Continuity Developer Information

TO DO Lists

• Continuity 7.0 Re-engineering plan

• Task List

• Future Plans

Obtaining, Compiling, and Understanding the Source code

• Obtaining the source from Git (Currently for collaborators only!)

• Setup blender_migration branch

• Compiling Continuity from source

• Understanding the Continuity source

• Description of Continuity Variables

• Description of Continuity Scripts

• How to edit unit types for a model editor

• Architecture of Continuity Parallel

• Anatomy of Continuity 6 Files

• Solvers used by Continuity 6

• Fixing the f2py problem

• Building Distributed SuperLU

• Running in batch mode

• Adding dynamically-compiled model binaries to the SVN Repository

• Creating a C Extension

• Dynamics Model

• Basis Function Refactor

• Instructions for wrapping Fortran codes with F2py

• Updating test cases

• Overview of the source code generation process

• Profiling the source code

Database Information

• Database development

• Basic Database Installation

• How to do things on the database

• How to export finite element geometries from the database

Tools and Libraries

• Creating the Continuity installer with Advanced Installer

• Creating the Continuity installer with Installshield **We no longer use this**

• Compiling Insight Toolkit (ITK) on Windows

• Compiling Insight Toolkit (ITK) on Linux

• Running with CUDA

• Using OpenMP

• Using PETSc

• Installing PyTrilinos (linux only)

• Using OpenNurbs

• Using the WiX installation system

• Packages removed from MglTools

• How to make changes to MglTools packages

Misc. Notes

• Documentation for the HexBlender plug-in for Blender 2.49b

• Setting up a web service

• Accessing the source from an off campus machine

• Updating NVIDIA graphics drivers on lys

• Upgrading to python 2.5

• Recommended SciTE settings

• Text editors that work well with Continuity

• Setting up a new system

• Using AFNI diffusion plugin

• Working with Windows 7

• Adding readline support to Mac

• Building Python 2.5, NumPy and SciPy on Mac OS X 10.6

• Miscellaneous notes on the Continuity website

• Notes on modifying PMW widgets

• Various example table files

• Miscellaneous notes on the Interfaces website

• Miscellaneous notes on using Swing/Instant to compile models

• Notes on Continuity’s Automated Build and Test System

• A map of the EP workflow

• Creating Markov model type ion channels in the EP ionic model editor (deprecated)

• A guide for sympy syntax in Continuity

• Some basics on how to debug in Python