fractal-server 0.2.1

Server component of the Fractal analytics platform

Fractal Server

Fractal is a framework to process high content imaging data at scale and prepare it for interactive visualization.

This is the server component of the fractal analytics platform. If you are interested in the client component, please refer to the main repository. If you are interested in the fractal tasks, please refer to the tasks repository.

Installation

You may pip install fractal-server

This will install the project and its dependencies. If you wish to also install Fractal core tasks, use

pip install fractal-server[core-tasks]

Environment and database

You will need to define some environment variables in order to use fractal-server. For your convenience, you may simply copy template.fractal_server.env to .fractal_server.env.

fractal-server requires a database to run. Once you set up the environment variables you need to initialise the database by invoking

alembic upgrade head

NOTE: as fractal-server is still in pre-alpha the database schema is not yet committed to the repository. As such you'll be required to first create a schema revision with alembic revision --autogenerate -m "[your commit message]".

Contributing

To contribute to the development of fractal-server you may fork and clone the repository.

We use poetry (v1.2) to manage the development environment and the dependencies. Running

poetry install [--with dev]

will take care of installing all the dependencies in a separate environment, optionally installing also the development dependencies.

It may be useful to use a different interpreter from the one installed in your system. To this end we recommend using pyenv. In the project folder, invoking

pyenv local 3.8.13
poetry env use 3.8
poetry install

will install Fractal in a development environment using python 3.8.13 instad of the system-wide interpreter.

Testing

We use pytest for unit and integration testing of Fractal. If you installed the development dependencies, you may run the test suite by invoking

poetry run pytest

Contributors

Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich (both in Switzerland). The project lead is with @gusqgm & @jluethi. The core development is done under contract by @mfranzon, @tcompa & @jacopo-exact from eXact lab S.r.l..

License

Fractal is released according to a BSD 3-Clause License. See LICENSE.