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  • 16. Developer Documentation

16. Developer Documentation¶

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

  • 16.1. Make a pull request to the afni repository
    • 16.1.1. Introduction
    • 16.1.2. How to make a pull request
    • 16.1.3. The quick version: Make a PR
  • 16.2. Elementary OpenMP in AFNI
    • 16.2.1. Overview
    • 16.2.2. Introduction
    • 16.2.3. Memory Concepts
    • 16.2.4. Compiling to use OpenMP
    • 16.2.5. Example #1 – A basic case
    • 16.2.6. Example #2 – A Little Bit of Restructuring
    • 16.2.7. Example #3 – OpenMP and malloc
    • 16.2.8. Example #4 – OpenMP and static variables
    • 16.2.9. Example #5 – OpenMP and random numbers – AlphaSim
    • 16.2.10. Example #6 – OpenMP and malloc() and memcpy() – 3dREMLfit
    • 16.2.11. Example #7 – Looping over voxels in 3dAutoTcorrelate
    • 16.2.12. OpenMP Library Functions
    • 16.2.13. Printing -help for OpenMP-ized programs
  • 16.3. Running tests
  • 16.4. Cmake for AFNI - making AFNI is a piece of C(m)ake
    • 16.4.1. Overview
    • 16.4.2. Quickstart
    • 16.4.3. Installation of development dependencies
    • 16.4.4. Basic approach to building and installing
    • 16.4.5. Modifying targets in the cmake build
    • 16.4.6. Adding new targets
    • 16.4.7. Linking against targets
    • 16.4.8. Linking against external software
    • 16.4.9. Other details
  • 16.5. Sphinx Documentation
    • 16.5.1. Setup for building sphinx
  • 16.6. Contribute Your Own Docs
    • 16.6.1. Rst & Sphinx Syntax:
  • 16.7. How to Format Help Strings
    • 16.7.1. C-programs
    • 16.7.2. C-GUI
    • 16.7.3. C-Shell Scripts
    • 16.7.4. R programs
    • 16.7.5. Python programs
    • 16.7.6. Building one help file

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Table of Contents

  • 1. Installation and Background
  • 2. Starting with AFNI
  • 3. Educational resources
  • 4. All program helps
  • 5. AFNI GUI (afni)
  • 6. SUMA GUI (suma)
  • 7. FATCAT
  • 8. NIFTI
  • 9. Statistics
  • 10. Templates & Atlases
  • 11. Non-human processing
  • 12. Tutorials, Examples
  • 13. Demo Material
  • 14. Codex: AFNI Code Examples from publications
  • 15. Citations and Reference Works
  • 16. Developer Documentation
    • 16.1. Make a pull request to the afni repository
    • 16.2. Elementary OpenMP in AFNI
    • 16.3. Running tests
    • 16.4. Cmake for AFNI - making AFNI is a piece of C(m)ake
    • 16.5. Sphinx Documentation
    • 16.6. Contribute Your Own Docs
    • 16.7. How to Format Help Strings
  • 17. Contributors
  • 18. Glossary
  • 19. Main AFNI pages

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