bella-companion 0.0.5__py3-none-any.whl → 0.0.6__py3-none-any.whl

bella_companion/cli.py

@@ -23,19 +23,19 @@ 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."
+        "sim-run", help="Run BEAST2 analyses on simulation datasets."
     ).set_defaults(func=run_beast)
 
     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)
 
     args = parser.parse_args()

bella_companion/fbd_empirical/run_beast.py

@@ -11,7 +11,7 @@ import src.config as cfg
 from src.utils import run_sbatch
 
 THIS_DIR = Path(__file__).parent
-
+AADD LAYERS RANGE
 
 def main():
     output_dir = cfg.BEAST_OUTPUTS_DIR / "fbd-empirical"

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-0.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.5
+Version: 0.0.6
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com

{bella_companion-0.0.5.dist-info → bella_companion-0.0.6.dist-info}/RECORD

@@ -1,5 +1,5 @@
 bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bella_companion/cli.py,sha256=fjCIIsguBUnm_u1dyuo42INGTDa5lh8laiW1yZN65So,1178
+bella_companion/cli.py,sha256=5GbOREOkW0C1Dt43i7Y-Xy1jTr8Tx779is-uQ1nlnUc,1162
 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
@@ -7,7 +7,7 @@ bella_companion/fbd_empirical/data/trees.nwk,sha256=zhvLvPLZelhMThVmvOENkmi3p2aP
 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=pUX4f77kQ_F_tJwRY7Sfz8NUql0sY4VKE1i8pZGte6Y,1952
 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-0.0.6.dist-info/METADATA,sha256=3smSTa-FBJ-RUBiIt7fiK3VGp4EBlw4nAaScxOkDUG8,576
+bella_companion-0.0.6.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+bella_companion-0.0.6.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
+bella_companion-0.0.6.dist-info/RECORD,,