GGMolVis Installation Guide as a Python Module

This guide provides instructions for installing GGMolVis as a Python module, along with its dependencies. Please note that this method of installation does not involve running Blender’s GUI; instead, you will interact with GGMolVis through Python.

Installation Steps

Install GGMolVis with `conda`

First, clone the GGMolVis repository from GitHub:
```
git clone git@github.com:yuxuanzhuang/ggmolvis.git
cd ggmolvis
```
Next, create and activate the conda environment specified in the repository:
```
conda env create -f devtools/conda-envs/test_env.yaml
conda activate ggmolvis-test
```
Then, install GGMolVis in editable mode:
```
python -m pip install -e .
```
Verify the installation by checking the version number:
```
python -c "import ggmolvis; print(ggmolvis.__version__)"
```
Note

Currently, only Python 3.11 is supported.

Install GGMolVis with `uv`

If you have [uv](https://github.com/astral-sh/uv) installed, you can do:

uv venv -p 3.11
source .venv/bin/activate
uv pip install 'ggmolvis @ https://github.com/yuxuanzhuang/ggmolvis.git'
uv pip install 'mdanalysis @ git+https://github.com/MDAnalysis/mdanalysis.git@develop#subdirectory=package'
# optionally: install jupyter-related things
uv pip install ipython ipykernel jupyter

Note

Currently, rendering in VSCode gives a PIL-related error, but the rendering itself finishes successfully, if you simply open the image saved on disk in /tmp

(Optional) Install a Different Version of MolecularNodes

If you need a development or alternative version of MolecularNodes, you can install it as follows:
```
git clone git@github.com:BradyAJohnston/MolecularNodes.git
cd MolecularNodes
python -m pip install -e .
```

Verification

Start JupyterLab using the ggmolvis-test environment:
```
jupyter lab
```
When JupyterLab opens, select the ggmolvis-test kernel in the Launcher or from the Kernel menu. No Blender GUI will appear during usage.
In a Jupyter notebook cell, run the following commands to confirm that GGMolVis is installed correctly:
```
import ggmolvis
print(ggmolvis.__version__)
print(ggmolvis.__file__)
```

If GGMolVis is properly installed, these commands will print the currently installed version and the file path for the GGMolVis module.

You are now ready to use GGMolVis as a Python module!