16. Developer Documentation

Building, testing, contributing… get it here while it’s hot.

• 16.1. So You Want to Write an AFNI Program
  • 16.1.1. Anatomy of an AFNI Program
  • 16.1.2. Datasets and Volumes
  • 16.1.3. Surfaces
  • 16.1.4. Communication: NIML and Live Data
  • 16.1.5. The Function Cookbook
• 16.2. Make a pull request to the afni repository
  • 16.2.1. Introduction
  • 16.2.2. How to make a pull request
  • 16.2.3. The quick version: Make a PR
• 16.3. Elementary OpenMP in AFNI
  • 16.3.1. Overview
  • 16.3.2. Introduction
  • 16.3.3. Memory Concepts
  • 16.3.4. Compiling to use OpenMP
  • 16.3.5. Example #1 – A basic case
  • 16.3.6. Example #2 – A Little Bit of Restructuring
  • 16.3.7. Example #3 – OpenMP and malloc
  • 16.3.8. Example #4 – OpenMP and static variables
  • 16.3.9. Example #5 – OpenMP and random numbers – AlphaSim
  • 16.3.10. Example #6 – OpenMP and malloc() and memcpy() – 3dREMLfit
  • 16.3.11. Example #7 – Looping over voxels in 3dAutoTcorrelate
  • 16.3.12. OpenMP Library Functions
  • 16.3.13. Printing -help for OpenMP-ized programs
• 16.4. Running tests
• 16.5. Cmake for AFNI - making AFNI is a piece of C(m)ake
  • 16.5.1. Overview
  • 16.5.2. Quickstart
  • 16.5.3. Installation of development dependencies
  • 16.5.4. macOS CMake builds
  • 16.5.5. Basic approach to building and installing
  • 16.5.6. Modifying targets in the cmake build
  • 16.5.7. Adding new targets
  • 16.5.8. Linking against targets
  • 16.5.9. Linking against external software
  • 16.5.10. Other details
• 16.6. Sphinx Documentation
  • 16.6.1. Setup for building sphinx
• 16.7. Contribute Your Own Docs
  • 16.7.1. Rst & Sphinx Syntax:
• 16.8. How to Format Help Strings
  • 16.8.1. C-programs
  • 16.8.2. C-GUI
  • 16.8.3. C-Shell Scripts
  • 16.8.4. R programs
  • 16.8.5. Python programs
  • 16.8.6. Building one help file