Contributing to Peter Moss Acute Myeloid & Lymphoblastic Leukemia AI Research Project projects

Peter Moss Acute Myeloid & Lymphoblastic Leukemia AI Research Project encourages and welcomes code contributions, bug fixes and enhancements from the Github community.

Ground rules & expectations

Before we get started, here are a few things we expect from you (and that you should expect from others):

Be kind and thoughtful in your conversations around projects. We all come from different backgrounds, which means we likely have different perspectives on "how open source is done." Try to listen to others rather than convince them that your way is correct.
All projects are released with a link to the Contributor Code of Conduct. By participating in our projects, you agree to abide by its terms.
Please ensure that your contribution complies with this document. If it does not, you will need to address and fix all issues before we can merge your contribution.
When adding content, please consider if it is widely valuable.

Overview

Being an Open Source project, everyone can contribute, provided that you respect the following points:

Before contributing any code, the author must make sure all the tests work (Our tests procedure is currently under discussion and angree).
Developed code must adhere to the syntax guidelines enforced by the linters.
Code must be developed following the SemVer (Semantic Versioning 2.0.0) branching model.
For any new feature added, unit tests must be provided, following the example of the ones already created.

How to contribute

If you'd like to contribute, start by searching through the relevant project issues and pull requests to see whether someone else has raised a similar idea or question.

If you don't see your idea listed, and you think it fits into the goals of this guide, do one of the following:

Bug Report
Feature Proposal
Feature Request

Repository Issues

The first step is to head to the repository issues tab and decide how you would like to contribute.

Bug reports

If you would like to contribute bug fixes or make the team aware of bugs you have identified in the project, please raise a Bug report issue in the issues section section. A template is provided that will allow you to provide your suggestions for your bug report / bug fix(es) which will be reviewed by the team.

Bug fix issues are the first step to creating a pull request for bug fixes, once you have created your issue and it has been approved you can proceed with your bug fixes.

Feature proposals

If you would like to contribute new features to a project, please raise a Feature proposal issue in the repository issues section. A template is provided that will allow you to provide your suggestions for your feature proposal.

Feature proposal issues are the first step to creating a pull request for feature proposals, once you have created your issue and it has been approved you can proceed with your feature proposal.

Feature requests

If you would like to suggest a new feature/new features for this project, please raise a Feature request issue in the repository issues section. A template is provided that will allow you to provide your suggestions for your feature request.

Community

Discussions about the Open Source Guides take place on this repository's issues and pull requests sections, or the repository discussions tab. Anybody is welcome to join these conversations.

Do not take these conversations to private channels, including contacting the maintainers directly. Keeping communication public means everybody can benefit and learn from the conversation.

Getting Started

In order to start contributing:

Fork the relevant repository clicking on the "Fork" button on the upper-right area of the page.
Clone your just forked repository:

git clone https://github.com/YourAccount/Your-Forked-Project.git

Add the main repository as a remote to your forked repository:

git remote add origin https://github.com/AmlResearchProject/Project-You-Forked.git

Before starting your contribution, remember to synchronize the latest dev branch in your forked repository with the dev branch in the main repository as specified by the CURRENT DEV BRANCH badge in the repository README. To do this, use following these steps

Change to your local dev branch (in case you are not in it already) replace 1.0.0 with the current dev branch of the repository:

git checkout 1.0.0

Fetch the remote changes:

git fetch origin

Merge them:

git rebase origin/1.0.0

Contributions following these guidelines will be added to the dev branch, and released in the next version. The release process is explained in the Releasing section below.

Documentation

Changes you make to the code in the repository or new projects that you make should be supported with documentation added to the docs directory.

It is the contributor's responsibility to ensure that the documentation is up to date. If you are contributing to an existing repository you will ensure that these documents are updated and/or added to to reflect your changes.

We use MKDocs along with Read the Docs. Use the Getting Started with MkDocs guide to find out how to update/create documentation for the project. The MKDocs config file and index file will already be provided in the repository structure, you will just need to modify these files to match your documentation structure.

Repository structure

Repository structures must be followed exactly for all contributions. Pull Requests that do not follow this structure will be rejected and closed with no further discussion.

- Project Root (Directory)
    - assets (Directory)
        - images (Directory)
            - project-banner.jpg (Image)
            - bug-report.jpg (Image)
            - feature-proposal.jpg (Image)
            - feature-request.jpg (Image)
            - fork.jpg (Image)
            - repo-issues.jpg (Image)
    - configuration (Directory)
        - config.json (File)
    - docs (Directory)
        - img (Directory)
            - project-banner.jpg (image)
        - installation (Directory)
            - ubuntu.md (File)
        - usage (Directory)
            - ubuntu.md (File)
        - index.md (File)
    - logs (Directory)
        - Auto generated log files
    - modules (Directory)
        - AbstractClassifier.py (File)
        - AbstractData.py (File)
        - AbstractModel.py (File)
        - AbstractServer.py (File)
        - helpers.py (File)
        - augmentation.py (File)
        - data.py (File)
        - model.py (File)
        - server.py (File)
    - model (Directory)
        - data (Directory)
            - test (Directory)
            - train (Directory)
            - plots (Directory)
        - model.json (File)
        - weights.h (File)
    - notebooks (Directory)
        - classifier.ipynb (File)
    - scripts
        - install.sh (File)
    - classifier.py (File)
    - CODE-OF-CONDUCT.md (File)
    - CONTRIBUTING.md (File)
    - LICENSE (File)
    - mkdocs.yml (File)
    - README.md (File)

Directories and files may be added to the above structure as required, but none must be removed.

Abstract Classes

Abstract classes are part of our "framework". Contributors may modify abstract classes by adding new methods or removing redundant methods. If you modify an abstract class make sure to add your attribution in the contributors area in the header.

Installation Scripts

The default installation script is install.sh found in the scripts directory.

You must include the installation commands for all libraries for the project using apt/pip/make etc. Replace # DEVELOPER TO ADD INSTALLATION COMMANDS FOR ALL REQUIRED LIBRARIES (apt/pip etc) with the relevant installation commands. If you are contributing an existing repository you will ensure that these scripts are updated to reflect your changes.

Logging

The helpers file handles all logging for the project. Loggig should be used in all cases rather than print(). The following logs are supported:

all
error
warning

Configuration

The project configuration file config.json can be found in the configuration directory.

All configurable variables should be held within this file and used wherever relevant throughout the project.

The helpers file loads the configuration and makes it available as helpers.confs.

You may remove redundent objects/arrays/values. from the configuration and/or add new ones.

Project Images

Images used in the project must be jpg. You must own rights to images you upload to the project, or include attribution. Contributors are solely responsible for any images they publish to our Github.

Naming Scheme

The following naming scheme must be used:

Directories: Snake case (snake_case)
Abstract Files: Camel case (CamelCase)
Files: Spinal case (spinal-case)
Images: Spinal case (spinal-case)

Please use descriptive but short names, and make sure to not use spaces in directory and file names.

Headers

All Python files must include the following header, replacing Module Title with a short but descriptive title for the module, and Module Description with a paragraph explaining what the module is for.

#!/usr/bin/env python3
""" Module Title.

Module Description.

MIT License

Copyright (c) 2021 Asociación de Investigacion en Inteligencia Artificial
Para la Leucemia Peter Moss

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files(the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and / or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

Contributors:

"""

Attribution

When you create a new module you should add your name to the Contributors section.
When you make a change to an existing module you should add your name to the Contributors section below existing contributors. You must not remove existing contributors from a header.

Footers

All READMEs and documentation should include the following footer (Replace/add contributors as required):

# Contributing
Asociación de Investigacion en Inteligencia Artificial Para la Leucemia Peter Moss encourages and welcomes code contributions, bug fixes and enhancements from the Github community.

Please read the [CONTRIBUTING](CONTRIBUTING.md "CONTRIBUTING") document for a full guide to forking our repositories and submitting your pull requests. You will also find our code of conduct in the [Code of Conduct](CODE-OF-CONDUCT.md) document.

## Contributors
- [Adam Milton-Barker](https://www.leukemiaairesearch.com/association/volunteers/adam-milton-barker "Adam Milton-Barker") - [Asociación de Investigacion en Inteligencia Artificial Para la Leucemia Peter Moss](https://www.leukemiaresearchassociation.ai "Asociación de Investigacion en Inteligencia Artificial Para la Leucemia Peter Moss") President/Founder & Lead Developer, Sabadell, Spain

&nbsp;

# Versioning
We use [SemVer](https://semver.org/) for versioning.

&nbsp;

# License
This project is licensed under the **MIT License** - see the [LICENSE](LICENSE "LICENSE") file for details.

&nbsp;

# Bugs/Issues
We use the [repo issues](issues "repo issues") to track bugs and general requests related to using this project. See [CONTRIBUTING](CONTRIBUTING.md "CONTRIBUTING") for more info on how to submit bugs, feature requests and proposals.

Remember to use relative URLs, and in the case of footers in the docs folder, you must us absolute URLs.

The contributors section should include a list of contributors that have contributed to the related document. In the case of the README footer, the Contributors section should include a list of contributors that have contributed to any part of the project.

You should add your details below existing contributors. Details should include:

Name
Company/University etc
Position
City
Country

Branching model

main: contains the tagged and released version
dev: the current dev branch is represented by the highest existing branch in the repository and contains the latest development code. New features and bugfixes are always merged to current dev branch before merging to main.

In order to start developing a new feature or refactoring, a new branch will be created following the SemVer scheme:

Given a version number MAJOR.MINOR.PATCH, increment the:

MAJOR version when you make incompatible code changes,
MINOR version when you add functionality in a backwards compatible manner, and
PATCH version when you make backwards compatible bug fixes.
If MAJOR is 1, this is the first major release
If MAJOR is 0, then Minor could mean the version is not backwards compatible
If MINOR is 1, this means the release is stable.

The branch will be created by our team depending on the nature of your issue. Once the new functionality has been completed, a Pull Request should be created from the feature branch to the relevant branch. Remember to check both the linters, and the tests before creating the Pull Request.

In order to contribute to the repository, the same scheme should be replicated in the forked repositories, so the new features or fixes should all come from the current version of dev branch and end up in the current dev branch again.

PEP 8 -- Style Guide for Python Code

All Python projects must align with the PEP 8 -- Style Guide for Python Code.

CII Best Practices

All projects must align with the CII Best Practice.

Changelog

The project contains a changelog that is automatically created from the description of the Pull Requests that have been merged into develop, thanks to the Release Drafter GitHub action.

Releasing

The process of making a release simply consists of creating the release in Github and providing the new tag name, this task is carried out by our team.

Version numbers

The version number will change for each release, following the SemVer scheme described previously.

Bugfix in releases

When a bug is found affecting a release, a branch will be created from the main branch. As a part of the patch, the release version will be increased in it's last number (Z). The patch then will be merged (via pull request (PR)) to the main branch, and a new version will be released.

Commits

Commits should be atomic, make commits to your fork until you have resolved/completed the work specified in your issue before submitting your PR, this keeps an easy to follow history of what work has been carried out and makes the review process easier and quicker

When making a commit, the subjects of each commit should be as follows, where XXX represents the issue number, # must :

Commit Title

Bug Fixes

fix #xxx
fixes #xxx
fixed #xxx

Partial Resolutions

partially resolves #xxx
partially resolved #xxx

Resolution

resolves #xxx
resolved #xxx

Alignment

aligns with #xxx

Closure

close #xxx
closes #xxx
closed #xxx

Commit Description

Your commit description should include a detailed description of the changes that have been made.

Committing

When you are ready to commit, you should do the following:

Show The Status Of All Changed/Added/Deleted files

git status

Diff

You may want to check the differences between changed files, you can do this using the following command.

git diff

Add All Changes

The following will add all changes shown by git status to your commit.

git add .

Add One Or More Changes

git add file1 file2 file5

Commit Added Changes

Commit your added changes to your local repository, remember to follow the Commit Title & Commit Description guides above.

To create your commit with both a title and description, use the following command which states the commit fixes issue ID 1 and provides a detailed description:

git commit -m "fixes #1" -m "Fixes the documentation typos described in issue #1"

Push Your Changes

When you have made your changes, ensured you have aligned with the procedures in this document, and made your commits to your local repository aligning with the guide above, you need to push your changes to your forked repository.

Push changes to your fork by using the following command:

git push

Pull Request protocol

Contributions to the ALL-Arduino-Nano-33-BLE-Sense-Classifier repository are done using a PR. The detailed "protocol" used in such PR is described below:

Direct commits to mains (even single-line modifications) are not allowed. Every modification has to come as a PR to the latest dev branch
PRs implement/fix submitted issues, the issue number has to be referenced in the subject of the relevant commit and PR
Anybody is welcome to provide comments to the PR (either direct comments or using the review feature offered by Github)
Use code line comments instead of general comments, for traceability reasons (see comments lifecycle below)
Comments lifecycle
- Comment is created, initiating a comment thread
- New comments can be added as responses to the original one, starting a discussion
- After discussion, the comment thread ends in one of the following ways:
  - Fixed in <commit hash> in case the discussion involves a fix in the PR branch (which commit hash is included as reference)
  - NTC, if finally nothing needs to be done (NTC = Nothing To Change)
PR can be merged when the following conditions are met:
- All comment threads are closed
- All the participants in the discussion have provided a LGTM general comment (LGTM = Looks good to me)
- All documentation has been updated to reflect your changes.
- No proprietory software or images have been added.
Self-merging is not allowed (except in rare and justified circumstances)

Some additional remarks to take into account when contributing with new PRs:

PR must include not only code contributions, but their corresponding pieces of documentation (new or modifications to existing one) and tests
Documentation must be added to the docs folder
In the case empty directories need to be uploaded, add a .gitkeep file inside.
The project banner is included in all documentation
Contributing, Versioning, Licensing, Bugs/Issues footer is included in all information
Contributors have been added to all Contributors footers
PR modifications must pass full regression based on existing tests in addition to whichever new test added due to the new functionality
PR should be of an appropriated size that makes review achievable. Too large PRs could be closed with a "please, redo the work in smaller pieces" without any further discussion

Files

CONTRIBUTING.md

Latest commit

History