From 2b582fc2a01165ad505c6bc4ddac54fed7cd574f Mon Sep 17 00:00:00 2001 From: mbsantiago Date: Sat, 8 Aug 2026 13:39:32 +0100 Subject: [PATCH 1/3] Fix typing issues --- src/batdetect2/outputs/formats/parquet.py | 9 +++++++-- src/batdetect2/plotting/detections.py | 8 ++++---- src/batdetect2/plotting/heatmaps.py | 4 ++-- 3 files changed, 13 insertions(+), 8 deletions(-) diff --git a/src/batdetect2/outputs/formats/parquet.py b/src/batdetect2/outputs/formats/parquet.py index 909fa9d..fdd3e7b 100644 --- a/src/batdetect2/outputs/formats/parquet.py +++ b/src/batdetect2/outputs/formats/parquet.py @@ -1,5 +1,5 @@ from pathlib import Path -from typing import List, Literal, Sequence +from typing import List, Literal, Sequence, TypedDict from uuid import UUID import numpy as np @@ -26,6 +26,11 @@ class ParquetOutputConfig(BaseConfig): include_geometry: bool = True +class ClipInfo(TypedDict): + clip: data.Clip + preds: list[Detection] + + class ParquetFormatter(OutputFormatterProtocol[ClipDetections]): def __init__( self, @@ -120,7 +125,7 @@ class ParquetFormatter(OutputFormatterProtocol[ClipDetections]): else: df = pd.read_parquet(path) - predictions_by_clip = {} + predictions_by_clip: dict[UUID, ClipInfo] = {} for _, row in df.iterrows(): clip_uuid = row["clip_uuid"] diff --git a/src/batdetect2/plotting/detections.py b/src/batdetect2/plotting/detections.py index f25a111..ef96532 100644 --- a/src/batdetect2/plotting/detections.py +++ b/src/batdetect2/plotting/detections.py @@ -185,25 +185,25 @@ def plot_clip_evaluation( label="found GT", edgecolor=gt_color, facecolor="none" if not fill else gt_color, - linestyle=gt_linestyle, + linestyle=gt_linestyle, # type: ignore ), patches.Patch( label="missed GT", edgecolor=missed_gt_color, facecolor="none" if not fill else missed_gt_color, - linestyle=missed_gt_linestyle, + linestyle=missed_gt_linestyle, # type: ignore ), patches.Patch( label="true Det", edgecolor=true_pred_color, facecolor="none" if not fill else true_pred_color, - linestyle=true_pred_linestyle, + linestyle=true_pred_linestyle, # type: ignore ), patches.Patch( label="false Det", edgecolor=false_pred_color, facecolor="none" if not fill else false_pred_color, - linestyle=false_pred_linestyle, + linestyle=false_pred_linestyle, # type: ignore ), ] ) diff --git a/src/batdetect2/plotting/heatmaps.py b/src/batdetect2/plotting/heatmaps.py index 9f4021f..8f10330 100644 --- a/src/batdetect2/plotting/heatmaps.py +++ b/src/batdetect2/plotting/heatmaps.py @@ -1,9 +1,9 @@ """Plot heatmaps.""" +import matplotlib.pyplot as plt import numpy as np import torch from matplotlib import axes, patches -from matplotlib.cm import get_cmap from matplotlib.colors import Colormap, LinearSegmentedColormap, to_rgba from batdetect2.plotting.common import create_ax @@ -80,7 +80,7 @@ def plot_classification_heatmap( raise ValueError("Inconsistent number of class names") if not isinstance(cmap, Colormap): - cmap = get_cmap(cmap) + cmap = plt.get_cmap(cmap) handles = [] From f4a0421ef3ae689d895550dab86b2ad4a3378649 Mon Sep 17 00:00:00 2001 From: mbsantiago Date: Sat, 8 Aug 2026 13:40:15 +0100 Subject: [PATCH 2/3] build: trim runtime dependencies --- pyproject.toml | 7 +- uv.lock | 4734 ++++++++++++++++++++++++------------------------ 2 files changed, 2371 insertions(+), 2370 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index b253de9..3be4922 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,10 +11,9 @@ dependencies = [ "deepmerge>=2.0", "hydra-core>=1.3.2", "librosa>=0.10.1", - "lightning[extra]==2.5.0", + "lightning==2.5.0", "loguru>=0.7.3", "matplotlib>=3.7.1", - "netcdf4>=1.6.5", "numpy>=1.23.5", "pandas>=1.5.3", "pydantic>=2.0.0", @@ -24,9 +23,10 @@ dependencies = [ "seaborn>=0.13.2", "soundevent[audio,geometry,plot]>=2.10.0", "soundfile>=0.12.1", - "tensorboard>=2.16.2", + "tabulate>=0.10.0", "torch>=2.0.0", "torchaudio>=2.0.0", + "tqdm>=4.70.0", "xarray>=2024.0.0", ] 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