ytree 3.3.0

An extension of yt for working with merger tree data.

ytree

This is ytree, a yt extension for working with tree data and especially merger trees.

Generally speaking, tree data defines a one-directional relationship between a series of objects. In trees, objects can have one or more ancestors, but only a single descendent.

Structure formation in cosmology proceeds in a hierarchical fashion, where dark matter halos grow via mergers with other halos. This type of evolution can be conceptualized as a tree, with small branches connecting to successively larger ones, and finally to the trunk. A merger tree describes the growth of halos in a cosmological simulation by linking a halo appearing in a given snapshot to its direct ancestors in a previous snapshot and its descendent in the next snapshot.

Merger trees are computationally expensive to generate and a great number of codes exist for computing them. However, each of these codes saves the resulting data to a different format. ytree is Python package for reading and working with merger tree data from multiple formats. If you are already familiar with using yt to analyze snapshots from cosmological simulations, then think of ytree as the yt of merger trees.

To load a merger tree data set with ytree and print the masses of all the halos in a single tree, one could do:

>>> import ytree
>>> a = ytree.load('tree_0_0_0.dat')
>>> my_tree = a[0]
>>> print(my_tree['tree', 'mass'].to('Msun'))
[6.57410072e+14 6.57410072e+14 6.53956835e+14 6.50071942e+14 ...
 2.60575540e+12 2.17122302e+12 2.17122302e+12] Msun

A list of all currently supported formats can be found in the online documentation. If you would like to see support added for another format, we would be happy to work with you to make it happen. In principle, any type of tree-like data where an object has one or more ancestors and a single descendent can be supported.

Installation

ytree can be installed with pip or conda:

pip installation

pip install ytree

conda installation

conda install -c conda-forge ytree

source installation

To get the development version, clone this repository and install like this:

git clone https://github.com/ytree-project/ytree
cd ytree
pip install -e .

Getting Started

The ytree documentation will walk you through installation, get you started analyzing merger trees, and help you become a contributor to the project. Have a look!

Sample Data

Sample data for all merger tree formats supported by ytree is available on the yt Hub in the ytree data collection.

Contributing

ytree would be much better with your contribution! As an extension of the yt Project, we follow the yt guidelines for contributing.

Citing ytree

If you use ytree in your work, please cite the following:

Smith et al., (2019). ytree: A Python package for analyzing merger trees.
Journal of Open Source Software, 4(44), 1881,
https://doi.org/10.21105/joss.01881

For BibTeX users:

  @article{ytree,
    doi = {10.21105/joss.01881},
    url = {https://doi.org/10.21105/joss.01881},
    year  = {2019},
    month = {dec},
    publisher = {The Open Journal},
    volume = {4},
    number = {44},
    pages = {1881},
    author = {Britton D. Smith and Meagan Lang},
    title = {ytree: A Python package for analyzing merger trees},
    journal = {Journal of Open Source Software}
  }

If you would like to also cite the specific version of ytree used in your work, include the following reference:

  @software{britton_smith_2023_8349044,
    author       = {Britton Smith and
                    Meagan Lang and
                    John Wise and
                    Juanjo Bazán},
    title        = {ytree-project/ytree: ytree 3.2.1 Release},
    month        = sep,
    year         = 2023,
    publisher    = {Zenodo},
    version      = {ytree-3.2.1},
    doi          = {10.5281/zenodo.8349044},
    url          = {https://doi.org/10.5281/zenodo.8349044}
  }

Resources

• The latest documentation can be found at https://ytree.readthedocs.io.

• The ytree paper in the Journal of Open Source Software.

• ytree is an extension of the yt Project. The yt-project community resources can be used for ytree-related communication. The ytree developers can usually be found on the yt project Slack channel.