Science Score: 62.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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✓Institutional organization owner
Organization becksteinlab has institutional domain (becksteinlab.physics.asu.edu) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.3%) to scientific vocabulary
Keywords
file-format
mdanalysis
molecular-dynamics
streaming
zarr
Last synced: 6 months ago
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JSON representation
·
Repository
zarrtraj MDAKit for @MDAnalysis
Basic Info
- Host: GitHub
- Owner: Becksteinlab
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://zarrtraj.readthedocs.io/
- Size: 27 MB
Statistics
- Stars: 9
- Watchers: 3
- Forks: 2
- Open Issues: 11
- Releases: 8
Topics
file-format
mdanalysis
molecular-dynamics
streaming
zarr
Created about 2 years ago
· Last pushed 7 months ago
Metadata Files
Readme
Changelog
Contributing
License
Code of conduct
Citation
Authors
README.md
zarrtraj
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Zarrtraj is an MDAnalysis MDAKit that provides the ability to read and write H5MD-formatted trajectory data in MDAnalysis using Zarr. Zarrtraj can read trajectories locally and from AWS S3, Google Cloud Buckets, and Azure Blob Storage & DataLakes. It can read both H5MD-formatted files stored in hdf5 (.h5md files) and H5MD-formatted files stored in Zarr (.zarrmd files).
Zarrtraj is installable via both pip and conda forge:
bash
pip install zarrtraj
bash
conda install -c conda-forge zarrtraj
For more information on installation and usage, see the zarrtraj documentation
Zarrtraj is bound by a Code of Conduct.
Copyright
The Zarrtraj source code is hosted at https://github.com/Becksteinlab/zarrtraj and is available under the MIT License (see the file LICENSE).
Copyright (c) 2024, Lawson Woods
Acknowledgements
Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using Zarrtraj in published work.
Owner
- Name: Becksteinlab
- Login: Becksteinlab
- Kind: organization
- Email: obeckste@asu.edu
- Location: Tempe, AZ
- Website: https://becksteinlab.physics.asu.edu
- Repositories: 56
- Profile: https://github.com/Becksteinlab
Computational Biophysics at Arizona State University
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: 'Zarrtraj: A Python package for streaming molecular dynamics trajectories from cloud services'
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Lawson
email: lawsonw84@gmail.com
family-names: Woods
orcid: 'https://orcid.org/0009-0003-0713-4167'
affiliation: >-
School of Computing and Augmented Intelligence,
Arizona State University, Tempe, Arizona, United
States of America
- given-names: Hugo
family-names: MacDermott-Opeskin
orcid: 'https://orcid.org/0000-0002-7393-7457'
affiliation: >-
Open Molecular Software Foundation, Davis, CA, United
States of America
email: hugomacdermott-opeskin@mdanalysis.org
- given-names: Edis
family-names: Jakupovic
orcid: 'https://orcid.org/0000-0001-8813-6356'
affiliation: >-
Center for Biological Physics, Arizona State
University, Tempe, AZ, United States of America
- given-names: Yuxuan
orcid: 'https://orcid.org/0000-0003-4390-8556'
family-names: Zhuang
affiliation: >-
Department of Computer Science, Stanford University,
Stanford, CA 94305, USA.
- given-names: Richard
orcid: 'https://orcid.org/0000-0002-3241-1846'
family-names: Gowers
name-particle: J
affiliation: Charm Therapeutics, London, United Kingdom
- given-names: Oliver
family-names: Beckstein
affiliation: >-
Center for Biological Physics, Arizona State
University, Tempe, AZ, United States of America
orcid: 'https://orcid.org/0000-0003-1340-0831'
identifiers:
- type: doi
value: 10.5281/zenodo.13887976
repository-code: 'https://github.com/Becksteinlab/zarrtraj'
url: 'https://zarrtraj.readthedocs.io/en/latest/index.html'
abstract: >-
Zarrtraj is an MDAnalysis MDAKit for streaming H5MD and
ZarrMD trajectory files from cloud storage like AWS S3,
Google Cloud Buckets, and Azure Data lakes and Blob
Storage
keywords:
- streaming
- molecular-dynamics
- file-format
- mdanalysis
- zarr
license: MIT
GitHub Events
Total
- Create event: 13
- Release event: 2
- Issues event: 18
- Watch event: 2
- Delete event: 4
- Issue comment event: 39
- Push event: 46
- Pull request event: 19
- Pull request review comment event: 22
- Pull request review event: 28
- Fork event: 1
Last Year
- Create event: 13
- Release event: 2
- Issues event: 18
- Watch event: 2
- Delete event: 4
- Issue comment event: 39
- Push event: 46
- Pull request event: 19
- Pull request review comment event: 22
- Pull request review event: 28
- Fork event: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 47
- Total pull requests: 41
- Average time to close issues: 2 months
- Average time to close pull requests: 11 days
- Total issue authors: 4
- Total pull request authors: 4
- Average comments per issue: 0.68
- Average comments per pull request: 1.32
- Merged pull requests: 39
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 12
- Pull requests: 18
- Average time to close issues: about 2 months
- Average time to close pull requests: 22 days
- Issue authors: 3
- Pull request authors: 4
- Average comments per issue: 0.58
- Average comments per pull request: 2.0
- Merged pull requests: 17
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ljwoods2 (25)
- hmacdope (19)
- orbeckst (6)
- PythonFZ (1)
Pull Request Authors
- ljwoods2 (58)
- hmacdope (4)
- orbeckst (4)
- richardjgowers (2)
Top Labels
Issue Labels
GSOC (5)
bug (2)
documentation (1)
wontfix (1)
user experience (1)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 40 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 2
pypi.org: zarrtraj
This is a kit that provides the ability to read and write trajectory data in the Zarr file format
- Documentation: https://zarrtraj.readthedocs.io/
- License: Copyright 2024 Lawson Woods Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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Latest release: 0.3.2
published 7 months ago
Rankings
Dependent packages count: 10.6%
Average: 35.2%
Dependent repos count: 59.7%
Last synced:
6 months ago
Dependencies
.github/workflows/gh-ci.yaml
actions
- MDAnalysis/install-mdanalysis main composite
- MDAnalysis/mdanalysis-compatible-python main composite
- actions/checkout v4 composite
- actions/setup-python v4 composite
- codecov/codecov-action v3 composite
- conda-incubator/setup-miniconda v2 composite
pyproject.toml
pypi
- MDAnalysis >=2.0.0