This document discusses the software development process and engineering practices used for tools created by the IU NanoBio group. It outlines the development cycle including requirements analysis, design, testing, deployment, maintenance, and community development. The group follows open source practices on GitHub for development and uses continuous integration, unit testing, and documentation on GitHub and nanoHUB. Quality assurance is conducted through detailed testing checklists. Tools and frameworks are on different release cycles, with tools receiving more rapid initial releases and maturing to longer cycles.

1. Tool Development Process and
Software Engineering
Supun Kamburugamuve
NSF Site Visit, CIB, Bloomington, IN
April 25, 2019

2. • Software
▪ https://github.com/IU-nanoBio
▪ Links to all projects
• Website
▪ https://nanohub.org/groups/nanobio
• Contact us
▪ iunanobio@googlegroups.com
Overview

3. Software Development Cycle
1. Use of Open Source Software Development
Guidelines
2. Market Research and Requirements Analysis
3. Tool Design
4. Quality Assurance (Testing, Validation)
5. Software Development
6. Tool Deployment
7. Tool Maintenance
8. Community Development
9. Tool Selection and Monitoring
10. Documentation

4. Software Development
• Follows the GitHub open source development model
▪ GitHub issues
▪ GitHub releases
▪ GitHub pull request (review then commit)
• Documentation on GitHub & nanoHUB
• Expand internal developer meetings to include users
▪ Create meetups

5. Nano Micro Macro DIPY/Odyssey/Fury Harp
Pull request
model
Yes Yes Yes Yes No
Unit tests In development In development In development Yes Yes
Validation tests In development In development In development Yes Yes
Functionality
testing / front end
Yes Yes Yes Yes N/A
UIs Rappture / Jupyter Jupyter / Rapture / Python
C++
Jupyter Python N/A, will be Python
Coding standards Yes Yes Yes Yes Yes
Public Forum
URL / Email
nanoHUB forums Gitter nanoHUB “Questions” and
physicell-users google
group
neuroimaging@python.org harp-users@googlegroups.c
om
Public Releases Github releases Github releases GitHub releases Github releases, Anaconda Github Releases
Languages C++, Python C++ C++, Python Python Java / C++ / Python in
development
Tools MPI, OpenMP, Machine
Learning
LLVM, LAPACK, SUNDIALS OpenMP VTK/GLSL Intel DAAL, MPI
Continuous
Builds
Yes WIll be added Yes (for most apps) Yes Yes
Documentation Available in Github and
nanoHub
Yes Yes Yes Yes
Development
method
Uses GitHub model Uses GitHub model Uses GitHub model Uses Github model Uses Github model
Software Engineering Practices

6. Quality Assurance
• Dedicated engineer for UI and functionality testing
▪ A detailed checklist on test points
▪ Cycle through the checklist each week
▪ Reports issues through GitHub
• Unit tests and integration tests are in development
▪ Will be integrated to Travis builds
In the past two months QA reported
11 issues and 7 of them are fixed

7. Deployment of Tools
• nanoHUB tools and underlying software frameworks are on
different development cycles
• Rapid releases at initial stages for nanoHUB tools
▪ Tools are small compared to back-end software
▪ We expect tools will move to longer release cycles as they mature
• e.g., PhysiCell cancer-immune model
▪ 4 Releases from February 2019
• Some back-end tools moving to a quick release cycle

8. xml2jupyter Tool (discussed in Macro slides)
• Provides an example of scripting a template (for nanoBIO
related applications)
▪ lower the barrier for others
▪ more modular (fix bugs and add features just one place)
▪ incorporate common tests, continuous integration, etc.

9. Documentation & Community
• GitHub documentation
• Tools have documentation on nanoHUB
• Engage with users on nanoHUB forums