bella-companion 0.0.25__py3-none-any.whl → 0.0.27__py3-none-any.whl

bella_companion/eucovid/run_beast.py

@@ -21,16 +21,16 @@ def run_beast():
     all_predictor_files = ",".join(glob(str(predictors_dir / "all" / "*.tsv")))
     all_predictors_data = " ".join(
         [
-            f"-D msa_file={msa_file}",
-            f"-D changeTimesFile={predictors_dir / 'changetimes_all_7e.tsv'}",
-            f"-D predictorFiles={all_predictor_files}",
+            f"-D aligned_fasta={msa_file}",
+            f"-D GLMpredictor_changetimes={predictors_dir / 'changetimes_all_7e.tsv'}",
+            f"-D GLMpredictor_files={all_predictor_files}",
         ]
     )
     flight_predictor_data = " ".join(
         [
-            f"-D msa_file={msa_file}",
-            f"-D changeTimesFile={predictors_dir / 'changetimes_flights_4e.tsv'}",
-            f"-D predictorFiles={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
+            f"-D aligned_fasta={msa_file}",
+            f"-D GLMpredictor_changetimes={predictors_dir / 'changetimes_flights_4e.tsv'}",
+            f"-D GLMpredictor_files={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
         ]
     )
 
@@ -41,13 +41,14 @@ def run_beast():
         " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
-                f"-D msa_file={msa_file}",
+                f"-D aligned_fasta={msa_file}",
                 f"-prefix {output_dir / 'Nonparametric'}{os.sep}",
                 str(beast_configs_dir / "Nonparametric.xml"),
             ]
         ),
         base_log_dir / "Nonparametric",
-        mem_per_cpu="256000",
+        cpus=128,
+        mem_per_cpu=12000,
     )
 
     os.makedirs(output_dir / "all-predictors-GLM", exist_ok=True)
@@ -55,14 +56,14 @@ def run_beast():
         " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
-                f"-D ReDimension='{5 * 7}'",
                 all_predictors_data,
                 f"-prefix {output_dir / 'all-predictors-GLM'}{os.sep}",
                 str(beast_configs_dir / "GLM.xml"),
             ]
         ),
         base_log_dir / "all-predictors-GLM",
-        mem_per_cpu="256000",
+        cpus=128,
+        mem_per_cpu=12000,
     )
 
     os.makedirs(output_dir / "flights-GLM", exist_ok=True)
@@ -70,16 +71,16 @@ def run_beast():
         " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
-                f"-D ReDimension='{5 * 4}'",
                 flight_predictor_data,
                 f"-prefix {output_dir / 'flights-GLM'}{os.sep}",
                 str(beast_configs_dir / "GLM.xml"),
             ]
         ),
         base_log_dir / "flights-GLM",
-        mem_per_cpu="256000",
+        cpus=128,
+        mem_per_cpu=12000,
     )
-
+    """
     os.makedirs(output_dir / "all-predictors-MLP", exist_ok=True)
     job_ids["all-predictors-MLP"] = submit_job(
         " ".join(
@@ -111,6 +112,7 @@ def run_beast():
         base_log_dir / "flights-MLP",
         mem_per_cpu="256000",
     )
+    """
 
     with open(base_output_dir / "eucovid_job_ids.json", "w") as f:
         json.dump(job_ids, f)

bella_companion/platyrrhine/run_beast.py

@@ -65,7 +65,7 @@ def run_beast():
         job_ids[i] = submit_job(
             command,
             Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / "platyrrhine" / str(i),
-            mem_per_cpu="12000",
+            mem_per_cpu=12000,
         )
 
     with open(base_output_dir / "platyrrhine_job_ids.json", "w") as f:

bella_companion/utils/slurm.py

@@ -4,7 +4,11 @@ from pathlib import Path
 
 
 def submit_job(
-    command: str, log_dir: Path, time: str = "240:00:00", mem_per_cpu: str = "2000"
+    command: str,
+    log_dir: Path,
+    time: str = "240:00:00",
+    cpus: int = 1,
+    mem_per_cpu: int = 2000,
 ) -> str | None:
     if log_dir.exists():
         print(f"Log directory {log_dir} already exists. Skipping.")
@@ -15,8 +19,9 @@ def submit_job(
             f"-J {log_dir}",
             f"-o {log_dir / 'output.out'}",
             f"-e {log_dir / 'error.err'}",
+            f"-c {cpus}",
             f"--time {time}",
-            f"--mem-per-cpu={mem_per_cpu}",
+            f"--mem-per-cpu {mem_per_cpu}",
             f"--wrap='{command}'",
         ]
     )

{bella_companion-0.0.25.dist-info → bella_companion-0.0.27.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.25
+Version: 0.0.27
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com

{bella_companion-0.0.25.dist-info → bella_companion-0.0.27.dist-info}/RECORD

@@ -1,9 +1,9 @@
 bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
 bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
-bella_companion/eucovid/beast_configs/GLM.xml,sha256=ng13sapf8qe1OGm3xSjl-N_4Fa0gWEOPU172z2XpyQM,11731
+bella_companion/eucovid/beast_configs/GLM.xml,sha256=YMvcyeSRIGQOhSSoj7FV0R-5wZHcGWwf9bKxamJ0q9k,20739
 bella_companion/eucovid/beast_configs/MLP.xml,sha256=qLvfP3qEIa_XEDigXrPGbegKDLddifRvoZjNmoDDmFo,11268
-bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=oDOxiXPlL5zwuvyOPkdZmdSprivYNbDScjT1IvWnZFI,11548
+bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=n-t4sUfDS9AzC02tbIk5mx_RDg2l62ELhdR3I3_jjHE,17783
 bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
 bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
 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
 bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
 bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
 bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
-bella_companion/eucovid/run_beast.py,sha256=mq7ZFlXPd0DTpuOs7cKCbyM48Y7vfDAc_dwOaGW50-M,3812
+bella_companion/eucovid/run_beast.py,sha256=Rj_Cf38TtyljP0JRyMn7G5Nt5Jv9T4CM5eJsKKfoy4E,3823
 bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
 bella_companion/platyrrhine/beast_config.xml,sha256=8A6E5iPu9FqDL3UdlsqDbabLFlC6Qhfa4Ta47niRkVA,7090
 bella_companion/platyrrhine/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
 bella_companion/platyrrhine/data/traits.csv,sha256=N_mCnaM9Gy0Qot7-l_mK0vMvr7e_5BZ4bgUHpcoG9UM,3949
 bella_companion/platyrrhine/data/trees.nwk,sha256=lpSiGUG5s3zE--IKPOyWrJ5vpJb_xAPnfxychs3YNIs,488232
 bella_companion/platyrrhine/results.py,sha256=qosxqstTy7uadHARRt1WqmxZzxnQ3hiTjtw6V-YWKGA,2556
-bella_companion/platyrrhine/run_beast.py,sha256=caUmebyZMzOukI8RdOlECsT3DStShi0NZNzEJ72qAaw,2554
+bella_companion/platyrrhine/run_beast.py,sha256=xYpK_QS5Qr-8jvq3_s-uXBW5yGsxE3c8AvHd12N6PFY,2552
 bella_companion/platyrrhine/summarize_logs.py,sha256=82N7rcmLthCyQqmP4Yub4KUsIjNzQl9vEuFLMvIv03o,951
 bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
 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
 bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7UpYw,480
 bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
 bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
-bella_companion/utils/slurm.py,sha256=v5DaG7YHVyK8KRFptgGDC6I8jxEhyJuMVK9N08pZSAI,1812
-bella_companion-0.0.25.dist-info/METADATA,sha256=oZu6C3m8LatujG5t26sTzJj_6V-L8ICRF9ad3Tz2Wts,576
-bella_companion-0.0.25.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-bella_companion-0.0.25.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
-bella_companion-0.0.25.dist-info/RECORD,,
+bella_companion/utils/slurm.py,sha256=xEyf-Jxk8fy71t3fko_Ic9WtUFSdLFE3w4tR17gaBPw,1868
+bella_companion-0.0.27.dist-info/METADATA,sha256=Sl37hKYlQ0qIq5NxxA1wNCmF-Mj109HazWo8EDq_pkk,576
+bella_companion-0.0.27.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+bella_companion-0.0.27.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
+bella_companion-0.0.27.dist-info/RECORD,,