Collaborative Scientific Software Development course, NORBIS & Digital Life Norway 2019

Instructors: David Grellscheid, Stefanie Hólmgeirsdóttir, Kidane M. Tekle, Kim Brügger, Matúš Kalaš

Preparation

Python (version >= 3.5)

Python packages: numpy, matplotlib, pytest

Create a user account on https://github.com/

Git version control

• Linux users: from your package manager
• Mac users: https://git-scm.com/download/mac or brew or macports
• Windows users: we recommend https://gitforwindows.org/ and using Git Bash included therein

Day 1 (Tuesday Mar 5th)

(all David except intro)

• Norbis intro (Ragna Breines)
• Code you want to read
• Python introduction
• Hands-on: Project Euler
  • 1, 2, 3 (to use basic language features)
  • 14, 17 (use dict), 57
  • 79 (file input), 102 (handle 2D points)
• Clean Code summary
• Python links: tutorial, PEP8 == coding style guidelines, library list, Python package index (PyPI)

Homework till next week: Project Euler number 3. Needs to complete within a minute!

Day 2 (Wednesday Mar 6th)

Keyword: Agile

• Collaborative software development (Kidane)
  • Additional material: Best practices (Kidane)
• Good project management is about people, caring and understanding; and some planning and documentation (Stefanie)
  • Requirements, solution proposal, team, project roles|responsibilites, changes, negotiations, evaluation, ...
• Team work: Projecting a kindergarden playground (Miss Claudia, alter ego of Stefanie)
• Useful tools: Trello
• Technical debt (Kidane)

Day 3 (Thursday Mar 7th)

• Creating better code (Kim)
  • Useful links: Software Carpentry lessons, ...
• Debugging (Kim)
• Hands-on: Debugging python code with PDB (Kim)
• Unit testing (Kim)
• Hands-on: Unit testing with pytest
• Refactoring (Kim)
• Hands-on: Refactoring Kim's code
• Live demo: Code review (and some refactoring; David)
• Tools: PDB, pytest, logger, PyCharm IDE (Integrated development environment), ...

Day 4 (Friday Mar 8th)

(all David)

• Object-oriented design
• Hands-on OO design: Freight train station
• Python: modules, OO, copying
• Python: Numpy, Scipy, Matplotlib
• Exercise 1: Bouncing dots
• Exercise 2: Landcover data

Day 5 (Monday Mar 11th)

• Documentation (Kim)
• Version control with git (Kidane)
• Group project descriptions
  • Genetic Bike (group work repo)
  • Traffic Jam (group work repo)
  • Mutation Analyser (group work repo)

Day 6 (Tuesday Mar 12th)

• Optimisation, profiling (David)
• Live demo: Profiling (David)
• Live demo: Linking code across programming languages (David)
• ELIXIR (Christine Stansberg)

Day 7 (Wednesday Mar 13th)

• Containers (Kidane)
• Open source, community, licensing, publishing (Matus)

Day 8 (Thursday Mar 14th)

• Packaging & continuous integration (Kim)
• Presentations of group projects and discussion (everyone)

Feedback form

• Please fill in our feedback form