BACKGROUND Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolki...

In recent years, Python has made great inroads as an introductory language in computer science education, but few emphasize its object-oriented nature; it is most often introduced with a procedural paradigm. For those teaching object orientation in CS1, Java remains the predominant language. We suggest that Python is an excellent choice for teaching an object-oriented CS1. Based on our experien...

Computer-aided diagnosis of neural diseases from EEG signals (or other physiological signals that can be treated as time series, e.g., MEG) is an emerging field that has gained much attention in past years. Extracting features is a key component in the analysis of EEG signals. In our previous works, we have implemented many EEG feature extraction functions in the Python programming language. As...

Scientific computing is usually associated with compiled languages for maximum efficiency. However, in a typical application program, only a small part of the code is time–critical and requires the efficiency of a compiled language. It is often advantageous to use interpreted high–level languages for the remaining tasks, adopting a mixed–language approach. This will be demonstrated for Python, ...

This paper presents the design and implementation of a complete embedded Python run-time system for the ARM Cortex-M3 microcontroller. The Owl embedded Python run-time system introduces several key innovations, including a toolchain that is capable of producing relocatable memory images that can be utilized directly by the run-time system and a novel foreign function interface that enables the ...

PyRovio is our Python implementation of the WowWee Rovio API. It allows direct control of a Rovio robot from Python programs. We have used PyRovio to implement Python-based actor-agents that participate in a live intermedia performance. We also use PyRovio as part of ongoing work in cognitive robotics to connect SNePS-based agent minds to their Rovio bodies in the world.

The PythonTEX package allows authors to combine computational and typesetting tasks by embedding Python code in TEX documents. This package allows access to many powerful Python modules, providing support for such things as symbolic mathematics, plotting, arbitrary precision numerical calculations, and networking. Python’s intuitive syntax, popularity, and extensibility along with TEX’s formatt...

Dynamic languages, like Python, are attractive because they guarantee that no correct program is rejected prematurely. However, this comes at a price of losing early error detection, and making both code optimization and certification harder tasks when compared with static typed languages. Having the static certification of Python programs as a goal, we developed a static type inference system ...

Automatic differentiation (AD) is an essential primitive for machine learning programming systems. Tangent is a new library that performs AD using source code transformation (SCT) in Python. It takes numeric functions written in a syntactic subset of Python and NumPy as input, and generates new Python functions which calculate a derivative. This approach to automatic differentiation is differen...

We present pylibjit, a Python library for generating machine code at load time or run time. The library can be used for dynamic code generation, although it is mainly aimed at optimizing compilation of existing Python function definitions. Python functions can be compiled by simply annotating them with a decorator specifying data types. The pylibjit compiler takes advantage of this type informa...