Developer Curriculum

How to use this curriculum

These materials represent an abbreviated and targeted curriculum designed to help you develop and maintain the Transposonmapper repository and code base. All of the resources listed below are free to access and use, and supplementary material like video lessons has been added where possible and relevant.

Materials were compiled by Maurits Kok and Ashley Cryan of the TU Delft Digital Competence Centre, with input from other DCC members Niket Agrawal, Jose Urra Llanusa, and Manuel Garcia Alvarez. The curriculum was compiled in September 2021.

Bash

• What is Bash? - of all the shells available, Bash is one of the most popular, the most powerful, and the most friendly
• Bash Essentials – Bash commands commonly used to navigate file directories in your Terminal/GitBash
• The Unix Shell lesson from Software Carpentries - use of the shell is fundamental to using a wide range of other powerful tools and computing resources. These lessons will start you on a path towards using these resources effectively
• Installation Instructions - particularly important for Windows users, as Bash comes pre-installed on Mac. Windows users will need to install GitBash following the instructions at this link
• Using the Terminal in Mac - The Terminal app allows you to control your Mac using a command prompt

Git

• What is Git?- 2-minute video overview of the technology and how it works
• Install Git from GitHub Guides - Check if Git is already installed on your machine; if not, follow these instructions to get started. Notes: If you've already installed GitBash on Windows OS, you will have Git already. Installing GitHub Desktop will also install the latest version of Git if you don't already have it.
• Installing Git from Software Carpentries - Alternative installation instructions from Software Carpentries, including videos and details per OS.
• Intro to version control with Git from Code Refinery – self-paced introductory lesson to version control using Git
• Git Intro video lesson from Code Refinery - Day 1 - Recorded lesson from a May 2021 Code Refinery workshop on material in Intro to version control with Git, part 1/2
• Git Intro video lesson from Code Refinery - Day 2 - Recorded lesson from a May 2021 Code Refinery workshop on material in Intro to version control with Git, part 2/2
• Branching and merging – lesson from Code Refinery on concept of branching in Git (featuring octopus diagram)
• What is .gitignore? – introduction to how and why to use the .gitignore file to not track some files in a project folder (e.g., because of their size or sensitivity)
• Git command cheat sheet – commonly used Git commands in one page that can also be downloaded

GitHub/GitLab (remote repositories)

• Understanding the GitHub flow – guide from GitHub on how and why to work with branches
• Collaborative distributed version control - We have learned how to make a git repository for a single person. What about sharing?
• SSH connection to GitHub – instructions to set up SSH connection to GitHub so that you do not need to input your login credentials with every push/pull
• GitLab and SSH keys – instructions to add an SSH key to your (TU Delft) GitLab account for the same reason as above
• GitHub without the Command Line from Code Refinery - practice collaborating and sharing using either the GitHub website or GitHub desktop application
• GitHub Guides: Mastering Markdown - Markdown is a lightweight and easy-to-use syntax for styling all forms of writing on the GitHub platform.

Jupyter Notebooks and JupyterLab

• Introduction to Jupyter and JupyterLab - lesson material on the user interface of JupyterLab, how Jupyter notebooks work, and what some common and powerful usecases are

Anaconda Navigator and managing conda environments

• Anaconda Installation Guide from Software Carpentries - Although one can install a plain-vanilla Python and all required libraries by hand, we recommend installing Anaconda, a Python distribution that comes with the latest version of Python and Jupyter Notebooks by default
• Intro to Anaconda Navigator - Anaconda Navigator is a graphical user interface to the conda package and environment manager. This 10-minute guide to Navigator will have you navigating the powerful conda program in a web-like interface without having to learn command line commands
• Introduction to Conda for (Data) Scientists - Conda is an open source package and environment management system that easily creates, saves, loads, and switches between environments on your local computer
• Managing Conda environments - documentation on performing a range of common tasks with Conda using the command line

Python

• Scientific Computing with Python - a free video course series that teaches the basics of using Python 3
• Applied Data Science with Python Specialization - Coursera course in which you can enroll for free
• LearnPython.org - Whether you are an experienced programmer or not, this website is intended for everyone who wishes to learn the Python programming language
• Programming with Python from Software Carpentries - this introduction to Python is built around a common scientific task: data analysis
• Plotting and Programming with Python from Software Carpentries - an introduction to programming in Python for people with little or no previous programming experience using plotting as its motivating example
• Can You Speak Python? - test your knowledge of some important features of the Python programming language and the NumPy and Pandas libraries

Modular Code and testing

• Writing tests - lesson from CodeRefinery on automated testing
• Video testing lesson - recording from software testing workshop by Code Refinery
• Modular coding - slides on modular code from Code Refinery

Docker

• Installing Docker - installation instructions for Windows, macOS, and Linux
• Install WSL2 update - manual WSL2 update for Windows
• Dockerfile reference - information on how to write a Dockerfile

VSCode

• Setting up VSCode for Linux - guide to getting started using VSCode with Windows Subsystem for Linux

Continuous Integration

• GitHub Actions introduction course - an introductory course from GitHub on how to use GitHub Actions

Reproducible Research

• Reproducible Research material from Code Refinery - demonstrates how version control, workflows, containers, and package managers can be used to record reproducible environments and computational steps
• Reproducible Research video lesson from Code Refinery - Recorded video lesson from Code Refinery workshop in May 2021 on Reproducible Research material
• Data + Code + Software = PDF - Slides to an overview on how to integrate data and software into a PDF.