Veusz is a scientific plotting package, designed to create publication-ready Postscript, PDF, or SVG output. It features an easy to use graphical interface as well as a command line interface and can be scripted or embedded in Python scripts. Graphs are constructed in a modular fashion from separate components. Datasets can be interactively modified or created from within the program.
Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Theano features tight integration with numpy, transparent use of a GPU, efficient symbolic differentiation, speed and stability optimizations, dynamic C code generation, and extensive unit-testing and self-verification. Theano has been powering large-scale computationally intensive scientific investigations since 2007. But it is also approachable enough to be used in the classroom (IFT6266 at the University of Montreal).
PyParticles is a particle simulation toolbox entirely written in Python. It simulates a particle-by-particle model with the most popular integrations methods, including Euler, Runge Kutta, and Midpoint. It represents the results on an OpenGL or Matplotlib plot, and offers an easy-to-use API.