Chestrays, like xrays but for chests

We use conda to setup dependencies:

conda env create -f environment.yml

To use the shared kaggle account run the following command in the directory of this README:

export KAGGLE_CONFIG_DIR=`pwd`/secrets

To check if worked run kaggle kernels list -m. It should list some kernels and not print any warnings or errors.

There are currently two tools in this package: krun and kfetch.

krun takes a notebook (with existing metadata file) and runs it as a kaggle kernel. Optionally waiting for it to complete and downloading the output.

kfetch takes a notebook (with existing metadata file) and waits for it to complete running, then fetches the output.

To initially fetch a notebook from a kernel and have the metadata created use: kaggle kernels pull -p kernels/create-dataturks-nih chestrays/create-pneumonia-dataturks-dataset This will fetch the kernel called chestrays/create-pneumonia-dataturks-dataset and put it in the kernels/create-dataturks-nih subdirectory.

To get access to the secrets stored in secrets/ install git-crypt and contact one of the people who have the key:

• Tim Head