Some thoughts

• Learning to program/data science is hard and we may not always explain in a way that is accessible to you - So if you don’t understand something ASK ,

• Programming gets better with practice and play - try the code, try variations on the ideas presented, make up stuff to try,

• Programming means making mistakes, expect it, stay calm and try again - if you get frustrated step away and come back; be creative

• Support each other - assign tasks but check each others work

Best Practices for Software Development

• Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, et al. (2014) Best Practices for Scientific Computing. PLoS Biol 12(1): e1001745. doi:10.1371/journal.pbio.1001745

• Blanton, B and Lenhardt, C 2014. A Scientist’s Perspective on Sustainable Scientific Software. Journal of Open Research Software 2(1):e17, DOI: http://dx.doi.org/10.5334/jors.ba

Alternative View

Summary of Best Practices

Wilson et al, Summary Box

Common Coding/Software Engineering Issues

• Unreadable code (hard to understand, easy to forget how it works, hard to find errors, hard to expand)
• Overly complex, disorganized code (hard to find errors; hard to modify-expand)
• Insufficient testing (both during development and after)
• Not tracking code changes (multiple versions, which is correct?)

Automated Tools for Best Practices in Software Engineering

Automated tools (really useful for more complex code development ( note that capstones’s often create programs > 100 lines of code)

Automated documentation- a program that helps you to generate documentation

https://en.wikipedia.org/wiki/Comparison_of_documentation_generators

http://roxygen.org/roxygen2-manual.pdf

Automated test case development

http://r-pkgs.had.co.nz/tests.html

Automated code evolution tracking (Version Control) This you already know https://github.com/