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Expand Up @@ -41,7 +41,7 @@ The schedule will very soon contain links to lesson material and exercises.

### Day 1 (Sep 16)

- 13:00-13:30 (0.5h) - **Welcome and introduction**
- 13:00-13:30 - **Welcome and introduction**
- Practical information (tools, communication, breaks, etc.)
- Motivation (reproducibility, robustness, distribution, improvement, trust, etc.)
- What will learn and achieve from this course?
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- Branching and merging
- Recovering from typical mistakes

- 16:45-18:00 (1.25h) - {ref}`documentation`
- 16:45-18:00 - {ref}`documentation`
- In-code documentation including docstrings
- Writing good README files
- Markdown
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- Merge vs. rebase
- Conflict resolution

- 16:45-18:00 (1.25h) - **Debriefing and Q&A**
- 16:45-18:00 - **Debriefing and Q&A**
- Participants work on their projects
- Together we study actual codes that participants wrote or work on
- Constructively we discuss possible improvements
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### Day 3 (Sep 18)

- 09:00-10:30 (1.5h) - {ref}`testing`
- 09:00-10:30 - {ref}`testing`
- Unit tests
- End-to-end tests
- pytest
- GitHub Actions

- 10:45-12:15 (1.5h) - {ref}`reusable`
- 10:45-12:15 - {ref}`reusable`
- Tracking dependencies with requirements.txt and environment.yml
- Recording environments in containers

- 13:00-14:45 (1.75h) - {ref}`refactoring`
- 13:00-14:45 - {ref}`refactoring`
- Naming (and other) conventions, project organization, modularity
- Refactoring (explained through examples)
- Design patterns: functional design vs. object-oriented design
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- Command-line interfaces
- Workflows with Snakemake

- 15:00-16:30 (1.5h) - {ref}`publishing`
- 15:00-16:30 - {ref}`publishing`
- Licenses
- Publishing the code via Zenodo
- Packaging the code
- Sharing the code via PyPI

- 16:45-18:00 (1.25h) - **Debriefing and Q&A**
- 16:45-18:00 - **Debriefing and Q&A**
- Participants work on their projects
- Together we study actual codes that participants wrote or work on
- Constructively we discuss possible improvements
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