graph_models

This site contains the API documentation for the graph_models package.

Overview

graph_models is the example package that ships with this Python project template. It provides a simple undirected-graph data structure (UGRAPH) to illustrate the intended project layout. Replace it with your own code.

Quick Start

from graph_models import UGRAPH

g = UGRAPH(nodes=["A", "B", "C"], edges=[("A", "B"), ("A", "C")])
print(g.num_nodes)         # 3
print(g.num_edges)         # 2
print(g.adjacency_matrix)

Installation

git clone https://github.com/your-org/your-repo.git
cd your-repo
make sync-venv

See the API Reference for detailed documentation.

Manuscript workflow (`paper/` and `notebooks/`)

The template ships with a paired paper/ and notebooks/ layout for projects that publish alongside a manuscript:

notebooks/ holds Jupyter notebooks (figure_creator.ipynb, table_creater.ipynb) that produce results from the package code and write them directly into paper/figures/ (PNG/PDF) or paper/tables/ (LaTeX fragments).
paper/ holds the LaTeX source. main.tex pulls in the generated artefacts via \includegraphics{figures/...} and \input{tables/...}, so re-running a notebook is the canonical way to refresh a result — the .tex skeleton stays put.

The shipped class file (paper/uai2026.cls) targets UAI 2026 purely as an example. Replace it with whatever class your publishing outlet requires (NeurIPS, ICML, ACL, IEEEtran, Springer LNCS, …); the notebook → paper/ artefact pipeline is venue-agnostic.

Developer Guide

Pre-commit hooks

The project uses pre-commit to enforce code quality before every commit and push. Hooks are defined in .pre-commit-config.yaml and include:

Hook	Stage	Purpose
`ruff`	commit	Linting and auto-formatting
`trailing-whitespace`, `end-of-file-fixer`, `check-yaml`, `check-added-large-files`	commit	General hygiene
`mypy`	commit	Static type checking (strict mode)
`bandit`	commit	Security vulnerability scanning
`pip-compile` (×2)	push	Re-pin `requirements.txt` and `requirements_dev.txt` from `pyproject.toml`

Install and run all hooks against every file in one step:

make precommit

This runs pre-commit install (registers the git hooks) and then pre-commit run --all-files. After that, hooks run automatically on git commit and git push.

To update hook versions to their latest releases:

pre-commit autoupdate

Documentation (MkDocs)

Docs are built with MkDocs and the Material theme. API reference pages are auto-generated from source docstrings via the mkdocstrings plugin.

Preview locally:

source venv_<your-repo>/bin/activate
mkdocs serve

Then open http://127.0.0.1:8000.

Build a static site:

mkdocs build          # output goes to site/

Deploy docs to GitHub Pages

Versioned docs are managed with mike, which pushes each release to the gh-pages branch of your repository.

Deploy a new version:

mike deploy --push --update-aliases <version> latest
# e.g.  mike deploy --push --update-aliases 0.1.0 latest

Set the default version (only needed once):

mike set-default --push latest

View available deployed versions:

mike list

Prerequisites: your GitHub repository must have GitHub Pages enabled (Settings → Pages → Source: gh-pages branch). The repo_url and site_url fields in mkdocs.yml must point at your actual repository.