Metadata-Version: 2.4
Name: aind-ibl-ephys-alignment-preprocessing
Version: 0.1.2
Summary: Library to prepare histology and ephys for the IBL ephys alignment GUI
Project-URL: Repository, https://github.com/AllenNeuralDynamics/aind-ibl-ephys-alignment-preprocessing/
Project-URL: Issues, https://github.com/AllenNeuralDynamics/aind-ibl-ephys-alignment-preprocessing/issues
Project-URL: Changelog, https://github.com/AllenNeuralDynamics/aind-ibl-ephys-alignment-preprocessing/blob/main/CHANGELOG.md
Author: Allen Institute for Neural Dynamics
Author-email: Galen Lynch <galen@galenlynch.com>
License-Expression: MIT
License-File: LICENSE
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.11
Requires-Dist: aind-anatomical-utils>=0.4
Requires-Dist: aind-ephys-ibl-gui-conversion>=0.2
Requires-Dist: aind-registration-utils>=0.4
Requires-Dist: aind-s3-cache>=0.1
Requires-Dist: aind-zarr-utils>=0.11.2
Requires-Dist: antspyx>=0.3.0
Requires-Dist: filelock
Requires-Dist: iblatlas>=0.4.0
Requires-Dist: numpy>=1.21.0
Requires-Dist: pandas>=1.3.0
Requires-Dist: pydantic>=2
Requires-Dist: simpleitk
Description-Content-Type: text/markdown

# AIND IBL Ephys Alignment Preprocessing

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Library to prepare histology and ephys for the IBL ephys alignment GUI

## Installation

If you choose to clone the repository, you can install the package by running the following command from the root directory of the repository:

```bash
pip install .
```

Otherwise, you can use pip:

```bash
pip install aind-ibl-ephys-alignment-preprocessing
```



To develop the code, run:
```bash
uv sync
```

## Development

Please test your changes using the full linting and testing suite:

```bash
./scripts/run_linters_and_checks.sh -c
```

Or run individual commands:
```bash
uv run --frozen ruff format          # Code formatting
uv run --frozen ruff check           # Linting
uv run --frozen mypy                 # Type checking
uv run --frozen interrogate -v       # Documentation coverage
uv run --frozen codespell --check-filenames  # Spell checking
uv run --frozen pytest --cov aind_ibl_ephys_alignment_preprocessing # Tests with coverage
```


### Documentation
```bash
sphinx-build -b html docs/source/ docs/build/html
```


## License

This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
