CMD"],
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+ os.environ["BELLA_RUN_BEAST_CMD"],
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  f"-seed {seed}",
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  f"-D msa_file={data_dir / 'msa.fasta'}",
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  f"-D changeTimesFile={data_dir / 'changetimes.csv'}",
{bella_companion-0.1.1.dist-info → bella_companion-0.1.3.dist-info}/METADATA 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: 0.1.1
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+ Version: 0.1.3
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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-0.1.1.dist-info → bella_companion-0.1.3.dist-info}/RECORD RENAMED
@@ -1,14 +1,13 @@
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- bella_companion/.DS_Store,sha256=1lFlJ5EFymdzGAUAaI30vcaaLHt3F1LwpG7xILf9jsM,6148
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  bella_companion/BELLA.jar,sha256=4mKDzPfz263rTqA9KS2f4Mc-UWGMuj8G48ZDonKSqVw,67408597
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  bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  bella_companion/cli.py,sha256=CrtV2CG6G1nKCCVu02gtNlpHNJHLnFtSaru-LFiHKKc,3014
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  bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
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- bella_companion/eucovid/beast_configs/GLM.xml,sha256=-SZWxJgJdBthp132ckPpRGooKoYfKKREi6VV3pF22aY,11532
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+ bella_companion/eucovid/beast_configs/GLM.xml,sha256=wm7aAa_4ALdzzYZIJdekClfDRZd6aMAOkLAAuNXYNMI,11496
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  bella_companion/eucovid/beast_configs/MLP.xml,sha256=C2d-Mcjw44CLFL-pCYgYdbZb1bNR-6OUBtaLWLUt5AU,10539
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  bella_companion/eucovid/data/changetimes.csv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
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  bella_companion/eucovid/data/flights.csv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
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  bella_companion/eucovid/data/msa.fasta,sha256=sWaVSINSJDDLjmwlpl31JWM5VnKF7yViSpERI69glQc,4839354
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- bella_companion/eucovid/run_beast.py,sha256=O9jULAMYIJOtQ_o4EQlG0Xh8s1Z2i27wmnGjYbvNWeM,1331
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+ bella_companion/eucovid/run_beast.py,sha256=61aPwb5eGA5suvUysSLwOYq-HfshBOQC6V17aFSUKLY,1333
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  bella_companion/features.py,sha256=xj0iwGHhLV_4jxLmG0M-jXWejuKVFJqpB0dK8Skc9n8,283
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  bella_companion/platyrrhine/__init__.py,sha256=gySgNPoKaEdhcZppKMsCmS-aAcYw_rDEw0viz72Udaw,259
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  bella_companion/platyrrhine/beast_config.xml,sha256=bLzavt-Zd8cmSgQQnlCBfZ9KyM7d1inOGx12VNjPFb4,7056
@@ -58,7 +57,7 @@ bella_companion/utils/explain/shap.py,sha256=ueCymQiVOcLIBy_Pf0yq7aOlI8ATehzhoxn
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  bella_companion/utils/explain/typeguards.py,sha256=U6N_lBosmXqFAiakB3zkjlHXzKd16e_cYkHLh76SSFY,591
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  bella_companion/utils/slurm.py,sha256=xEyf-Jxk8fy71t3fko_Ic9WtUFSdLFE3w4tR17gaBPw,1868
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  bella_companion/version.xml,sha256=Gr3nsYqFhVNP0Mszl_IfilxefsPN8ZpQlGlB8OJSwnE,522
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- bella_companion-0.1.1.dist-info/WHEEL,sha256=M6du7VZflc4UPsGphmOXHANdgk8zessdJG0DBUuoA-U,78
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- bella_companion-0.1.1.dist-info/entry_points.txt,sha256=Jmns5P9G0EXcV26VD5Na81SD2Fri_SiUISy9Rfz5ZYI,52
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- bella_companion-0.1.1.dist-info/METADATA,sha256=f_dbV3ST1DaBgVxI2t-cMnTN9U5197hPA8yGf4HN38U,472
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- bella_companion-0.1.1.dist-info/RECORD,,
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+ bella_companion-0.1.3.dist-info/WHEEL,sha256=M6du7VZflc4UPsGphmOXHANdgk8zessdJG0DBUuoA-U,78
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+ bella_companion-0.1.3.dist-info/entry_points.txt,sha256=Jmns5P9G0EXcV26VD5Na81SD2Fri_SiUISy9Rfz5ZYI,52
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+ bella_companion-0.1.3.dist-info/METADATA,sha256=TQM6EYAjz0H7eIwRRMpccHdLJIz0GfseUsVrBH7NzRw,472
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+ bella_companion-0.1.3.dist-info/RECORD,,
bella_companion/.DS_Store DELETED
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