bella-companion 0.0.43__py3-none-any.whl → 0.0.44__py3-none-any.whl

bella_companion/cli.py

@@ -15,6 +15,18 @@ from bella_companion.simulations import summarize_logs as summarize_simulations
 
 def main():
     load_dotenv(Path(os.getcwd()) / ".env")
+    os.environ["BELLA_RUN_BEAST_CMD"] = " ".join(
+        [
+            "java",
+            os.getenv("JAVA_OPTIONS", ""),
+            f"-jar {Path(__file__).parent / 'BELLA.jar'}",
+            f"-version_file {Path(__file__).parent / 'version.xml'}",
+            "-seed 42",
+            "-overwrite",
+            "-statefile /tmp/state",
+            "-DFout /dev/null",
+        ]
+    )
 
     parser = argparse.ArgumentParser(
         prog="bella",

bella_companion/simulations/figures/__init__.py

@@ -1,15 +1,7 @@
-from bella_companion.simulations.figures.epi_multitype_results import (
-    plot_epi_multitype_results,
-)
-from bella_companion.simulations.figures.epi_skyline_results import (
-    plot_epi_skyline_results,
-)
-from bella_companion.simulations.figures.fbd_2traits_results import (
-    plot_fbd_2traits_results,
-)
-from bella_companion.simulations.figures.fbd_no_traits_results import (
-    plot_fbd_no_traits_results,
-)
+from bella_companion.simulations.figures.epi_multitype import plot_epi_multitype_results
+from bella_companion.simulations.figures.epi_skyline import plot_epi_skyline_results
+from bella_companion.simulations.figures.fbd_2traits import plot_fbd_2traits_results
+from bella_companion.simulations.figures.fbd_no_traits import plot_fbd_no_traits_results
 from bella_companion.simulations.figures.scenarios import plot_scenarios
 
 __all__ = [

bella_companion/simulations/figures/{epi_skyline_results.py → epi_skyline.py}

@@ -14,8 +14,7 @@ from bella_companion.simulations.scenarios.epi_skyline import REPRODUCTION_NUMBE
 
 
 def plot_epi_skyline_results():
-    output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "epi-skyline"
-    os.makedirs(output_dir, exist_ok=True)
+    base_output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "epi-skyline"
 
     for i, reproduction_number in enumerate(REPRODUCTION_NUMBERS, start=1):
         summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"]) / f"epi-skyline_{i}"
@@ -26,6 +25,8 @@ def plot_epi_skyline_results():
         }
         true_values = {"reproductionNumberSP": reproduction_number}
 
+        output_dir = base_output_dir / str(i)
+        os.makedirs(output_dir, exist_ok=True)
         for log_summary in logs_summaries.values():
             step(
                 [
@@ -35,12 +36,10 @@ def plot_epi_skyline_results():
             )
         step(reproduction_number, color="k", linestyle="--")
         plt.ylabel("Reproduction number")  # pyright: ignore
-        plt.savefig(output_dir / f"predictions-{i}.svg")  # pyright: ignore
+        plt.savefig(output_dir / "predictions.svg")  # pyright: ignore
         plt.close()
 
         plot_coverage_per_time_bin(
-            logs_summaries, true_values, output_dir / f"coverage-{i}.svg"
-        )
-        plot_maes_per_time_bin(
-            logs_summaries, true_values, output_dir / f"maes-{i}.svg"
+            logs_summaries, true_values, output_dir / "coverage.svg"
         )
+        plot_maes_per_time_bin(logs_summaries, true_values, output_dir / "maes.svg")

bella_companion/simulations/figures/{fbd_no_traits_results.py → fbd_no_traits.py}

@@ -14,8 +14,7 @@ from bella_companion.simulations.scenarios.fbd_no_traits import RATES
 
 
 def plot_fbd_no_traits_results():
-    output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "fbd-no-traits"
-    os.makedirs(output_dir, exist_ok=True)
+    base_output = Path(os.environ["BELLA_FIGURES_DIR"]) / "fbd-no-traits"
 
     for i, rates in enumerate(RATES, start=1):
         summaries_dir = (
@@ -28,6 +27,7 @@ def plot_fbd_no_traits_results():
         }
         true_values = {"birthRateSP": rates["birth"], "deathRateSP": rates["death"]}
 
+        output_dir = base_output / str(i)
         for id, rate in true_values.items():
             for log_summary in logs_summaries.values():
                 step(
@@ -41,18 +41,18 @@ def plot_fbd_no_traits_results():
             plt.ylabel(  # pyright: ignore
                 r"$\lambda$" if id == "birthRateSP" else r"$\mu$"
             )
-            plt.savefig(output_dir / f"{id}-predictions-{i}-.svg")  # pyright: ignore
+            plt.savefig(output_dir / f"{id}-predictions.svg")  # pyright: ignore
             plt.close()
 
         plot_coverage_per_time_bin(
             logs_summaries,
             true_values,
-            output_dir / f"coverage-{i}.svg",
+            output_dir / "coverage.svg",
             reverse_xticks=True,
         )
         plot_maes_per_time_bin(
             logs_summaries,
             true_values,
-            output_dir / f"maes-{i}.svg",
+            output_dir / "maes.svg",
             reverse_xticks=True,
         )

bella_companion/simulations/metrics.py

@@ -36,9 +36,10 @@ def _avg_ci_width(summary: pl.DataFrame, true_values: dict[str, float]) -> float
 
 
 def print_metrics():
+    base_summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"])
     metrics = {}
     for name, scenario in SCENARIOS.items():
-        summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"]) / name
+        summaries_dir = base_summaries_dir / name
         summaries = {
             Path(log_summary).stem: pl.read_csv(log_summary)
             for log_summary in glob(str(summaries_dir / "*.csv"))
@@ -54,5 +55,5 @@ def print_metrics():
             }
             for target, true_values in scenario.targets.items()
         }
-    with open("simulation-metrics.json", "w") as f:
+    with open(base_summaries_dir / "sim-metrics.json", "w") as f:
         json.dump(metrics, f)

bella_companion/version.xml

@@ -0,0 +1,13 @@
+<addon name='BELLA' version='0.0.1'>
+    <depends on="BEAST.base" atleast="2.7.0" atmost="2.7.9"/>
+    <depends on="BEAST.app" atleast="2.7.0" atmost="2.7.9"/>
+
+    <service type="beast.base.core.BEASTInterface">
+        <provider classname="bella.BayesMLP"/>
+        <provider classname="bella.ReLu"/>
+        <provider classname="bella.SoftPlus"/>
+        <provider classname="bella.Sigmoid"/>
+        <provider classname="bella.Tanh"/>
+        <provider classname="bella.SkylineNodeTreeLogger"/>
+    </service>
+</addon>

{bella_companion-0.0.43.dist-info → bella_companion-0.0.44.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bella-companion
-Version: 0.0.43
+Version: 0.0.44
 Summary: Add your description here
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{bella_companion-0.0.43.dist-info → bella_companion-0.0.44.dist-info}/RECORD

@@ -1,5 +1,7 @@
+bella_companion/BELLA.jar,sha256=4mKDzPfz263rTqA9KS2f4Mc-UWGMuj8G48ZDonKSqVw,67408597
 bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
+bella_companion/cli.py,sha256=2Xa49zHn85UfgsJ-hxsVfacfZDMTQZG0JatEtkFBO6k,2796
+bella_companion/version.xml,sha256=Gr3nsYqFhVNP0Mszl_IfilxefsPN8ZpQlGlB8OJSwnE,522
 bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
 bella_companion/eucovid/run_beast.py,sha256=etaD_4SVdy_Pmz5s4jvDLzp2K_QV8leEY8Pe3xySBsk,3443
 bella_companion/eucovid/beast_configs/GLM.xml,sha256=b5rAeKVEam3u2AGSJsm7EHB6LcC0l9bp1SyZT2QyjpI,10892
@@ -33,7 +35,7 @@ bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZ
 bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
 bella_companion/simulations/generate_data.py,sha256=edfhXrs76hl30i_xizup4z6qgzXZyaDzX_PVC62Ytpw,849
 bella_companion/simulations/generate_figures.py,sha256=layMgoj3Bfl78Ceb1oE7YirAQ8zhjDyD9IrxDRXf6go,657
-bella_companion/simulations/metrics.py,sha256=duIkPb8cCXmIzjKA2yk9HLf4Y9eFIB_hRWaH05uIDws,1876
+bella_companion/simulations/metrics.py,sha256=dg85Z5umewEzPXpfhQEEHtbQPCLT7LB0BEIPW8tAQYc,1934
 bella_companion/simulations/run_beast.py,sha256=qniy326i-vDCeHzzHpQRrSnY2ULqNNrO0z3GEsWx4Mc,3208
 bella_companion/simulations/summarize_logs.py,sha256=Shf3Dx9k4lTbmO__MSLw-aIA8a8kTCXhbctBcV6Izug,1216
 bella_companion/simulations/beast_configs/epi-multitype/GLM.xml,sha256=VymAYsaZVuB3EPE0DCQSXpKepVq8pPjKaB5yhEpaVkE,4334
@@ -48,11 +50,11 @@ bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml,sha256=e
 bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml,sha256=Caq7Gxqx-wYAu3_YkMikVqni3DjBv1Wt00sc1Upo1X8,4743
 bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml,sha256=JE_cGh2DW5yPAXyXXr0D3DlovmV-aIbze7qrhENHK3w,4275
 bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml,sha256=m2xaHZwskCFInvVY1QH1fwQqH6p_fgESlPX2BbBeUhk,2822
-bella_companion/simulations/figures/__init__.py,sha256=aBYbJntH4egFmkSSWiVMYDEApXPYxJD7eA3TCPNNegM,658
-bella_companion/simulations/figures/epi_multitype_results.py,sha256=j85WgvN5AyAtX-CalMegr2lwlAZBmzyJxkikBPXRjCc,2629
-bella_companion/simulations/figures/epi_skyline_results.py,sha256=jwognQspt0e1qvrhaYA-MQScsDxpDZd3YKJ5-RHfU6U,1659
-bella_companion/simulations/figures/fbd_2traits_results.py,sha256=JiXrbYkH1HwdJQhTHXj6KhMEXYgQmQ6LmDboAIO1CPA,2728
-bella_companion/simulations/figures/fbd_no_traits_results.py,sha256=kwDbgUTQUk-LXAvMGvKf1kInFvK7kTJld4BWpgS1sVU,1950
+bella_companion/simulations/figures/__init__.py,sha256=LeHPeBb4vxJo0pxLZi_9s6iRBKvWC32yhAZBByqK2_8,590
+bella_companion/simulations/figures/epi_multitype.py,sha256=j85WgvN5AyAtX-CalMegr2lwlAZBmzyJxkikBPXRjCc,2629
+bella_companion/simulations/figures/epi_skyline.py,sha256=5wPGpQujxnSPasetM9lU07Or5ZC5j_h-LfVs6jdDzWc,1677
+bella_companion/simulations/figures/fbd_2traits.py,sha256=JiXrbYkH1HwdJQhTHXj6KhMEXYgQmQ6LmDboAIO1CPA,2728
+bella_companion/simulations/figures/fbd_no_traits.py,sha256=Hh2wDQFtk5nQTRSgApmtamn5xenWC5XhAlIk_xhOSII,1935
 bella_companion/simulations/figures/scenarios.py,sha256=gbMz1TUxxT2RSIq2kQlFioNdgSHk-gQY2OQuf6-7Fww,2817
 bella_companion/simulations/figures/utils.py,sha256=0M5OrxaEuqcj9rR2uAc_O7utQvhEceZGH0sKrGRWaWs,3129
 bella_companion/simulations/figures/explain/__init__.py,sha256=DnmVIWO65nTT5VsWnbS7NyYgKEY_eo4oMCtCY_ML2Vk,260
@@ -69,8 +71,8 @@ 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=xEyf-Jxk8fy71t3fko_Ic9WtUFSdLFE3w4tR17gaBPw,1868
-bella_companion-0.0.43.dist-info/METADATA,sha256=FHwaRLEDuz_6yvFM2QExhAlXKFQ3gdgV_Ez--8kk3BM,347
-bella_companion-0.0.43.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bella_companion-0.0.43.dist-info/entry_points.txt,sha256=SVEYDBrkBWPrOGwnEH2aO5TSVIAvfKE37sqm-9ut9jg,51
-bella_companion-0.0.43.dist-info/top_level.txt,sha256=q0loZYv4vf3zF_tOATyAJqeyLOEuPyLbObNqIGP7Fmc,16
-bella_companion-0.0.43.dist-info/RECORD,,
+bella_companion-0.0.44.dist-info/METADATA,sha256=yLCkFJaRBy303yaBpSoeoOOlzpPanoTybeG7PFr1sf0,347
+bella_companion-0.0.44.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bella_companion-0.0.44.dist-info/entry_points.txt,sha256=SVEYDBrkBWPrOGwnEH2aO5TSVIAvfKE37sqm-9ut9jg,51
+bella_companion-0.0.44.dist-info/top_level.txt,sha256=q0loZYv4vf3zF_tOATyAJqeyLOEuPyLbObNqIGP7Fmc,16
+bella_companion-0.0.44.dist-info/RECORD,,