Installation¶

On a Deep Origin workstation¶

No installation needed!

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

Recommended installation¶

This sections describes how to install the Deep Origin CLI and Python client on your computer using our recommendations. We recommend:

Using the uv package and environment manager
Using Jupyter Lab to run the Deep Origin Python client

macOS/LinuxWindows

First, create a folder to contain your project. This can be any name (except deeporigin).

mkdir do-client
cd do-client

Now use this one liner to install deeporigin using the uv package manager.

curl -LsSf https://client-docs.deeporigin.io/install.sh | sh

Now start a Jupyter Lab instance that uses this environment, allowing you to use the deeporigin python client in it:

# run jupyter using this environment
uv run --with jupyter jupyter lab

# make a folder for your project
# this can be any name (except deeporigin)
mkdir do-client
cd do-client

# install uv if needed
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

# If uv tells you to add something to PATH,
# you may need to do that first
uv init

# we use the latest stable version of python
uv python install 3.13

# install deeporigin in the current environment
uv add deeporigin

# if you're using Deep Origin tools (like FEP), use:
uv add deeporigin --extra tools

# also install as a uv tool to run from the command line
uv tool install deeporigin

# run jupyter using this environment
uv run --with jupyter jupyter lab

Upgrading to a new version¶

If you followed the recommended installation steps, you can upgrade to the latest version of the Deep Origin Python client by running:

uv add --upgrade deeporigin

in your project root.

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, use 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 3.10+ and GNU 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 test this package by running the following commands:

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

OS and python support¶

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

Python	macOS	Windows	Ubuntu
3.10		✅	✅
3.11		✅	✅
3.12		✅	✅
3.13	✅	✅	✅