Module 1.4b Coding best practice 2023 (outline)
Theme 1: Getting started with bioinformatics
Note: this module was removed from the 2024 course edition, to free up more time for introducting bash and python
Coding best practice
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Time |
Activity description |
ILOs |
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13.00 - 13.45 |
Lecture: “Key principles of good coding practice” |
· Describe what is meant by “documentation” · Outline the main reasons for why documentations matters · Give examples of how code sharing can be facilitated · Explain what git and github is about, and how it can facilitate code-sharing and maintenance |
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14.00 - 16.30 |
Practical: “Getting started with git and github” |
· Use basic git commands from the command-line (clone, config, add, commit, status, log, diff) · Generate and merge branches · Work with a remote repository (remote add, fetch, pull, push) |
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Details
In this session, we aim to get the participants started with some good habits when writing code.
In the lecture, we will focus on the importance of good documentation and using version-control software, using real-life scenarios. In the practical, the participants will create their own repositories. They will learn the most basic commands needed to use such a repository, and upload the code they have written in the first two days. For the remainder of the course, the participants will continue adding code to their repositories, and thereby get more comfortable with the procedure.