Package Health Score

75 / 100

security
No known security issues
popularity
Limited
maintenance
Healthy
community
Active

Popularity

Limited

GitHub Stars: 56
Forks: 13
Contributors: 20

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package tsinfer, we found that it has been starred 56 times.

Security

No known security issues

Security and license risk for latest version

Release Date: Jul 17, 2024
Direct Vulnerabilities: 0
C
0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 0
H
0
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

GPL-3.0

Non-Permissive License

We noticed that this project uses a license which requires less permissive conditions such as disclosing the source code, stating changes or redistributing the source under the same license. It is advised to further consult the license terms before use.

Security Policy

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Maintenance

Healthy

Commit Frequency

Open Issues: 119
Open PR: 6
Last Release: 5 months ago
Last Commit: 1 month ago

Further analysis of the maintenance status of tsinfer based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that tsinfer demonstrates a positive version release cadence with at least one new version released in the past 12 months.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Active

Readme: Yes
Contributing.md: No
Code of Conduct: Yes
Contributors: 20
Funding: No

With more than 10 contributors for the tsinfer repository, this is possibly a sign for a growing and inviting community.

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Package

Python Versions Compatibility: >=3.9

Age: 7 years
Latest Release: 4 months ago
Dependencies: 5 Direct
Versions: 14
Maintainers: 2
Wheels: Linux, macOS, Windows

Readme

tsinfer

Infer a tree sequence from genetic variation data

The documentation contains details of how to use this software, including installation instructions.

The initial algorithm, its rationale, and results from testing on simulated and real data are described in the following Nature Genetics paper:

> Jerome Kelleher, Yan Wong, Anthony W Wohns, Chaimaa Fadil, Patrick K Albers and Gil McVean (2019) Inferring whole-genome histories in large population datasets. Nature Genetics 51: 1330-1338

Tsinfer versions 0.2.0 onwards allow missing data and provide a fully parameterised Li & Stephens matching algorithm (i.e. which allows mismatch). These improvements are described in the following Science paper:

> Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2022) A unified genealogy of modern and ancient genomes. Science 375: eabi8264

Please cite either or both of these if you use tsinfer in your work. Code to reproduce the results in the first paper is present in a separate GitHub repository.

Note that tsinfer does not attempt to infer node times (i.e. branch lengths of the inferred trees). If you require a tree sequence where the dates of common ancestors are expressed in calendar or generation times, you should post-process the tsinfer output using software such as tsdate.

tsinfer dependencies

daiquiri humanize lmdb sortedcontainers tqdm

FAQs

What is tsinfer?

Infer tree sequences from genetic variation data. Visit Snyk Advisor to see a full health score report for tsinfer, including popularity, security, maintenance & community analysis.

Is tsinfer popular?

The python package tsinfer receives a total of 293 weekly downloads. As such, tsinfer popularity was classified as limited. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is tsinfer well maintained?

We found that tsinfer demonstrated a healthy version release cadence and project activity. It has a community of 20 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is tsinfer safe to use?

The python package tsinfer was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 30 November-2024, at 17:06 (UTC).

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tsinfer

Infer tree sequences from genetic variation data. For more information about how to use this package see README

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Package Health Score

Popularity

Direct Usage Popularity

Security

Security and license risk for latest version

Non-Permissive License

Maintenance

Commit Frequency

Community

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Package

Readme

tsinfer

tsinfer dependencies

FAQs

What is tsinfer?

Is tsinfer popular?

Is tsinfer well maintained?

Is tsinfer safe to use?

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Package Health Score

Direct Usage Popularity

Security and license risk for latest version

Commit Frequency

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Readme

tsinfer

tsinfer dependencies

FAQs

What is tsinfer?

Is tsinfer popular?

Is tsinfer well maintained?

Is tsinfer safe to use?

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Source Code

Open Source

Container

Config

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