jabs-behavior-classifier 0.36.0__tar.gz

jabs_behavior_classifier-0.36.0/PKG-INFO

@@ -0,0 +1,325 @@
+Metadata-Version: 2.3
+Name: jabs-behavior-classifier
+Version: 0.36.0
+Summary: 
+Author: Glen Beane, Brian Geuther, Keith Sheppard
+License: Proprietary
+Requires-Dist: h5py>=3.10.0,<4.0.0
+Requires-Dist: markdown2>=2.5.1,<3.0.0
+Requires-Dist: numpy>=2.0.0,<3.0.0
+Requires-Dist: opencv-python-headless>=4.8.1.78,<5.0.0
+Requires-Dist: pandas>=2.2.2,<3.0.0
+Requires-Dist: pyside6>=6.8.0,!=6.9.0
+Requires-Dist: scikit-learn>=1.5.0,<2.0.0
+Requires-Dist: shapely>=2.0.1,<3.0.0
+Requires-Dist: tabulate>=0.9.0,<1.0.0
+Requires-Dist: toml>=0.10.2,<0.11.0
+Requires-Dist: xgboost>=2.0.0,<3.0.0
+Requires-Dist: pyarrow>=20.0.0,<21.0.0
+Requires-Dist: rich>=14.0.0,<15.0.0
+Requires-Dist: rich-argparse>=1.7.1,<2.0.0
+Requires-Dist: intervaltree>=3.1.0,<4.0.0
+Requires-Dist: qt-material-icons>=0.2.0,<0.3.0
+Requires-Dist: jsonschema>=4.25.1,<5.0.0
+Requires-Dist: click>=8.2.1
+Requires-Python: >=3.10, <3.14
+Project-URL: Issues, https://github.com/KumarLabJax/JABS-behavior-classifier/issues
+Project-URL: Repository, https://github.com/KumarLabJax/JABS-behavior-classifier
+Description-Content-Type: text/markdown
+
+# JAX Animal Behavior System (JABS)
+
+![JABS Screen Shot](img/jabs_screenshot.png)
+
+## ReadTheDocs Tutorial and User Guide
+
+https://jabs-tutorial.readthedocs.io/en/latest/index.html
+
+[User Guide (Markdown)](https://github.com/KumarLabJax/JABS-behavior-classifier/blob/main/src/jabs/resources/docs/user_guide/user_guide.md)
+
+## Copyright
+
+Copyright 2023 The Jackson Laboratory -- All rights reserved.
+
+## Contact
+
+email us at jabs@jax.org
+
+## License
+
+JABS is licensed under a non-commercial use license, see LICENSE for more information. Contact us for information about
+licensing for commercial use.
+
+## Pose Files
+
+JABS requires pose files generated from the Kumar Lab's mouse pose estimation neural networks. Single mouse pose files 
+are generated from [this repository](https://github.com/KumarLabJax/deep-hrnet-mouse). Multi-mouse is still under development. Contact us for more information.
+
+## Requirements
+
+JABS was initially developed and tested on Python 3.10. See the `pyproject.toml` for a list of required Python 
+packages. These packages are available from the Python Package Index (PyPI).
+
+Currently, JABS supports Python 3.10 through 3.13.
+
+## Python Environment Setup
+
+We recommend creating a Python Virtualenv for JABS:
+
+```
+python -m venv jabs.venv
+
+# Linux and MacOS
+source jabs.venv/bin/activate
+
+# Windows
+jabs.venv\Scripts\activate.bat
+```
+
+### JABS Installation
+
+Developers should follow the Developer Setup section below. This section describes how to install JABS into a Python 
+environment for a non-developer user.
+
+#### PyPI
+
+JABS is not available on PyPI at this time, but we hope to begin publishing it there soon.
+
+#### Pip install from Github
+
+With the jabs.venv virtualenv activated, run the following command to install JABS from our git repository. This will 
+install the latest commit from the main branch: 
+`pip install git+https://github.com/KumarLabJax/JABS-behavior-classifier.git`
+
+you can also specify a branch or tag:
+
+`pip install git+https://github.com/KumarLabJax/JABS-behavior-classifier.git@branch-name`
+
+or a specific commit:
+
+`pip install git+https://github.com/KumarLabJax/JABS-behavior-classifier.git@commit-hash`
+
+#### Pip install from local source
+
+If you've cloned the JABS repository, you can install by running the following command in the project root directory:
+
+`pip install .`
+
+#### Windows .bat scripts
+
+There are two scripts that Windows users can use to simplify installing and running JABS. These can be executed by 
+double-clicking on them in Windows Explorer.
+
+* setup_windows.bat: this will create a Python virtualenv called jabs.venv in the project root and then install JABS as 
+a Python package.
+* launch_jabs.bat: this script will activate the jabs.venv environment and then launch the JABS GUI.
+
+### Running JABS
+
+After installing JABS, five commands will be added to the bin directory of your Python virtualenv:
+
+* jabs: launch the JABS GUI
+* jabs-init: initialize a new JABS project directory from the command line
+* jabs-classify: run a trained classifier from the command line
+* jabs-stats: print accuracy statistics for the given classifier
+* jabs-convert-parquet: convert parquet pose file to JABS pose file format
+
+You can run the `<jabs command> --help` to get usage information for each of the commands.
+
+**NOTE: On some platforms, the first time you run the JABS GUI it might take several minutes to launch. Subsequent 
+startup times should be significantly reduced.**
+
+### Developer Setup
+
+The following instructions are for Linux or macOS Developers. Commands for JABS developers using Windows might be 
+slightly different.
+
+This project now uses **uv** for dependency management and building. Poetry is no longer required.
+
+JABS developers will need to install uv by following the instructions on 
+[uv's official website](https://docs.astral.sh/uv/getting-started/installation/).
+
+1) **Clone** the repository and enter the project directory.
+
+2) **Create/activate** a virtual environment (uv recommended):
+
+Note, if you don't want to activate the virtualenv, you can use `uv run <command>` to run commands in the virtualenv.
+If you don't want to activate the virtualenv, you can skip this step.
+
+```bash
+uv venv
+source .venv/bin/activate   # Linux/macOS
+# .venv\Scripts\Activate.ps1 # Windows PowerShell
+```
+
+3) **Install dependencies** in editable mode:
+
+```bash
+uv sync
+```
+
+This will install all dependencies and JABS will be installed in "editable" mode, meaning that the JABS Python modules 
+installed in the virtualenv will be links to the files in the cloned git repository. JABS code changes will be 
+reflected immediately in the Python environment.
+
+Note to Developers: JABS uses package metadata to determine the version number. If you change the version number in the 
+pyproject.toml file, you will need to run `uv sync` to update the version number in the installed package so 
+that the GUI will display the correct version.
+
+
+#### Adding Dependencies
+```
+uv add <package>            # runtime dependency
+uv add --dev <package>      # dev-only dependency
+```
+
+
+#### Code Style
+
+JABS uses [ruff](https://docs.astral.sh/ruff/) for linting and formatting. Developers should run `ruff check` and `ruff format` before 
+committing code. A pre-commit hook is provided to run these commands automatically.
+
+To install pre-commit hooks for linting and formatting run:
+
+```commandline
+pre-commit install
+```
+
+You can also run [ruff](https://docs.astral.sh/ruff/) directly from command line:
+
+```commandline
+ruff check src/packagepath/modulename.py
+ruff format src/packagepath/modulename.py
+```
+
+#### Building Python Packages
+
+Build wheels and source distributions with uv:
+
+```bash
+uv build
+```
+
+This will produce both a .tar.gz and a Python Wheel file (.whl) in the dist directory. 
+
+The wheel file can be installed with pip:
+```
+pip install jabs_behavior_classifier-<version>-py3-none-any.whl
+```
+
+Since the Wheel does not contain any compiled code it is platform independent.
+
+### Enabling XGBoost Classifier
+
+The XGBoost Classifier has a dependency on the OpenMP library. This does not ship with macOS. XGBoost should work "out 
+of the box" on other platforms. On macOS, you can install libomp with Homebrew (preferred) with the following 
+command `brew install libomp`. You can also install libomp from source if you can't use Homebrew, but this is beyond 
+the scope of this Readme.
+
+### Singularity/Linux
+
+We supply a tested pair of singularity definition files. The [first vm](vm/behavior-classifier-vm.def) is intended for command-line use on 
+compute clusters when scaling inferences. The [second vm](vm/behavior-classifier-vm-gui.def) is designed for interacting with the GUI in a portable 
+environment. Please inspect the definition files for related linux packages to run the software.
+
+# JABS Project Portability
+
+We have 4 version numbers in our software:
+
+* JABS Python package version. This gets bumped every release.
+* Feature version. This gets bumped every time we change feature values or the format used to store 
+calculated features.
+* Classifier version. This gets bumped every time we change characteristics of classifiers.
+* Prediction version. This gets bumped every time we change how predictions are stored.
+
+## Long Term Support of JABS-based Classifiers
+
+There are multiple JABS Classifier artifacts that have different compatibility and portability characteristics.
+
+* Project folders. These are the most compatible for upgrades. The vast majority of our upgrades to JABS will allow
+transparent upgrades (e.g. re-generation of features) within the project folder without user interaction. We will
+provide instructions for changes that are not.
+* Exported training data. These are compatible across computers, but should generally not be considered compatible
+across JABS package versions. Once we add the appropriate version checks, the error message should be a bit more
+clear when and why these aren't compatible across versions.
+* Classifier pickle files. These are only compatible within a specific install of the package (e.g. mac will not
+be compatible with windows). These are the serialized trained classifiers, so load really fast, but should not be 
+considered portable beyond the computer and specific JABS install that created them.
+
+Project folders are big, but are almost always compatible across JABS versions.
+
+Exported classifiers are smaller and easier to move around, but might require the same JABS package version to run. These 
+are good for sharing or archiving specific versions (e.g. a version we use in a paper). A comon use case is to export
+training data from a project folder, transfer it to our HPC cluster, and then train a and run classifier using the 
+`jabs-classify` command from same version of JABS that was used to export the training file.
+
+Pickle files are tiny and efficient, but are not transferable across computers. We use these for large-scale 
+predictions in pipelines (for example, using exported training data to train a classifier saved as a .pickle file, 
+which can then be used to classify many videos as part of a pipeline).
+
+## CI/CD and Release Management
+
+JABS uses GitHub Actions for continuous integration and automated releases to PyPI. 
+The CI/CD pipeline is defined in `.github/workflows/` and automatically manages package building, testing, and publishing.
+
+### Pull Request Checks
+
+Pull requests to the `main` branch trigger automated checks to ensure code quality and functionality:
+
+1. **Code Formatting and Linting**: Ensures code adheres to style guidelines
+2. **Test Execution**: Runs the full test suite to verify functionality
+
+### Automated Release Process
+
+The release process is triggered automatically when the version number in `pyproject.toml` is changed on the `main` branch:
+
+1. **Version Detection**: The workflow monitors changes to `pyproject.toml` and extracts the version number
+2. **Pre-release Detection**: Versions containing letters (e.g., `1.0.0a1`, `2.1.0rc1`) are automatically marked as pre-releases
+3. **Build Pipeline**: If version changed, the system runs:
+   - Code formatting and linting checks
+   - Test execution
+   - Package building with `uv build`
+4. **PyPI Publishing**: Successfully built packages are automatically published to PyPI
+5. **GitHub Release**: A corresponding GitHub release is created with build artifacts
+
+### Release Workflow Files
+
+- **`.github/workflows/release.yml`**: Main release workflow that orchestrates the entire process
+- **`.github/workflows/_format-lint-action.yml`**: Reusable workflow for code quality checks
+- **`.github/workflows/_run-tests-action.yml`**: Reusable workflow for test execution
+- **`.github/workflows/pull-request.yml`**: CI checks for pull requests
+
+### Creating a New Release
+
+To create a new release:
+
+1. Update the version number in `pyproject.toml`:
+   ```toml
+   version = "X.Y.Z"  # for stable releases
+   version = "X.Y.Za1" # for alpha pre-releases
+   version = "X.Y.Zrc1" # for release candidates
+   ```
+
+2. Re-lock the uv lock file:
+   ```bash
+   uv lock
+   ```
+
+3. Commit and push the change:
+   ```bash
+   git add pyproject.toml uv.lock
+   git commit -m "Bump version to X.Y.Z"
+   ```
+   
+4. Merge your changes into the `main` branch via a pull request.
+
+3. The CI/CD pipeline will automatically:
+   - Detect the version change
+   - Run all quality checks and tests
+   - Build and publish the package to PyPI
+   - Create a GitHub release with generated release notes
+
+### Environment Requirements
+
+The release workflow requires:
+- **PyPI API Token**: Stored as `PYPI_API_TOKEN` in GitHub repository secrets

jabs_behavior_classifier-0.36.0/README.md

@@ -0,0 +1,296 @@
+# JAX Animal Behavior System (JABS)
+
+![JABS Screen Shot](img/jabs_screenshot.png)
+
+## ReadTheDocs Tutorial and User Guide
+
+https://jabs-tutorial.readthedocs.io/en/latest/index.html
+
+[User Guide (Markdown)](https://github.com/KumarLabJax/JABS-behavior-classifier/blob/main/src/jabs/resources/docs/user_guide/user_guide.md)
+
+## Copyright
+
+Copyright 2023 The Jackson Laboratory -- All rights reserved.
+
+## Contact
+
+email us at jabs@jax.org
+
+## License
+
+JABS is licensed under a non-commercial use license, see LICENSE for more information. Contact us for information about
+licensing for commercial use.
+
+## Pose Files
+
+JABS requires pose files generated from the Kumar Lab's mouse pose estimation neural networks. Single mouse pose files 
+are generated from [this repository](https://github.com/KumarLabJax/deep-hrnet-mouse). Multi-mouse is still under development. Contact us for more information.
+
+## Requirements
+
+JABS was initially developed and tested on Python 3.10. See the `pyproject.toml` for a list of required Python 
+packages. These packages are available from the Python Package Index (PyPI).
+
+Currently, JABS supports Python 3.10 through 3.13.
+
+## Python Environment Setup
+
+We recommend creating a Python Virtualenv for JABS:
+
+```
+python -m venv jabs.venv
+
+# Linux and MacOS
+source jabs.venv/bin/activate
+
+# Windows
+jabs.venv\Scripts\activate.bat
+```
+
+### JABS Installation
+
+Developers should follow the Developer Setup section below. This section describes how to install JABS into a Python 
+environment for a non-developer user.
+
+#### PyPI
+
+JABS is not available on PyPI at this time, but we hope to begin publishing it there soon.
+
+#### Pip install from Github
+
+With the jabs.venv virtualenv activated, run the following command to install JABS from our git repository. This will 
+install the latest commit from the main branch: 
+`pip install git+https://github.com/KumarLabJax/JABS-behavior-classifier.git`
+
+you can also specify a branch or tag:
+
+`pip install git+https://github.com/KumarLabJax/JABS-behavior-classifier.git@branch-name`
+
+or a specific commit:
+
+`pip install git+https://github.com/KumarLabJax/JABS-behavior-classifier.git@commit-hash`
+
+#### Pip install from local source
+
+If you've cloned the JABS repository, you can install by running the following command in the project root directory:
+
+`pip install .`
+
+#### Windows .bat scripts
+
+There are two scripts that Windows users can use to simplify installing and running JABS. These can be executed by 
+double-clicking on them in Windows Explorer.
+
+* setup_windows.bat: this will create a Python virtualenv called jabs.venv in the project root and then install JABS as 
+a Python package.
+* launch_jabs.bat: this script will activate the jabs.venv environment and then launch the JABS GUI.
+
+### Running JABS
+
+After installing JABS, five commands will be added to the bin directory of your Python virtualenv:
+
+* jabs: launch the JABS GUI
+* jabs-init: initialize a new JABS project directory from the command line
+* jabs-classify: run a trained classifier from the command line
+* jabs-stats: print accuracy statistics for the given classifier
+* jabs-convert-parquet: convert parquet pose file to JABS pose file format
+
+You can run the `<jabs command> --help` to get usage information for each of the commands.
+
+**NOTE: On some platforms, the first time you run the JABS GUI it might take several minutes to launch. Subsequent 
+startup times should be significantly reduced.**
+
+### Developer Setup
+
+The following instructions are for Linux or macOS Developers. Commands for JABS developers using Windows might be 
+slightly different.
+
+This project now uses **uv** for dependency management and building. Poetry is no longer required.
+
+JABS developers will need to install uv by following the instructions on 
+[uv's official website](https://docs.astral.sh/uv/getting-started/installation/).
+
+1) **Clone** the repository and enter the project directory.
+
+2) **Create/activate** a virtual environment (uv recommended):
+
+Note, if you don't want to activate the virtualenv, you can use `uv run <command>` to run commands in the virtualenv.
+If you don't want to activate the virtualenv, you can skip this step.
+
+```bash
+uv venv
+source .venv/bin/activate   # Linux/macOS
+# .venv\Scripts\Activate.ps1 # Windows PowerShell
+```
+
+3) **Install dependencies** in editable mode:
+
+```bash
+uv sync
+```
+
+This will install all dependencies and JABS will be installed in "editable" mode, meaning that the JABS Python modules 
+installed in the virtualenv will be links to the files in the cloned git repository. JABS code changes will be 
+reflected immediately in the Python environment.
+
+Note to Developers: JABS uses package metadata to determine the version number. If you change the version number in the 
+pyproject.toml file, you will need to run `uv sync` to update the version number in the installed package so 
+that the GUI will display the correct version.
+
+
+#### Adding Dependencies
+```
+uv add <package>            # runtime dependency
+uv add --dev <package>      # dev-only dependency
+```
+
+
+#### Code Style
+
+JABS uses [ruff](https://docs.astral.sh/ruff/) for linting and formatting. Developers should run `ruff check` and `ruff format` before 
+committing code. A pre-commit hook is provided to run these commands automatically.
+
+To install pre-commit hooks for linting and formatting run:
+
+```commandline
+pre-commit install
+```
+
+You can also run [ruff](https://docs.astral.sh/ruff/) directly from command line:
+
+```commandline
+ruff check src/packagepath/modulename.py
+ruff format src/packagepath/modulename.py
+```
+
+#### Building Python Packages
+
+Build wheels and source distributions with uv:
+
+```bash
+uv build
+```
+
+This will produce both a .tar.gz and a Python Wheel file (.whl) in the dist directory. 
+
+The wheel file can be installed with pip:
+```
+pip install jabs_behavior_classifier-<version>-py3-none-any.whl
+```
+
+Since the Wheel does not contain any compiled code it is platform independent.
+
+### Enabling XGBoost Classifier
+
+The XGBoost Classifier has a dependency on the OpenMP library. This does not ship with macOS. XGBoost should work "out 
+of the box" on other platforms. On macOS, you can install libomp with Homebrew (preferred) with the following 
+command `brew install libomp`. You can also install libomp from source if you can't use Homebrew, but this is beyond 
+the scope of this Readme.
+
+### Singularity/Linux
+
+We supply a tested pair of singularity definition files. The [first vm](vm/behavior-classifier-vm.def) is intended for command-line use on 
+compute clusters when scaling inferences. The [second vm](vm/behavior-classifier-vm-gui.def) is designed for interacting with the GUI in a portable 
+environment. Please inspect the definition files for related linux packages to run the software.
+
+# JABS Project Portability
+
+We have 4 version numbers in our software:
+
+* JABS Python package version. This gets bumped every release.
+* Feature version. This gets bumped every time we change feature values or the format used to store 
+calculated features.
+* Classifier version. This gets bumped every time we change characteristics of classifiers.
+* Prediction version. This gets bumped every time we change how predictions are stored.
+
+## Long Term Support of JABS-based Classifiers
+
+There are multiple JABS Classifier artifacts that have different compatibility and portability characteristics.
+
+* Project folders. These are the most compatible for upgrades. The vast majority of our upgrades to JABS will allow
+transparent upgrades (e.g. re-generation of features) within the project folder without user interaction. We will
+provide instructions for changes that are not.
+* Exported training data. These are compatible across computers, but should generally not be considered compatible
+across JABS package versions. Once we add the appropriate version checks, the error message should be a bit more
+clear when and why these aren't compatible across versions.
+* Classifier pickle files. These are only compatible within a specific install of the package (e.g. mac will not
+be compatible with windows). These are the serialized trained classifiers, so load really fast, but should not be 
+considered portable beyond the computer and specific JABS install that created them.
+
+Project folders are big, but are almost always compatible across JABS versions.
+
+Exported classifiers are smaller and easier to move around, but might require the same JABS package version to run. These 
+are good for sharing or archiving specific versions (e.g. a version we use in a paper). A comon use case is to export
+training data from a project folder, transfer it to our HPC cluster, and then train a and run classifier using the 
+`jabs-classify` command from same version of JABS that was used to export the training file.
+
+Pickle files are tiny and efficient, but are not transferable across computers. We use these for large-scale 
+predictions in pipelines (for example, using exported training data to train a classifier saved as a .pickle file, 
+which can then be used to classify many videos as part of a pipeline).
+
+## CI/CD and Release Management
+
+JABS uses GitHub Actions for continuous integration and automated releases to PyPI. 
+The CI/CD pipeline is defined in `.github/workflows/` and automatically manages package building, testing, and publishing.
+
+### Pull Request Checks
+
+Pull requests to the `main` branch trigger automated checks to ensure code quality and functionality:
+
+1. **Code Formatting and Linting**: Ensures code adheres to style guidelines
+2. **Test Execution**: Runs the full test suite to verify functionality
+
+### Automated Release Process
+
+The release process is triggered automatically when the version number in `pyproject.toml` is changed on the `main` branch:
+
+1. **Version Detection**: The workflow monitors changes to `pyproject.toml` and extracts the version number
+2. **Pre-release Detection**: Versions containing letters (e.g., `1.0.0a1`, `2.1.0rc1`) are automatically marked as pre-releases
+3. **Build Pipeline**: If version changed, the system runs:
+   - Code formatting and linting checks
+   - Test execution
+   - Package building with `uv build`
+4. **PyPI Publishing**: Successfully built packages are automatically published to PyPI
+5. **GitHub Release**: A corresponding GitHub release is created with build artifacts
+
+### Release Workflow Files
+
+- **`.github/workflows/release.yml`**: Main release workflow that orchestrates the entire process
+- **`.github/workflows/_format-lint-action.yml`**: Reusable workflow for code quality checks
+- **`.github/workflows/_run-tests-action.yml`**: Reusable workflow for test execution
+- **`.github/workflows/pull-request.yml`**: CI checks for pull requests
+
+### Creating a New Release
+
+To create a new release:
+
+1. Update the version number in `pyproject.toml`:
+   ```toml
+   version = "X.Y.Z"  # for stable releases
+   version = "X.Y.Za1" # for alpha pre-releases
+   version = "X.Y.Zrc1" # for release candidates
+   ```
+
+2. Re-lock the uv lock file:
+   ```bash
+   uv lock
+   ```
+
+3. Commit and push the change:
+   ```bash
+   git add pyproject.toml uv.lock
+   git commit -m "Bump version to X.Y.Z"
+   ```
+   
+4. Merge your changes into the `main` branch via a pull request.
+
+3. The CI/CD pipeline will automatically:
+   - Detect the version change
+   - Run all quality checks and tests
+   - Build and publish the package to PyPI
+   - Create a GitHub release with generated release notes
+
+### Environment Requirements
+
+The release workflow requires:
+- **PyPI API Token**: Stored as `PYPI_API_TOKEN` in GitHub repository secrets

jabs_behavior_classifier-0.36.0/pyproject.toml

@@ -0,0 +1,75 @@
+[project]
+name = "jabs-behavior-classifier"
+version = "0.36.0"
+description = ""
+readme = "README.md"
+requires-python = ">=3.10,<3.14"
+license = { text = "Proprietary" }
+
+authors = [
+  { name = "Glen Beane" },
+  { name = "Brian Geuther" },
+  { name = "Keith Sheppard" },
+]
+
+dependencies = [
+  "h5py>=3.10.0,<4.0.0",
+  "markdown2>=2.5.1,<3.0.0",
+  "numpy>=2.0.0,<3.0.0",
+  "opencv-python-headless>=4.8.1.78,<5.0.0",
+  "pandas>=2.2.2,<3.0.0",
+  "pyside6>=6.8.0,!=6.9.0",
+  "scikit-learn>=1.5.0,<2.0.0",
+  "shapely>=2.0.1,<3.0.0",
+  "tabulate>=0.9.0,<1.0.0",
+  "toml>=0.10.2,<0.11.0",
+  "xgboost>=2.0.0,<3.0.0",
+  "pyarrow>=20.0.0,<21.0.0",
+  "rich>=14.0.0,<15.0.0",
+  "rich-argparse>=1.7.1,<2.0.0",
+  "intervaltree>=3.1.0,<4.0.0",
+  "qt-material-icons>=0.2.0,<0.3.0",
+  "jsonschema>=4.25.1,<5.0.0",
+  "click>=8.2.1",
+]
+
+[dependency-groups]
+dev = [
+  {include-group = "lint"},
+  {include-group = "test"},
+  "pre-commit>=4.2.0,<5.0.0",
+]
+test = [
+  "pytest>=8.3.4,<9.0.0",
+  "matplotlib>=3.9.3,<4.0.0",
+]
+lint = [
+  "ruff>=0.11.5,<0.12.0",
+]
+
+[project.urls]
+Repository = "https://github.com/KumarLabJax/JABS-behavior-classifier"
+Issues = "https://github.com/KumarLabJax/JABS-behavior-classifier/issues"
+
+[project.scripts]
+jabs = "jabs.scripts.gui_entrypoint:main"
+"jabs-classify" = "jabs.scripts.classify:main"
+"jabs-init" = "jabs.scripts.initialize_project:main"
+"jabs-features" = "jabs.scripts.generate_features:main"
+"jabs-stats" = "jabs.scripts.stats:main"
+"jabs-convert-parquet" = "jabs.scripts.convert_parquet:main"
+"jabs-project-merge" = "jabs.scripts.merge_projects:main"
+"jabs-cli" = "jabs.scripts.cli:main"
+
+# Poetry-specific config kept for src/ layout and Poetry's own dev group
+[tool.poetry]
+packages = [
+  { include = "jabs", from = "src" },
+]
+
+[build-system]
+requires = ["uv_build>=0.7.19,<0.8.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-name = "jabs"

jabs_behavior_classifier-0.36.0/src/jabs/__init__.py

@@ -0,0 +1 @@
+"""JABS Behavior Classifier"""