bella-companion 0.0.11__py3-none-any.whl → 0.0.12__py3-none-any.whl

bella_companion/fbd_empirical/run_beast.py

@@ -22,9 +22,6 @@ def _get_migration_rates_init(types: list[str], init_rate: float = 1) -> str:
 
 
 def run_beast():
-    from dotenv import load_dotenv
-
-    load_dotenv()
     base_output_dir = Path(os.environ["BELLA_BEAST_OUTPUT_DIR"])
     output_dir = base_output_dir / "fbd-empirical"
     os.makedirs(output_dir, exist_ok=True)
@@ -42,18 +39,16 @@ def run_beast():
     change_times = (
         pl.read_csv(change_times_file, has_header=False).to_series().to_numpy()
     )
+    time_bins = [0, *change_times]
+    T = len(time_bins)
 
     types: list[str] = sorted(traits["type"].unique())
     types.remove("?")
     N = len(types)
 
-    time_predictor = " ".join(list(map(str, np.repeat([0, *change_times], N))))
-    log10BM_predictor = " ".join(
-        [t.split("_")[0] for t in types] * (len(change_times) + 1)
-    )
-    midlat_predictor = " ".join(
-        [t.split("_")[1] for t in types] * (len(change_times) + 1)
-    )
+    time_predictor = " ".join(list(map(str, np.repeat(time_bins, N))))
+    log10BM_predictor = " ".join([t.split("_")[0] for t in types] * T)
+    midlat_predictor = " ".join([t.split("_")[1] for t in types] * T)
 
     job_ids = {}
     for i, tree in enumerate(tqdm(trees)):
@@ -66,19 +61,19 @@ def run_beast():
                 f"-D birthRateUpper=5",
                 f"-D deathRateUpper=5",
                 f"-D samplingRateUpper=5",
-                f'-D samplingRateInit="{" ".join(["2.5"] * N)}"',
+                f'-D samplingRateInit="{" ".join(["2.5"] * T)}"',
                 f"-D migrationRateUpper=5",
                 f'-D migrationRateInit="{_get_migration_rates_init(types, 2.5)}"',
                 f'-D nodes="16 8"',
                 f'-D layersRange="0,1,2"',
-                f"-D tree_file={tree_file}",
+                f"-D treeFile={tree_file}",
                 f"-D treeIndex={i}",
                 f"-D changeTimesFile={change_times_file}",
                 f"-D traitsFile={traits_file}",
                 f"-D processLength={process_length}",
                 f'-D timePredictor="{time_predictor}"',
-                f'-D log10BM_predictor="{log10BM_predictor}"',
-                f'-D midlat_predictor="{midlat_predictor}"',
+                f'-D log10BMPredictor="{log10BM_predictor}"',
+                f'-D midlatPredictor="{midlat_predictor}"',
                 f"-prefix {output_dir}{os.sep}",
                 str(Path(os.environ["BELLA_BEAST_CONFIGS_DIR"]) / "fbd-empirical.xml"),
             ]

{bella_companion-0.0.11.dist-info → bella_companion-0.0.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.11
+Version: 0.0.12
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com

{bella_companion-0.0.11.dist-info → bella_companion-0.0.12.dist-info}/RECORD

@@ -5,7 +5,7 @@ bella_companion/fbd_empirical/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSq
 bella_companion/fbd_empirical/data/traits.csv,sha256=cxNKYmgtBCKHsm9qnOpS29Rkx9cQKe0oxpgaXSIukJg,5422
 bella_companion/fbd_empirical/data/trees.nwk,sha256=JAsdfGhTIzGmJz6g6-0s5SVfqNuxawOMc9gbt0srue4,539385
 bella_companion/fbd_empirical/results.py,sha256=0FENY5EpgNQ6rwPsEiOT2ZEO5oBbIAK6TzPvk11SDnk,3116
-bella_companion/fbd_empirical/run_beast.py,sha256=Vvh0xognC92tAI7GhUyzU901N1x6t8UjUDccvB2JcVA,3309
+bella_companion/fbd_empirical/run_beast.py,sha256=MPW4A10NiXc8y3JS3ZN17DL-Oh8IoIdTv1Y5QLLrcxo,3229
 bella_companion/fbd_empirical/summarize_logs.py,sha256=OoT43DMjim9o4qsjYCgGKnBKp3dHXzVP6sVtzqR8lMQ,955
 bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
 bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
@@ -35,7 +35,7 @@ bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7
 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-0.0.11.dist-info/METADATA,sha256=NQPoh1JxQYhkfvNRr_CrdJx1_t46j5o8P6lHlnEy83k,577
-bella_companion-0.0.11.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-bella_companion-0.0.11.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
-bella_companion-0.0.11.dist-info/RECORD,,
+bella_companion-0.0.12.dist-info/METADATA,sha256=0XKEli6E-1urNh-LiUEm9nqBm5FR6CWqZHXo4ow4rK4,577
+bella_companion-0.0.12.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+bella_companion-0.0.12.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
+bella_companion-0.0.12.dist-info/RECORD,,