bella-companion 0.0.29__py3-none-any.whl → 0.0.30__py3-none-any.whl

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Files changed (7) hide show
  1. bella_companion/eucovid/beast_configs/GLM.xml +6 -5
  2. bella_companion/eucovid/run_beast.py +5 -11
  3. bella_companion/platyrrhine/run_beast.py +1 -6
  4. {bella_companion-0.0.29.dist-info → bella_companion-0.0.30.dist-info}/METADATA +1 -1
  5. {bella_companion-0.0.29.dist-info → bella_companion-0.0.30.dist-info}/RECORD +7 -7
  6. {bella_companion-0.0.29.dist-info → bella_companion-0.0.30.dist-info}/WHEEL +0 -0
  7. {bella_companion-0.0.29.dist-info → bella_companion-0.0.30.dist-info}/entry_points.txt +0 -0
bella_companion/eucovid/beast_configs/GLM.xml CHANGED
@@ -109,11 +109,12 @@
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  <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
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  <Uniform name="distr" lower="0" upper="0.057"/>
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  </distribution>
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- <plate var="n" range="$(layersRange)">
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- <prior name="distribution" x="@migrationW$(n)">
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- <Normal name="distr" mean="0.0" sigma="1.0"/>
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- </prior>
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- </plate>
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+ <prior name="distribution" x="@migrationRateW">
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+ <Normal name="distr" mean="0.0" sigma="1.0"/>
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+ </prior>
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+ <prior name="distribution" x="@migrationRateScaler">
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+ <LogNormal name="distr" M="0.0" S="0.8"/>
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+ </prior>
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  <prior name="distribution" x="@gammaShape">
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  <Exponential name="distr" mean="0.5"/>
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  </prior>
bella_companion/eucovid/run_beast.py CHANGED
@@ -1,4 +1,3 @@
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- import json
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  import os
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  from glob import glob
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  from pathlib import Path
@@ -34,10 +33,8 @@ def run_beast():
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  ]
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  )
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- job_ids = {}
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-
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  os.makedirs(output_dir / "Nonparametric", exist_ok=True)
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- job_ids["Nonparametric"] = submit_job(
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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"],
@@ -52,7 +49,7 @@ def run_beast():
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  )
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  os.makedirs(output_dir / "all-predictors-GLM", exist_ok=True)
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- job_ids["all-predictors-GLM"] = submit_job(
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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"],
@@ -67,7 +64,7 @@ def run_beast():
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  )
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  os.makedirs(output_dir / "flights-GLM", exist_ok=True)
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- job_ids["flights-GLM"] = submit_job(
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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"],
@@ -82,7 +79,7 @@ def run_beast():
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  )
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  os.makedirs(output_dir / "all-predictors-MLP", exist_ok=True)
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- job_ids["all-predictors-MLP"] = submit_job(
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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"],
@@ -98,7 +95,7 @@ def run_beast():
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  )
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  os.makedirs(output_dir / "flights-MLP", exist_ok=True)
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- job_ids["flights-MLP"] = submit_job(
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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"],
@@ -112,6 +109,3 @@ def run_beast():
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  cpus=128,
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  mem_per_cpu=12000,
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  )
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-
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- with open(base_output_dir / "eucovid_job_ids.json", "w") as f:
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- json.dump(job_ids, f)
bella_companion/platyrrhine/run_beast.py CHANGED
@@ -1,4 +1,3 @@
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- import json
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  import os
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  from pathlib import Path
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@@ -33,7 +32,6 @@ def run_beast():
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  time_predictor = " ".join(list(map(str, np.repeat(time_bins, len(types)))))
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  log10BM_predictor = " ".join(types * T)
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- job_ids = {}
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  for i, tree in enumerate(
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  tqdm(trees, desc="Submitting BEAST jobs for platyrrhine datasets")
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  ):
@@ -64,11 +62,8 @@ def run_beast():
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  str(Path(__file__).parent / "beast_config.xml"),
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  ]
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  )
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- job_ids[i] = submit_job(
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+ submit_job(
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  command,
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  Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / "platyrrhine" / str(i),
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  mem_per_cpu=12000,
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  )
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-
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- with open(base_output_dir / "platyrrhine_job_ids.json", "w") as f:
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- json.dump(job_ids, f)
{bella_companion-0.0.29.dist-info → bella_companion-0.0.30.dist-info}/METADATA 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: 0.0.29
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+ Version: 0.0.30
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  Summary:
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  Author: gabriele-marino
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  Author-email: gabmarino.8601@gmail.com
{bella_companion-0.0.29.dist-info → bella_companion-0.0.30.dist-info}/RECORD RENAMED
@@ -1,7 +1,7 @@
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  bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
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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=_pqs2-ADRGSmaBxCmMepuVMWiNEyce3azgE-qD6FNrs,10828
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+ bella_companion/eucovid/beast_configs/GLM.xml,sha256=b5rAeKVEam3u2AGSJsm7EHB6LcC0l9bp1SyZT2QyjpI,10892
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  bella_companion/eucovid/beast_configs/MLP.xml,sha256=M0_B6t0bZpjCAQqAmjrFshW96pt9sNREcoLUjwchX6Q,10616
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  bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=n-t4sUfDS9AzC02tbIk5mx_RDg2l62ELhdR3I3_jjHE,17783
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  bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
@@ -20,14 +20,14 @@ bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv,sha256=pPVT5
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  bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
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  bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
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  bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
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- bella_companion/eucovid/run_beast.py,sha256=DU3T0xVVQ6y0ZClyFyouMd939V7sf5KGfadEzTDQf6I,3712
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+ bella_companion/eucovid/run_beast.py,sha256=etaD_4SVdy_Pmz5s4jvDLzp2K_QV8leEY8Pe3xySBsk,3443
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  bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
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  bella_companion/platyrrhine/beast_config.xml,sha256=bLzavt-Zd8cmSgQQnlCBfZ9KyM7d1inOGx12VNjPFb4,7056
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  bella_companion/platyrrhine/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
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  bella_companion/platyrrhine/data/traits.csv,sha256=N_mCnaM9Gy0Qot7-l_mK0vMvr7e_5BZ4bgUHpcoG9UM,3949
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  bella_companion/platyrrhine/data/trees.nwk,sha256=lpSiGUG5s3zE--IKPOyWrJ5vpJb_xAPnfxychs3YNIs,488232
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  bella_companion/platyrrhine/results.py,sha256=qosxqstTy7uadHARRt1WqmxZzxnQ3hiTjtw6V-YWKGA,2556
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- bella_companion/platyrrhine/run_beast.py,sha256=fnUmpJue3o0vZn9GWmwlmV0z2HIzXc4t_U2LFIKOq_I,2621
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+ bella_companion/platyrrhine/run_beast.py,sha256=_9Ex2B65zu6I68uY6s3_dohPYPaFP3E7u-uyWuDLAJc,2477
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  bella_companion/platyrrhine/summarize_logs.py,sha256=82N7rcmLthCyQqmP4Yub4KUsIjNzQl9vEuFLMvIv03o,951
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  bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
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  bella_companion/simulations/beast_configs/epi-multitype/GLM.xml,sha256=VymAYsaZVuB3EPE0DCQSXpKepVq8pPjKaB5yhEpaVkE,4334
@@ -69,7 +69,7 @@ bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7
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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
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- bella_companion-0.0.29.dist-info/METADATA,sha256=GfkFvoMcKT2VpMWy3vrbyeKPMoR8xEo7UlZtLcVEon0,576
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- bella_companion-0.0.29.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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- bella_companion-0.0.29.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
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- bella_companion-0.0.29.dist-info/RECORD,,
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+ bella_companion-0.0.30.dist-info/METADATA,sha256=DndfOvgcd48t3HfXC_ZsSuJ_PKC6GBOx-6hxkDSZPKY,576
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+ bella_companion-0.0.30.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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+ bella_companion-0.0.30.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
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+ bella_companion-0.0.30.dist-info/RECORD,,