Course Material for the Software Carpentry workshop Würzburg 2017-06-26/2017-06-27

1 About

This is the course material for the Software Carpentry workshop taking place in Würzburg July 3rd and 4th, 2017. The course is an introduction for novices to the Unix Shell, Python and git.

2 Schedule

2.0 Check installation while people are arriving

2.1 Welcome and introduction [9:00 - 9:30]

• Introduction of the instructors and helpers
• Name tags
• Sticky notes
• Introduction of the participants
• Ice breaker - Sort people by the following values:
  • Are you a PhD or Postdoc?
  • Sort by time after graduation
  • Group by research field
  • Considering the course topic - how strong do you feel about knowing this already?
• Code of Conduct https://software-carpentry.org/conduct/ => Be excellent to each other!
• Photos
• Social media, Hash Tag #SWCWue
• Breaks
• Coffee/Tea
• Bathroom
• Material of the course
  • https://swcarpentry.github.io/shell-novice/
  • https://swcarpentry.github.io/python-novice-inflammation/
  • https://swcarpentry.github.io/git-novice/
• The etherpad
  • http://pad.software-carpentry.org/2017-07-03-wuerzburg
  • Short URL: http://bit.ly/2uAm6wR
  • Exercise - add your name to the list of participants
• Motivation
  • Automation
  • Reproducibility / Transparency
• Who has still issue with installation?

2.2 Unix Shell (Konrad) [9:30 - 12:00]

• Files, folders, locations
• Manipulating files and folders
• Connecting tools with pipes
• for loops
• Shell scripting

2.3 Python [13:00 - 16:00]

2.3.0 Check Jupyter notebook

2.3.1 Session 1 (Markus):

• Print, literal constants
• Variables
• String format operators
• Data structures: str, int, float, list, dict
• File handling
• Conditionals if else startement
• for loop

2.3.2 Session 2 (Konrad):

• Function definition
• Writing Python scripts

2.4 Git (Markus/Konrad) [9:00 - 12:00]

• The Softare Carpentry Git lesson
• Setup
• Creating a Repository
• Tracking Changes
• Exploring History
• Ignoring things
• Remote repositories
• GitHub

2.5 Open Session [13:00 - 16:00]

This session offers space for further exercises, questions and related topics like open source / open content licenses, open science practices, reproducible research.

• Fill out the post- workshop survey of SWC
• Fill out the feedback form of the GSLS

2.6 Discussion and feedback [16:00 - 16:30]

3 Sources

• The Unix Shell
• Programming with Python
• Version Control with Git

4 Links and hints from our discussions

• Text Editors / IDEs (integrated development environment)

  • Try for something that suits your needs and taste. It should ideally have features like autocompletion and syntax highlighting.
  • vim
  • emacs
  • gedit
  • kate
  • Spyder
  • PyCharm
  • Atom

• Main ways to work with Python

  • Script
  • interactive after calling "python" or "ipython" (REPL)
  • Jupyter notebook

• Literate programming

• Markdown - A markup language

• Python 2.7 (legacy!) vs Python 3 (currently 3.6)

• Comparison of R to Python

• Useful Python libraries

  • pandas
  • numpy
  • scipy
  • Biopython
  • scikit-learn - Machine learning
  • scikit-image - Image analysis
  • matplotlib - 2D plotting library
  • seaborn - statistical data visualization
  • bokeh
  • statsmodel

5 License

This work by Markus Ankenbrand and Konrad Förstner is licensed under a Creative Commons Attribution 4.0 International License.