ytree
ytree: A Python package for analyzing merger trees - Published in JOSS (2019)
Science Score: 98.0%
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✓DOI references
Found 7 DOI reference(s) in README and JOSS metadata -
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Repository
A Python package for analyzing tree data and especially merger trees.
Basic Info
Statistics
- Stars: 16
- Watchers: 6
- Forks: 10
- Open Issues: 5
- Releases: 14
Topics
Metadata Files
README.md
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('tree000.dat') mytree = 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 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 it. Citation instructions
can be found here.
Resources
The latest documentation can be found at https://ytree.readthedocs.io.
The ytree paper in the Journal of Open Source Software.
ytreeis an extension of the yt Project. The yt-project community resources can be used for ytree-related communication. Theytreedevelopers can usually be found on the yt project Slack channel.
Owner
- Name: ytree-project
- Login: ytree-project
- Kind: organization
- Repositories: 2
- Profile: https://github.com/ytree-project
JOSS Publication
ytree: A Python package for analyzing merger trees
Authors
University of Edinburgh
University of Illinois at Urbana-Champaign
Editor
Juanjo Bazán
Tags
astronomy astrophysics merger tree structure formation galaxiesCitation (CITATION.rst)
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_2025_17045610,
author = {Britton Smith and
Meagan Lang and
John Wise and
Juanjo Bazán},
title = {ytree-project/ytree: ytree 3.3.1 Release},
month = sep,
year = 2025,
publisher = {Zenodo},
version = {ytree-3.3.1},
doi = {10.5281/zenodo.17045610},
url = {https://doi.org/10.5281/zenodo.17045610},
}
GitHub Events
Total
- Create event: 3
- Release event: 2
- Issues event: 3
- Watch event: 3
- Delete event: 1
- Issue comment event: 6
- Push event: 19
- Pull request event: 38
Last Year
- Create event: 3
- Release event: 2
- Issues event: 3
- Watch event: 3
- Delete event: 2
- Issue comment event: 6
- Push event: 20
- Pull request event: 39
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Britton Smith | b****h@g****m | 1,266 |
| langmm | c****8@g****m | 40 |
| Juanjo Bazán | j****n@g****m | 1 |
| John Wise | j****7 | 1 |
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 24
- Total pull requests: 120
- Average time to close issues: 4 months
- Average time to close pull requests: about 1 month
- Total issue authors: 7
- Total pull request authors: 4
- Average comments per issue: 3.29
- Average comments per pull request: 0.74
- Merged pull requests: 101
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 2
- Pull requests: 30
- Average time to close issues: N/A
- Average time to close pull requests: about 19 hours
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.5
- Average comments per pull request: 0.03
- Merged pull requests: 23
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- brittonsmith (12)
- TobiBu (5)
- manodeep (3)
- PauCaBu (1)
- cspotz (1)
- Morkney (1)
- milanq14 (1)
Pull Request Authors
- brittonsmith (116)
- matthewturk (2)
- jwise77 (1)
- dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 264 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 3
(may contain duplicates) - Total versions: 27
- Total maintainers: 1
pypi.org: ytree
A Python package for analyzing tree data and especially merger trees.
- Homepage: https://github.com/ytree-project/ytree
- Documentation: https://ytree.readthedocs.io/en/stable/index.html
- License: BSD License
-
Latest release: 3.3.1
published 4 months ago
Rankings
Maintainers (1)
conda-forge.org: ytree
- Homepage: https://github.com/ytree-project/ytree
- License: BSD-3-Clause
-
Latest release: 3.1.2
published over 3 years ago
Rankings
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- pypa/gh-action-pypi-publish v1.5.0 composite
- configparser *
- h5py *
- more_itertools >=8.4
- numpy *
- unyt >=3.0.1
- yt >=4.2