util

Utility modules for Python, for use with other Python programs.

Features

Logging

The log submodule contains many functions for building and interacting with Python logging objects. Static logging configurations can be loaded from the logging.yml file, and the default location for log output is typically set to a local logs directory. Additionally, the classes submodule contains the LoggedObject class which can be used to create objects which have their own logging instances.

Email

The mutt submodule is a flexible wrapper to the mutt system program, and can be used to send emails. A common use-case is send the contents of a submodule or object's log file as the body of an email to users as a notification of program completion. File attachments can also be sent, allowing you to also send some of the files created by your program with the email.

Qsub

The qsub submodule includes the Job class for submitting jobs to a compute cluster and monitoring them for completion. Currently configured for the phoenix system at NYULMC running SGE.

Git

The git submodule contains functions for interacting with git installed on the system. For example, it is possible to check the current repository's branch information, in case you want prevent the program from running if not on the master branch.

Find

The find submodule contains the find function which can be used to search the system for desired files or directories. This function has been modeled off of the standard GNU find program and supports multiple inclusion and exclusion patterns, and search depth limits, among others.

Software

Designed and tested with Python 2.7

Designed for use on Linux system with Sun Grid Engine (SGE) installed

Some modules may make system calls relying on standard GNU utilities

Credits

sh.py is used as an included dependency.