bella-companion 0.0.42__tar.gz → 0.0.44__tar.gz

{bella_companion-0.0.42 → bella_companion-0.0.44}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bella-companion
-Version: 0.0.42
+Version: 0.0.44
 Summary: Add your description here
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{bella_companion-0.0.42 → bella_companion-0.0.44}/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-0.0.44/bella_companion/simulations/figures/__init__.py

@@ -0,0 +1,13 @@
+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__ = [
+    "plot_epi_multitype_results",
+    "plot_epi_skyline_results",
+    "plot_fbd_2traits_results",
+    "plot_fbd_no_traits_results",
+    "plot_scenarios",
+]

bella_companion-0.0.42/bella_companion/simulations/figures/epi_skyline_results.py → bella_companion-0.0.44/bella_companion/simulations/figures/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-results"
-    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-0.0.42 → bella_companion-0.0.44}/bella_companion/simulations/figures/explain/shap.py

@@ -1,6 +1,7 @@
 from functools import partial
 from itertools import product
 from pathlib import Path
+from typing import Callable
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -43,13 +44,18 @@ def plot_shap_features_importance(
     )  # shape: (n_runs, n_features)
     features_importances /= features_importances.sum(axis=1, keepdims=True)
 
-    for i, (feature_name, feature) in enumerate(features.items()):
-        sns.violinplot(
-            y=features_importances[:, i],
-            x=[feature_name] * len(features_importances),
-            cut=0,
-            color="#E74C3C" if feature.is_relevant else "gray",
-        )
+    def _plot_violins(group_check: Callable[[Feature], bool]):
+        for i, (feature_name, feature) in enumerate(features.items()):
+            if group_check(feature):
+                sns.violinplot(
+                    y=features_importances[:, i],
+                    x=[feature_name] * len(features_importances),
+                    cut=0,
+                    color="#E74C3C" if feature.is_relevant else "gray",
+                )
+
+    _plot_violins(lambda f: not f.is_binary)
+    _plot_violins(lambda f: f.is_binary)
     plt.xlabel("Feature")  # pyright: ignore
     plt.ylabel("Importance")  # pyright: ignore
     plt.savefig(output_file)  # pyright: ignore

bella_companion-0.0.42/bella_companion/simulations/figures/fbd_no_traits_results.py → bella_companion-0.0.44/bella_companion/simulations/figures/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-predictions"
-    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-0.0.42 → bella_companion-0.0.44}/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-0.0.44/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-0.0.42 → bella_companion-0.0.44}/bella_companion.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bella-companion
-Version: 0.0.42
+Version: 0.0.44
 Summary: Add your description here
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{bella_companion-0.0.42 → bella_companion-0.0.44}/bella_companion.egg-info/SOURCES.txt

@@ -1,7 +1,9 @@
 README.md
 pyproject.toml
+bella_companion/BELLA.jar
 bella_companion/__init__.py
 bella_companion/cli.py
+bella_companion/version.xml
 bella_companion.egg-info/PKG-INFO
 bella_companion.egg-info/SOURCES.txt
 bella_companion.egg-info/dependency_links.txt
@@ -57,10 +59,10 @@ bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml
 bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml
 bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml
 bella_companion/simulations/figures/__init__.py
-bella_companion/simulations/figures/epi_multitype_results.py
-bella_companion/simulations/figures/epi_skyline_results.py
-bella_companion/simulations/figures/fbd_2traits_results.py
-bella_companion/simulations/figures/fbd_no_traits_results.py
+bella_companion/simulations/figures/epi_multitype.py
+bella_companion/simulations/figures/epi_skyline.py
+bella_companion/simulations/figures/fbd_2traits.py
+bella_companion/simulations/figures/fbd_no_traits.py
 bella_companion/simulations/figures/scenarios.py
 bella_companion/simulations/figures/utils.py
 bella_companion/simulations/figures/explain/__init__.py

{bella_companion-0.0.42 → bella_companion-0.0.44}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "bella-companion"
-version = "0.0.42"
+version = "0.0.44"
 description = "Add your description here"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -28,5 +28,8 @@ bella = "bella_companion.cli:main"
 requires = ["setuptools>=42"]
 build-backend = "setuptools.build_meta"
 
+[tool.setuptools]
+packages = ["bella_companion"]
+
 [tool.setuptools.package-data]
 bella_companion = ["**/*"]

bella_companion-0.0.42/bella_companion/simulations/figures/__init__.py

@@ -1,21 +0,0 @@
-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.scenarios import plot_scenarios
-
-__all__ = [
-    "plot_epi_multitype_results",
-    "plot_epi_skyline_results",
-    "plot_fbd_2traits_results",
-    "plot_fbd_no_traits_results",
-    "plot_scenarios",
-]

{bella_companion-0.0.42 → bella_companion-0.0.44}/bella_companion/simulations/scenarios/fbd_2traits.py

@@ -89,9 +89,9 @@ SCENARIO = Scenario(
     features={
         f"{rate}Rate": {
             "timePredictor": Feature(is_binary=False, is_relevant=True),
-            "randomPredictor": Feature(is_binary=False, is_relevant=False),
             "trait1Predictor": Feature(is_binary=True, is_relevant=True),
             "trait2Predictor": Feature(is_binary=True, is_relevant=False),
+            "randomPredictor": Feature(is_binary=False, is_relevant=False),
         }
         for rate in RATES
     },