bella-companion 0.0.42__py3-none-any.whl → 0.0.43__py3-none-any.whl

bella_companion/simulations/figures/epi_skyline_results.py

@@ -14,7 +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"
+    output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "epi-skyline"
     os.makedirs(output_dir, exist_ok=True)
 
     for i, reproduction_number in enumerate(REPRODUCTION_NUMBERS, start=1):

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/simulations/figures/fbd_no_traits_results.py

@@ -14,7 +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"
+    output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "fbd-no-traits"
     os.makedirs(output_dir, exist_ok=True)
 
     for i, rates in enumerate(RATES, start=1):

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
     },

{bella_companion-0.0.42.dist-info → bella_companion-0.0.43.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bella-companion
-Version: 0.0.42
+Version: 0.0.43
 Summary: Add your description here
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown

{bella_companion-0.0.42.dist-info → bella_companion-0.0.43.dist-info}/RECORD

@@ -50,27 +50,27 @@ bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml,sha256=JE_cGh2DW
 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=gI5Ha-OIEShcZLmqVuy0W8hJzkrsydQE-Coa65_BFCo,1667
+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=fLsgpV3IbLLtxQEFNOL9K4jEEJrG324ziUM0rxIv7_k,1962
+bella_companion/simulations/figures/fbd_no_traits_results.py,sha256=kwDbgUTQUk-LXAvMGvKf1kInFvK7kTJld4BWpgS1sVU,1950
 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
 bella_companion/simulations/figures/explain/pdp.py,sha256=3n3ssgufW_43pn2hO5V5J_jgcJH3Fpb8stIRtTnlQ8w,3801
-bella_companion/simulations/figures/explain/shap.py,sha256=qRfOMNwkU-hsBy5MHMTfVFAszaPESVOugCKQTVY8Q4Y,1940
+bella_companion/simulations/figures/explain/shap.py,sha256=1PkbCgynbW-PXkkRpIcY7JoBYqOxqmu1OEOif_roFY8,2207
 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=fTkFeGHxyV_1f2nX3g_Oyr_e6wkorhXEicJjIAgeZKA,2439
 bella_companion/simulations/scenarios/epi_skyline.py,sha256=JqnOVATECxBUqEbkR5lBlMI2O8k4hO6ipR8k9cHUsm0,2365
-bella_companion/simulations/scenarios/fbd_2traits.py,sha256=5UmrDlxdCMWOF0v9_0c1Yh0TyaE_FKEdxhSzHNofwQY,3541
+bella_companion/simulations/scenarios/fbd_2traits.py,sha256=-amB3NX0GsVgYbFuHH71t93FuXUEnRUyhWf2Qpcpia4,3541
 bella_companion/simulations/scenarios/fbd_no_traits.py,sha256=R6CH0fVeQg-Iesl39pq2uY8ICVEO4VZbvUVUCGwauJU,2520
 bella_companion/simulations/scenarios/scenario.py,sha256=_FRWAyOFbw94lAzd3zCD-1ek4TrssoiXfXRQPShLiIA,620
 bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7UpYw,480
 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-0.0.42.dist-info/METADATA,sha256=FY_Ja-RMCMyymPVti1WDLQLOtd5ie4rzWl3Zjj6ZJCg,347
-bella_companion-0.0.42.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bella_companion-0.0.42.dist-info/entry_points.txt,sha256=SVEYDBrkBWPrOGwnEH2aO5TSVIAvfKE37sqm-9ut9jg,51
-bella_companion-0.0.42.dist-info/top_level.txt,sha256=q0loZYv4vf3zF_tOATyAJqeyLOEuPyLbObNqIGP7Fmc,16
-bella_companion-0.0.42.dist-info/RECORD,,
+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,,