# refinebio-py
A python client for the refine.bio API.
## Usage
`pyrefinebio` can be installed via pip
```
$ pip install pyrefinebio
```
You can then import and start using it right away!
```python
import pyrefinebio
pyrefinebio.download_dataset(
"./ds.zip",
"foo@bar.com",
dataset_dict={
"SRP066781": ["ALL"]
}
)
```
See the [documentation](https://alexslemonade.github.io/refinebio-py/index.html) for more help!
## Testing
Tests can be run with:
```
python -m unittest discover tests -b
```
## Releasing to PyPI
`pyrefinebio` can automatically be released to PyPI via a GitHub action.
To trigger the action, create a new release via GitHub:
- go to the [GitHub repo's release page](https://github.com/AlexsLemonade/refinebio-py/releases)
- click `Draft a new release`
- fill out the form
- the Tag version should be in the form `vX.X.X`
- click `Publish release`
- the action should automatically be triggered
## Documentation
The docs are generated using [sphinx autodoc](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html).
### Generating the Docs
Before you can generate the docs you must install pyrefienbio and sphinx requirements.
I recommend setting up a [virtual environment](https://docs.python.org/3/tutorial/venv.html)
before installing the requirements, but that step is optional.
To install the requirements:
```bash
$ pip install -r requirements.txt
$ pip install -r docs-requirements.txt
```
Then, to generate the docs navigate to `./docs` and run the command:
```
$ make html
```
The output will be in `./docs/_build`
Open `./docs/_build/html/*` in a browser to view the docs
### Deploying the Docs to Github Pages
First, set the variable `release` in `./docs/conf.py` to the correct version.
Then, clone the branch `gh-pages` into a folder `./doc-output`
You can use the following command to do this:
```
$ git clone --single-branch --branch gh-pages https://github.com/AlexsLemonade/refinebio-py.git doc-output
```
Navigate tho `./docs` and run the command:
```
$ make github
```
Navigate to `./doc-output` and commit and push any changes
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"description": "# refinebio-py\n\nA python client for the refine.bio API.\n\n## Usage\n\n`pyrefinebio` can be installed via pip\n\n```\n$ pip install pyrefinebio\n```\n\nYou can then import and start using it right away!\n\n```python\nimport pyrefinebio\n\npyrefinebio.download_dataset(\n \"./ds.zip\",\n \"foo@bar.com\",\n dataset_dict={\n \"SRP066781\": [\"ALL\"]\n }\n)\n```\n\nSee the [documentation](https://alexslemonade.github.io/refinebio-py/index.html) for more help!\n\n## Testing\n\nTests can be run with:\n\n```\npython -m unittest discover tests -b\n```\n\n## Releasing to PyPI\n\n`pyrefinebio` can automatically be released to PyPI via a GitHub action.\n\nTo trigger the action, create a new release via GitHub:\n- go to the [GitHub repo's release page](https://github.com/AlexsLemonade/refinebio-py/releases)\n- click `Draft a new release`\n- fill out the form\n - the Tag version should be in the form `vX.X.X`\n- click `Publish release`\n- the action should automatically be triggered\n\n## Documentation\n\nThe docs are generated using [sphinx autodoc](https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html).\n\n### Generating the Docs\n\nBefore you can generate the docs you must install pyrefienbio and sphinx requirements.\n\nI recommend setting up a [virtual environment](https://docs.python.org/3/tutorial/venv.html)\nbefore installing the requirements, but that step is optional.\n\nTo install the requirements:\n\n```bash\n$ pip install -r requirements.txt\n$ pip install -r docs-requirements.txt\n```\n\nThen, to generate the docs navigate to `./docs` and run the command:\n\n```\n$ make html\n```\n\nThe output will be in `./docs/_build`\n\nOpen `./docs/_build/html/*` in a browser to view the docs\n\n### Deploying the Docs to Github Pages\n\nFirst, set the variable `release` in `./docs/conf.py` to the correct version.\n\nThen, clone the branch `gh-pages` into a folder `./doc-output`\n\nYou can use the following command to do this:\n\n```\n$ git clone --single-branch --branch gh-pages https://github.com/AlexsLemonade/refinebio-py.git doc-output\n```\n\nNavigate tho `./docs` and run the command:\n\n```\n$ make github\n```\n\nNavigate to `./doc-output` and commit and push any changes\n",
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