Add MobileNet ONNX species classification and modernize BatBot

.gitattributes

@@ -2,3 +2,4 @@ examples/example3.wav filter=lfs diff=lfs merge=lfs -text
 examples/example4.wav filter=lfs diff=lfs merge=lfs -text
 examples/example1.wav filter=lfs diff=lfs merge=lfs -text
 examples/example2.wav filter=lfs diff=lfs merge=lfs -text
+batbot/classifier/models/onnx/batbot.mobilenet.9dc57ea3.onnx filter=lfs diff=lfs merge=lfs -text

.github/workflows/python-publish.yaml

@@ -1,4 +1,4 @@
-name: Wheel
+name: Python distributions
 
 on:
   pull_request:
@@ -9,123 +9,98 @@ on:
       - main
     tags:
       - v*
-  schedule:
-    - cron: '0 16 * * *' # Every day at 16:00 UTC (~09:00 PT)
 
 jobs:
-  build_wheels:
-    name: Build on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [3.12]
-
-    steps:
-      - name: Checkout code
-        uses: nschloe/action-cached-lfs-checkout@v1.2.3
-        with:
-          exclude: "examples/example[2-4].wav"
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v6
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Build wheel
-        run: |
-          pip install --upgrade pip
-          pip install build
-          python -m build --wheel --outdir dist/ .
-
-      - uses: actions/upload-artifact@v6
-        with:
-          name: artifact-wheel-${{ matrix.os }}-${{ matrix.python-version }}
-          path: ./dist/*.whl
-
-  build_sdist:
-    name: Build source distribution
+  build:
+    name: Build wheel and source distribution
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
         uses: nschloe/action-cached-lfs-checkout@v1.2.3
         with:
           exclude: "examples/example[2-4].wav"
 
-      - name: Set up Python 3.12
+      - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: '3.11'
+          cache: pip
 
-      - name: Build sdist
+      - name: Build and validate distributions
         run: |
-          pip install --upgrade pip
-          pip install build
-          python -m build --sdist --outdir dist/ .
+          python -m pip install --upgrade pip
+          python -m pip install build twine
+          python -m build --outdir dist/ .
+          python -m twine check dist/*
 
-      - uses: actions/upload-artifact@v6
+      - name: Upload distributions
+        uses: actions/upload-artifact@v6
         with:
-          name: artifact-sdist
-          path: ./dist/*.tar.gz
+          name: python-distributions
+          path: dist/
+          if-no-files-found: error
 
-  test_wheel:
-    needs: [build_wheels, build_sdist]
+  test-wheel:
+    name: Test the installed wheel and bundled model
+    needs: build
     runs-on: ubuntu-latest
-
-    # test wheel
-    if: github.event_name == 'push'
     steps:
-      - name: Set up Python 3.12
+      - name: Set up Python
         uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: '3.11'
+          cache: pip
 
-      - uses: actions/download-artifact@v7
+      - name: Download distributions
+        uses: actions/download-artifact@v7
         with:
-          path: artifact
+          name: python-distributions
+          path: dist
 
       - name: Install wheel
         run: |
-          pip install --upgrade pip
-          pip install wheel
-          find .
-          mkdir dist
-          cp artifact/*-ubuntu-*/*.whl dist/
-          cp artifact/*/*.tar.gz dist/
-          pip install dist/*.whl
+          python -m pip install --upgrade pip
+          python -m pip install dist/*.whl
 
-      - name: Test module
+      - name: Smoke test wheel outside the checkout
+        working-directory: ${{ runner.temp }}
         run: |
-          python -c "import batbot;"
-
-      # - name: Test CLI
-      #   run: |
-      #     batbot example
-
-  upload_pypi:
-    needs: [test_wheel]
-    runs-on: ubuntu-latest
-    # upload to PyPI on every tag starting with 'v'
+          python -I -c "import batbot; assert batbot.__version__"
+          batbot --help
+          python -I - <<'PY'
+          import tempfile
+          from pathlib import Path
+
+          import cv2
+          import numpy as np
+
+          from batbot import classifier
+
+          with tempfile.TemporaryDirectory() as directory:
+              image = Path(directory) / 'smoke.png'
+              cv2.imwrite(str(image), np.zeros((300, 700, 3), dtype=np.uint8))
+              result = classifier.Classifier().classify(image)[0]
+              assert result['label'] in classifier.CLASSES
+              assert len(result['scores']) == len(classifier.CLASSES)
+          PY
+
+  publish:
+    name: Publish to PyPI
+    needs: test-wheel
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+    runs-on: ubuntu-latest
     environment:
       name: pypi
       url: https://pypi.org/p/batbot
     permissions:
       id-token: write
+      contents: read
     steps:
-      - uses: actions/download-artifact@v7
+      - name: Download distributions
+        uses: actions/download-artifact@v7
         with:
-          path: artifact
+          name: python-distributions
+          path: dist
 
-      - name: Install wheel
-        run: |
-          find .
-          mkdir dist
-          cp artifact/*-ubuntu-*/*.whl dist/
-          cp artifact/*/*.tar.gz dist/
-
-      - name: Publish package distributions to PyPI
+      - name: Publish distributions with trusted publishing
         uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.BATBOT_PYPI_TOKEN }}

.github/workflows/testing.yaml

@@ -1,24 +1,24 @@
-# This workflow will install Python dependencies, run tests and lint with multiple versions of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Testing
 
-on: push
+on:
+  push:
+  pull_request:
+    branches:
+      - main
 
 jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.11', '3.12', '3.13', '3.14']
 
     env:
       OS: ubuntu-latest
       PYTHON: ${{ matrix.python-version }}
 
     steps:
-      # Checkout and env setup
       - name: Checkout code
         uses: nschloe/action-cached-lfs-checkout@v1.2.3
         with:
@@ -28,25 +28,21 @@ jobs:
         uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
+          cache: pip
 
-      - name: Install dependencies
+      - name: Install project and test tools
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements/runtime.txt
-          pip install -r requirements/optional.txt
-          pip install -e .
+          python -m pip install -e ".[test]" pre-commit
 
       - name: Check with pre-commit
-        run: |
-          SKIP=hadolint pre-commit
-          SKIP=hadolint pre-commit run --all-files
+        run: SKIP=hadolint pre-commit run --all-files
 
       - name: Run tests and coverage
-        run: |
-          set -ex
-          pytest --cov=batbot --cov-append --cov-report=xml --random-order-seed=1
+        run: pytest --cov-report=xml --random-order-seed=1
 
       - name: Upload coverage to Codecov
+        if: matrix.python-version == '3.11'
         continue-on-error: true
         uses: codecov/codecov-action@v5
         with:

.gitignore

@@ -21,3 +21,4 @@ example*.json
 .vscode/*
 
 assets/*.key
+assets/*.png

.pre-commit-config.yaml

@@ -2,46 +2,46 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/hadolint/hadolint
-    rev: v2.13.1-beta
+    rev: v2.15.1
     hooks:
       - id: hadolint
         name: Hadolint for Dockerfiles
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.20.0
+    rev: v3.21.2
     hooks:
       - id: pyupgrade
         name: pyupgrade
         description: Run PyUpgrade on Python code.
+        args: [--py311-plus]
   - repo: https://github.com/pycqa/isort
-    rev: 6.0.1
+    rev: 9.0.0b5
     hooks:
       - id: isort
-        args: [--settings-path setup.cfg]
+        args: [--settings-path, pyproject.toml]
         name: isort
         description: Run import sorting (isort) on Python code.
   - repo: https://github.com/psf/black
-    rev: 25.1.0
+    rev: 26.5.1
     hooks:
       - id: black
         name: Black for Python code formatting
         language_version: python3
-        args: ["--skip-string-normalization", "--target-version", "py310", "--line-length", "100"]
   - repo: https://github.com/pycqa/flake8
-    rev: 7.2.0
+    rev: 7.3.0
     hooks:
       - id: flake8
         name: Flake8 for Python code linting
-        args: ["--config", ".flake8"]
+        additional_dependencies: [flake8-pyproject==1.2.4]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: double-quote-string-fixer
         name: Format single quotes
-      - id: requirements-txt-fixer
-        name: Format requirements.txt
       - id: check-yaml
         name: Format YAML files
         args: ['--unsafe']
+      - id: check-toml
+        name: Format TOML files
       - id: trailing-whitespace
         name: Fix Whitespace
       - id: mixed-line-ending

.readthedocs.yaml

@@ -7,9 +7,9 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-   os: ubuntu-22.04
+   os: ubuntu-24.04
    tools:
-     python: "3.10"
+     python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -18,6 +18,7 @@ sphinx:
 # Optionally declare the Python requirements required to build your docs
 python:
    install:
-   - requirements: requirements/documentation.txt
    - method: pip
      path: .
+     extra_requirements:
+       - docs

CHANGELOG.rst

@@ -1,7 +1,13 @@
-=========
 Changelog
 =========
 
+Version 0.2.0
+-------------
+
+* Add MobileNet ONNX species classification for spectrogram images and WAV files.
+* Add ``classify``, ``classify-wav``, and ``classify-bulk`` CLI commands.
+* Add mirrored model retrieval, bulk species summaries, and a performance plotting example.
+
 TODO
 ----
 

Dockerfile

@@ -26,11 +26,8 @@ WORKDIR /code
 
 COPY ./ /code
 
-RUN python3 -m venv /venv
-
 # hadolint ignore=DL3003,DL3013
-RUN /venv/bin/pip install --no-cache-dir -r requirements/runtime.txt \
- && /venv/bin/pip install --no-cache-dir -r requirements/optional.txt \
+RUN python3 -m venv /venv \
  && /venv/bin/pip install --no-cache-dir -e .
  # && if [ "$(uname -m)" != "aarch64" ] \
  #       ; then \

ISSUES.rst

@@ -1,4 +1,3 @@
-============
 Known Issues
 ============
 

MANIFEST.in

@@ -6,3 +6,7 @@ include LICENSE
 
 # Include examples files for testing
 include examples/example1.wav
+include examples/plot_classifier_performance.py
+
+# Include the classifier model in source distributions
+recursive-include batbot/classifier/models/onnx *.onnx