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RSE-UP

Welcome

Getting Started

Running Example and Project Organization
Software to Install
Python Refresher

Code, Documentation and Licensing

Writing Readable Code
Documenting Programs
Software Licenses

Working with the Shell

Introduction to Bash
The Basics of the Unix Shell
Bash Basics Exercises
Building Tools with the Unix Shell
Bash Tool Exercises
Bash Advanced
Bash Advanced Exercises

Version Control with Git

Version Control
Using Git at the Command Line
Exercise Version Control
Using SSH on Gitlab and Github
Writing good commit messages
Going Further with Git
Forking on Github
Exercises Git Advanced

Markdown, READMEs, Notebooks and Computational Narratives

Markdown
README Files
Jupyter Notebooks
Computational Narratives

Testing and Error Handling

Introduction to Testing
Testing Software
Exercises - Testing
Introduction to Error Handling
Handling Errors
Exercises - Error Handling

Working in teams

Working in Teams
Exercise - Work Teams

Workflows

Data Analysis Workflows

Requirements, Architecture and Design

Application Classes, Software Requirements, Architecture and Design

Building Command-Line Tools

Introduction to CLI application using Python
Building Command-Line Tools with Python
Exercises - Scripting Python for CLI tools

Configuration and Packaging

Introduction to Configuration
Introduction to Packaging Python Software
- Creating Packages with Python
- Exercises - Packaging

Workflows and Automation

Introduction to Make and Snakemake
Introduction to CI/CD
- CI/CD Basics

Tracking Provenance

Tracking Provenance
Exercises - Provenance

Open Science

Software Citation and FAIR

Appendix

Solutions
Working Remotely
Project Tree
Bibliography

Repository
Open issue

Index

By Software Engineering Group - University of Potsdam

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