sleap-nn 0.0.1__tar.gz

sleap_nn-0.0.1/.claude/commands/coverage.md

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+Run tests with coverage.
+
+Command to run:
+```
+pytest -q --maxfail=1 --cov=sleap_nn --cov-branch tests/ && rm -f .coverage.* && python -m coverage annotate
+```
+
+The result will be the terminal output and the line-by-line coverage will be in files sitting next to each module with the file naming `{module_name.py},cover`. 
+
+If you are working on a PR, figure out which files were changed and look for coverage specifically in those. If you don't know which files to look for coverage in, use this:
+
+```
+git diff --name-only $(git merge-base origin/main HEAD) | jq -R . | jq -s .
+```

sleap_nn-0.0.1/.claude/commands/lint.md

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+Run linting with `black` and `ruff`.
+
+Command:
+
+```
+black sleap_nn tests && ruff check --fix sleap_nn tests
+```
+
+Then manually fix any remaining errors which cannot be automatically fixed by ruff.

sleap_nn-0.0.1/.claude/commands/pr-description.md

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+Update PR description.
+
+Use the `gh` CLI to fetch the current PR description, then update it with a comprehensive description of the changes made in this PR.
+
+If there is an associated issue (linked in the PR metadata or mentioned in the PR description), then use the `gh` CLI to fetch that too to contextualize the work done in the PR.
+
+Include a summary, example usage (for enhancements), API changes, and other notes for future consideration (including reasoning behind design decisions).

sleap_nn-0.0.1/.dockerignore

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+README.md
+docs/
+*.egg-info/
+
+
+# Test artifacts
+tests/
+*.pytest_cache/
+
+*.ruff_cache
+codecov.yml
+
+# Git files
+.github/
+.gitignore

sleap_nn-0.0.1/.github/workflows/build.yml

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+# Package builds
+name: Build
+
+on:
+  release:
+    types:
+      - published
+  workflow_dispatch:
+    inputs:
+      testpypi:
+        description: 'Publish to TestPyPI'
+        required: false
+        type: boolean
+        default: false
+
+jobs:
+  pypi:
+    name: PyPI Wheel
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write  # Required for PyPI trusted publishing
+    steps:
+
+    - name: Checkout repo
+      uses: actions/checkout@v4
+
+    - name: Setup UV
+      uses: astral-sh/setup-uv@v6
+      with:
+        python-version: "3.12"
+
+    - name: Build distributions
+      run: |
+        uv build
+
+    - name: Determine index and publish
+      run: |
+        # Manual override for TestPyPI
+        if [[ "${{ github.event.inputs.testpypi }}" == "true" ]]; then
+          echo "Manual TestPyPI publishing..."
+          uv publish --index testpypi --trusted-publishing always
+        else
+          echo "Publishing to PyPI..."
+          uv publish
+        fi

sleap_nn-0.0.1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  pull_request:
+    types: [opened, reopened, synchronize]
+    paths:
+      - "sleap_nn/**"
+      - "tests/**"
+      - ".github/workflows/ci.yml"
+      - "pyproject.toml"
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: false
+
+      - name: Set up Python
+        run: uv python install 3.11
+
+      - name: Install dev dependencies and torch
+        run: uv sync --extra dev --extra torch-cpu
+
+      - name: Run Black
+        run: uv run black --check sleap_nn tests
+
+      - name: Run Ruff
+        run: uv run ruff check sleap_nn/
+
+  tests:
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu", "windows", "mac", "self-hosted-gpu"]
+        include:
+          - os: ubuntu
+            runs-on: ubuntu-latest
+          - os: windows
+            runs-on: windows-latest
+          - os: mac
+            runs-on: macos-14
+          - os: self-hosted-gpu
+            runs-on: [self-hosted, puma, gpu, 2xgpu]
+        python: [3.12]
+
+    name: Tests (${{ matrix.os }}, Python ${{ matrix.python }})
+    runs-on: ${{ matrix.runs-on }}
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: false
+
+      - name: Set up Python (non-self-hosted GPU)
+        if: matrix.os != 'self-hosted-gpu'
+        run: uv python install ${{ matrix.python }}
+
+      - name: Install dev dependencies and torch (self-hosted GPU)
+        if: matrix.os == 'self-hosted-gpu'
+        run: uv sync --extra dev --extra torch-cuda128
+
+      - name: Install dev dependencies and torch (non-self-hosted GPU)
+        if: matrix.os != 'self-hosted-gpu'
+        run: uv sync --extra dev --extra torch-cpu
+
+      - name: Print environment info
+        run: |
+          echo "=== UV Environment ==="
+          uv run python --version
+          uv run python -c "import sys; print('Python executable:', sys.executable)"
+          echo "=== UV Environment NumPy Check ==="
+          uv run python -c "import numpy; print('NumPy version:', numpy.__version__); print('NumPy location:', numpy.__file__)" || echo "NumPy import failed in uv environment"
+          echo "=== CUDA Availability Check ==="
+          uv run python -c "
+          import torch
+          print(f'PyTorch version: {torch.__version__}')
+          print(f'CUDA available: {torch.cuda.is_available()}')
+          print(f'CUDA device count: {torch.cuda.device_count()}')
+          if torch.cuda.is_available():
+              print(f'CUDA version: {torch.version.cuda}')
+              print(f'Current device: {torch.cuda.current_device()}')
+              print(f'Device name: {torch.cuda.get_device_name(0)}')
+          else:
+              print('CUDA is not available')
+          " || echo "CUDA check failed"
+          echo "=== PIP EXECUTABLE COMPARISON ==="
+          uv run python -c "import subprocess; print('pip from uv run python:', subprocess.check_output(['pip', '--version']).decode().strip())" || echo "pip not found from python"
+          uv run pip --version || echo "uv run pip failed"
+          echo "=== UV pip list vs python -m pip list ==="
+          echo "--- uv run pip list ---"
+          uv run pip list | head -20
+          echo "--- uv run python -m pip list ---"
+          uv run python -m pip list | head -20
+          echo "=== UV ENVIRONMENT CHECK ==="
+          uv run python -c "import os; print('VIRTUAL_ENV:', os.environ.get('VIRTUAL_ENV', 'Not set'))"
+          echo "=== Import Test ==="
+          uv run python -c "import torch; import lightning; import kornia; print('All imports successful')" || echo "Import test failed"
+
+      - name: Check MPS backend (macOS only)
+        if: runner.os == 'macOS'
+        run: |
+          echo "=== macOS MPS Backend Check ==="
+          uv run python -c "
+          import torch
+          print(f'PyTorch version: {torch.__version__}')
+          print(f'MPS available: {torch.backends.mps.is_available()}')
+          print(f'MPS built: {torch.backends.mps.is_built()}')
+          if torch.backends.mps.is_available():
+              print('MPS backend is available and ready to use!')
+              device = torch.device('mps')
+              test_tensor = torch.randn(3, 3).to(device)
+              print(f'Test tensor on MPS: {test_tensor.device}')
+          else:
+              print('MPS backend is not available on this macOS system')
+          "
+
+      - name: Run pytest
+        run: |
+          echo "=== Final environment check before tests ==="
+          uv run python -c "import numpy, torch, lightning, kornia; print(f'All packages available: numpy={numpy.__version__}, torch={torch.__version__}')"
+          echo "=== Running pytest ==="
+          uv run pytest --cov=sleap_nn --cov-report=xml --durations=-1 tests/
+
+      - name: Upload coverage
+        uses: codecov/codecov-action@v5
+        with:
+          fail_ci_if_error: true
+          verbose: false
+          token: ${{ secrets.CODECOV_TOKEN }}

sleap_nn-0.0.1/.github/workflows/codespell.yml

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+# Codespell configuration is within pyproject.toml
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

sleap_nn-0.0.1/.github/workflows/docs.yml

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+name: Docs
+
+on:
+  release:
+    types:
+      - published
+  push:
+    branches:
+      - main
+    paths:
+      - "sleap_nn/**"
+      - "docs/**"
+      - "mkdocs.yml"
+      - ".github/workflows/docs.yml"
+
+jobs:
+  docs:
+    name: Docs
+    runs-on: "ubuntu-latest"
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      - name: Install sleap-nn with docs dependencies
+        run: |
+            pip install -e ".[docs]"
+
+      - name: Print environment info
+        run: |
+            which python
+            pip freeze
+
+      - name: Setup Git user
+        run: |
+            git config --global user.name "github-actions[bot]"
+            git config --global user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Build and upload docs (release)
+        if: ${{ github.event_name == 'release' && github.event.action == 'published' }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+            mike deploy --update-aliases --allow-empty --push "${{ github.event.release.tag_name }}" latest
+
+      - name: Build and upload docs (dev)
+        if: ${{ github.event_name == 'push' }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+            mike deploy --update-aliases --allow-empty --push dev

sleap_nn-0.0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# ruff
+.ruff_cache/
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+.vscode/
+
+wandb/
+
+# Serena
+.serena/
+
+# macOS
+.DS_Store

sleap_nn-0.0.1/CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Common Development Commands
+
+### Testing
+- Run all tests: `pytest tests`
+- Run specific test file: `pytest tests/path/to/test_file.py`
+- Run with coverage: `pytest --cov=sleap_nn --cov-report=xml tests/`
+- Run tests with duration info: `pytest --durations=-1 tests/`
+
+### Code Quality
+- Format code: `black sleap_nn tests`
+- Check formatting: `black --check sleap_nn tests`
+- Run linter: `ruff check sleap_nn/`
+
+### Environment Setup
+- GPU (Windows/Linux): `mamba env create -f environment.yml`
+- CPU (Windows/Linux/Intel Mac): `mamba env create -f environment_cpu.yml`
+- Apple Silicon (M1/M2 Mac): `mamba env create -f environment_osx-arm64.yml`
+- Activate environment: `mamba activate sleap-nn`
+
+## Architecture Overview
+
+sleap-nn is a PyTorch-based neural network backend for animal pose estimation. The codebase follows a modular architecture:
+
+### Core Components
+
+1. **Model Architecture** (`sleap_nn/architectures/`)
+   - Backbone networks: UNet, ConvNext, SwinT (via `model.py:get_backbone`)
+   - Head modules for different tasks: confidence maps, centroids, PAFs, etc.
+   - Model configuration via Hydra/OmegaConf
+
+2. **Data Pipeline** (`sleap_nn/data/`)
+   - Providers for reading SLEAP files (`providers.py`)
+   - Data augmentation, normalization, resizing
+   - Confidence map and edge map generation
+   - Instance cropping and centroid computation
+
+3. **Training System** (`sleap_nn/training/`)
+   - Lightning-based training modules (`lightning_modules.py`)
+   - ModelTrainer class for orchestrating training (`model_trainer.py`)
+   - Custom losses and callbacks
+   - Configuration via `TrainingJobConfig`
+
+4. **Inference Pipeline** (`sleap_nn/inference/`)
+   - Different predictors for each model type (single instance, top-down, bottom-up)
+   - Peak finding and PAF grouping for multi-instance
+   - Unified prediction interface via `predictors.py`
+
+5. **Tracking** (`sleap_nn/tracking/`)
+   - Instance tracking across frames
+   - Candidate generation with fixed windows and local queues
+
+### Configuration System
+
+The project uses a hierarchical configuration system with three main sections:
+- `data_config`: Data pipeline configuration
+- `model_config`: Model architecture configuration  
+- `trainer_config`: Training hyperparameters and Lightning configuration
+
+Configurations are managed via Hydra and can be specified in YAML files (see `docs/config_*.yaml` examples).
+
+### Key Entry Points
+
+- Training: `sleap_nn/train.py` - Hydra-based training entry point
+- Inference: `sleap_nn/predict.py` - Run inference on trained models
+- CLI: `sleap_nn/cli.py` - Command-line interface (currently minimal)
+- Evaluation: `sleap_nn/evaluation.py` - Model evaluation utilities
+
+### Model Types
+
+The system supports multiple model architectures for pose estimation:
+- Single Instance: One animal per frame
+- Centered Instance: Crop-based single instance
+- Centroid: Animal center detection
+- Top-Down: Centroid → Instance detection
+- Bottom-Up: Multi-instance with PAFs
+
+Each model type has corresponding head modules, data processing, and inference pipelines.