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<!DOCTYPE html>
<html>
<head>
<title>Hammers and Saws: What We've Learned from Teaching Research Software Engineering with Python and R</title>
<meta charset="utf-8">
<link rel="stylesheet" href="custom.css">
</head>
<body>
<textarea id="source">
# Hammers and Saws
<div align="center">
<h3>
What We've Learned from Teaching Research Software Engineering
<br/>
with Python and R
</h3>
</div>
<div class="flex-row">
<div class="flex-col narrow">
<p>
<img class="column" src="./img/py-rse-cover.jpg" alt="Research Software Engineering with Python (cover)"/>
</p>
</div>
<div class="flex-col">
<br/>
<table>
<tr>
<td><a href="https://damienirving.github.io/">Damien Irving</a></td>
<td><a href="https://katehertweck.com/">Kate Hertweck</a></td>
</tr>
<tr>
<td><a href="https://lukewjohnston.com/">Luke Johnston</a></td>
<td><a href="https://joelostblom.com/">Joel Ostblom</a></td>
</tr>
<tr>
<td><a href="https://www.cwick.co.nz/">Charlotte Wickham</a></td>
<td><a href="https://third-bit.com">Greg Wilson</a></td>
</tr>
</table>
<div align="center">
<p>
<a href="https://www.routledge.com/Research-Software-Engineering-with-Python-Building-software-that-makes/Irving-Hertweck-Johnston-Ostblom-Wickham-Wilson/p/book/9780367698324">Chapman and Hall/CRC, 2021, 978-0367698324</a>
</p>
<p>
<a href="https://merely-useful.tech/py-rse/">https://merely-useful.tech/py-rse/</a>
</p>
</div>
</div>
</div>
---
# TL;DR
- Wrote a book to bridge the gap between introductory programming and research software engineering
- Based on over 50 years of collective teaching experience
- Narrative follows logical progression of package development
- Can be used to teach a semester-long course (complete with exercises)
- Free to read online
- Learned a few things along the way…
---
# What We Care About
<p class="hanging-indent">
<strong>Open science</strong>:
making data, methods, and results freely available
to all by publishing them under open licenses.
</p>
<p class="hanging-indent">
<strong>Reproducible research</strong>:
ensuring that anyone with access to the data and software can feasibly reproduce results,
both to check them and to build on them.
</p>
<p class="hanging-indent">
<strong>Software sustainability</strong>:
the ease of maintaining and extending it rather than replacing it,
which depends on skills and culture as well as technology.
</p>
<p class="hanging-indent">
<strong>Graphic design</strong>:
judging from these slides, not so much…
</p>
---
# Audience
<div class="flex-row">
<div class="flex-col wide">
<img class="column" src="./img/amira-khan.png" alt="Amira Khan" />
</div>
<div class="flex-col">
<p>
<strong>Amira</strong>:
Master's in Library Science;
some stats courses;
learned some R doing data science courses online;
wants to tidy up and share scripts, datasets, and reports.
</p>
</div>
</div>
<div class="flex-row">
<div class="flex-col">
<p>
<strong>Jun</strong>:
PhD in geology plus a 4-month data science bootcamp;
now does forensic audits;
uses a variety of machine learning and visualization tools;
wants to open source his work.
</p>
</div>
<div class="flex-col wide">
<img class="column" src="./img/jun-hsu.png" alt="Jun Hsu" />
</div>
</div>
<div class="flex-row">
<div class="flex-col wide">
<img class="column" src="./img/sami-virtanen.png" alt="Sami Virtanen" />
</div>
<div class="flex-col">
<p>
<strong>Sami</strong>:
BSc in applied math and computer science;
works for university's computing center;
wants to help researchers build and run data pipelines.
</p>
</div>
</div>
---
# Trajectory
| Novice | Competent | RSE |
| ---- | ---- | ---- |
| Email attachments | Git repository | Branching workflow |
| "Just do it" | Slack/mailing list | Martha's Rules |
| Interactive analysis | A pile of scripts | Build tools / CI |
| Word / Google Docs | LaTeX | Site generator |
| "It doesn't crash" | "Are there any NAs?" | Assertions / unit tests |
| "Um, hi?" | README | LICENSE + CoC |
---
# Main Topics
- Automation
- Unix shell
- Make
- Travis CI
- Robust programming
- Command-line Python scripts
- Configuration
- Testing
- Error handling
- Package development
- Collaboration
- Git and GitHub
- Data provenance
- Teamwork
<div align="center">
<p>
<em>
Actual order is different so that learners score some early wins.
</em>
</p>
</div>
---
# Automation
<ul>
<li>The Unix shell is the unavoidable duct tape of research computing
<ul>
<li>Many other things don't make sense until you've seen it</li>
</ul>
</ul>
<ul>
<li>Make is past its best-by date
<ul>
<li>But none of its would-be replacements has achieved critical mass</li>
</ul>
</ul>
<ul>
<li>If we were starting over, we'd use GitHub Actions instead of Travis CI
<ul>
<li>Though we are nervous about how reliant open science is on GitHub</li>
</ul>
</ul>
---
# Robust Programming
<div align="center">
<p>
<em>
Based on <a href="https://doi.org/10.1371/journal.pcbi.1005412">Taschuk's Rules</a>
</em>
</p>
</div>
<ul>
<li>Command-line Python scripts
<ul>
<li>Assume learners know <code>for</code> loops and functions</li>
<li>Show them how to handle command-line arguments, stdin/stdout, etc.</li>
</ul>
</ul>
<ul>
<li>Configuration
<ul>
<li>Also serves as a lesson in software design</li>
</ul>
</ul>
<ul>
<li>Testing
<ul>
<li>Though we punt on "what tests should I write?"</li>
</ul>
</ul>
<ul>
<li>Error handling
<ul>
<li>Because testing is never perfect</li>
<li>And neither are people</li>
</ul>
</ul>
<ul>
<li>Package development
<ul>
<li>Only for code, not data</li>
</ul>
</ul>
---
# Collaboration
<ul>
<li>Git and GitHub
<ul>
<li>From zero to a branch-based workflow</li>
<li>You can do a lot with GitHub without using Git</li>
</ul>
</ul>
<ul>
<li>Data provenance
<ul>
<li>How to actually implement the <a href="https://www.go-fair.org/fair-principles/">FAIR Principles</a></li>
</ul>
</ul>
<ul>
<li>Teamwork
<ul>
<li>Licensing</li>
<li>Issue tracking</li>
<li>Running meetings and making decisions</li>
<li>Including everyone (especially <a href="https://doi.org/10.1371/journal.pcbi.1007296">newcomers</a>)</li>
</ul>
</ul>
---
# What we learned about Python and R
<ul>
<li>Planned to write two books in parallel
<ul>
<li>Realized we needed to focus on one to complete</li>
<li>Python version was further along</li>
<li>R version should arrive in 2022</li>
</ul>
</ul>
<ul>
<li>Our experience is that:
<ol>
<li>Python users tend to arrive with more computing skills than R users</li>
<li>The tidyverse is easier to teach than Pandas</li>
</ol>
</ul>
<div align="center">
<table>
<tr><th>Topic</th><th>Python</th><th>R</th></tr>
<tr><td>Unix shell</td><td>Yes</td><td>No</td></tr>
<tr><td>Make</td><td>Yes</td><td>No</td></tr>
<tr><td>Git</td><td>Command line</td><td>GUI</td></tr>
<tr><td>Packages</td><td>Code only</td><td>Code and data</td></tr>
</table>
</div>
---
# What we learned about writing books
<div align="center">
<p>
It takes longer than you expect.
</p>
</div>
---
# What we learned about writing together
- It's a lot more fun than writing solo
- Modeling the collaborative approaches covered in the books
- Content is better: not one person's opinion and preferences
---
# What we learned about writing tools
- All available options are frustrating
---
<div align="center">
<h1>Thank you</h1>
</div>
<div class="flex-row">
<div class="flex-col narrow">
<p>
<img class="column" src="./img/py-rse-cover.jpg" alt="Research Software Engineering with Python (cover)"/>
</p>
</div>
<div class="flex-col">
<br/>
<table>
<tr>
<td><a href="https://damienirving.github.io/">Damien Irving</a></td>
<td><a href="https://katehertweck.com/">Kate Hertweck</a></td>
</tr>
<tr>
<td><a href="https://lukewjohnston.com/">Luke Johnston</a></td>
<td><a href="https://joelostblom.com/">Joel Ostblom</a></td>
</tr>
<tr>
<td><a href="https://www.cwick.co.nz/">Charlotte Wickham</a></td>
<td><a href="https://third-bit.com">Greg Wilson</a></td>
</tr>
</table>
<div align="center">
<p>
<a href="https://www.routledge.com/Research-Software-Engineering-with-Python-Building-software-that-makes/Irving-Hertweck-Johnston-Ostblom-Wickham-Wilson/p/book/9780367698324">Chapman and Hall/CRC, 2021, 978-0367698324</a>
</p>
<p>
<a href="https://merely-useful.tech/py-rse/">https://merely-useful.tech/py-rse/</a>
</p>
</div>
</div>
</div>
</textarea>
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