Upload the python package to pypi¶

1. Prepare a `init.py` and `main.py` file for your package.¶

├── h1d
│   ├── AsymmetricTad.py
│   ├── HiCmetric.py
│   ├── MultiTypeScore.py
│   ├── Multi_samples_metrics.py
│   ├── __init__.py
│   ├── __main__.py

__init__.py is required to import the directory as a package, and can simply be an empty file.

For example, I prepared the __init__.py file as:

# -*- coding: utf-8 -*-
print("nothing")

def hello():
    print("hello world")

'__main__' is the name of the scope in which top-level code executes. A module’s name is set equal to '__main__' when read from standard input, a script, or from an interactive prompt.
if __name__ == "__main__":
    # execute only if run as a script
    main()
For a package, the same effect can be achieved by including a __main__.py module, the contents of which will be executed when the module is run with -m.

Simply speaking, __main__.py will be automatically run, when we use the whole module (here is h1d directory).

I prepared the __main__.py file as:

import argparse

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("type",help="type anything",type=str)
    args = parser.parse_args()
    print(args.type)

if __name__=='__main__':
    main()

Now our folder h1d is a module. We can test our module via command line:

python -m h1d 1234abcd

This command will use h1d>>__init__.py>>__main__.py, so the output will be:

nothing
1234abcd

Please note we can also run

python h1d 1234abcd

In this case, the script will run as the __main__.pymodule instead of the h1d module

So the output will be

1234abcd

2.prepare the file `setup.py`¶

Create the new files listed below:

├── LISENSE
├── README.md
├── h1d
│   ├── AsymmetricTad.py
│   ├── HiCmetric.py
│   ├── MultiTypeScore.py
│   ├── Multi_samples_metrics.py
│   ├── __init__.py
│   ├── __main__.py
│   ├── __pycache__
│   ├── calcuDiffCI.py
│   ├── calculateMetrics.py
│   ├── calculateTwoSample.py
│   ├── callDirectionalTAD.py
│   ├── calldTADAllchr.py
│   ├── discrete.py
│   ├── geneDensity
│   ├── loadfile.py
│   ├── plotMetrics.py
│   ├── plotTwoSample.py
│   └── test.py
└── setup.py

README.md is used to store long description.
LISENCE tells users who install your package the terms under which they can use your package. Choose a license according to https://choosealicense.com/

setup.py is the build script for setuptools. It tells setuptools about your package (such as the name and version) as well as which code files to include.

from setuptools import setup

with open("README.md", "r", encoding="utf-8") as fh:
    readme = fh.read()

setup(
    name='h1d',  #distribution name of your package 
    version='0.0.4',   #package version
    author='wangjiankng', 
    author_email='wangjk321@gmail.com',
    url='https://github.com/wangjk321/HiC1Dmetrics',
    description='HiC1Dmetrics pip version',   #short description
    long_description=readme,     #detailed description of the package
    long_description_content_type="text/markdown",  #what type of markup is used
    packages=['h1d'],     #a list of all packages that should be included 
    install_requires=["pandas","numpy","scikit-learn"],  #specify dependencies
    classifiers=[    #gives index and pip  additional metadata about your package
        "Programming Language :: Python :: 3", #only compatible with Python 3
        "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
        "Operating System :: OS Independent",
    ],
    entry_points={
        'console_scripts': [
            'h1dtest=h1d:hello',
            'h1d=h1d.__main__:main',
        ]}
)

Use “console_script” entry points to register your script interfaces.

This entry_ponits means we can directly use h1dtest and h1d in command-line interface (CLI ).

h1dtest will use the hello function defined in __init__.py
h1d will use the main function defined in __main__.py

3. Generating distribution archives¶

Make sure you have the latest versions of setuptools , twineand wheel installed

pip install --user --upgrade setuptools wheel twine

Run the following command from the same directory where setup.py is located:

python3 setup.py sdist bdist_wheel

This command should generate two files in the distdirectory:

dist
├── h1d-0.0.4-py3-none-any.whl
└── h1d-0.0.4.tar.gz

The tar.gz file is a Source Archive
The .whl file is a Built Distribution.
Newer pip versions preferentially install built distributions, but will fall back to source archives if needed.

4. Register an account on PyPI¶

https://pypi.org/account/register/

5. Uploading the distribution archives¶

python3 -m twine upload --repository-url https://upload.pypi.org/legacy/ dist/*
## if exsiting error, add ""--skip-existing"

The output will be:

Uploading distributions to https://upload.pypi.org/legacy/
Enter your username: XXXXXX
Enter your password: XXXXXX
Uploading h1d-0.0.4-py3-none-any.whl
100%|██████████████████████████████████████████████████████████████████████████████████| 37.0k/37.0k [00:02<00:00, 18.0kB/s]
Uploading h1d-0.0.4.tar.gz
100%|██████████████████████████████████████████████████████████████████████████████████| 32.2k/32.2k [00:01<00:00, 21.5kB/s]

View at:
https://pypi.org/project/h1d/0.0.4/

6. Try the new package¶

In other PC, try:

pip install h1d

The output:

Collecting h1d
  Downloading h1d-0.0.4-py3-none-any.whl (26 kB)
Requirement already satisfied: pandas in ./software/anaconda3/lib/python3.6/site-packages (from h1d) (1.1.5)
Requirement already satisfied: numpy in ./software/anaconda3/lib/python3.6/site-packages (from h1d) (1.19.2)
Requirement already satisfied: scikit-learn in ./software/anaconda3/lib/python3.6/site-packages (from h1d) (0.22.2.post1)
Requirement already satisfied: python-dateutil>=2.7.3 in ./software/anaconda3/lib/python3.6/site-packages (from pandas->h1d) (2.8.1)
Requirement already satisfied: pytz>=2017.2 in ./software/anaconda3/lib/python3.6/site-packages (from pandas->h1d) (2020.4)
Requirement already satisfied: six>=1.5 in ./software/anaconda3/lib/python3.6/site-packages (from python-dateutil>=2.7.3->pandas->h1d) (1.15.0)
Requirement already satisfied: scipy>=0.17.0 in ./software/anaconda3/lib/python3.6/site-packages (from scikit-learn->h1d) (1.5.2)
Requirement already satisfied: joblib>=0.11 in ./software/anaconda3/lib/python3.6/site-packages (from scikit-learn->h1d) (1.0.0)
Installing collected packages: h1d
Successfully installed h1d-0.0.4

Then we can use the new pacakge in python:

>>> import h1d
nothing here

Or by command line:

h1dtest

Output:

hello world