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!

import pyrefinebio

pyrefinebio.download_dataset(
    "./ds.zip",
    "foo@bar.com",
    dataset_dict={
        "SRP066781": ["ALL"]
    }
)

See the documentation 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
• 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.

Generating the Docs

Before you can generate the docs you must install pyrefienbio and sphinx requirements.

I recommend setting up a virtual environment before installing the requirements, but that step is optional.

To install the requirements:

$ 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