How-to: Run Tests and Check Coverage

Author:

Rohit Goswami

Problem

You want to run tests and check coverage across all optional dependency sets.

Quick Start

Single Environment (uv)

For basic development:

cd rgpycrumbs
uv sync --extra test
uv run pytest tests/ -m pure

Full Coverage (pixi)

pixi manages multiple environments with different optional deps:

pixi run cov

This runs:

Environment	Deps	Test marker	Covers
test	numpy, scipy, ase, click	pure, eon	CLI, parsers, basetypes, interpolation
surfaces	jax	surfaces	Surface models, kernels, gradient-enhanced GP
fragments	IRA, tblite, pyvista	fragments, ira, align	Geometry analysis, IRA alignment, fragments

Each env writes COVERAGE_FILE=.coverage.<env>, then cov combines them all.

Individual Environments

pixi run -e test test-base          # base tests
pixi run -e surfaces test-surfaces  # jax surface models
pixi run -e fragments test-fragments # IRA + geometry

How It Works

digraph coverage_flow {
    fontname="Jost"; fontsize=12;
    node [fontname="Jost", fontsize=12, shape=box, style=filled, fillcolor=white];
    edge [fontname="Jost", fontsize=11];

    clean [label="cov-clean\nremove .coverage.*", fillcolor="#F1DB4B"];
    test [label="test-base\n(numpy, scipy, ase)"];
    surfaces [label="test-surfaces\n(+ jax)"];
    fragments [label="test-fragments\n(+ IRA, tblite)"];
    combine [label="coverage combine\n.coverage.test + .coverage.surfaces + .coverage.fragments", fillcolor="#FF655D", fontcolor=white];
    report [label="coverage report", fillcolor="#004D40", fontcolor=white];

    clean -> test -> combine;
    clean -> surfaces -> combine;
    clean -> fragments -> combine;
    combine -> report;
}

Quality Guidelines

• New modules must have tests in the same PR

• Plot functions: at least smoke tests

• Parsers: synthetic input + output schema validation

• Conda-only deps (IRA, jax, tblite): tested in their pixi env, not mocked