bella-companion 0.0.11__tar.gz → 0.0.13__tar.gz

{bella_companion-0.0.11 → bella_companion-0.0.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.11
+Version: 0.0.13
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com
@@ -10,7 +10,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: arviz (>=0.22.0,<0.23.0)
-Requires-Dist: bella-lumiere (>=0.0.13,<0.0.14)
+Requires-Dist: bella-lumiere (>=0.0.14,<0.0.15)
 Requires-Dist: dotenv (>=0.9.9,<0.10.0)
 Requires-Dist: phylogenie (>=2.1.30,<3.0.0)
 Requires-Dist: seaborn (>=0.13.2,<0.14.0)

{bella_companion-0.0.11 → bella_companion-0.0.13}/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 → bella_companion-0.0.13}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bella-companion"
-version = "0.0.11"
+version = "0.0.13"
 description = ""
 authors = ["gabriele-marino <gabmarino.8601@gmail.com>"]
 
@@ -8,7 +8,7 @@ authors = ["gabriele-marino <gabmarino.8601@gmail.com>"]
 python = "^3.10"
 
 arviz = "^0.22.0"
-bella-lumiere = "^0.0.13"
+bella-lumiere = "^0.0.14"
 dotenv = "^0.9.9"
 phylogenie = "^2.1.30"
 seaborn = "^0.13.2"