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CITATION.cff

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@@ -40,4 +40,4 @@ repository: 'https://github.com/biocypher/biochatter'
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repository-code: 'https://github.com/biocypher/biochatter'
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repository-artifact: 'https://pypi.org/project/biochatter/'
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url: 'https://biochatter.org/'
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license: MIT
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license: Apache-2.0

CONTRIBUTING.md

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on a pull request.
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Before joining the community, please also make sure that you agree with our
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[Code of Conduct](CODE_OF_CONDUCT.md).
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[Code of Conduct](CODE_OF_CONDUCT.md) and our [License](LICENSE).

LICENSE

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MIT License
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Copyright (c) 2023 biocypher
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Apache License
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Version 2.0, January 2004
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http://www.apache.org/licenses/
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TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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NOTICE

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BioChatter
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Copyright (c) 2023–2026 BioChatter developers
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This product includes software developed by the BioChatter contributors.
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0

README.md

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| | | | |
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| --- | --- | --- | --- |
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| __License__ | [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) | __Python__ | [![Python](https://img.shields.io/pypi/pyversions/biochatter)](https://www.python.org) |
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| __License__ | [![License: Apache 2.0](https://img.shields.io/badge/license-Apache%202-blue)](https://opensource.org/license/apache-2-0) | __Python__ | [![Python](https://img.shields.io/pypi/pyversions/biochatter)](https://www.python.org) |
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| __Package__ | [![PyPI version](https://img.shields.io/pypi/v/biochatter)](https://pypi.org/project/biochatter/) [![Downloads](https://static.pepy.tech/badge/biochatter)](https://pepy.tech/project/biochatter) [![DOI](https://zenodo.org/badge/650181006.svg)](https://zenodo.org/doi/10.5281/zenodo.10777945) | __Build status__ | [![CI](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml/badge.svg)](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml) [![Docs](https://github.com/biocypher/biochatter/actions/workflows/docs.yaml/badge.svg)](https://github.com/biocypher/biochatter/actions/workflows/docs.yaml) |
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| __Tests__ | [![Coverage](https://raw.githubusercontent.com/biocypher/biochatter/coverage/coverage.svg)](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml) | __Docker__ | [![Latest image](https://img.shields.io/docker/v/biocypher/chatgse)](https://hub.docker.com/repository/docker/biocypher/chatgse/general) [![Image size](https://img.shields.io/docker/image-size/biocypher/chatgse/latest)](https://hub.docker.com/repository/docker/biocypher/chatgse/general) |
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| __Development__ | [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://black.readthedocs.io/en/stable/) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) | __Contributions__ | [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CONTRIBUTING.md) |

docs/index.md

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particular focus on the currently emerging "foundation models." You can read
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it [here](https://www.embopress.org/doi/full/10.1038/s44320-024-00041-w).
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[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![Python](https://img.shields.io/pypi/pyversions/biochatter)](https://www.python.org) [![PyPI version](https://img.shields.io/pypi/v/biochatter)](https://pypi.org/project/biochatter/) [![Downloads](https://static.pepy.tech/badge/biochatter)](https://pepy.tech/project/biochatter) [![CI](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml/badge.svg)](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml) [![Latest image](https://img.shields.io/docker/v/biocypher/chatgse)](https://hub.docker.com/repository/docker/biocypher/chatgse/general) [![Image size](https://img.shields.io/docker/image-size/biocypher/chatgse/latest)](https://hub.docker.com/repository/docker/biocypher/chatgse/general) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://black.readthedocs.io/en/stable/) [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](https://github.com/biocypher/biochatter/blob/main/CONTRIBUTING.md)
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[![License: Apache 2.0](https://img.shields.io/badge/license-Apache%202-blue)](https://opensource.org/license/apache-2-0) [![Python](https://img.shields.io/pypi/pyversions/biochatter)](https://www.python.org) [![PyPI version](https://img.shields.io/pypi/v/biochatter)](https://pypi.org/project/biochatter/) [![Downloads](https://static.pepy.tech/badge/biochatter)](https://pepy.tech/project/biochatter) [![CI](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml/badge.svg)](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml) [![Latest image](https://img.shields.io/docker/v/biocypher/chatgse)](https://hub.docker.com/repository/docker/biocypher/chatgse/general) [![Image size](https://img.shields.io/docker/image-size/biocypher/chatgse/latest)](https://hub.docker.com/repository/docker/biocypher/chatgse/general) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://black.readthedocs.io/en/stable/) [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](https://github.com/biocypher/biochatter/blob/main/CONTRIBUTING.md)

pyproject.toml

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{name = "Francesco Carli", email = "francesco.carli94@gmail.com"}
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]
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repository = "https://github.com/biocypher/biochatter"
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license = "MIT"
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license = {text = "Apache-2.0"}
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readme = "README.md"
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requires-python = ">=3.10,<3.13"
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packages = [
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"Development Status :: 3 - Alpha",
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"Intended Audience :: Developers",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"License :: OSI Approved :: Apache Software License",
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"Operating System :: OS Independent",
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"Programming Language :: Python",
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"Natural Language :: English",

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