The base_schemas folder is a python package that contains the definition of main schemas (ensemble of tables) that are shared across distinct pipelines. The actual main schemas are mice and exp, and they are illustrated in the following diagram:
Main schemas definitions should be the same for all pipelines, so the organization via separate package helps to isolate the code during development and deployment.
For the development version, clone the repository, and run
# for development
pip install -e .
# for usage
pip install .
Alternatively, the package can be directly installed using one of the following commands (main can be replaced by a commit hash or branch):
pip install "git+ssh://git@github.com/SCENE-Collaboration/Base-schemas.git@main"
pip install "git+https://github.com/SCENE-Collaboration/Base-schemas.git@main"
To build an installable package (source release or wheel), run:
pip install build
python -m build .
which will create the release files in the dist/ subfolder.
For example, for version "1.1.0", it will create:
dist
dist/base_schemas-1.1.0.tar.gz
dist/base_schemas-1.1.0-py3-none-any.whl
The wheel can be directly installed with pip:
pip install dist/base_schemas-1.1.0-py3-none-any.whl
This workflow is useful when e.g. distributing package versions for use within a Docker container.
from base_schemas.schemas import mice, exp
print(mice.Mouse())We thank Prof. Mackenzie Mathis, Dr. Tanmay Nath, Dr. Gary Kane, and Dr. Mariia Popova for their early contributions to this codebase, which helped establish the foundation of the shared schemas used across pipelines.