Hey there, I’m Stephen.

Welcome to my work-in-progress website.

## Insertion Sort: Go

This post shows an implementation of insertion sort written in Go. Insertion sort builds a sorted array at the beginning of the original array, iterating through the unsorted portion to add another element to the sorted portion with each pass. For a more detailed walkthrough, see my original post with an implementation in C.

func insertionSort(arr []int) {
arrLen := len(arr)
for i := 1; i < arrLen; i++ {
key := arr[i]
j := i - 1
for j >= 0 && arr[j] > key {
arr[j+1] = arr[j]
j--
}
arr[j+1] = key
}
}

## Creating an Advent of Code Application Using Go Plugins

The best way to learn programming is to write code. The advice is almost always “build something,” but it can be hard to figure out what a good “something” would be, especially for beginners. In my mind, that’s where coding puzzles come in. Some of my favorites are Advent of Code, Project Euler (for the more mathematically inclined) and Rosalind (focused on bioinformatics). I’ve spent a fair bit of time working through Advent of Code puzzles in a few different languages – R, Python, Julia, and Go so far. I can’t say that I’ve completed all 25 challenges for a year, nor that I’ve done all four of those languages for every puzzle that I’ve completed. But I’ve gotten a tremendous amount of enjoyment and satisfaction from doing the puzzles that I have worked on, and I’ve learned a ton.

In this post, I’m going to talk about how I have structured my Go solutions (later posts will get into the puzzle solutions themselves in detail). I really wanted to embed my solutions in a single application and have everything runnable through a common command. I found the Go Plugin package to be just about the best solution for doing this, though not without its challenges. Most things I read about the plugin package said that it wasn’t mature enough, or that it’s too clunky to work well. While it definitely is a little clunky, I think it does alright for this job.

The main challenge that I was facing was how to dynamically include different Go source files for execution from a main program. I wanted to specify at runtime which package to import and run, which is not possible as far as I know. I didn’t want to run the solution code, write the answers to disk, and then have the main program just read in those answers. The other solution that I had come across was to create a map with dates pointing to solution functions. I definitely thought about how I might do that, but decided that manually importing every solution file and filling in the map with the functions from each file was just too much of a pain, and not a very elegant solution.

## Go Plugins

So what exactly is a Go plugin? From the package docs:

A plugin is a Go main package with exported functions and variables that have been built with:

go build -buildmode=plugin


Importantly, even though a Go plugin is a main package, the main() function is not run. This is nice because it can allow you to export functionality from a main package that you may have written for some other purpose. But it is a pain because Go will not compile a main package without a main() function, so you still need one even if you’re creating a package specifically to be a plugin, and you know you won’t actually use main(). The other irritating part is that you have to provide type information to the caller program about the entities from the plugin that you want to use. I was able to make this work by having every plugin implement a function with the signature func Solve(fname string), which takes the path to the problem input as its argument, runs the solution functions, and prints the answers. That way, I can have the same code in my main program regardless of the intermediate steps involved in any given day’s solution.

## Program Structure

You can find the full source code on GitHub.

So given this brief overview of Go plugins, how does it work in practice? The project has this overall file structure:

.
|__ AOC.go
|__ puzzles/
|  |__ 2018/
|  |  |__ 01/
|  |  |  |__ input.txt
|  |  |  |__ main.go


AOC.go is the main Advent of Code program file. It includes the code to load plugins and execute the solution function from those plugins. The puzzles/ directory contains sub-directories for each day’s puzzle, where input.txt is the puzzle input (generated for each unique user of adventofcode.com) and main.go contains the source code for the solutions.

As mentioned above, all of the main.go solution files contain a function with the signature func Solve(fname string). Beyond that, they also generally contain a func readInput(fname string) as well as functions for the different parts of the puzzle, taking in the data structure(s) produced by readInput(). They also all contain a blank func main(){} so that they can be compiled as main packages, as required by the plugin package. For any puzzle solution, we have to compile it as a plugin to provide a .so file with a predictable name that the AOC.go file can locate and access. To do this, we run:

$cd puzzles/$YEAR/$DAY$ go build -buildmode=plugin -o $YEAR$DAY.so

AOC.go is the most interesting file as far as the plugin system is concerned. After reading in the year and day for the desired puzzle, it has to attempt to locate a solution directory and .so (shared object) file for that date:

import (
"fmt"
"os"
"path/filepath"
"plugin"
)

dir := filepath.Join("puzzles", year, day)
// Check for solution directory
if s, err := os.Stat(dir); os.IsNotExist(err) || !s.IsDir() {
fmt.Println("No solution available for", year, day)
os.Exit(1)
}
// Check for .so file
pluginPath := filepath.Join(dir, year+day+".so")
p, err := plugin.Open(pluginPath)
if err != nil {
fmt.Printf("No such file %s.so\n", year+day)
os.Exit(1)
}

Assuming that our program survives through that point (i.e. we have the correct subdirectory inside the puzzles/ directory and that we have compiled it with -buildmode=plugin to create a .so file), we then need to find the Solve() function and run it. We need to know the name of the symbol that we’re looking up, as well as its type/signature.

symbol, err := p.Lookup("Solve")
if err != nil {
fmt.Println(err.Error())
os.Exit(1)
}

solve, ok := symbol.(func(string))
if !ok {
fmt.Println("Plugin has no 'Solve' function")
os.Exit(1)
}

All that’s left is to provide the path to the puzzle’s input file and run the Solve() function.

inputFile := filepath.Join(dir, "input.txt")
solve(inputFile)

I have set things up so that the Solve() functions print out the answers, rather than returning them as a string. So once we call solve() in the parent program, we’re all done! Running from the command line is as easy as

$go build -o AOC$ ./AOC 2018 1

## Helper Scripts

It would definitely get tedious to create new solution directories by hand, write the solution code, then compile it with the -buildmode=plugin flag by hand. Especially when it turns out that the solution needs to be fixed or refactored, and then needs to be compiled yet again. So I created a couple of different helper scripts to make these tasks a little easier.

### new_puzzle.sh

When I want to start working on a new solution, I like having a template for the files ready to go. In the project root, I have a directory called template containing input.txt.templ, which is blank (the input is taken from the AOC website), and main.go.templ which contains a skeleton file with func Solve(fname string), func ReadInput(fname string), func Part1(), and func Part2(), as well as the empty func main(){}. new_puzzle.sh copies the basic templates into a new directory for the year and day that I want to solve. After doing some input validation (which I won’t get into here), the main part of the script creates the directory, creates a basic README.md, and copies over a couple of templates for the source code and the input file.

YEAR=$1 DAY=$2

DIR="puzzles/$YEAR/$DAY"
mkdir -p $DIR cp template/input.txt.templ$DIR/input.txt
cp template/main.go.templ $DIR/main.go README="# [$YEAR Day $DAY:](https://adventofcode.com/$YEAR/day/$DAY)\n\n" echo -e$README > $DIR/README.md ### build_plugin.sh It’s also nice to be able to build a plugin from the project root, without worrying about changing directories, making sure the .so file is in the right place, and typing everything out by hand. Once again skipping over input validation in this post, the script is fairly straightforward: YEAR=$1
DAY=$2 DIR="puzzles/$YEAR/$DAY" if [[ -d$DIR ]]; then
cd $DIR go build -buildmode=plugin -o$YEAR$DAY.so else echo "$DIR does not exist"
exit 1
fi

### build_all_plugins.sh

Finally, it’s sometimes helpful to be able to compile every plugin you’ve got, instead of just one at a time. This is especially useful after cloning the git repository, since the .so files are ignored. This was a great opportunity for me to learn more about control flow in bash. Again, it’s not a very complex script, but I find it incredibly useful.

cd puzzles

# every subdir in puzzles/ is a year
for YEAR in *; do
# cd into the year's dir
cd $YEAR echo "$YEAR"

# every subdir in puzzles/$YEAR/ is a day for DAY in *; do # cd into day's dir cd$DAY
echo -e "\t$DAY" # if there's a main.go file, build it if [[ -f main.go ]]; then go build -buildmode=plugin -o$YEAR\$DAY.so
fi

# cd back into the year dir
cd ..
done
done

## Conclusion

Go’s plugin system does have a lot of restrictions – it’s only available on MacOS and Linux, it requires the plugin and the caller program to be compiled with the exact same version of Go and of any dependencies that are be imported in both, etc. But if you are working solo or if the plugins and the calling program will be built on the same machine at roughly the same time, it’s not a bad solution. My Advent of Code use case is obviously not the most complex or technically demanding application, so I can’t speak to the usefulness of Go plugins in other contexts. But I’ve enjoyed working with them and have learned a lot from the experience. If it looks like the plugin package might be useful for you, I’d strongly encourage you to give it a try!

## Selection Sort: C

Next up in my “learning in public” push is selection sort, and an implementation in C. Like insertion sort, selection sort sorts the array in place, starting with a sorted beginning portion and an unsorted end. We iterate through the unsorted portion, and find the smallest value. We then swap that element with the first element in the unsorted portion. From there, the unsorted portion begins one index later, and we repeat the process until the entire array is sorted.

## Insertion Sort: C

In my first post in my “learning in public” push, I’m going to be talking about the insertion sort algorithm and an implemention in C. The general idea of insertion sort is to build a sorted array in place, at the beginning of the original array, shifting the unsorted elements toward the end of the array as necessary. It relies on the fact that an array of length 1 is sorted by definition.

I’m going to show and walk through some pseudocode, touch on the efficiency of the algorithm, and then show an implementation in C.

## Pseudocode

NB: I use zero-indexed arrays and half-open array slicing in this pseudocode.

A = Array(...)
N = A.length
for i from 1 to N:
A[0:i] is sorted
key = array[i]
j = i - 1  // index of last element in the sorted portion
while j >= 0 and A[j] > key:
A[j + 1] = A[j]
j = j - 1
A[j + 1] = key


### Example

• Start with A = [3 1 2]
• First iteration: i = 1
• A[0:i] --> A[0:1] --> [3] is sorted by definition
• key = A[i] --> A[1] --> 1
• j = i - 1 --> 0
• Loop condition: 0 >= 0 and 3 > 1 --> TRUE
• A[j + 1] = A[j] --> A[1] = 3, A = [3 3 2]
• j = j - 1 --> -1
• Loop condition: FALSE (j < 0)
• A[j + 1] = key --> A[0] = 1, A = [1 3 2]
• A = [1 3 2]
• Second iteration: i = 2
• A[0:i] --> A[0:2] --> [1 3] is already sorted
• key = A[i] --> A[2] --> 2
• j = i - 1 --> 1
• Loop condition: 1 >= 0 and 3 > 2 --> TRUE
• A[j + 1] = A[j] --> A[2] = 3, A = [1 3 3]
• j = j - 1 -- > 0
• Loop condition: FALSE (!(1 > 2))
• A[j + 1] = key --> A[1] = 2, A = [1 2 3]
• A = [1 2 3]
• i == N so no third iteration

## Efficiency

• Worst-case
• Array is reverse sorted
• O(n2)
• Best-case
• Ω(n)

## Implementation

insertionSort() takes as input an integer, n, the length of the array, and an array of integers, arr. It sorts the array in place, so it doesn’t return anything.

void insertionSort(int n, int arr[])
{
for (int i = 1; i < n; i++)
{
int key = arr[i];
int j = i - 1;

while (j >= 0 && arr[j] > key)
{
arr[j + 1] = arr[j];
j--;
}
arr[j + 1] = key;
}
}

## Learning and Working in Public

Having a new baby, settling into a new apartment in a new city, and hunting for a new job while taking care of said baby full-time have made my life just a little hectic this summer. Which is to say that I have not been as productive in my side-projects and learning agenda as I would like. So this post is step 1 in my push to be more deliberate about advancing my knowledge and portfolio. [Read More]

## Hugo Workflow

I recently ported my pretty defunct blog over to Hugo, after some considerable searching about the best option for my needs. I wanted to be able to work with R Markdown files, but not have to mess too much with the internals. I had messed around with Blogdown a couple years ago, and thought it may be a good starting place. The issue is that I don’t want to have to work in RStudio for all of my website work. [Read More]

I’m updating my first R-related blog post, from back in 2016. In it, I used reshape2 to do some data cleaning on a messy dataset. In this update, I’m going to use tools from the tidyverse instead. I’m keeping most of the text the same, but changing the code chunks. [Read More]

## Mental Health and Data Donation

This morning I was listening to a really good (though now a bit old) episode of the awesome podcast Partially Derivative. The episode featured Glen Coppersmith, the founder and CEO of Qntfy (pronounced “Quantify”). Qntfy is working to tap into non-healthcare data to gain insights into mental health processes and outcomes. The episode does a great job discussing the barriers to communication between fields as disparate as statistics/data science and clinical mental health. [Read More]

## Rescaling Variables with R

In doing some RA work, I’ve needed to rescale or normalize different variables. Working with survey data, it can be very difficult to compare ordinal results across questions. Say for instance that we want to get the correlation of perceived economic status and perceived social status. The Latinobarómetro survey asks the first question with a scale from 0 to 10. The second item, though, is reported on a five-point scale. If we want to easily interpret correlation, it helps to have these on the same scale. [Read More]

## ioslides with R Markdown

Over the weekend, I decided to write up some slides for my stats section on Monday. Having really gotten into the groove of using R Markdown, and having gotten a little rusty on using LaTeX with knitr, I decided to play around with HTML5 slides instead of going the beamer route. In the spirit of results first, the finished presentation is shown below. Click inside the frame, then use your left and right arrows to navigate. [Read More]