programming_and_version_control_class.Rmd

---
title: 'Programming and Version Control'
author: "[Brian High](https://github.com/brianhigh)"
date: "![CC BY-SA 4.0](cc_by-sa_4.png)"
output:
  ioslides_presentation:
    fig_caption: yes
    fig_retina: 1
    fig_width: 6
    fig_height: 4
    keep_md: yes
    smaller: yes
    logo: logo_128.png
---

## Common Programming Issues

* Poorly formatted, not following "best practices" style guides
    - Long sections of poorly commented code with obscure vairable names
    - Not enough blank lines separating code sections
    - No spaces between list items, function parameters
* Too much copy and paste
    - Difficult to read, debug and maintain
* Fail to check for problems
    - Packages, utilities, files or folders missing
    - Invalid data entry
* Inefficient 
    - Redoing work already done (installing, downloading, etc.)
    - Processing more data than needed, usinfg more RAM
    - Looping more times than needed
    - Not taking advantage of language features

## Common Programming Solutions

* Code reuse, modular design (functions, loops)

```
function task:
    do steps: [1, 2, 3, 4, 5]

mylist = [A, B, C, D]
foreach item in mylist: do task to item
```

* Consider dependencies, anticipate problems
* Validate input (with e.g., regular expressions)
* Use resources wisely (RAM, CPU, storage)
* Use language "idiomatically" - as designed to be used
* Use clear comments, descriptive and consistent variable naming scheme

## Programming Examples

* Web programming: [Panopto Link Maker](https://github.com/brianhigh/panopto-linkmaker) (HTML/JavaScript/Regex)
    - Input validation with Regular Expressions
    - Completely client-side programming: completely portable
* API Programming: [Amazon Search](https://github.com/brianhigh/amzn-srch) (Python/R)
    - Embedding non-R system commands in Rmd
    - Small "remove duplicates" Python script to use from shell with pipe
* Functions: [Reddit Wordclouds](https://github.com/brianhigh/reddit-wordclouds) (Python/R)
    - Loops versus *apply functions
    - Example of Rmd ioslides presentation with license info and icon
* Regular expressions filtering, streaming: [Filter-fastq](https://github.com/brianhigh/filter-fastq) (Python/Perl/Regex)
* Validation: [Get-logo-png](https://github.com/brianhigh/research-computing/blob/master/get_logo_png.sh) (Bash/Regex)
    - Checking requirements, command-line arguments
    - Input validation with Regular Expressions
    - Automation using CLI tools, pipes

## Version Control

Different systems: an _evolution_ of version control systems (VCS)

- RCS: Revision Conrtrol System (1982, single user)
- CVS: Concurrent Versions System (1990, multi user, central server)
- SVN: Subversion (2000, updated, improved, CVS-like, central server)
- various distributed VCS: Git (2005), Mercurial (2005), Bazarr (2005)

Demo basic "git" workflow:

* fork, clone, pull, edit, commit, push, pull-request
    - From RStudio GUI
    - From command line
    - From other GUI or web browser (GitHub site)

## Exercise: Practice Git

Try to fork, clone, commit, push, and send a "pull request" with these projects.

Pick a project (from course modules page, GitHub):

- [Panopto-linkmaker](https://github.com/brianhigh/panopto-linkmaker) (HTML, JavaScript, CSS)
- [Airquality-example](https://github.com/brianhigh/airquality-example) (R)
- [WA Water Quality](https://github.com/brianhigh/wa-water-quality) (R)
- [Medicare-ipps](https://github.com/brianhigh/medicare-ipps) (R)
- [Amazon-search](https://github.com/brianhigh/amzn-srch) (R, Python)
- [Reddit-wordclouds](https://github.com/brianhigh/reddit-wordclouds) (R, Python)
- [Filter-fastq](https://github.com/brianhigh/filter-fastq) (Python, Perl)
- [Get-logo-png](https://github.com/brianhigh/research-computing/blob/master/get_logo_png.sh) (Bash)