kbase_sdk

Core utilities for KBase SDK apps. Note: experimental

Installation

$ pip install --extra-index-url https://test.pypi.org/simple kbase_sdk

This package currently only lives in test PyPi

Usage

Initialize app context

import kbase_sdk

context = kbase_sdk.init_context()

# You can also explicitly pass in the root directory of your app
# Useful if it is not your current working directory
context = kbase_sdk.init_context(root_directory)

Run another app as a remote job

import kbase_sdk

job = kbase_sdk.run_app(context, {
    app: 'AssemblyUtil',
    method: 'get_assembly_as_fasta',
    params: { 'ref': 'x/y/z' }
})

Development

Before working, activate a virtualenv with python3 and install dependencies

# Init the virtual environment
$ python3 -m venv env
$ source env/bin/activate

# Install package dependencies
$ pip install -e .

# Install dev dependencies
$ pip install -r dev-requirements.txt

Tests

# Make sure you are in a virtualenv
$ source env/bin/activate
# Make sure dependencies are installed
$ pip install -e .
$ pip install -r dev-requirements.txt

# Run all tests
$ make test

# Run a single test module
$ python -m unittest test/test_something.py

Build

Pip

# Generates a build file into dist/
$ python setup.py bdist_wheel 
# Uploads the build to pypi
$ twine upload --repository-url https://test.pypi.org/legacy/ dist/x

Project anatomy

The python packages are found in /kbase_sdk/. Tests are found in /test/.

Key files:

Makefile -- targets for testing and publishing
setup.py -- python setuptools configuration for pip packaging
conda_recipe -- config for conda packaging

jayrbolton / kbase_sdk