This is an intermediate-level course in collaborative research software engineering and development skills, using Python as an example language. It teaches these skills in a way that mimics a typical software development process working as a part of a team, starting from an existing piece of software. The lesson is developed using The Carpentries Jekyll lesson template.
A typical learner for this course may be someone who has gained basic software development skills either by self-learning or attending a foundational course such as the novice Software Carpentry Python course. However, their software development-related projects are now becoming larger and more complex and they need more intermediate software engineering skills to help them design more robust software code, automate the process of testing and verifying its correctness and support collaborations with others.
⚠️ The course material can change at any point - if you are planning a workshop using this material, either let the maintainers know or make sure you use your own fork of the lesson.
The lesson uses patient inflammation data for code examples, from the Software Carpentry Python "inflammation" lesson.
Check out the variant of this lesson that uses river catchment data in code examples (more suited for Earth and environmental scientists).
The course is in a stable beta - it has been run over 15 times times with different cohorts by the lesson authors as well as independently by people not directly involved in the lesson development and is in a good state to be reused and taught by others.
The lesson is suitable for both instructor-led teaching or guided self-learning where helpers provide help and answer questions (synchronously or asynchrounously) as learners go through the course on their own. Initially, in sections 1-3 of the lesson, learners are working on a software project and going though exercises individually. In sections 4 and 5, they are grouped and work in teams, as they would when collaborating on a team software project development.
The lesson has 5 sections; each section can be delivered in one day by an instructor or worked through in self-learning mode over a half a day to a day, depending on the pace.
If you would like to teach this lesson to your audience and help with more beta testing,
please let the lesson developers know by opening an issue with your workshop details and a
label .
We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any questions, concerns, or experience any difficulties along the way.
We'd like to ask you to familiarise yourself with our Contribution Guide and have a look at the more detailed guidelines on proper formatting, instructions on compiling and rendering the lesson locally, and making any changes and adding new content or episodes.
Please see the current list of issues for ideas for contributing to this
repository. For making your contribution, we use the GitHub flow, which is
nicely explained in the chapter Contributing to a Project in Pro Git
by Scott Chacon.
Look for tags 
Current maintainers of this lesson (in alphabetical order) are:
- Matthew Bluteau
- Steve Crouch
- Kamilla Kopec-Harding
- Doug Lowe
- Aleksandra Nenadic (lead Maintainer for the period 1 October 2023 - 31 March 2024)
The maintainer team aims to meet at 11:00 UK time (BST or GMT) on the fourth Wednesday each month. The meetings alternate between operations meetings and co-working sprints. Meeting notes are kept in the Google doc.
A list of all contributors to the lesson can be found in AUTHORS.
Instructional material from this lesson is made available under the Creative Commons Attribution (CC BY 4.0) licence. Except where otherwise noted, example programs and software included as part of this lesson are made available under the MIT licence. For more information, see LICENSE.md.
To cite this lesson, please consult with CITATION.
To get in touch with the lesson maintainers, send an email to python-inter-inflammation@lists.carpentries.org.
Original lesson authors Aleksandra Nenadic, James Graham, and Steve Crouch were supported by the UK's Software Sustainability Institute via the EPSRC, BBSRC, ESRC, NERC, AHRC, STFC and MRC grant EP/S021779/1.