The CodeRefinery Project

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# The CodeRefinery Project

## Radovan Bast

## slides: [bit.ly/niasc-2016](http://bit.ly/niasc-2016)

[coderefinery.org](http://coderefinery.org) | [@coderefine](https://twitter.com/coderefine) | [neic.nordforsk.org](https://neic.nordforsk.org)

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## Software is transforming research

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- Quality of scientific software is **increasingly becoming critical** for the advancement of knowledge

- Scientists often **lack the necessary training** in practices to
  enable them to collaboratively write high-quality scientific software
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## Many researchers struggle with code complexity

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## Goals: Better science with better software

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(c) The New Yorker, Oct 17, 2016
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- Provide researchers with **infrastructure**, **training**, and **guides** in the necessary tools
  and techniques to create sustainable, modular, reusable, and reproducible
  software
- Build **strong partnerships** with related initiatives
- This project is not about efficient code but rather about **efficient coding**
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## CodeRefinery launched September 2016

- Nordic e-Infrastructure Collaboration project
- Funded for two years
- We are a team of enthusiasts located in DK, FI, NO, SE

### Team

- Aleksi Kallio
- Bjørn Lindi
- Erik Edelmann
- Jyry Suvilehto
- Lukasz Bartosz Berger
- Michaela Barth
- Nikolai Denissov
- Pinja Koskinen
- Radovan Bast
- Sabry Razick
- Sri Harsha Vathsavayi
- Thor Wikfeldt
]

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## Version control: record every change

*"I don't need version control because it is just me."*

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## Version control: make it possible to collaborate

- We plan to deploy a Nordic-wide code repository hosting platform

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## Automated testing

```python
def get_bmi(mass_kg, height_m):
    """
    Calculates the body mass index.
    """
    return mass_kg/(height_m**2)

def test_get_bmi():
    bmi = get_bmi(mass_kg=90.0, height_m=1.91)
    expected_result = 24.670376
    assert abs(bmi - expected_result) < 1.0e-6
```

### Bonus

- Robust code
- Best documentation
- Simplify collaboration
- Guides towards modular code structure

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- Suiting up to modify untested code
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### Good code (pure)

```python
# function which computes the body mass index
def get_bmi(mass_kg, height_m):
    return mass_kg/(height_m**2)

# compute the body mass index
bmi = get_bmi(mass_kg=90.0, height_m=1.91))
```

### Less good code (side effects)

```python
mass_kg = 90.0
height_m = 1.91
bmi = 0.0

# function which computes the body mass index
def get_bmi():
    global bmi
    bmi = mass_kg/(height_m**2)

# compute the body mass index
get_bmi()
```

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## Continuous integration service

- [Travis CI](https://travis-ci.org)
- [Jenkins](https://jenkins.io)
- Test every changeset
- We plan to deploy a service which will make it easier for researchers to test their code

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## Documentation

- Close to the code (minimize barrier)
- **Versions**: If the project has versions, the documentation should too
- Lightweight markup (LaTeX is not lightweight enough)
- Readable on any device
- Division into tutorials and keyword reference
- Tutorials contain good defaults
- Ready examples that one can copy-paste to get quickly started
- Prose, written by humans

### Current gold standard (in my opinion):

### [GitHub](https://github.com)/[GitLab](https://gitlab.com)/[Bitbucket](https://bitbucket.org) -> [RST](http://docutils.sourceforge.net/rst.html)/[Sphinx](http://www.sphinx-doc.org) -> [Read the Docs](https://readthedocs.org)

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## How can you publish a Nature paper?

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## How to publish a Nature paper

- Ask the Nature IT admins to give you access to their server
- Promise to submit a high quality paper
  in the right place and using the right format and style
- Once you get access simply upload your article sources
- Make sure the issue looks good
- If somebody complains later, make corrections

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## Use code review

### Peer review process in publishing

- Papers are reviewed before they are published
- Maintain standards of quality
- Improve performance
- Provide credibility

### Code review

- Code is reviewed before it is integrated
- Improve quality
- Learning
- Knowledge transfer
- [GitHub](https://github.com)/[GitLab](https://gitlab.com)/[Bitbucket](https://bitbucket.org) offer a web solution for code review
- Consider code reading sessions

*"We don't need code review because we are just two."*

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## Code review workflow

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## Modular code development

### Modular design is good - examples:

- Lego
- Car manufacturing
- Design of your phone or laptop
- Modular composition when you order a laptop
- Success of USB
- Erasmus study program

### Advantages

- Separation of concerns
- Composability
- Leveraging functionality

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## Automate All the Things!

### DevOps tools

- Vagrant
- Ansible
- Puppet
- Docker

## Motivation

- Automatize configuration of the servers
- Build, maintain, and distribute virtual development environments
- Fast to create a development environment
- Everyone has identical environment
- Reproducible environments
- Containerisation

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## Code sharing platform

### Open-source software

- [GitHub](https://github.com)/[GitLab](https://gitlab.com)/[Bitbucket](https://bitbucket.org)
- Often anonymous download

### Closed-source software

- Typically has paid maintainers
- Own distribution websites

### Open-use software

- Typically no budget
- Often "home-cooked" solutions
- Often anonymous download not enough
- Maintenance burden

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## Code complexity/viscosity: simple vs. easy

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## Coming to a city near you

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- Dec 2016 - Helsinki
- Feb 2017 - Stockholm
- May 2017 - Copenhagen
- May 2017 - Umeå
- Jun 2017 - Tromsø
- Aug 2017 - Reykjavík
- Oct 2017 - Aarhus
- Nov 2017 - Linköping
- Dec 2017 - Helsinki
- Feb 2018 - Trondheim
- Mar 2018 - Turku
- Apr 2018 - Odense
- May 2018 - Uppsala
- Jun 2018 - Oslo
]

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## Get in touch! Slides: [bit.ly/niasc-2016](http://bit.ly/niasc-2016)

### [@coderefine](https://twitter.com/coderefine)

### [github.com/coderefinery](https://github.com/coderefinery)
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