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!

Tests can be run with:

python -m unittest discover tests -b

pyrefinebio can automatically be released to PyPI via a GitHub action.

To trigger the action, create a new release via GitHub:

The docs are generated using sphinx autodoc.

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

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

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution for pyrefinebio 0.4.11
File	Size	Uploaded
pyrefinebio-0.4.11.tar.gz	43.8 kB	Nov 14, 2023	Details

Table of built distributions (wheels) for pyrefinebio 0.4.11
File	Interpreter	ABI	Platform	Reset
pyrefinebio-0.4.11-py3-none-any.whl 66.8 kB Nov 14, 2023	Python 3	none	any	Details

Total release size: 110.5 kB

Download URL	pyrefinebio-0.4.11.tar.gz
Size	43.8 kB
Tags	Source
SHA-256 checksum How to use checksums	`ac314a7e4ab4e4edd665e4242a3423712504d4497cd6f1b39d89cea02b60be2c`
BLAKE2b-256 checksum How to use checksums	`67c8749c19dd95236917ee6ebab6edf24df0531e09b70fccb228b46057d3f84e`
Upload date	Nov 14, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.12.0`

Download URL	pyrefinebio-0.4.11-py3-none-any.whl
Size	66.8 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`7229ce0fe41dccf75495ab40c6149a4dda07f06c30370201f9c060faef5dc255`
BLAKE2b-256 checksum How to use checksums	`2da92d6827c791f0f5f828e1f8c13e979faedf6604f473c5a4bf4ee29cfbc284`
Upload date	Nov 14, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.12.0`