Installation¶

On a Deep Origin workstation¶

No installation needed!

The Deep Origin CLI and Python client are installed on every workstation.

On your local computer¶

Run the command below for your favorite package manager to install the Deep Origin CLI and Python client.

pippixipipxpipenvpoetryuvmicromambaflit

pip install deeporigin

pixi add deeporigin

pipx install deeporigin

pipenv install deeporigin

poetry add deeporigin

uv pip install deeporigin

micromamba install -c https://repo.prefix.dev/deeporigin-public deeporigin

flit install deeporigin

For developers¶

Developers only

If you intend to contribute this package, we recommend installing this package via the instructions below. If you simply intend to use this package, we recommend following the instructions above.

Get the code¶

First, run the following command to clone the source code repository:

git clone git@github.com:deeporiginbio/deeporigin-client.git

Install the development dependencies for this package¶

Second, install Python 3.9+ and make.

To verify that both are installed, run the following commands:

python3 --version
# Python 3.12.3

make --version
# GNU Make 4.4.1

Create an editable installation of this package from the cloned source code¶

Third, navigate to the directory you cloned the code to, and run the following command:

make install

This will install this package in an "editable" mode. In this mode, changes to the source code will take effect immediately.

Run the linting and tests for this package¶

Once installed, you can lint and test this package by running the following commands:

make lint
make test

Compiling and serving the documentation for this package¶

You can compile and serve the documentation for this package by running:

make docs-serve

Supported Python versions¶

deeporigin is tested against the following versions of Python in Ubuntu Linux and Windows:

3.9
3.10
3.11
3.12