[Replace the contents this README.MD file with the appropriate "Users manual" needed for the python tool.]

Python Tool Template

Introduction

This page gives details concerning guiding principles and formatting required for developing python tool.

Requirements

• Git and Github accounts

  Follow this installation guide HERE to install Git in your local machine. Additionally, direct to Github sign up page if you do not have the account.

• PIP

  Follow official PIP link for installation instruction.

Installation

Getting started with the Python Tool Template:

• Click on "Use this Template" button and fill out the new repository informations (name/description/access).
• Finally click on "Create repository from template" and you now have a new repository based on the Python tools Template following the standard layouts.

Alternatively,

• Direct to Github Create New Repository and select the "biobakery/python-tools-template". Fill out other information (Repository name/description/access)
• Finally click on "Create repository" and you now have a new repository based on the Bioconductor Template.

NOTE: Make your repository "Private" unless it is ready to be released.

Getting started with a public python tools

• Clone your recently created repository in your local development environment either using:

      git clone https://github.com/biobakery/Python-tool-template.git
  

  or using the "Clone or Download" button.

Picking A Name

Python module/package names should generally follow the following constraints:

• All lowercase
• Unique on pypi, even if you don’t want to make your package publicly available (you might want to specify it privately as a dependency later)
• Underscore-separated or no word separators at all (don’t use hyphens)

Packaging

The main setup config file, setup.py, should contain a single call to setuptools.setup(), like so:

from setuptools import setup
setup(name='<Package Name>',
      version='<Version>',
      description='<Description of the package>',
      author='Author Name',
      author_email='Author Email',
      license='MIT',
      packages=['<package name>'],
      zip_safe=False)

Addition parameter included in the sample setup.py template file. Now we can install the package locally (for use on our system), with:

$ pip install .

We can also install the package with a symlink, so that changes to the source files will be immediately available to other users of the package on our system:

$ pip install -e .

Anywhere else in our system using the same Python, we can do this now:

>>> from template.tools import sample_function
>>> print sample_function.transpose()

Note: Edit the setup.py file with relevent information about the package.

For more packaging information, see official python packaging documentation

Test workflow

Two of the main frameworks for testing python tools are Unittests and pytest.

For this template, we are using unittest:

• To set up your package to use unittest, run: Either use the module and class name

  python -m unittest template.tests.sample_test.TestStringMethods
  

  Or use the path:

  python template/tests/sample_test.py 
  

  This will run your test cases of the class or the test file. For more information on running your test cases through command line, see Python unit test documentation.