bella-companion 0.0.44__tar.gz → 0.0.45__tar.gz

{bella_companion-0.0.44 → bella_companion-0.0.45}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: bella-companion
-Version: 0.0.44
+Version: 0.0.45
 Summary: Add your description here
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Requires-Dist: arviz>=0.22.0
 Requires-Dist: bella-lumiere>=0.0.14
 Requires-Dist: dotenv>=0.9.9
-Requires-Dist: phylogenie>=3.1.2
+Requires-Dist: phylogenie>=3.1.3
 Requires-Dist: poetry>=2.2.1
 Requires-Dist: seaborn>=0.13.2

{bella_companion-0.0.44 → bella_companion-0.0.45}/bella_companion/cli.py

@@ -7,10 +7,10 @@ from dotenv import load_dotenv
 from bella_companion.eucovid import run_beast as run_eucovid_beast
 from bella_companion.platyrrhine import plot_platyrrhine_results
 from bella_companion.platyrrhine import run_beast as run_platyrrhine
-from bella_companion.platyrrhine import summarize_logs as summarize_platyrrhine
+from bella_companion.platyrrhine import summarize as summarize_platyrrhine
 from bella_companion.simulations import generate_data, generate_figures, print_metrics
 from bella_companion.simulations import run_beast as run_simulations
-from bella_companion.simulations import summarize_logs as summarize_simulations
+from bella_companion.simulations import summarize as summarize_simulations
 
 
 def main():

bella_companion-0.0.45/bella_companion/platyrrhine/__init__.py

@@ -0,0 +1,5 @@
+from bella_companion.platyrrhine.results import plot_platyrrhine_results
+from bella_companion.platyrrhine.run_beast import run_beast
+from bella_companion.platyrrhine.summarize import summarize
+
+__all__ = ["plot_platyrrhine_results", "run_beast", "summarize"]

bella_companion-0.0.45/bella_companion/platyrrhine/results.py

@@ -0,0 +1,109 @@
+import os
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import numpy as np
+import polars as pl
+from numpy.typing import NDArray
+from phylogenie import draw_tree, get_node_depths, load_newick, load_nexus
+
+
+def _plot_tree(output_dir: Path, tree_file: str | Path):
+    sample_trees = load_nexus(tree_file)
+    trees = [sample_trees[f"STATE_{i*100_000}"] for i in range(11, 101)]
+
+    for tree in trees:
+        for node in tree:
+            if node.parent is not None and not node.branch_length:
+                node.parent.remove_child(node)
+
+    avg_tree = trees[0].copy()
+    for node in avg_tree:
+        node.clear()
+    for avg_node, nodes in zip(avg_tree, zip(*trees)):
+        avg_node.set("birthRateSP", np.mean([n["birthRateSP"] for n in nodes]))
+        avg_node.set("deathRateSP", np.mean([n["deathRateSP"] for n in nodes]))
+
+    avg_tree.ladderize()
+    for rate in ["birthRateSP", "deathRateSP"]:
+        ax = plt.gca()
+        draw_tree(
+            avg_tree,
+            ax,
+            color_by=rate,
+            hist_axes_kwargs={
+                "loc": "upper left",
+                "bbox_to_anchor": (0.06, 0, 1, 1),
+                "bbox_transform": ax.transAxes,
+            },
+        )
+        height = avg_tree.height
+        ticks = np.arange(height, 0, -10)
+        ax.set_xticks(ticks, [str(round(height - t)) for t in ticks])  # pyright: ignore
+        plt.xlabel("Time (mya)")  # pyright: ignore
+        plt.savefig(output_dir / f"{rate}-tree.svg")  # pyright: ignore
+        plt.close()
+
+
+def _plot_predictions(output_dir: Path, log_summary_file: str | Path):
+    log_summary = pl.read_csv(log_summary_file)
+
+    data_dir = Path(__file__).parent / "data"
+    change_times = (
+        pl.read_csv(data_dir / "change_times.csv", has_header=False)
+        .to_series()
+        .to_list()
+    )
+    max_time = max(
+        max(get_node_depths(tree).values())
+        for tree in load_newick(data_dir / "trees.nwk")
+    )
+    time_bins = list(reversed([0.0, *change_times, max_time]))
+
+    gradient = np.linspace(0.4, 0.9, 4)
+    colors: dict[str, NDArray[np.floating]] = {
+        "birthRateSP": plt.cm.Blues(gradient),  # pyright: ignore
+        "deathRateSP": plt.cm.Oranges(gradient),  # pyright: ignore
+        "diversificationRateSP": plt.cm.Greens(gradient),  # pyright: ignore
+    }
+    for rate in colors:
+        for type in [0, 1, 2, 3]:
+            if rate == "diversificationRateSP":
+                estimates = log_summary.select(
+                    [
+                        pl.col(f"birthRateSPi{i}_{type}_median")
+                        - pl.col(f"deathRateSPi{i}_{type}_median")
+                        for i in range(len(change_times) + 1)
+                    ]
+                ).to_numpy()
+            else:
+                estimates = log_summary.select(
+                    [
+                        pl.col(f"{rate}i{i}_{type}_median")
+                        for i in range(len(change_times) + 1)
+                    ]
+                ).to_numpy()
+            median = np.median(estimates, axis=0)
+            color = colors[rate][type]
+            plt.step(  # pyright: ignore
+                time_bins, [median[0], *median], color=color, label=type
+            )
+
+        plt.gca().invert_xaxis()
+        plt.legend(title="Body mass")  # pyright: ignore
+        plt.xlabel("Time (mya)")  # pyright: ignore
+        plt.ylabel(  # pyright: ignore
+            r"$\lambda$"
+            if rate == "birthRateSP"
+            else r"$\mu$" if rate == "deathRateSP" else r"$d$"
+        )
+        plt.savefig(output_dir / f"{rate}-predictions.svg")  # pyright: ignore
+        plt.close()
+
+
+def plot_platyrrhine_results():
+    summaries_dir = Path(os.environ["BELLA_SUMMARIES_DIR"]) / "platyrrhine"
+    output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "platyrrhine"
+    os.makedirs(output_dir, exist_ok=True)
+    _plot_predictions(output_dir, summaries_dir / "MLP.csv")
+    _plot_tree(output_dir, summaries_dir / "sample-trees.nexus")

bella_companion-0.0.44/bella_companion/platyrrhine/summarize_logs.py → bella_companion-0.0.45/bella_companion/platyrrhine/summarize.py

@@ -5,13 +5,13 @@ from pathlib import Path
 
 import joblib
 import polars as pl
-from phylogenie import Tree, load_nexus
+from phylogenie import Tree, dump_newick, load_nexus
 from tqdm import tqdm
 
 from bella_companion.utils import read_weights_dir, summarize_logs_dir
 
 
-def summarize_logs():
+def summarize():
     data_dir = Path(__file__).parent / "data"
     change_times = pl.read_csv(data_dir / "change_times.csv", has_header=False)
     n_time_bins = len(change_times) + 1
@@ -28,14 +28,14 @@ def summarize_logs():
     )
     weights = read_weights_dir(logs_dir)
 
-    summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"], "platyrrhine")
+    summaries_dir = Path(os.environ["BELLA_SUMMARIES_DIR"], "platyrrhine")
     os.makedirs(summaries_dir, exist_ok=True)
     summaries.write_csv(summaries_dir / "MLP.csv")
     joblib.dump(weights, summaries_dir / "MLP.weights.pkl")
 
     trees: list[Tree] = []
     for tree_file in tqdm(glob(str(logs_dir / "*.trees")), "Summarizing trees"):
-        trees.extend(list(load_nexus(tree_file).values())[:-10])
-    joblib.dump(trees, summaries_dir / "trees.pkl")
+        trees.extend(list(load_nexus(tree_file).values())[-10:])
+    dump_newick(trees, summaries_dir / "trees.nwk")
 
-    shutil.copy(logs_dir / "0.trees", summaries_dir / "sample-tree.nexus")
+    shutil.copy(logs_dir / "0.trees", summaries_dir / "sample-trees.nexus")

{bella_companion-0.0.44 → bella_companion-0.0.45}/bella_companion/simulations/__init__.py

@@ -2,12 +2,12 @@ from bella_companion.simulations.generate_data import generate_data
 from bella_companion.simulations.generate_figures import generate_figures
 from bella_companion.simulations.metrics import print_metrics
 from bella_companion.simulations.run_beast import run_beast
-from bella_companion.simulations.summarize_logs import summarize_logs
+from bella_companion.simulations.summarize import summarize
 
 __all__ = [
     "generate_data",
     "generate_figures",
     "print_metrics",
     "run_beast",
-    "summarize_logs",
+    "summarize",
 ]

{bella_companion-0.0.44 → bella_companion-0.0.45}/bella_companion/simulations/figures/epi_multitype.py

@@ -58,10 +58,10 @@ def plot_epi_multitype_results():
     output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "epi-multitype"
     os.makedirs(output_dir, exist_ok=True)
 
-    log_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"]) / "epi-multitype"
+    summaries_dir = Path(os.environ["BELLA_SUMMARIES_DIR"]) / "epi-multitype"
     model = "MLP-32_16"
-    log_summary = pl.read_csv(log_dir / f"{model}.csv")
-    weights = joblib.load(log_dir / f"{model}.weights.pkl")
+    log_summary = pl.read_csv(summaries_dir / f"{model}.csv")
+    weights = joblib.load(summaries_dir / f"{model}.weights.pkl")
     weights = [w["migrationRate"] for w in weights]
 
     _plot_predictions(log_summary, output_dir)

{bella_companion-0.0.44 → bella_companion-0.0.45}/bella_companion/simulations/figures/epi_skyline.py

@@ -17,7 +17,7 @@ def plot_epi_skyline_results():
     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}"
+        summaries_dir = Path(os.environ["BELLA_SUMMARIES_DIR"]) / f"epi-skyline_{i}"
         logs_summaries = {
             "Nonparametric": pl.read_csv(summaries_dir / "Nonparametric.csv"),
             "GLM": pl.read_csv(summaries_dir / "GLM.csv"),

{bella_companion-0.0.44 → bella_companion-0.0.45}/bella_companion/simulations/figures/fbd_2traits.py

@@ -58,10 +58,10 @@ def _plot_predictions(log_summary: pl.DataFrame, output_dir: Path):
 def plot_fbd_2traits_results():
     output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "fbd-2traits"
 
-    log_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"]) / "fbd-2traits"
+    summaries_dir = Path(os.environ["BELLA_SUMMARIES_DIR"]) / "fbd-2traits"
     model = "MLP-32_16"
-    log_summary = pl.read_csv(log_dir / f"{model}.csv")
-    weights = joblib.load(log_dir / f"{model}.weights.pkl")
+    log_summary = pl.read_csv(summaries_dir / f"{model}.csv")
+    weights = joblib.load(summaries_dir / f"{model}.weights.pkl")
 
     for rate in RATES:
         os.makedirs(output_dir / rate, exist_ok=True)

{bella_companion-0.0.44 → bella_companion-0.0.45}/bella_companion/simulations/figures/fbd_no_traits.py

@@ -17,9 +17,7 @@ def plot_fbd_no_traits_results():
     base_output = Path(os.environ["BELLA_FIGURES_DIR"]) / "fbd-no-traits"
 
     for i, rates in enumerate(RATES, start=1):
-        summaries_dir = (
-            Path(os.environ["BELLA_LOG_SUMMARIES_DIR"]) / f"fbd-no-traits_{i}"
-        )
+        summaries_dir = Path(os.environ["BELLA_SUMMARIES_DIR"]) / f"fbd-no-traits_{i}"
         logs_summaries = {
             "Nonparametric": pl.read_csv(summaries_dir / "Nonparametric.csv"),
             "GLM": pl.read_csv(summaries_dir / "GLM.csv"),

{bella_companion-0.0.44 → bella_companion-0.0.45}/bella_companion/simulations/metrics.py

@@ -36,7 +36,7 @@ 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"])
+    base_summaries_dir = Path(os.environ["BELLA_SUMMARIES_DIR"])
     metrics = {}
     for name, scenario in SCENARIOS.items():
         summaries_dir = base_summaries_dir / name

bella_companion-0.0.44/bella_companion/simulations/summarize_logs.py → bella_companion-0.0.45/bella_companion/simulations/summarize.py

@@ -8,13 +8,13 @@ from bella_companion.simulations.scenarios import SCENARIOS
 from bella_companion.utils import read_weights_dir, summarize_logs_dir
 
 
-def summarize_logs():
+def summarize():
     output_dir = Path(os.environ["BELLA_BEAST_OUTPUT_DIR"])
     with open(output_dir / "simulations_job_ids.json", "r") as f:
         job_ids: dict[str, dict[str, dict[str, str]]] = json.load(f)
 
     for scenario_name, scenario in SCENARIOS.items():
-        summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"]) / scenario_name
+        summaries_dir = Path(os.environ["BELLA_SUMMARIES_DIR"]) / scenario_name
         os.makedirs(summaries_dir, exist_ok=True)
         for model in job_ids[scenario_name]:
             logs_dir = output_dir / scenario_name / model

{bella_companion-0.0.44 → bella_companion-0.0.45}/bella_companion.egg-info/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.4
 Name: bella-companion
-Version: 0.0.44
+Version: 0.0.45
 Summary: Add your description here
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Requires-Dist: arviz>=0.22.0
 Requires-Dist: bella-lumiere>=0.0.14
 Requires-Dist: dotenv>=0.9.9
-Requires-Dist: phylogenie>=3.1.2
+Requires-Dist: phylogenie>=3.1.3
 Requires-Dist: poetry>=2.2.1
 Requires-Dist: seaborn>=0.13.2

{bella_companion-0.0.44 → bella_companion-0.0.45}/bella_companion.egg-info/SOURCES.txt

@@ -10,8 +10,12 @@ bella_companion.egg-info/dependency_links.txt
 bella_companion.egg-info/entry_points.txt
 bella_companion.egg-info/requires.txt
 bella_companion.egg-info/top_level.txt
+bella_companion/__pycache__/__init__.cpython-310.pyc
+bella_companion/__pycache__/cli.cpython-310.pyc
 bella_companion/eucovid/__init__.py
 bella_companion/eucovid/run_beast.py
+bella_companion/eucovid/__pycache__/__init__.cpython-310.pyc
+bella_companion/eucovid/__pycache__/run_beast.cpython-310.pyc
 bella_companion/eucovid/beast_configs/GLM.xml
 bella_companion/eucovid/beast_configs/MLP.xml
 bella_companion/eucovid/beast_configs/Nonparametric.xml
@@ -35,7 +39,12 @@ bella_companion/platyrrhine/__init__.py
 bella_companion/platyrrhine/beast_config.xml
 bella_companion/platyrrhine/results.py
 bella_companion/platyrrhine/run_beast.py
-bella_companion/platyrrhine/summarize_logs.py
+bella_companion/platyrrhine/summarize.py
+bella_companion/platyrrhine/__pycache__/__init__.cpython-310.pyc
+bella_companion/platyrrhine/__pycache__/results.cpython-310.pyc
+bella_companion/platyrrhine/__pycache__/run_beast.cpython-310.pyc
+bella_companion/platyrrhine/__pycache__/summarize.cpython-310.pyc
+bella_companion/platyrrhine/__pycache__/summarize_logs.cpython-310.pyc
 bella_companion/platyrrhine/data/change_times.csv
 bella_companion/platyrrhine/data/traits.csv
 bella_companion/platyrrhine/data/trees.nwk
@@ -45,7 +54,15 @@ bella_companion/simulations/generate_data.py
 bella_companion/simulations/generate_figures.py
 bella_companion/simulations/metrics.py
 bella_companion/simulations/run_beast.py
-bella_companion/simulations/summarize_logs.py
+bella_companion/simulations/summarize.py
+bella_companion/simulations/__pycache__/__init__.cpython-310.pyc
+bella_companion/simulations/__pycache__/features.cpython-310.pyc
+bella_companion/simulations/__pycache__/generate_data.cpython-310.pyc
+bella_companion/simulations/__pycache__/generate_figures.cpython-310.pyc
+bella_companion/simulations/__pycache__/metrics.cpython-310.pyc
+bella_companion/simulations/__pycache__/run_beast.cpython-310.pyc
+bella_companion/simulations/__pycache__/summarize.cpython-310.pyc
+bella_companion/simulations/__pycache__/summarize_logs.cpython-310.pyc
 bella_companion/simulations/beast_configs/epi-multitype/GLM.xml
 bella_companion/simulations/beast_configs/epi-multitype/MLP.xml
 bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml
@@ -65,9 +82,19 @@ 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/__pycache__/__init__.cpython-310.pyc
+bella_companion/simulations/figures/__pycache__/epi_multitype.cpython-310.pyc
+bella_companion/simulations/figures/__pycache__/epi_skyline.cpython-310.pyc
+bella_companion/simulations/figures/__pycache__/fbd_2traits.cpython-310.pyc
+bella_companion/simulations/figures/__pycache__/fbd_no_traits.cpython-310.pyc
+bella_companion/simulations/figures/__pycache__/scenarios.cpython-310.pyc
+bella_companion/simulations/figures/__pycache__/utils.cpython-310.pyc
 bella_companion/simulations/figures/explain/__init__.py
 bella_companion/simulations/figures/explain/pdp.py
 bella_companion/simulations/figures/explain/shap.py
+bella_companion/simulations/figures/explain/__pycache__/__init__.cpython-310.pyc
+bella_companion/simulations/figures/explain/__pycache__/pdp.cpython-310.pyc
+bella_companion/simulations/figures/explain/__pycache__/shap.cpython-310.pyc
 bella_companion/simulations/scenarios/__init__.py
 bella_companion/simulations/scenarios/common.py
 bella_companion/simulations/scenarios/epi_multitype.py
@@ -75,7 +102,18 @@ bella_companion/simulations/scenarios/epi_skyline.py
 bella_companion/simulations/scenarios/fbd_2traits.py
 bella_companion/simulations/scenarios/fbd_no_traits.py
 bella_companion/simulations/scenarios/scenario.py
+bella_companion/simulations/scenarios/__pycache__/__init__.cpython-310.pyc
+bella_companion/simulations/scenarios/__pycache__/common.cpython-310.pyc
+bella_companion/simulations/scenarios/__pycache__/epi_multitype.cpython-310.pyc
+bella_companion/simulations/scenarios/__pycache__/epi_skyline.cpython-310.pyc
+bella_companion/simulations/scenarios/__pycache__/fbd_2traits.cpython-310.pyc
+bella_companion/simulations/scenarios/__pycache__/fbd_no_traits.cpython-310.pyc
+bella_companion/simulations/scenarios/__pycache__/scenario.cpython-310.pyc
 bella_companion/utils/__init__.py
 bella_companion/utils/beast.py
 bella_companion/utils/explain.py
-bella_companion/utils/slurm.py
+bella_companion/utils/slurm.py
+bella_companion/utils/__pycache__/__init__.cpython-310.pyc
+bella_companion/utils/__pycache__/beast.cpython-310.pyc
+bella_companion/utils/__pycache__/explain.cpython-310.pyc
+bella_companion/utils/__pycache__/slurm.cpython-310.pyc

{bella_companion-0.0.44 → bella_companion-0.0.45}/bella_companion.egg-info/requires.txt

@@ -1,6 +1,6 @@
 arviz>=0.22.0
 bella-lumiere>=0.0.14
 dotenv>=0.9.9
-phylogenie>=3.1.2
+phylogenie>=3.1.3
 poetry>=2.2.1
 seaborn>=0.13.2

{bella_companion-0.0.44 → bella_companion-0.0.45}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "bella-companion"
-version = "0.0.44"
+version = "0.0.45"
 description = "Add your description here"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -8,7 +8,7 @@ dependencies = [
     "arviz>=0.22.0",
     "bella-lumiere>=0.0.14",
     "dotenv>=0.9.9",
-    "phylogenie>=3.1.2",
+    "phylogenie>=3.1.3",
     "poetry>=2.2.1",
     "seaborn>=0.13.2",
 ]

bella_companion-0.0.44/bella_companion/platyrrhine/__init__.py

@@ -1,5 +0,0 @@
-from bella_companion.platyrrhine.results import plot_platyrrhine_results
-from bella_companion.platyrrhine.run_beast import run_beast
-from bella_companion.platyrrhine.summarize_logs import summarize_logs
-
-__all__ = ["plot_platyrrhine_results", "run_beast", "summarize_logs"]

bella_companion-0.0.44/bella_companion/platyrrhine/results.py

@@ -1,69 +0,0 @@
-import os
-from pathlib import Path
-
-import matplotlib.pyplot as plt
-import numpy as np
-import polars as pl
-from numpy.typing import NDArray
-from phylogenie import get_node_depths, load_newick
-
-
-def _plot_predictions(output_dir: Path):
-    log_summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"])
-    log_summary = pl.read_csv(log_summaries_dir / "platyrrhine" / "MLP.csv")
-
-    data_dir = Path(__file__).parent / "data"
-    change_times = (
-        pl.read_csv(data_dir / "change_times.csv", has_header=False)
-        .to_series()
-        .to_list()
-    )
-    max_time = max(
-        max(get_node_depths(tree).values())
-        for tree in load_newick(data_dir / "trees.nwk")
-    )
-    time_bins = list(reversed([0.0, *change_times, max_time]))
-
-    colors: dict[str, NDArray[np.floating]] = {
-        "birth": plt.cm.Blues(np.linspace(0.4, 0.9, 4)),  # pyright: ignore
-        "death": plt.cm.Oranges(np.linspace(0.4, 0.9, 4)),  # pyright: ignore
-        "diversification": plt.cm.Greens(np.linspace(0.4, 0.9, 4)),  # pyright: ignore
-    }
-    for rate in ["birth", "death", "diversification"]:
-        for type in [0, 1, 2, 3]:
-            if rate == "diversification":
-                estimates = log_summary.select(
-                    [
-                        pl.col(f"birthRateSPi{i}_{type}_median")
-                        - pl.col(f"deathRateSPi{i}_{type}_median")
-                        for i in range(len(change_times) + 1)
-                    ]
-                ).to_numpy()
-            else:
-                estimates = log_summary.select(
-                    [
-                        pl.col(f"{rate}RateSPi{i}_{type}_median")
-                        for i in range(len(change_times) + 1)
-                    ]
-                ).to_numpy()
-            median = np.median(estimates, axis=0)
-            color = colors[rate][type]
-            plt.step(  # pyright: ignore
-                time_bins, [median[0], *median], color=color, label=type
-            )
-
-        ax = plt.gca()
-        ax.invert_xaxis()
-        plt.legend(title="Body mass")  # pyright: ignore
-        plt.xlabel("Time (mya)")  # pyright: ignore
-        plt.ylabel(  # pyright: ignore
-            r"$\lambda$" if rate == "birth" else r"$\mu$" if rate == "death" else r"$d$"
-        )
-        plt.savefig(output_dir / f"{rate}-predictions.svg")  # pyright: ignore
-        plt.close()
-
-
-def plot_platyrrhine_results():
-    output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "platyrrhine"
-    os.makedirs(output_dir, exist_ok=True)
-    _plot_predictions(output_dir)