Online CodeRefinery workshop

Registration (closed)

Registration closed

Contact

support@coderefinery.org

Course goals and format

In this course, you will become familiar with tools and best practices for version control and reproducibility in modern research software development. The main focus is on using Git for efficiently writing and maintaining research software.

We will not teach programming, but we teach the tools you need to use programming well. We assume that you are familiar with the programming language that you use in your work and research. We try to keep the course as language-independent as possible but we will show some basic code examples in Python.

This is an informal and interactive event with type-along type of presentations, live coding, and demos. Short tutorials alternate with practical exercises.

Prerequisites

• You should be able to navigate the file tree in a terminal session and edit text files in the terminal. This Linux shell crash course (video) contains the essentials.
• Basics in one or more programming languages.
• You need to install some software (see below).
• It is useful if you have a basic idea of how Git works. We will start from the basics anyway, but please go through this Git-refresher material for a basic overview and important configuration steps.
• Make sure that Git is configured, and verify the configuration (see below).

Software requirements

You need to install some software before CodeRefinery (why we ask you to do this). Please do this - and check it - in advance, otherwise you’ll start off behind.

Note that, e.g., a working Python executable on your laptop is not sufficient - a version greater than 3.4 is strongly recommended and a number of extra packages need to be installed as detailed on the Python installation page. You also need to check your git configuration (video: how to configure Git). If you have an institutional laptop with limited rights, start in advance and/or ask for help to translate these instructions to work on your system.

• Bash
• Editor
• Git, including some configuration
• (optional) Visual diff tools
• Python
• Jupyter and JupyterLab
• (optional) Snakemake
• Zoom

You should either a) drop by one of our verification sessions in advance, or b) verify with your team’s helper before the workshop.

Schedule

All times are in Europe/Stockholm time Time converter

The schedule includes frequent breaks.

Helper onboarding

• Nov 10 (Tue) 13:00 - 14:00
• Nov 11 (Wed) 10:00 - 11:00

Installation help and verification times

• Nov 10 (Tue) 14:00 - 15:00
• Nov 11 (Wed) 11:00 - 12:00
• Join anytime during this (preferably not everyone at the very start and end)

Day 1 (Nov 17, Tue)

• 9:00 - 9:20 Welcome and practical information (Thor)
• 9:20 - 12:00 Introduction to version control - part 1/2 (“Motivation” to “Undoing”) (Sabry)

Day 2 (Nov 18, Wed)

• 9:00 - 12:00 Introduction to version control - part 2/2 (“Branching and merging” to “Inspecting history”) (Sabry and Matus)

Day 3 (Nov 19, Thu)

• 9:00 - 12:00 Collaborative distributed version control (Thor)

Day 4 (Nov 24, Tue)

• 9:00 - 9:15 Mini-intro (Thor)
• 9:00 - 11:00 Reproducible research and FAIR data (Anne)
• 11:00 - 12:00 Social coding and open software (Annika)

Day 5 (Nov 25, Wed)

• 9:00 - 10:30 Jupyter (Radovan)
• 10:30 - 12:00 Documentation (Pavlin)

Day 6 (Nov 26, Thu)

• 9:00 - 10:30 Automated testing (Anne)
• 10:45 - 11:45 Modular code development (Radovan)
• 11:45 - 12:00 Concluding remarks and where to go from here (Thor)

Location

The workshop will be held online by Zoom. Helpers and accepted learnes will receive a link.

Price

Free of charge, funded by the Nordic e-Infrastructure Collaboration.

Contact

support@coderefinery.org

Who the course is for

Are you doing any of these things below:

• You write scripts to process data.
• You change scripts written by your colleagues.
• You write code that is used in research by you or others.

If yes, then this course is for you. This is not designed for “professional code developers” or computer scientists.

If you develop research code and you know all the tools already, join us as a helper! It’s fun, and you always learn something new about a subject by teaching it.

How to join

We are normally limited by number of helpers, thus why not allow groups to bring their own helper?:

• We have the concept of teams that bring their own breakout room.
• Anyone may register as a learner, we will try to take as many as we can.
• Or you can register as a helper. If you are somewhat comfortable with these tools, you can be a helper! (see below)
• Register as a team, one helper and 4-6 learners.
  • We will accept all complete teams.
  • Everyone on the team must register separately.
  • Decide some team name, and when registering, everone enter this same name so that we can link you together.
  • During the exercise sessions in breakout rooms, the helper has primary responsibility for their group’s hands-on exercises. Still, instructors drop by to check and help as needed, so don’t worry if you don’t know everything.
  • This is a great opportunity to bring your friends and colleagues and prepare for the future together.

If you’ve been to a CodeRefinery before and have used git some after that, you are definitely capable of being a helper. If you routinely use git and know Python somewhat well, you are also very qualified to be a helper.

We arrange a helper onboarding sessions (see under Schedule). It is strongly recommended for the first-time helpers to attend this onboarding session. Please join one of the following sessions that fits your schedule.

What we will not teach

This is not a course about a specific programming language or the Linux/Unix terminal shell. We assume that you are familiar with the programming language that you use in your work and research. We try to keep the course as language-independent as possible but we will show some basic code examples in Python.

Host

• Naoe Tatara

Instructors

• Radovan Bast
• Anne Fouilloux
• Matus Kalas
• Pavlin Mitev
• Sabry Razick
• Annika Rockenberger
• Thor Wikfeldt

Expert helpers

• Richard Darst
• Max R. Eckardt
• Juho Lehtonen
• Emiliano Molinaro
• Stefan Negru
• Samantha Wittke

Helpers

• Octavian Andrei
• Raphaela Heil
• Johan Hellsvik
• Patric Holmvall
• Diana Iusan
• Matthew Morris
• Athanasios Protopapas
• Annajiat Alim Rasel
• Anthony Scemama
• Ingrid Strandberg

(Tips for helpers).

FAQ

• Why should I come as a team? If you will work together later, learning the tools at the same time is a great way to do it.

• Am I good enough to be a helper? If you are asking this question, probably you are. You should have some familiarity with git, provide some initial advice on obvious error messages, and be able to call us for advanced help when it’s needed.

• How does the waiting list work? Anyone can register, but you go to the waitlist until we can be sure we have enough helpers. We’ll continually approve people as we get space. We know this may be more unpredictable for you, but the way to make sure you get in is join a team with a helper (or find us more helpers in general).

• If it’s online, why did you close? CodeRefinery workshops are interactive, with lots of interaction between instructors, helpers, and learners. We can scale one-to-many easily, but we reached the limits of an interactive format.

• How can I be notified of updates? Currently, we don’t have any way. Follow @coderefine on Twitter.