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ispy-readii

Running READII to perform radiomic feature extraction on the I-SPY cohort for radiogenomic analysis.

Development

Installing Pixi

Pixi is a tool for managing conda environments and managing dependencies.

To install pixi, visit the pixi website and follow the instructions for your operating system.

Cloning the repository

Clone the repository to your local machine using the following command:

git clone https://github.com/bhklab/RECIST-play.git

Installing dependencies

To install the dependencies for the handbook, run the following command:

pixi install

This will install the dependencies specified in the pixi.toml file.

Adding dependencies

To add a new dependency, run the following command:

pixi add <package_name>

This will add the specified package to the pixi.toml file.

Directory Structure

Run the following command in your terminal in the ispy-readii directory to set up the project directory structure:

mkdir -p procdata rawdata results workflow/{config,envs,logs,notebooks,scripts}

You should now have the following directory structure:

├── README.md
├── procdata        # output from any processing steps of rawdata
├── rawdata         # data as it is downloaded from the source
├── results         # final output from the pipeline
└── workflow
    ├── config
    ├── envs
    ├── logs
    ├── notebooks   # Jupyter, R notebooks
    └── scripts     # Where any code scripts are kept (Python, R, etc.)

Contributing

Please use the following angular commit message format:

<type>(optional scope): short summary in present tense

(optional body: explains motivation for the change)

(optional footer: note BREAKING CHANGES here, and issues to be closed)

<type> refers to the kind of change made and is usually one of:

  • feat: A new feature.
  • fix: A bug fix.
  • docs: Documentation changes.
  • style: Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc).
  • refactor: A code change that neither fixes a bug nor adds a feature.
  • perf: A code change that improves performance.
  • test: Changes to the test framework.
  • build: Changes to the build process or tools.

scope is an optional keyword that provides context for where the change was made. It can be anything relevant to your package or development workflow (e.g., it could be the module or function - name affected by the change).