Generates network topologies, i.e., arrangements of nodes and edges using Python and exports the topologies for use in CiCL studies built on top of interactive-network-base.

Uses Python 3.10.13 and pip 23.3.1 with a virtual environment. To get started, first clone this repository:

git clone https://github.com/comanlab/gentopo.git

Everything in this repository is meant to run within a virtual environment, which is activated from the root of this repository.

TODO: If .python-version is already present, will skipping to mkvirtualenv gentopo successfully install and use 3.10.13 from pyenv?

Use Pyenv within the root directory of this project to use the desired Python version via

pyenv local 3.10.13

After installing and setting the local directory's Python version, ensure pyenv local returns 3.10.13 to confirm the intended Python version is in use from those installed by pyenv on your local machine. (Note: For those bringing their own Python virtual environment manager, e.g. conda, this project is tested for Python >=3.10.)

mkvirtualenv gentopo

This will create and activate the virtual environment called gentopo.

To activate the virtual environment, run

workon gentopo

If already in the activated environment, the previous command should do nothing.

Check that the virtual environment has the expected Python version using

which python
# should result in: $HOME/.virtualenvs/gentopo/bin/python

and

python --version
# should result in: Python 3.10.13 when using pyenv

Locally, Then, install the package dependencies for this project via

pip install -r requirements.txt

To use a Jupyter notebook locally, install a new kernel for the virtual environment via

python -m ipykernel install --user --name=gentopo

Then, start a JupyterLab instance with

jupyter lab

Select the genetopo kernel to from the Launcher to start a new notebook. Or, select an existing file to work on from the File Browser.