Installation
Requirements
Python 3.10 or newer
Git (required to install the DCA dependency from source)
Standard install
Clone the repository and install in editable mode so local changes are reflected immediately:
git clone https://github.com/dulithaprasanna/ALSEBO.git
cd ALSEBO
pip install -e .
This installs all dependencies declared in setup.cfg, including the
dca package which is fetched directly from GitHub:
dca @ git+https://github.com/utdal/py-mfdca.git@vae_dependency
Note
Because dca is a Git-only dependency, make sure Git is available in
the environment where you run pip install.
Virtual environment (recommended)
python -m venv .venv
source .venv/bin/activate # Windows: .venv\Scripts\activate
pip install -e .
Dependencies
The following packages are installed automatically:
Package |
Purpose |
|---|---|
|
Array operations and data I/O |
|
Gaussian Process Regression, t-SNE, PCA, k-means |
|
FASTA parsing in sequence space and VAE data loading |
|
ESM protein language model embeddings |
|
VAE training (encoder–decoder architecture) |
|
Plotting utilities |
|
Mean-field Direct Coupling Analysis features |
Verify the installation
import alsebo
print(alsebo.__version__)
Building the documentation locally
pip install tox
tox -e viewdocs # builds HTML and serves at http://localhost:8000