Have you ever tried to use someone else’s code and spent a whole day trying to install it? Have you ever decided not to use a tool because installing it was a massive pain? Both of those have happened to me and, to be honest, it is a massive shame. The authors may spend large amounts of time developing these tools and in the end, no one uses them because they can’t get them to work. So I have decided to try and make all code I develop as easy and painless as possible to install and use. <\/p>\n\n\n\n\n\n\n\n
Say you have just developed a new deep-learning tool in python (lets call it ABlooper<\/a>). To maximize usage, you want to make it as easy to install as possible. What could be easier than this? \ud83d\ude0d<\/p>\n Okay, so now that we know where we want to get to, the question is how to get there.<\/p>\n Python actually makes it quite straightforward for us to achieve this with packages such as The first thing we need to do is organise our code in the right way. I would recommend the following structure for a python package. This is just a skeleton however and I am sure many people would disagree on some of the details. But this will work, so unless you have a better way of doing it, it is good enough.<\/p>\n If you are planning on sharing your code you should probably already have some code files, a The key file that will be doing most of the work is Not all of the parameters used here a necessary, and there are many additional keywords that can be added to the This way users will not even need to know any python to use your code!<\/p>\n There are two other files left to discuss:<\/p>\n$ pip install ABlooper\n<\/code><\/pre>\nsetuptools<\/code>, build<\/code> and twine<\/code>. It even provides a server for people to easily share python packages.<\/p>\nPackage structure and required files<\/h4>\n
ABlooper\/\n\u251c\u2500\u2500 ABlooper\/\n\u2502 \u251c\u2500\u2500 some_code.py\n\u2502 \u251c\u2500\u2500 more_code.py\n\u2502 \u251c\u2500\u2500 __init__.py\n\u2502 \u2514\u2500\u2500 data\/\n\u2502 \u2514\u2500\u2500 model_weights\n\u251c\u2500\u2500 LICENSE\n\u251c\u2500\u2500 README.md\n\u251c\u2500\u2500 MANIFEST.in\n\u2514\u2500\u2500 setup.py\n<\/code><\/pre>\nREADME.md<\/code> and a LICENSE<\/code>. If the code you are sharing is machine learning based, you will probably have weights stored in a non-python file. We will have to explicitly tell setuptools<\/code> to include these in the package.<\/p>\nsetup.py<\/code>. Here is an template of what it should look like:<\/p>\nfrom setuptools import setup, find_packages\n\nwith open("README.md", "r", encoding="utf-8") as readme:\n long_description = readme.read()\nsetup(\n name='ABlooper', # Name of the package. This is what people will be installing\n version='1.0.0', # Version. Usually if you are not planning on making any major changes after this 1.0.0 is a good way to go.\n description='Set of functions to predict CDR structure', # Short description\n license='BSD 3-clause license', \n maintainer='Brennan Abanades',\n long_description=long_description, # This just makes your README.md the description shown on pypi\n long_description_content_type='text\/markdown',\n maintainer_email='youremail@stats.ox.ac.uk',\n include_package_data=True, # If you have extra (non .py) data this should be set to True \n packages=find_packages(include=('ABlooper', 'ABlooper.*')), # Where to look for the python package\n install_requires=[ # All Requirements\n 'numpy',\n 'torch>=1.6',\n ],\n)\n<\/code><\/pre>\nsetup<\/code> function. A full list of keywords can be found here<\/a>. For example, you can make a python function runnable from the command line using the entry_points<\/code> keyword:<\/p>\nentry_points={'console_scripts': ['ABlooper=ABlooper.more_code:main']},\n<\/code><\/pre>\n\n
__init__.py<\/code> – Is used to let python know that the directory is a python package and can be an empty file.<\/li>\nMANIFEST.in<\/code> – Enumerates all additional (non-python) data needed to run the package. In our case this would contain one line: include ABlooper\/data\/*<\/code>.<\/li>\n<\/ul>\nUploading to PyPi<\/h4>\n