Here is a list of all files with brief descriptions:

magiks/__init__.py
magiks/geometry/__init__.py
magiks/jacobian/__init__.py
magiks/jointspace/__init__.py
magiks/magiks_core/__init__.py
magiks/specific_geometries/__init__.py
magiks/specific_geometries/pr2/__init__.py
math_tools/__init__.py
math_tools/algebra/__init__.py
complex.py	This module provides tools by which you can work with complex numbers
cost_function.py
endeffector.py	: This module provides a class containing a set of reference positions and orientations in the taskspace together with their associated poses
function_library.py
functions.py
general_magiks.py
general_math.py
geometry.py	This module contains a comprehensive data structure with relevant method and properties for identities in three-dimensional geometry like a point, a rotation or orinetation in 3D space, an ellipsoid and etc
inverse_kinematics.py	This module provides a functor class regaring the inverse kinematic calculations of a manipulator
jacobian.py	This module provides three classes representing the geometric, analytic and error jacobians of a manipulator
kinematic_manager.py	This module contains the main class for handling the kinematics of a manipulator
link_point.py
log_manager.py	This module provides classes containing data structure for IK test log data
manipulator_configuration.py
manipulator_geometry.py
manipulator_library.py	Contains a function that defines geometric parameters and joint limits for a number of known manipulators Some examples: (PUMA, PA10, EXO, AILA Arm and PR2 Arm)
optimization.py	This module provides fast solution to some typical optimization problems
polynomials.py	This module provides everything you need to work with polynomials including tools by which you can fit a curve through a set of points
pose_metric.py	: This module provides a class representing the residual error between the actual and desired endeffector poses including methods for calculating residual functions based on various conventions for both position and orientation
pr2_arm_kinematics.py
pr2_kinematics.py
pr2_symbolics.py
pyride_interpreter.py	Contains simplified functions to control PR2 using pyride engine
pyride_synchronizer.py	Contains simplified functions to control PR2 using pyride engine
quaternions.py	This module provides some useful functions dealing with quaternions
skilled_pr2.py	Contains a class inherited from PyRide_PR2 in pyride_synchronizer.py which is connected to a real-time robot, a real PR2 or PR2 in simulation that have special skills like drawing
task_frame.py	: This module provides a class representing the reference orientation of an endeffector and the desired value for it
task_point.py	: This module provides a class representing the reference poisition of an endeffector and the desired value for it
task_reference.py	: This module provides a class representing the reference poisitions and orientations of an endeffector and the desired value for it
trajectory.py	This module provides a class containing a trajectory in the multi-dimensional space
vectors_and_matrices.py	This module provides some useful functions dealing with numpy vectors and matrices
workspace.py	: This module provides a class containing methods and properties regarding the workspace of a manipulator
writer_pr2.py	Contains a class inherited from Skilled_PR2 in skilled_pr2.py which is connected to a real-time robot, a real PR2 or PR2 in simulation that have special writing skills