<!--
<p align="center">
<img src="https://github.com/BioDataFuse/pyBiodatafuse/raw/main/docs/source/logo.png" height="150">
</p>
-->
<h1 align="center">
pyBioDataFuse
</h1>
<p align="center">
<a href="https://github.com/BioDataFuse/pyBiodatafuse/actions/workflows/tests.yml">
<img alt="Tests" src="https://github.com/BioDataFuse/pyBiodatafuse/workflows/Tests/badge.svg" />
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<a href="https://github.com/BioDataFuse/pyBiodatafuse/blob/main/LICENSE">
<img alt="PyPI - License" src="https://img.shields.io/pypi/l/pyBiodatafuse" />
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<a href='https://pyBiodatafuse.readthedocs.io/en/latest/?badge=latest'>
<img src='https://readthedocs.org/projects/pyBiodatafuse/badge/?version=latest' alt='Documentation Status' />
</a>
<a href="https://codecov.io/gh/BioDataFuse/pyBiodatafuse/branch/main">
<img src="https://codecov.io/gh/BioDataFuse/pyBiodatafuse/branch/main/graph/badge.svg" alt="Codecov status" />
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<img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" />
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</a>
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<img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/>
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</p>
A python package for integrating data from multiple resources
## 💪 Getting Started
> TODO show in a very small amount of space the **MOST** useful thing your package can do.
> Make it as short as possible! You have an entire set of docs for later.
### Command Line Interface
The pyBiodatafuse command line tool is automatically installed. It can
be used from the shell with the `--help` flag to show all subcommands:
```shell
$ pyBiodatafuse --help
```
> TODO show the most useful thing the CLI does! The CLI will have documentation auto-generated
> by `sphinx`.
## 🚀 Installation
The most recent release can be installed from
[PyPI](https://pypi.org/project/pyBiodatafuse/) with:
```shell
$ pip install pyBiodatafuse
```
The most recent code and data can be installed directly from GitHub with:
```bash
$ pip install git+https://github.com/BioDataFuse/pyBiodatafuse.git
```
## 👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See
[CONTRIBUTING.md](https://github.com/BioDataFuse/pyBiodatafuse/blob/master/.github/CONTRIBUTING.md) for more information on getting involved.
## 👋 Attribution
### ⚖️ License
The code in this package is licensed under the MIT License.
<!--
### 📖 Citation
Citation goes here!
-->
<!--
### 🎁 Support
This project has been supported by the following organizations (in alphabetical order):
- [Harvard Program in Therapeutic Science - Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/)
-->
<!--
### 💰 Funding
This project has been supported by the following grants:
| Funding Body | Program | Grant |
|----------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------|-----------------|
| DARPA | [Automating Scientific Knowledge Extraction (ASKE)](https://www.darpa.mil/program/automating-scientific-knowledge-extraction) | HR00111990009 |
-->
### 🍪 Cookiecutter
This package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.
## 🛠️ For Developers
<details>
<summary>See developer instructions</summary>
The final section of the README is for if you want to get involved by making a code contribution.
### Development Installation
To install in development mode, use the following:
```bash
$ git clone git+https://github.com/BioDataFuse/pyBiodatafuse.git
$ cd pyBiodatafuse
$ pip install -e .
```
### 🥼 Testing
After cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be
run reproducibly with:
```shell
$ tox
```
Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/BioDataFuse/pyBiodatafuse/actions?query=workflow%3ATests).
### 📖 Building the Documentation
The documentation can be built locally using the following:
```shell
$ git clone git+https://github.com/BioDataFuse/pyBiodatafuse.git
$ cd pyBiodatafuse
$ tox -e docs
$ open docs/build/html/index.html
```
The documentation automatically installs the package as well as the `docs`
extra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins
like `texext` can be added there. Additionally, they need to be added to the
`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).
### 📦 Making a Release
After installing the package in development mode and installing
`tox` with `pip install tox`, the commands for making a new release are contained within the `finish` environment
in `tox.ini`. Run the following from the shell:
```shell
$ tox -e finish
```
This script does the following:
1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`,
`src/pyBiodatafuse/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix
2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build)
3. Uploads to PyPI using [`twine`](https://github.com/pypa/twine). Be sure to have a `.pypirc` file configured to avoid the need for manual input at this
step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can
use `tox -e bumpversion -- minor` after.
</details>
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See\n[CONTRIBUTING.md](https://github.com/BioDataFuse/pyBiodatafuse/blob/master/.github/CONTRIBUTING.md) for more information on getting involved.\n\n## \ud83d\udc4b Attribution\n\n### \u2696\ufe0f License\n\nThe code in this package is licensed under the MIT License.\n\n<!--\n### \ud83d\udcd6 Citation\n\nCitation goes here!\n-->\n\n<!--\n### \ud83c\udf81 Support\n\nThis project has been supported by the following organizations (in alphabetical order):\n\n- [Harvard Program in Therapeutic Science - Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/)\n\n-->\n\n<!--\n### \ud83d\udcb0 Funding\n\nThis project has been supported by the following grants:\n\n| Funding Body | Program | Grant |\n|----------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------|-----------------|\n| DARPA | [Automating Scientific Knowledge Extraction (ASKE)](https://www.darpa.mil/program/automating-scientific-knowledge-extraction) | HR00111990009 |\n-->\n\n### \ud83c\udf6a Cookiecutter\n\nThis package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s\n[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s\n[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.\n\n## \ud83d\udee0\ufe0f For Developers\n\n<details>\n <summary>See developer instructions</summary>\n\nThe final section of the README is for if you want to get involved by making a code contribution.\n\n### Development Installation\n\nTo install in development mode, use the following:\n\n```bash\n$ git clone git+https://github.com/BioDataFuse/pyBiodatafuse.git\n$ cd pyBiodatafuse\n$ pip install -e .\n```\n\n### \ud83e\udd7c Testing\n\nAfter cloning the repository and installing `tox` with `pip install tox`, the unit tests in the `tests/` folder can be\nrun reproducibly with:\n\n```shell\n$ tox\n```\n\nAdditionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/BioDataFuse/pyBiodatafuse/actions?query=workflow%3ATests).\n\n### \ud83d\udcd6 Building the Documentation\n\nThe documentation can be built locally using the following:\n\n```shell\n$ git clone git+https://github.com/BioDataFuse/pyBiodatafuse.git\n$ cd pyBiodatafuse\n$ tox -e docs\n$ open docs/build/html/index.html\n``` \n\nThe documentation automatically installs the package as well as the `docs`\nextra specified in the [`setup.cfg`](setup.cfg). `sphinx` plugins\nlike `texext` can be added there. 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