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DrugEx Test Runner

Run unit and other tests for DrugEx in GPU-enabled Docker containers.

# define important variables
export NVIDIA_VISIBLE_DEVICES=0 # ids of the GPUs to use
export BASE_IMAGE_TAG="12.0.1-cudnn8-runtime-ubuntu22.04" # cuda base image tag, translated to nvidia/cuda:12.0.1-cudnn8-runtime-ubuntu22.04
export PYTHON_VERSION="3.10" # python version for the conda base environment
export DRUGEX_REPO="https://<username>:<access-token>@your_hosting_service.com/DrugEx.git"
export DRUGEX_REVISION="master" # can be branch, commit ID or a tag
export QSPRPRED_REPO="https://<username>:<access-token>@your_hosting_service.com/QSPRPred.git"
export QSPRPRED_REVISION="main" # can be branch, commit ID or a tag

# spawn a runner with the given settings
./runner.sh # make sure you are in the 'docker' group so that you have correct permissions

A few tips:

  • Use any repo URLs format that git will understand, but remember the docker image will not have access to your ssh keys by default.

  • You can customize the tests.sh script to change what tests to run or do other stuff inside the runner container.

  • When you run the runner.sh script logs are saved to the logs folder in the current directory.

  • It is possible to permanently set the environment variables in a .env file that you can save in this directory. In this case, it would have the following contents:

    NVIDIA_VISIBLE_DEVICES=0
DRUGEX_REPO=https://<gitlab-username>:<access-token>@<gitlab-repo-url>
DRUGEX_REVISION=master
QSPRPRED_REPO=https://<gitlab-username>:<access-token>@<gitlab-repo-url>
QSPRPRED_REVISION=main