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<!DOCTYPE html>

<head>

<title>ORMIR - Guidelines</title>

<!-- =======================================================

* Template Name: Tempo

* Updated: Jan 09 2024 with Bootstrap v5.3.2

* Template URL: https://bootstrapmade.com/tempo-free-onepage-bootstrap-theme/

* Author: BootstrapMade.com

* License: https://bootstrapmade.com/license/

======================================================== -->

</head>

<body>

<ul>

<li class="dropdown"><a href="#"><span>About us</span> <i class="bi bi-chevron-down"></i></a>

<ul>

<li><a href="motivation.html">Why a community</a></li>

<li><a href="groups.html#">Working groups</a></li>

<li><a href="boards.html">Advisors & Outreach</a></li>

</ul>

</li>

<ul>

<li><a href="software.html">Software</a></li>

<li><a href="templates.html">Templates</a></li>

<li><a href="guidelines.html">Guidelines</a></li>

</ul>

</li>

<ul>

<li><a href="datasets.html">Datasets</a></li>

<li><a href="policies.html">Policies</a></li>

</ul>

</li>

<span>Outreach</span>

<ul>

<li><a href="publications.html">Publications</a></li>

<li><a href="events.html">Events</a></li>

<li><a href="funding.html">Funding</a></li>

</ul>

</li>

<span>Joining & Q</span>

<ul>

<li><a href="contact.html">Questions?</a></li>

</ul>

</li>

</ul>

</nav>

</div>

</header>

<h2>Coding guidelines</h2>

</div>

Here are our guidelines for <a href="#code">code</a>, <a href="#data">data</a>, and <a href="#publications">publications</a>

</div>

<br>

<h4>Python code</h4>

What Python <i>code</i> style do I use?

</button>

We follow the <a class="reference external" href="https://www.python.org/dev/peps/pep-0008/"> Style Guide for Python Code</a>. In summary:

<br>

<h6 style="color:#90bc00">Naming Style</h6>

<ul>

<li>

Variables, functions, methods, modules, packages:

<br>

<code-text>lower_case_with_underscores</code-text>

</li>

<li>

Constants:

<br>

<code-text>ALL_CAPS_WITH_UNDERSCORES</code-text>

</li>

<li>

Classes and exceptions:

<br>

<code-text>CapWords</code-text>

</li>

</ul>

<br>

<h6 style="color:#90bc00">Indentation</h6>

<ul>

<li>

4 spaces or 1 tab

</li>

</ul>

<br>

<h6 style="color:#90bc00">Space</h6>

<ul>

<li>

Leave space between operators in case of assignment and arithmetic operations:

<br>

<code-text>var = 4</code-text>

</li>

<li>

Leave space after a comma:

<br>

<code-text>var_1, var_2 = get_values(num_1, num_2)</code-text>

</li>

</ul>

<br>

<h6 style="color:#90bc00">Comments</h6>

<ul>

<li>

Comments are introduced by <code-text>#</code-text> positioned above the code they refer to, and they are indented to align with the code are commenting on:

<br>

<code-text># assign variable</code-text>

<br>

<code-text>a = 5</code-text>

<br>

<i>Why are comments important?</i> As part of a community, we want to write code that can be readable and reusable by others. Let's be generous and precise with our comments!

</li>

</ul>

</div>

How do I quickly translate existing code to Python?

</button>

If you already know Python: ChatGPT! Example of command:

<br>

<code-text>translate the following code from Matlab to Python: [paste your code]</code-text>

<br>

<i>Important</i>: Double-check the content of ChatGPT output!

<br>

If you don't know Python, team up with some ORMIR community members who know Python and work on the translation together!

</div>

<br>

<h4>Python documentation</h4>

What Python <i>documentation</i> style (docstrings) do I use?

</button>

We use <a class="reference external" href="https://numpydoc.readthedocs.io/en/latest/format.html">Numpy style docstrings</a> to document our code.

Docstrings describe functionalities and parameters of the subsequent code and are enclosed in triple quotes (<code-text>"""..."""</code-text>).

They are typically placed at the beginning of the module, class, function, or method they describe. Here is the example of Numpy style docstrings for functions:

<br>

<code-text>

<br>

def my_function (input1, input2):

<br>

    """This functions does ...

<br>

    Parameters

<br>

    ----------

<br>

    input_1 : type

<br>

        Description of the parameter `input_1`

<br>

    input_2 : type

<br>

        Description of the parameter `input_2`

<br>

    Returns

<br>

    -------

<br>

    output: int

<br>

        Description of the variable `output`

<br>

    """

<br>

    # function body

<br>

    return output

</code-text>

<br>

The documentation is between the header and the body, and it contains at least the following sections:

<ul>

<li>

Description: An explanation of what the function does

</li>

<li>

Parameters: A description of each parameter the function accepts, including name, data type, definition, and default values

</li>

<li>

Returns: A description of the values returned by the function, including name, data type, definition, and any special cases

</li>

</ul>

You can find a complete description of Numpy style docstrings on <a class="reference external" href="https://numpydoc.readthedocs.io/en/latest/format.html">the Numpy website</a>

</div>

How do I create Numpy-style documentation (docstrings) fast?

</button>

With ChatGPT! Example of command:

<br>

<code-text>write docstrings in Numpy style for the following function: [paste your function]</code-text>

<br>

<i>Important</i>: Double-check the content of ChatGPT output and correct wherever needed!

</div>

How do I publish documentation <i>automatically</i> using Read the Docs?

</button>

<a href="https://docs.readthedocs.io/en/stable/">Read the Docs</a> is a tool to genereate code from docstrings and to host and publish documentation on the web.

To learn how to use Read the Docs follow their step-by-step <a href="https://docs.readthedocs.io/en/stable/tutorial/index.html">tutorial</a>.

An excellent example of Read the Docs is the <a href="https://ciclope.readthedocs.io/en/"> documentation</a> of Ciclope.

</div>

How do I publish documentation <i>manually</i> using Sphynx?

</button>

<a href="https://www.sphinx-doc.org/en">Sphynx</a> is a tool to write and generate documentation from docstrings.

You can find guidelines on how to use Sphynx <a href="assets/documents/ORMIR_Sphinx_SOP.pdf">here</a>

</div>

How do I create a website using Jupyter Book?

</button>

You can find comprehensive guidelines and a template on the <a href="https://jupyterbook.org/en/stable/intro.html">Jupyter Book website</a>. In a nutshell:

<ol>

<li> For each website page, create one <code-text>.md</code-text> or <code-text>.ipynb</code-text> file and write the content using markdown</li>

<li> Create a <code-text>_toc.yml</code-text> and a <code-text>_config.yml</code-text> files (see examples <a href="https://jupyterbook.org/en/stable/start/create.html#anatomy-of-a-jupyter-book">here</a>)</li>

<li> Install Jupyter Book with the command <code-text>pip install jupyter-book</code-text></li>

<li> Create your book with the command <code-text>jupyter-book build book_name</code-text>

</ol>

The created <code-text>.html</code-text> files will be in the folder <code-text>_build/html</code-text>

</div>

How do I deploy my Jupyter Book website on GitHub using CI?

</button>

CI (Continuous Integration) is a tool that allows you to automate procedures, and in GitHub it is called <i>Actions</i>.

Deploying a Jupyter Book website using Actions is very convenient because it automates the building process, ensuring that your site is continuously and seamlessly updated with every change pushed to the repository. You can find detailed information on how to deploy a Jupyter Book website using Actions <a href="https://jupyterbook.org/en/stable/publish/gh-pages.html">here</a>.

Briefly:

<ol>

<li> Make sure that your repository contains all the website content files, (that is, <code-text>.md</code-text> and/or <code-text>.ipynb</code-text> files, together with figures, etc.), <code-text>_config.yml</code-text> and <code-text>_toc.yml</code-text>. Note: You do <i>not</i> need to push the <code-text>_built</code-text> folder because GitHub Action will create the <code-text>.html</code-text> files of your website

</li>

<li> In the same repository, add the following files from

<a href="https://github.com/ORMIRcommunity/templates/tree/main/github_actions_jupyter_book">this</a> ORMIR template folder:

<a href="https://github.com/ORMIRcommunity/templates/blob/main/github_actions_jupyter_book/requirements.txt">requirements.txt</a>,

<a href="https://github.com/ORMIRcommunity/templates/blob/main/github_actions_jupyter_book/.nojekyll">.nojekyll</a>, and

<a href="https://github.com/ORMIRcommunity/templates/blob/main/github_actions_jupyter_book/.github/workflows/ci.yml">.github/workflows/ci.yml</a> (note that <code-text>.nojekyll</code-text> and <code-text>.github/workflows/ci.yml</code-text> are hidden files)

</li>

<li>Go to your GitHub repository on GitHub.com. In the top bar, click on <code-text>Settings</code-text>, and in the appearing left panel, click on <code-text>Pages</code-text>. Under <code-text>Build and deployment</code-text>, <code-text>Source</code-text>, select <code-text>GitHub Actions</code-text>

</li>

<li>Every time you push new content to the repository, the book will be automatically created and the new <code-text>.html</code-text> files will be automatically deployed to your website. You can follow the progress by clicking <code-text>Actions</code-text> on the top bar of the GitHub repository

</ol>

</div>

<br>

<h4>Code license</h4>

What license do I use for my code?

</button>

You can choose a permissive license (e.g. BDS, MIT, Apache) or a copyleft license (e.g. GNU GPL, Mozilla).

If you are not familiar with open-source licenses, you can browse

<a class="reference external" href="https://choosealicense.com/licenses/">choosealicense.com</a>,

read the paper

<a class="reference external" href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002598">A Quick Guide to Software Licensing for the Scientist-Programmer</a>,

or watch

<a class="reference external" href="https://www.youtube.com/watch?v=GlAnKGBnhFY">this video</a> (from minute 4)

</div>

<br>

<h4>Jupyter notebook</h4>

What are Jupyter notebooks useful for?

</button>

Jupyter notebooks are useful not only to draft code, but also to create use cases, demos, or examples for Python packages

</div>

How do I structure a Jupyter notebook?

</button>

We created a Jupyter notebook <i>template</i> that you can download

<a class="reference external" href="https://github.com/ORMIRcommunity/templates/blob/main/ORMIR_nb_template.ipynb">here</a>.

Just like when you write a paper, you fill out a journal template with your content, you can fill out the ORMIR community notebook template with your narrative and code.

<br>

<i>Why should I use the template?</i> We usually use notebooks to create use-cases for our Python packages.

Using the template allows us to harmonize our use-cases and to make sure we remember to include authors, licenses, references, etc.

</div>

<br>

<h4>GitHub</h4>

How do I structure the readme file of a GitHub repository?

</button>

We created a GitHub readme <i>template</i> that you can download

<a class="reference external" href="https://github.com/ORMIRcommunity/templates/blob/main/ORMIR_readme_template.md">here</a>.

A readme file template allows us to harmonize our repositories and make sure we remember to include all sections, such as authors, licenses, use-cases, references, etc.

</div>

<br>

What image file formats and folder structure should I use?

</button>

Our pipelines usually start with <code-text>.dcm</code-text> images for CT/MR acquisitions or <code-text>.isq</code-text> images for µCT/HR-pQCT acquisitions.

We recommend to organize image files and folders following the <a href="https://ormir-mids.github.io/specs">ORMIR-MIDS specifications</a> implemented by the <a href="https://github.com/ormir-mids/ormir-mids">ORMIR-MIDS Python package</a>.

</div>

<br>

<h4>Publishing</h4>

In what journal can I publish my Python package?

</button>

Consider publishing in the <a class="reference external" href="https://joss.theoj.org/">Journal of Open Source Software (JOSS)</a>.

The paper is only a few pages and reviewers check your repository, helping you improve it.

</div>

How do I get a DOI for my code?

</button>

To get a permanent Digital Object Identifier (DOI) for your code so that it can be referenced, you can link your GitHub repository to Zenodo. You can find instructions on

<a class="reference external" href="https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content">this webpage </a>

or in

<a class="reference external" href="https://www.youtube.com/watch?v=gp3D4mf6MHQ">this video</a>.

</div>

<br>

<strong>Do you have some questions that we didn't address? <a href="mailto:[email protected]">Contact us!</a> </strong>

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