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lucidtronix committed Mar 12, 2024
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* [Setting up a remote VM](#setting-up-a-remote-vm)
* Modeling/Data Sources/Tests [(`ml4h/DATA_MODELING_TESTS.md`)](ml4h/DATA_MODELING_TESTS.md)
* [Contributing Code](#contributing-code)
* [Releases and Versioning](#releases)
* [Command line interface](#command-line-interface)

Advanced Topics:
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Step 5: open the folder you want to work on in the VM, type in your Broad password, and you are good to go!




## Contributing code

Want to contribute code to this project? Please see [CONTRIBUTING](./CONTRIBUTING.md) for developer setup and other details.

## Citation
If you use ML4H for research, you can use this citation format:
```
@misc{ml4h,
title = {ml4h},
copyright = {BSD 3-Clause License, 2021},
url = {https://github.com/broadinstitute/ml4h},
author = {{Data Sciences Platform at Broad Institute of MIT and Harvard}},
abstract = {ML4H is a toolkit for machine learning on clinical data of all kinds including genetics, labs, imaging, clinical notes, and more.},
urldate = {2021-03-31},
publisher = {Broad Institute},
month = mar,
year = {2021},
note = {original-date: 2019-04-10}
}
```
## Releases
Ideally, each release should be available on our [github releases page](https://github.com/broadinstitute/ml4h/releases)
In addition, the version # in setup.py should be incremented.
The pip installable [ml4h package on pypi should also be updated](https://pypi.org/project/ml4h/).

If the release changed the docker image, the new dockers both (CPU & GPU) should update the “latest” tag and should be pushed to both gcr: `gcr.io/broad-ml4cvd/deeplearning`, and the [ml4h github docker repo](https://github.com/broadinstitute/ml4h/pkgs/container/ml4h) with appropriate tags: ` ghcr.io/broadinstitute/ml4h`


## Command line interface
The ml4h package is designed to be accessable through the command line using "recipes".
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