Metadata-Version: 2.1
Name: aind-metadata-mapper
Version: 0.18.3
Summary: Package to manage mapping of source data into aind-data-schema metadata files.
Author: Allen Institute for Neural Dynamics
License: MIT
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: aind-data-schema-models >=0.3.2
Requires-Dist: pydantic-settings >=2.0
Provides-Extra: all
Requires-Dist: aind-metadata-mapper[bergamo] ; extra == 'all'
Requires-Dist: aind-metadata-mapper[bruker] ; extra == 'all'
Requires-Dist: aind-metadata-mapper[mesoscope] ; extra == 'all'
Requires-Dist: aind-metadata-mapper[openephys] ; extra == 'all'
Requires-Dist: aind-metadata-mapper[dynamicrouting] ; extra == 'all'
Requires-Dist: aind-metadata-mapper[u19] ; extra == 'all'
Provides-Extra: bergamo
Requires-Dist: aind-metadata-mapper[schema] ; extra == 'bergamo'
Requires-Dist: scanimage-tiff-reader ==1.4.1.4 ; extra == 'bergamo'
Requires-Dist: numpy >=1.26.4 ; extra == 'bergamo'
Provides-Extra: bruker
Requires-Dist: aind-metadata-mapper[schema] ; extra == 'bruker'
Requires-Dist: bruker2nifti ==1.0.4 ; extra == 'bruker'
Provides-Extra: dev
Requires-Dist: aind-metadata-mapper[all] ; extra == 'dev'
Requires-Dist: black ; extra == 'dev'
Requires-Dist: coverage ; extra == 'dev'
Requires-Dist: flake8 ; extra == 'dev'
Requires-Dist: interrogate ; extra == 'dev'
Requires-Dist: isort ; extra == 'dev'
Requires-Dist: furo ; extra == 'dev'
Provides-Extra: doc
Requires-Dist: Sphinx <6.0 ; extra == 'doc'
Requires-Dist: furo ; extra == 'doc'
Provides-Extra: dynamicrouting
Requires-Dist: aind-metadata-mapper[schema] ; extra == 'dynamicrouting'
Requires-Dist: pyyaml >=6.0.0 ; extra == 'dynamicrouting'
Provides-Extra: mesoscope
Requires-Dist: aind-metadata-mapper[bergamo] ; extra == 'mesoscope'
Requires-Dist: pillow >=10.4.0 ; extra == 'mesoscope'
Requires-Dist: tifffile ==2024.2.12 ; (python_version >= "3.9") and extra == 'mesoscope'
Provides-Extra: openephys
Requires-Dist: aind-metadata-mapper[schema] ; extra == 'openephys'
Requires-Dist: h5py >=3.11.0 ; extra == 'openephys'
Requires-Dist: np-session >=0.1.39 ; extra == 'openephys'
Requires-Dist: scipy >=1.11.0 ; extra == 'openephys'
Requires-Dist: pandas >=2.2.2 ; extra == 'openephys'
Requires-Dist: numpy >=1.26.4 ; extra == 'openephys'
Requires-Dist: npc-ephys >=0.1.18 ; (python_version >= "3.9") and extra == 'openephys'
Provides-Extra: schema
Requires-Dist: aind-data-schema <2.0,>=1.0.0 ; extra == 'schema'
Requires-Dist: pydantic <2.9 ; extra == 'schema'
Provides-Extra: u19
Requires-Dist: aind-metadata-mapper[schema] ; extra == 'u19'
Requires-Dist: pandas >=2.2.2 ; extra == 'u19'

# aind-metadata-mapper

[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
![Code Style](https://img.shields.io/badge/code%20style-black-black)
[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
![Interrogate](https://img.shields.io/badge/interrogate-100.0%25-brightgreen)
![Coverage](https://img.shields.io/badge/coverage-86%25-yellow?logo=codecov)
![Python](https://img.shields.io/badge/python->=3.10-blue?logo=python)

Repository to contain code that will parse source files into aind-data-schema models.

## Usage

## Installation
To use the software, in the root directory, run
```bash
pip install -e .[all]
```

It's possible to install just a small subset of dependencies. For example,
```bash
pip install -e .[bergamo]
```

To develop the code, run
```bash
pip install -e .[dev]
```

## Issues and Discussions
If you've found a bug in the schemas or would like to make a minor change, open an [issue](https://github.com/AllenNeuralDynamics/aind-metadata-mapper/issues) and please use the provided templates. If you'd like to propose a large change or addition, or generally have a question about how things work, head start a new Discussion!

## Contributing
Contributions are more than welcome for this project! If you'd like to develop the code, please follow the standards outlined in the [contribution guide](https://github.com/AllenNeuralDynamics/aind-metadata-mapper/blob/dev/CONTRIBUTING.md).

### Documentation
To generate the rst files source files for documentation, run
```bash
sphinx-apidoc -o docs/source/ src 
```
Then to create the documentation HTML files, run
```bash
sphinx-build -b html doc_template/empty_source/ doc_template/build/html
```
More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).


More information including a user guide and contributor guidelines can be found at [readthedocs](https://aind-metadata-mapper.readthedocs.io/en/latest/).
