RasmussenLab / MOVE

MOVE (Multi-Omics Variational autoEncoder) for integrating multi-omics data and identifying cross modal associations
https://move-dl.readthedocs.io/
MIT License
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Organize code #5

Closed ri-heme closed 2 years ago

ri-heme commented 2 years ago

I suggest the following way to organize the files and folders of the project. As discussed earlier with @valentas1, we can move the diff code snippets into their own modules (e.g., move.analysis and move.models).

.
└── move/
    ├── .github/workflows   <= CI workflows to lint and test code
    ├── conf/               <= Configuration files
    │   ├── data/           <= Default data configuration (e.g., batch size)
    │   ├── model/          <= Default model configuration (e.g., layers)
    │   └── training/       <= Default model training (e.g., epochs, steps)
    │
    ├── notebooks/          <= Jupyter notebooks (step-by-step tutorials)
    ├── src/                <= Source code
    │   └── move/
    │       ├── analysis/   <= Scripts for post-analysis (e.g. feature
    │       │                  importance)
    │       ├── data/       <= Scripts to encode data, create datasets, and 
    │       │                  data loaders
    │       ├── models/     <= Architectures and custom layers
    │       └── viz/        <= Scripts to create visualization
    │
    ├── tests/              <= Unit tests
    ├── LICENSE             <= License
    ├── README.md           <= README.md
    ├── requirements.txt    <= Requirements file for reproducing the analysis
    └── setup.py            <= Setup script