1.
Good Practices for Developing
Scientific Software Frameworks
The WRENCH framework example (and some others)
Rafael Ferreira da Silva
https://rafaelsilva.com
https://wrench-project.org
In collaboration with:

2.
What is the best way to write
secure and reliable applications?
2

3.
3
No Code!
Write
nothing,
deploy
nowhere!

4.
How to proceed?
Here are some guidelines…
4

5.
Good Enough Practices in Scientific Computing
• Among several recommendations, this paper emphasizes the following
aspects for software development:
• Place a brief explanatory comment at the start of every program
• Decompose programs into functions
• Be ruthless about eliminating duplication
• Always search for well-maintained software libraries that do what you need
• Test libraries before relying on them
• Give functions and variables meaningful names
• Make dependencies and requirements explicit
• Do not comment and uncomment sections of code to control a program's behavior
• Provide a simple example or test data set
• Submit code to a reputable DOI-issuing repository
5
https://arxiv.org/abs/1609.00037

6.
Best Practices for Scientific Computing
• This paper focuses on the development of scientific software for science
domains:
• Write programs for people, not computers
• Let the computer do the work
• Make incremental changes
• Do not repeat yourself (or others)
• Plan for mistakes
• Optimize software only after it works correctly
• Document design and purpose, not mechanics
• Collaborate
6
https://doi.org/10.1371/journal.pbio.1001745

7.
Scientific Software Best Practices
• This page highlights best-practices for scientific software development:
• Designing your software
• Software Requirements Specification
• Test-driven Development
• Version Control
• Branching Strategy
• Versioning of Releases
• Creating Citable Code
• Coding Guidelines and Code Review
• Continuous Integration
• Gamification
• Integrated Development Environment
7
https://scientific-software-best-practices.readthedocs.io/en/latest/

8.
Best Practices for Scientific Software
• This blog post focuses on domain science software:
• Hosting
• Packaging / installation
• Documentation
• Assistance
• Testing
• Academic publishing
8
https://software.ac.uk/blog/2017-11-29-best-practices-scientific-software

9.
However, there are no actual
recommendations for developing
scientific software frameworks!
Here it is our approach for the
WRENCH Software Framework…
9

10.
The WRENCH Simulation Framework
10
• Objective: Make it easy to develop simulators of complex
Cyberinfrastructure application executions
• Provides high-level, reusable simulation abstractions
• Produces accurate and scalable simulations
https://wrench-project.org

11.
Hosting: Open Source Project
• Some numbers
• > 26K lines of code
• C++, Javascript
• > 300 files
• ~3000 commits
• 16 contributors
• 12 releases
• 7 branches
• Version control
• Issues Tracking
11
https://github.com/wrench-project/wrench

12.
License
12
https://choosealicense.com

13.
Documentation
• Installation Guide
• Getting started
• APIs reference
• Tutorials
• Examples
• Focused guides
• 101, 102, etc.
• Tools
• Doxygen
• Sphynx
13
https://wrench-project.org/wrench/1.8

14.
Testing: Code Coverage
• Unit Tests
• Google Tests
• Integration Tests
• CodeCov
• >88% code coverage
• Other free options
• Coveralls
• SonarCloud
14
https://codecov.io/gh/wrench-project/wrench

15.
Code Quality Analysis
• Automated code review
• Identify issues through static
code review analysis
• Duplication
• Vulnerability
• Etc.
• Tools
• CodeFactor
• Codacy
• SonarCloud
15
https://www.codefactor.io/repository/github/wrench
-project/wrench/overview/master

16.
Continuous Integration (CI) / Deployment (CD)
• Merging in small code
changes frequently
• Automated builds, testing,
and deployment
• Tools
• GitHub Actions
• TravisCI
• AppVeyor
• Jenkins
• Bamboo
16
https://github.com/wrench-project/wrench/actions

17.
Continuous Delivery (CD)
• Kubernetes
https://kubernetes.io
• Amazon AWS / Google
Cloud / Microsoft Azure
• Ansible
https://www.ansible.com
• Packer
https://www.packer.io
17
https://dz2cdn1.dzone.com/storage/temp/11914589-what-
is-continuous-delivery.jpg

18.
Core Infrastructure Initiative (CII)
18
https://bestpractices.coreinfrastructure.org/en/projects/2357

19.
Gamification
• Getting a little badge to appear notifying you, gives a
(small) feeling of accomplishment and can be a good
motivator to write better pull requests
19

20.
Statistics /
Usage
20

21.
Outreach
• Website
• Presentations
• Publications
21

22.
Releases
• Semantic versioning
https://semver.org
22

23.
Some very successful scientific
software framework examples…
23

24.
24
Pegasus Workflow
Management System
http://pegasus.isi.edu
• Open source project since 2001
• Documentation with examples
and tutorial
• Tests and continuous
Integration
• Thousands of citations

25.
Scikit-learn
• Open source Python
library used for
millions of data
scientists
• Tests code coverage:
98%
25

26.
and many, many others…
26

27.
Thank you!
Questions?
27