Contributing

This project follows the all contributors specification. Contributions in many different ways are welcome!

Contribution Types

Report Bugs

Report bugs at https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/issues.

If you are reporting a bug, please include:

Your operating system name and version.
Any details about your local setup that might be helpful in troubleshooting.
Detailed steps to reproduce the bug.

Fix Bugs

Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.

Implement Features

Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.

Write Documentation

MIALSRTK could always use more documentation, whether as part of the official MIALSRTK docs, in docstrings, or even on the web in blog posts, articles, and such.

Submit Feedback

The best way to send feedback is to create an issue at https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/issues.

If you are proposing a feature:

Explain in detail how it would work.
Keep the scope as narrow as possible, to make it easier to implement.
Remember that this is a volunteer-driven project, and that contributions are welcome :)

Get Started!

Ready to contribute? Here’s how to set up MIALSRTK for local development.

Fork the mialsuperresolutiontoolkit repo on GitHub.

Clone your fork locally:

git clone git@github.com:your_name_here/mialsuperresolutiontoolkit.git
cd mialsuperresolutiontoolkit

Create a branch for local development:

git checkout -b name-of-your-bugfix-or-feature

Now you can make your changes locally. If you add a new node in a pipeline or a completely new pipeline, we encourage you to rebuild the BIDS App Docker image (See BIDS App build instructions) and test it on the sample dataset (mialsuperresolutiontoolkit/data/).

Note

Please keep your commit the most specific to a change it describes. It is highly advice to track unstaged files with git status, add a file involved in the change to the stage one by one with git add <file>. The use of git add . is highly disencouraged. When all the files for a given change are staged, commit the files with a brieg message using git commit -m "[COMMIT_TYPE]: Your detailed description of the change." that describes your change and where [COMMIT_TYPE] can be [FIX] for a bug fix, [ENH] for a new feature, [MAINT] for code maintenance and typo fix, [DOC] for documentation, [CI] for continuous integration testing.

When you’re done making changes, push your branch to GitHub:
```
git push origin name-of-your-bugfix-or-feature
```
Submit a pull request through the GitHub website.

Pull Request Guidelines

Before you submit a pull request, check that it meets these guidelines:

If the pull request adds functionality, the docs should be updated (See documentation build instructions).
The pull request should work for Python 3.6. Check https://app.circleci.com/pipelines/github/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit and make sure that the tests pass.

How to build the BIDS App locally

Go to the clone directory of your fork and run the script build_bidsapp.sh
```
cd mialsuperresolutiontoolkit
sh build_bidsapp.sh
```

Note that the tag of the version of the image will be extracted from pymialsrtk/info.py where you might need to change the version to not overwrite an other existing image with the same version.

How to install `pyMIALSTK` locally

Install the MIALSRTK conda environment pymialsrtk-env that provides a Python 3.6 environment:
```
cd mialsuperresolutiontoolkit
conda env create -f docker/bidsapp/environment.yml
```
Activate the pymialsrtk-env conda environment and install pymialsrtk
```
conda activate pymialsrtk-env
pip install .
```

How to build the documentation locally

Install the MIALSRTK conda environment pymialsrtk-env with sphinx and all extensions to generate the documentation:
```
cd mialsuperresolutiontoolkit
conda env create -f docker/bidsapp/environment.yml
```
Activate the MIALSRTK conda environment pymialsrtk-env and install pymialsrtk
```
conda activate pymialsrtk-env
pip install .
```
Run the script build_sphinx_docs.sh to generate the HTML documentation in documentation/_build/html:
```
bash build_sphinx_docs.sh
```

Note

Make sure to have activated the conda environment pymialsrtk-env before running the script build_sphinx_docs.sh.

Not listed as a contributor?

This is easy, MIALSRTK has the all contributors bot installed.

Just comment on Issue or Pull Request (PR), asking @all-contributors to add you as contributor:

@all-contributors please add <github_username> for <contributions>

<contribution>: See the Emoji Key Contribution Types Reference for a list of valid contribution types.

The all-contributors bot will create a PR to add you in the README and reply with the pull request details.

When the PR is merged you will have to make an extra Pull Request where you have to:

add your entry in the zenodo.json (for that you will need an ORCID ID - https://orcid.org/). Doing so, you will appear as a contributor on Zenodo in the future version releases of MIALSRTK. Zenodo is used by MIALSRTK to publish and archive each of the version release with a unique Digital Object Identifier (DOI), which can then be used for citation.

update the content of the table in documentation/contributors.rst with the new content generated by the bot in the README. Doing so, you will appear in the Contributing Page.

This document has been inspired and adapted from these great contributing guidelines.