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Pip Package Manager

There are few package managers specific for Python, and pip is the preferred one.

Homebrew doesn't know how to install pip or distribute. Luckily both can be easily installed with python scripts available on web, if needed. pip is shipped with python by default.

Installation

$ curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
$ python get-pip.py

Version check
$ pip -V
$ pip2 -V
$ pip3 -V

# Upgrading pip
$ pip install -U pip

# Check for any conflicts in installed packages
$ pip check

# Update list of pinned requirements
$ pip freeze > requirements.txt

Packages

# Vectors and matrices in Python
$ pip install numpy

# Other scientific computing tools
$ pip install scipy

# Dataframes in Python!
$ pip install pandas

# Most commonly used Biocomputing Python library
$ pip install biopython

# IPython Notebook is part of Jupyter now. Another populate Biocomputing tool
$ pip install jupyter

Note: If you already have a requirements.txt file listing all desired depedencies, then run $ pip install -r requirements.txt or $ pip install --requirement requirements.txt.

Additional options:

  • -U - upgrade if it had already installed
  • --no-index - ignore package index (only looking at --find-links url instead)
  • -f, --find-links <URL> - If a URL or path to an HTML file, then parse for links to archives. If a local path or file:// URL that's a directory, then look for archives in the directory listing.

Special case

Often, you will want a fast install from local archives, without probing PyPI.

First, download the archives that fulfill your requirements:

$ pip install --download <DIR> -r requirements.txt

Then, install using –find-links and –no-index:

$ pip install --no-index --find-links=[file://]<DIR> -r requirements.txt

Managing requirements

  • Create and active your virtual environment
  • Installed desired dependencies in the virtual environment
  • Call $pip freeze > requirements.txt to export all installed dependencies into the file.

Note: once you export all dependencies, it may require some cleanup because of previously installed dependencies in the source copy of python depdencies.

Last update: November 4, 2023