bella-companion 0.0.5__py3-none-any.whl → 0.0.7__py3-none-any.whl

bella_companion/cli.py

@@ -4,12 +4,10 @@ from pathlib import Path
 
 from dotenv import load_dotenv
 
-from bella_companion.simulations import (
-    generate_data,
-    generate_figures,
-    run_beast,
-    summarize_logs,
-)
+from bella_companion.fbd_empirical import run_beast as run_fbd_empirical
+from bella_companion.simulations import generate_data, generate_figures
+from bella_companion.simulations import run_beast as run_simulations
+from bella_companion.simulations import summarize_logs
 
 
 def main():
@@ -23,20 +21,24 @@ def main():
     subparsers = parser.add_subparsers(dest="command", required=True)
 
     subparsers.add_parser(
-        "generate-simulation-data", help="Generate simulated data."
+        "sim-data", help="Generate synthetic simulation datasets."
     ).set_defaults(func=generate_data)
 
     subparsers.add_parser(
-        "beast-run-simulations", help="Run BEAST2 on simulated data."
-    ).set_defaults(func=run_beast)
+        "sim-run", help="Run BEAST2 analyses on simulation datasets."
+    ).set_defaults(func=run_simulations)
 
     subparsers.add_parser(
-        "summarize-simulation-logs", help="Summarize BEAST2 logs for simulations data."
+        "sim-summary", help="Summarize BEAST2 log outputs for simulations."
     ).set_defaults(func=summarize_logs)
 
     subparsers.add_parser(
-        "generate-simulation-figures", help="Generate figures for simulations data."
+        "sim-figures", help="Generate plots and figures from simulation results."
     ).set_defaults(func=generate_figures)
 
+    subparsers.add_parser(
+        "fbd-empirical-run", help="Run BEAST2 analyses on empirical FBD datasets."
+    ).set_defaults(func=run_fbd_empirical)
+
     args = parser.parse_args()
     args.func()

bella_companion/fbd_empirical/__init__.py

@@ -0,0 +1,3 @@
+from bella_companion.fbd_empirical.run_beast import run_beast
+
+__all__ = ["run_beast"]

bella_companion/fbd_empirical/run_beast.py

@@ -1,3 +1,4 @@
+import json
 import os
 from pathlib import Path
 
@@ -7,48 +8,61 @@ from phylogenie import load_newick
 from phylogenie.utils import get_node_depths
 from tqdm import tqdm
 
-import src.config as cfg
-from src.utils import run_sbatch
+from bella_companion.utils import submit_job
 
 THIS_DIR = Path(__file__).parent
 
 
-def main():
-    output_dir = cfg.BEAST_OUTPUTS_DIR / "fbd-empirical"
+def run_beast():
+    base_output_dir = Path(os.environ["BELLA_BEAST_OUTPUT_DIR"])
+    output_dir = base_output_dir / "fbd-empirical"
     os.makedirs(output_dir, exist_ok=True)
 
-    tree_file = THIS_DIR / "data" / "trees.nwk"
-    change_times_file = THIS_DIR / "data" / "change_times.csv"
-    sampling_change_times_file = THIS_DIR / "data" / "sampling_change_times.csv"
+    data_dir = THIS_DIR / "data"
+    tree_file = data_dir / "trees.nwk"
+    change_times_file = data_dir / "change_times.csv"
 
+    trees = load_newick(str(tree_file))
+    assert isinstance(trees, list)
     change_times = (
         pl.read_csv(change_times_file, has_header=False).to_series().to_numpy()
     )
-    time_predictor = " ".join(
-        list(map(str, np.repeat(np.insert(change_times, 0, 0), 4)))
-    )
+    time_predictor = " ".join(list(map(str, np.repeat([0, *change_times], 4))))
     body_mass_predictor = " ".join(["0", "1", "2", "3"] * (len(change_times) + 1))
 
-    trees = load_newick(str(tree_file))
-    assert isinstance(trees, list)
+    job_ids = {}
     for i, tree in enumerate(tqdm(trees)):
         process_length = max(get_node_depths(tree).values())
-        for model in ["hidden-relu", "hidden-tanh"]:
-            command = " ".join(
-                [
-                    cfg.RUN_BEAST,
-                    f'-D treeFile={tree_file},treeIndex={i},typeTraitFile={THIS_DIR / "data" / "body_mass.csv"},changeTimesFile={change_times_file},samplingChangeTimesFile={sampling_change_times_file},processLength={process_length},timePredictor="{time_predictor}",bodyMassPredictor="{body_mass_predictor}"',
-                    f"-DF {THIS_DIR / 'params.json'}",
-                    f"-prefix {output_dir / model}",
-                    str(cfg.BEAST_CONFIGS_DIR / "fbd-empirical" / f"{model}.xml"),
-                ]
-            )
-            run_sbatch(
-                command,
-                cfg.SBATCH_LOGS_DIR / "fbd-empirical" / model / str(i),
-                mem_per_cpu="12000",
-            )
-
-
-if __name__ == "__main__":
-    main()
+        command = " ".join(
+            [
+                os.environ["BELLA_RUN_BEAST_CMD"],
+                f"-D types=0,1,2,3",
+                f'-D startTypePriorProbs="0.25 0.25 0.25 0.25"',
+                f"-D birthRateUpper=2",
+                f"-D deathRateUpper=2",
+                f"-D samplingRateUpper=10",
+                f'-D samplingRateInit="5 5 5 5 5 5 5"',
+                f"-D migrationRateUpper=10",
+                f'-D migrationRateInit="0.5 0 0 0.5 0.5 0 0 0.5 0.5 0 0 0.5"',
+                f'-D nodes="16 8"',
+                f'-D layersRange="0,1,2"',
+                f"-D treeFile={tree_file}",
+                f"-D treeIndex={i}",
+                f"-D changeTimesFile={change_times_file}",
+                f"-D samplingChangeTimesFile={data_dir / 'sampling_change_times.csv'}",
+                f"-D typeTraitFile={data_dir / 'body_mass.csv'}",
+                f"-D processLength={process_length}",
+                f'-D timePredictor="{time_predictor}"',
+                f'-D bodyMassPredictor="{body_mass_predictor}"',
+                f"-prefix {output_dir}{os.sep}",
+                str(Path(os.environ["BELLA_BEAST_CONFIGS_DIR"]) / "fbd-empirical.xml"),
+            ]
+        )
+        job_ids[i] = submit_job(
+            command,
+            Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / "fbd-empirical" / str(i),
+            mem_per_cpu="12000",
+        )
+
+    with open(base_output_dir / "fbd_empirical_job_ids.json", "w") as f:
+        json.dump(job_ids, f)

bella_companion/simulations/run_beast.py

@@ -66,6 +66,7 @@ def run_beast():
                         [
                             *base_command,
                             f'-D nodes="{" ".join(map(str, nodes))}"',
+                            f'-D layersRange="{",".join(map(str, range(len(nodes) + 1)))}"',
                             str(inference_configs_dir / "MLP.xml"),
                         ]
                     )

{bella_companion-0.0.5.dist-info → bella_companion-0.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.5
+Version: 0.0.7
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com

{bella_companion-0.0.5.dist-info → bella_companion-0.0.7.dist-info}/RECORD

@@ -1,13 +1,13 @@
 bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bella_companion/cli.py,sha256=fjCIIsguBUnm_u1dyuo42INGTDa5lh8laiW1yZN65So,1178
+bella_companion/cli.py,sha256=2QM1czJxsfQsOX-miE-OeReXtjMHaR7lX9i73zKki1o,1471
+bella_companion/fbd_empirical/__init__.py,sha256=I-G5rD59c1mNBYuoVNSfq59jD6IuwwJBDkNUCLcY7Qo,87
 bella_companion/fbd_empirical/data/body_mass.csv,sha256=-UkKNtm9m3g4PjY3BcfdP6z5nL_I6p9cq6cgZ-bWKI8,30360
 bella_companion/fbd_empirical/data/change_times.csv,sha256=zmc9_z91-XMwKyIoP9v9dVlLcf4MeIHkQiHLjoMriOo,120
 bella_companion/fbd_empirical/data/sampling_change_times.csv,sha256=Gwi9RcMFy89RyvfxKVZ_MoKVRHOZLuwB_3LEaq8asMQ,32
 bella_companion/fbd_empirical/data/trees.nwk,sha256=zhvLvPLZelhMThVmvOENkmi3p2aPAARb8KMdHTm6mss,4645318
 bella_companion/fbd_empirical/figure.py,sha256=4paOXCB1EcxuHzLPxDSleQU2AQ_ndTedtzS1ugiKICs,1018
 bella_companion/fbd_empirical/notbooks.ipynb,sha256=O45kmz0lZENRDFbKXEWPsIKATfF5GVeS5tCYmrGLnqk,83326
-bella_companion/fbd_empirical/params.json,sha256=hU23LniClZL_GSBAxIEJUJgMa93AM8zdtFOq6mt3vkI,311
-bella_companion/fbd_empirical/run_beast.py,sha256=2sV2UmxOfWmbueiU6D0p3lueMYiZyIkSKYoblTMrYuA,1935
+bella_companion/fbd_empirical/run_beast.py,sha256=Y2Mcl7tLer-CIgb5rcpZ0sCq7VL6VUejnbZ9mvkRxkU,2532
 bella_companion/fbd_empirical/summarize_logs.py,sha256=O6rhE606Wa98a8b1KKlLPjUOro1pfyqVTLdQksQMG0g,1439
 bella_companion/simulations/__init__.py,sha256=EBZAcI8skNPKjrA7CjrqH9ea7DTntmydAD0RqsxNUMM,352
 bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
@@ -22,7 +22,7 @@ bella_companion/simulations/figures/fbd_no_traits_results.py,sha256=O6hx_OZVSHmW
 bella_companion/simulations/figures/scenarios.py,sha256=OKh9_-ZvzNgWsO3-Vd0Aw3ndjVf76i_OuCvsKI-5r2s,2795
 bella_companion/simulations/generate_data.py,sha256=H8OV4ZlTGZB-jXaROTPmOsK3UxRiU-GrX40l-shliw8,728
 bella_companion/simulations/generate_figures.py,sha256=layMgoj3Bfl78Ceb1oE7YirAQ8zhjDyD9IrxDRXf6go,657
-bella_companion/simulations/run_beast.py,sha256=xOuwE0w4IbOqqCSym6kHsAEhfGT2mWdA-jmUZuviMbc,3121
+bella_companion/simulations/run_beast.py,sha256=Sw9wKNe1VlGNvYr-yiYv3LqUYVlcjcMAz_9Pzr-xyL0,3214
 bella_companion/simulations/scenarios/__init__.py,sha256=3Kl1lKcFpfb3vLX64DmSW4XCF5kXU1ZoHtstFH-ZIzU,876
 bella_companion/simulations/scenarios/common.py,sha256=_ddaSuTvEVdttGkXB4HPc2B7IB1F_GBOCW3cVOPZ-ZM,807
 bella_companion/simulations/scenarios/epi_multitype.py,sha256=GWGIiqvYwX_FrT_3RXkZKYGDht9nZ7ceHRBKUvXDPnA,2432
@@ -36,7 +36,7 @@ bella_companion/utils/beast.py,sha256=5Vsv98VTE9HrY56WzUSMECjD_rIPxHTMRMD1ZzmA6w
 bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
 bella_companion/utils/plots.py,sha256=dB_GiJ1HGrZ93cqODz6kB-HeDRPwlm2MkMe9rJZGnfs,3117
 bella_companion/utils/slurm.py,sha256=v5DaG7YHVyK8KRFptgGDC6I8jxEhyJuMVK9N08pZSAI,1812
-bella_companion-0.0.5.dist-info/METADATA,sha256=IIRIUzr8WcpcLOApct-WoFLrEBkzAxhjXPIY6HucbOk,576
-bella_companion-0.0.5.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-bella_companion-0.0.5.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
-bella_companion-0.0.5.dist-info/RECORD,,
+bella_companion-0.0.7.dist-info/METADATA,sha256=w-O11B88lzyTN6ENgW_0XTR2UhZEuj6Ar9hxmX_JDWs,576
+bella_companion-0.0.7.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+bella_companion-0.0.7.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
+bella_companion-0.0.7.dist-info/RECORD,,

bella_companion/fbd_empirical/params.json

@@ -1,11 +0,0 @@
-{
-    "types": "0,1,2,3",
-    "startTypePriorProbs": "0.25 0.25 0.25 0.25",
-    "birthRateUpper": 2,
-    "deathRateUpper": 2,
-    "samplingRateUpper": 10,
-    "samplingRateInit": "5 5 5 5 5 5 5",
-    "migrationRateUpper": 10,
-    "migrationRateInit": "0.5 0 0 0.5 0.5 0 0 0.5 0.5 0 0 0.5",
-    "nodes": "16 8"
-}