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Developer instructions

Development mode installation

  • We recommend doing development work in a conda environment. For information on setting up conda for the first time, see this article.
  • This method allows you to modify the source code for example DataJoint workflows (e.g. workflow-array-ephys) and their dependencies (e.g., element-array-ephys).
  • Launch a new terminal and change directory to where you want to clone the repositories (e.g., bash cd ~/Projects)
  • Clone the relevant workflow and refer to the requirements.txt in the workflow for the list of Elements to clone and install as editable. You will also need to install element-interface 
    deps=("lab" "animal" "session" "interface" "<others>")
for repo in $deps # clone each
do 
    git clone https://github.com/datajoint/element-$repo
done
for repo in $(ls -d ./{element,workflow}*) # editable install 
do 
    pip install -e ./$repo
done

Drop schemas

If you need to drop all schemas to start fresh, you'll need to do following the dependency order. Refer to the workflow's notebook (notebooks/06-drop-optional.ipynb) for the drop order.

Pytests

  • Download the test dataset to your local machine. Note the directory where the dataset is saved (e.g. /tmp/testset).
  • Create an .env file within the docker directory with the following content. Replace /tmp/testset with the directory where you have the test dataset downloaded. TEST_DATA_DIR=/tmp/testset
  • If testing an unreleased version of the element or your fork of an element or the workflow, within the Dockerfile uncomment the lines from the different options presented. This will allow you to install the repositories of interest and run the integration tests on those packages. Be sure that the element package version matches the version in the requirements.txt of the workflow.
  • Run the Docker container. 
    docker-compose -f ./docker/docker-compose-test.yaml up --build