Nautilus gas-grain code for astrochemistry

Python CLI for the Nautilus gas-grain astrochemistry code.

This package is part of the Nautilus project.

It provides the nautilus-astrochem command, a front-end to the Fortran Nautilus code shipped by the companion package nautilus-astrochem-code, plus plotting and post-processing helpers built on xarray.

Installation

You can use classical tools like pip to install the package, in a virtual environment or system wide. However, system wide installation, using pip, is not recommended, and virtual environments may make the use of the package more difficult.

The recommended way to install nautilus-astrochem is to use the uv. This tool allows managing python installation, environment and global installed tools easily.

After installing uv, you can install the package globally with:

uv tool install nautilus-astrochem@latest

uv will install the package in its own virtual environment, and make available the nautilus-astrochem command. The binaries from the nautilus-astrochem-code package can also be made available.

[!tip] You can specify a version of the package to install as such: uv tool install nautilus-astrochem@<version>. latest will query PyPI for the latest version.

Usage

Each command and subcommand has its own help message.

nautilus-astrochem --help            # show help
nautilus-astrochem run --help        # run a simulation
nautilus-astrochem run-rates --help  # compute reaction rates
nautilus-astrochem plot --help       # plot abundances / major reactions
nautilus-astrochem clean --help      # clean simulation intermediates
nautilus-astrochem version           # Get version of the code

Getting started

To get started with nautilus-astrochem, we offer a repository nautilus-doc, with scientific documentation and examples of use cases ready to run. This repository is used to provide the documentation website, where the content of the documentation is available.

Tab completion

Tab completion will only work if you have installed the nautilus-astrochem package, and it is available in your PATH

The CLI is implemented with tyro, and it provides support for tab completion in several shells. You can follow the instructions below extracted from the official documentation. Refer to it for more details, in them, you will see python 01_functions.py, replace it by nautilus-astrochem. All credits go to the authors of tyro.

Fish

# (1) Create the completions directory if it doesn't exist.
mkdir -p ~/.config/fish/completions/

# (2) Write the completion script.
nautilus-astrochem --tyro-write-completion fish ~/.config/fish/completions/nautilus-astrochem.fish

Zsh

# (1) Make directory for local completions.
mkdir -p ~/.zfunc

# (2) Write completion script.
nautilus-astrochem --tyro-write-completion zsh ~/.zfunc/_nautilus-astrochem

And if it’s not in your .zshrc already:

# (3) Add .zfunc to our function search path, then initialize completions.
# Ideally this should go in your .zshrc!
fpath+=~/.zfunc
autoload -Uz compinit && compinit

Bash

# (1) Find and make completion directory.
completion_dir=${BASH_COMPLETION_USER_DIR:-${XDG_DATA_HOME:-$HOME/.local/share}/bash-completion}/completions/
mkdir -p $completion_dir

# (2) Write completion scripts. The name of the completion script must match
# the name of the file.
nautilus-astrochem --tyro-write-completion bash ${completion_dir}/nautilus-astrochem

Contact

Requests or questions can be sent to valentine.wakelam@u-bordeaux.fr.