atomistic-cookbook-utils

Small shared utilities used by the recipes in the Atomistic Cookbook.

The goal is to keep recipe code focused on the science: any boilerplate that would otherwise be copy-pasted across many recipes lives here.

Installation

pip install atomistic-cookbook-utils

For a recipe's environment.yml, add it under pip: with a semantic version range, e.g.

- atomistic-cookbook-utils >=0.1,<0.2

Contents

download_with_retry

Download a file with automatic retries on transient HTTP errors (429, 500, 502, 503, 504). Skips the download if the file already exists, creates parent directories as needed.

from atomistic_cookbook_utils import download_with_retry

download_with_retry(
    "https://zenodo.org/records/10566825/files/gaas_training.xyz",
    "data/gaas_training.xyz",
)

run_command

Run a shell-like command string without invoking a shell. The string is split with shlex.split, so quoting works as expected; pipes, redirection and globs do not — for those, use subprocess directly.

By default the child inherits the parent's stdout and stderr. Pass print_output=True to capture the command's combined output and re-emit it via print() — this makes the output visible in sphinx-gallery rendered cells (which capture sys.stdout but not raw file-descriptor writes from child processes).

from atomistic_cookbook_utils import run_command

run_command("mtt train options.yaml")
run_command("ls -la", cwd="data", print_output=True)

Source

This package is developed inside the cookbook repository at src/atomistic-cookbook-utils/. See CONTRIBUTING.rst at the repo root for development workflow.