Introduction

Reproducibility: Definitions, Advantages, and Barriers

It's code all the way down...

Turtles All GIFfrom Turtles GIFs

... and it's a mess

xkcd.com/2347

Many, Many Tools Wanting to Help

Conda
Anaconda
Miniconda
Mamba
Pixi
pip
virtualenv
Pipenv
pyenv
Poetry
requirements.txt
environment.yml
renv
uv
just

A Time-Capsule for the Future

Python


                  $ pip freeze > requirements.txt

What does the file contain?
Re-create this environment with:


                  $ pip install -r requirements.txt

Self-study: Carpentries Lesson

R

Initialize renv, and then “save” and “load” the state of your project library.


                  renv::init()
                  renv::snapshot()  # save
                  renv::restore()   # load

Self-study: Carpentries Lesson

Upload to GitHub

Add

VS Code: click '+' next to 'Changes' (or files)
RStudio: click 'Staged'

N.B.: also include .RProfile and activate.R

git: git add [filenames]

Commit

IDEs: Write "add dependencies", click 'Commit'
git: git commit -m "add dependencies"

Push

IDEs: Click 'Push'
git: git push

Software Documentation

How to make software easier to understand

## Docstrings

Using regular comments:

<pre style="width: fit-content; font-size: 50%;"><code data-trim class="language-python">
                  # This function converts a temperature in Fahrenheit to Celsius.
                  def fahrenheit_to_celsius(temp_f: float) -> float:
                      temp_c = (temp_f - 32.0) * (5.0/9.0)
                      return temp_c
                </code></pre>

Using docstrings:

<pre style="width: fit-content; font-size: 50%;"><code data-trim class="language-python">
                  def fahrenheit_to_celsius(temp_f: float) -> float:
                      """
                      Converts a temperature in Fahrenheit to Celsius.

Parameters
                      ----------
                      temp_f : float
                          The temperature in Fahrenheit.

Returns
                      -------
                      float
                          The temperature in Celsius.
                      """
                      return (temp_f - 32.0) * (5.0/9.0)
                </code></pre>

For-

matting

Follow style guides without altering functionality
Increase readability and reduce chance for merge conflicts
Formatter can fix issues, if requested

## Defining a Function

<pre style="width: fit-content; float: left; font-size: 47%;"><code data-trim class="language-python">
                  def my_function(parameters):
                      # perform action
                      # return value

def fahr_to_kelvin(temp):
                    kelvin = ((temp - 32) * (5 / 9)) + 273.15
                    return kelvin
                   
                </code></pre>

<pre style="width: fit-content; float: right; font-size: 47%;"><code data-trim class="language-r">
                  my_function <- function(parameters) {
                    # perform action
                    # return value
                  }

fahr_to_kelvin <- function(temp) {
                    kelvin <- ((temp - 32) * (5 / 9)) + 273.15
                    return(kelvin)
                  }
                </code></pre>

<pre class="fragment" style="width: 100%; font-size: 47%; float: left; margin-left: auto;"><code data-trim class="language-python">
                  # freezing point of water
                  fahr_to_kelvin(32)  # 273.15

# boiling point of water
                  fahr_to_kelvin(212)  # 373.15
                </code></pre>

Next Steps

How to make your code reusable