bella-companion 0.0.29__tar.gz → 0.0.30__tar.gz

{bella_companion-0.0.29 → bella_companion-0.0.30}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.29
+Version: 0.0.30
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com

{bella_companion-0.0.29 → bella_companion-0.0.30}/bella_companion/eucovid/beast_configs/GLM.xml

@@ -109,11 +109,12 @@
                 <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
                     <Uniform name="distr" lower="0" upper="0.057"/>
                 </distribution>
-                <plate var="n" range="$(layersRange)">
-                    <prior name="distribution" x="@migrationW$(n)">
-                        <Normal name="distr" mean="0.0" sigma="1.0"/>
-                    </prior>
-                </plate>
+                <prior name="distribution" x="@migrationRateW">
+                    <Normal name="distr" mean="0.0" sigma="1.0"/>
+                </prior>
+                <prior name="distribution" x="@migrationRateScaler">
+                    <LogNormal name="distr" M="0.0" S="0.8"/>
+                </prior>
                 <prior name="distribution" x="@gammaShape">
                     <Exponential name="distr" mean="0.5"/>
                 </prior>

{bella_companion-0.0.29 → bella_companion-0.0.30}/bella_companion/eucovid/run_beast.py

@@ -1,4 +1,3 @@
-import json
 import os
 from glob import glob
 from pathlib import Path
@@ -34,10 +33,8 @@ def run_beast():
         ]
     )
 
-    job_ids = {}
-
     os.makedirs(output_dir / "Nonparametric", exist_ok=True)
-    job_ids["Nonparametric"] = submit_job(
+    submit_job(
         " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
@@ -52,7 +49,7 @@ def run_beast():
     )
 
     os.makedirs(output_dir / "all-predictors-GLM", exist_ok=True)
-    job_ids["all-predictors-GLM"] = submit_job(
+    submit_job(
         " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
@@ -67,7 +64,7 @@ def run_beast():
     )
 
     os.makedirs(output_dir / "flights-GLM", exist_ok=True)
-    job_ids["flights-GLM"] = submit_job(
+    submit_job(
         " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
@@ -82,7 +79,7 @@ def run_beast():
     )
 
     os.makedirs(output_dir / "all-predictors-MLP", exist_ok=True)
-    job_ids["all-predictors-MLP"] = submit_job(
+    submit_job(
         " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
@@ -98,7 +95,7 @@ def run_beast():
     )
 
     os.makedirs(output_dir / "flights-MLP", exist_ok=True)
-    job_ids["flights-MLP"] = submit_job(
+    submit_job(
         " ".join(
             [
                 os.environ["BELLA_RUN_BEAST_CMD"],
@@ -112,6 +109,3 @@ def run_beast():
         cpus=128,
         mem_per_cpu=12000,
     )
-
-    with open(base_output_dir / "eucovid_job_ids.json", "w") as f:
-        json.dump(job_ids, f)

{bella_companion-0.0.29 → bella_companion-0.0.30}/bella_companion/platyrrhine/run_beast.py

@@ -1,4 +1,3 @@
-import json
 import os
 from pathlib import Path
 
@@ -33,7 +32,6 @@ def run_beast():
     time_predictor = " ".join(list(map(str, np.repeat(time_bins, len(types)))))
     log10BM_predictor = " ".join(types * T)
 
-    job_ids = {}
     for i, tree in enumerate(
         tqdm(trees, desc="Submitting BEAST jobs for platyrrhine datasets")
     ):
@@ -64,11 +62,8 @@ def run_beast():
                 str(Path(__file__).parent / "beast_config.xml"),
             ]
         )
-        job_ids[i] = submit_job(
+        submit_job(
             command,
             Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / "platyrrhine" / str(i),
             mem_per_cpu=12000,
         )
-
-    with open(base_output_dir / "platyrrhine_job_ids.json", "w") as f:
-        json.dump(job_ids, f)

{bella_companion-0.0.29 → bella_companion-0.0.30}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bella-companion"
-version = "0.0.29"
+version = "0.0.30"
 description = ""
 authors = ["gabriele-marino <gabmarino.8601@gmail.com>"]