bella-companion 0.0.24__py3-none-any.whl → 0.0.26__py3-none-any.whl

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Files changed (9) hide show
  1. bella_companion/eucovid/beast_configs/GLM.xml +377 -128
  2. bella_companion/eucovid/beast_configs/Nonparametric.xml +331 -146
  3. bella_companion/eucovid/run_beast.py +17 -15
  4. bella_companion/platyrrhine/run_beast.py +1 -1
  5. bella_companion/utils/slurm.py +6 -1
  6. {bella_companion-0.0.24.dist-info → bella_companion-0.0.26.dist-info}/METADATA +1 -1
  7. {bella_companion-0.0.24.dist-info → bella_companion-0.0.26.dist-info}/RECORD +9 -9
  8. {bella_companion-0.0.24.dist-info → bella_companion-0.0.26.dist-info}/WHEEL +0 -0
  9. {bella_companion-0.0.24.dist-info → bella_companion-0.0.26.dist-info}/entry_points.txt +0 -0
bella_companion/eucovid/run_beast.py CHANGED
@@ -21,16 +21,16 @@ def run_beast():
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  all_predictor_files = ",".join(glob(str(predictors_dir / "all" / "*.tsv")))
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  all_predictors_data = " ".join(
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  [
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- f"-D msa_file={msa_file}",
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- f"-D changeTimesFile={predictors_dir / 'changetimes_all_7e.tsv'}",
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- f"-D predictorFiles={all_predictor_files}",
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+ f"-D aligned_fasta={msa_file}",
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+ f"-D GLMpredictor_changetimes={predictors_dir / 'changetimes_all_7e.tsv'}",
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+ f"-D GLMpredictor_files={all_predictor_files}",
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  ]
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  )
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  flight_predictor_data = " ".join(
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  [
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- f"-D msa_file={msa_file}",
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- f"-D changeTimesFile={predictors_dir / 'changetimes_flights_4e.tsv'}",
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- f"-D predictorFiles={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
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+ f"-D aligned_fasta={msa_file}",
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+ f"-D GLMpredictor_changetimes={predictors_dir / 'changetimes_flights_4e.tsv'}",
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+ f"-D GLMpredictor_files={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
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  ]
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  )
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@@ -41,13 +41,14 @@ def run_beast():
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  " ".join(
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  [
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  os.environ["BELLA_RUN_BEAST_CMD"],
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- f"-D msa_file={msa_file}",
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+ f"-D aligned_fasta={msa_file}",
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  f"-prefix {output_dir / 'Nonparametric'}{os.sep}",
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  str(beast_configs_dir / "Nonparametric.xml"),
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  ]
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  ),
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  base_log_dir / "Nonparametric",
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- mem_per_cpu="64000",
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+ cpus=128,
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+ mem_per_cpu=12000,
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  )
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  os.makedirs(output_dir / "all-predictors-GLM", exist_ok=True)
@@ -55,14 +56,14 @@ def run_beast():
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  " ".join(
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  [
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  os.environ["BELLA_RUN_BEAST_CMD"],
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- f"-D ReDimension='{5 * 7}'",
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  all_predictors_data,
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  f"-prefix {output_dir / 'all-predictors-GLM'}{os.sep}",
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  str(beast_configs_dir / "GLM.xml"),
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  ]
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  ),
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  base_log_dir / "all-predictors-GLM",
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- mem_per_cpu="64000",
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+ cpus=128,
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+ mem_per_cpu=12000,
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  )
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  os.makedirs(output_dir / "flights-GLM", exist_ok=True)
@@ -70,16 +71,16 @@ def run_beast():
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  " ".join(
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  [
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  os.environ["BELLA_RUN_BEAST_CMD"],
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- f"-D ReDimension='{5 * 4}'",
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  flight_predictor_data,
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  f"-prefix {output_dir / 'flights-GLM'}{os.sep}",
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  str(beast_configs_dir / "GLM.xml"),
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  ]
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  ),
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  base_log_dir / "flights-GLM",
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- mem_per_cpu="64000",
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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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+ """
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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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  " ".join(
@@ -93,7 +94,7 @@ def run_beast():
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  ]
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  ),
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  base_log_dir / "all-predictors-MLP",
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- mem_per_cpu="64000",
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+ mem_per_cpu="256000",
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  )
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  os.makedirs(output_dir / "flights-MLP", exist_ok=True)
@@ -109,8 +110,9 @@ def run_beast():
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  ]
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  ),
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  base_log_dir / "flights-MLP",
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- mem_per_cpu="64000",
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+ mem_per_cpu="256000",
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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
@@ -65,7 +65,7 @@ def run_beast():
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  job_ids[i] = 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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+ mem_per_cpu=12000,
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  )
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  with open(base_output_dir / "platyrrhine_job_ids.json", "w") as f:
bella_companion/utils/slurm.py CHANGED
@@ -4,7 +4,11 @@ from pathlib import Path
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  def submit_job(
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- command: str, log_dir: Path, time: str = "240:00:00", mem_per_cpu: str = "2000"
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+ command: str,
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+ log_dir: Path,
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+ time: str = "240:00:00",
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+ cpus: int = 1,
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+ mem_per_cpu: int = 2000,
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  ) -> str | None:
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  if log_dir.exists():
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  print(f"Log directory {log_dir} already exists. Skipping.")
@@ -17,6 +21,7 @@ def submit_job(
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  f"-e {log_dir / 'error.err'}",
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  f"--time {time}",
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  f"--mem-per-cpu={mem_per_cpu}",
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+ f"-c={cpus}",
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  f"--wrap='{command}'",
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  ]
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  )
{bella_companion-0.0.24.dist-info → bella_companion-0.0.26.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: 0.0.24
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+ Version: 0.0.26
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  Summary:
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  Author: gabriele-marino
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  Author-email: gabmarino.8601@gmail.com
{bella_companion-0.0.24.dist-info → bella_companion-0.0.26.dist-info}/RECORD RENAMED
@@ -1,9 +1,9 @@
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  bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
2
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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=ng13sapf8qe1OGm3xSjl-N_4Fa0gWEOPU172z2XpyQM,11731
4
+ bella_companion/eucovid/beast_configs/GLM.xml,sha256=YMvcyeSRIGQOhSSoj7FV0R-5wZHcGWwf9bKxamJ0q9k,20739
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  bella_companion/eucovid/beast_configs/MLP.xml,sha256=qLvfP3qEIa_XEDigXrPGbegKDLddifRvoZjNmoDDmFo,11268
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- bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=oDOxiXPlL5zwuvyOPkdZmdSprivYNbDScjT1IvWnZFI,11548
6
+ 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
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  bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
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  bella_companion/eucovid/data/msa.fasta,sha256=sWaVSINSJDDLjmwlpl31JWM5VnKF7yViSpERI69glQc,4839354
@@ -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=nBSwRItcxlfRJeXwGe1oFuO4Q-_xTY4u651YW6V-OmY,3807
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+ bella_companion/eucovid/run_beast.py,sha256=Rj_Cf38TtyljP0JRyMn7G5Nt5Jv9T4CM5eJsKKfoy4E,3823
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  bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
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  bella_companion/platyrrhine/beast_config.xml,sha256=8A6E5iPu9FqDL3UdlsqDbabLFlC6Qhfa4Ta47niRkVA,7090
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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
30
- bella_companion/platyrrhine/run_beast.py,sha256=caUmebyZMzOukI8RdOlECsT3DStShi0NZNzEJ72qAaw,2554
30
+ bella_companion/platyrrhine/run_beast.py,sha256=xYpK_QS5Qr-8jvq3_s-uXBW5yGsxE3c8AvHd12N6PFY,2552
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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
@@ -68,8 +68,8 @@ bella_companion/simulations/summarize_logs.py,sha256=Shf3Dx9k4lTbmO__MSLw-aIA8a8
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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=v5DaG7YHVyK8KRFptgGDC6I8jxEhyJuMVK9N08pZSAI,1812
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- bella_companion-0.0.24.dist-info/METADATA,sha256=P6X18g_ClPSSr_Q1m-0W9ajzOLeWKouQm8Z5yLhk6yQ,576
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- bella_companion-0.0.24.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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- bella_companion-0.0.24.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
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- bella_companion-0.0.24.dist-info/RECORD,,
71
+ bella_companion/utils/slurm.py,sha256=mKxeSzSX0TnQdgMUR-02hjxufepgzjPxUFnEjXVjjCQ,1868
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+ bella_companion-0.0.26.dist-info/METADATA,sha256=GOVBIP656gDA6JuP0TAe7aj73SEdOlhQ6f8U-tknD7I,576
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+ bella_companion-0.0.26.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
74
+ bella_companion-0.0.26.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
75
+ bella_companion-0.0.26.dist-info/RECORD,,