Science Score: 67.0%
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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
Found 6 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.1%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Hetnets in Python (relocated from dhimmel/hetio)
Basic Info
- Host: GitHub
- Owner: hetio
- License: other
- Language: Python
- Default Branch: main
- Homepage: https://het.io/software
- Size: 798 KB
Statistics
- Stars: 98
- Watchers: 8
- Forks: 30
- Open Issues: 5
- Releases: 14
Topics
Metadata Files
README.md
Hetnets in Python
Overview
Hetnetpy is a Python 3 package for creating, querying, and operating on hetnets. This software provides convenient data structures for hetnets, as well as algorithms for edge prediction. It is specifically tailored and streamlined for hetnets compared to other more generic network software. See https://het.io/software for additional software packages designed specifically for hetnets.
Package relocation
Note that this package was previously named hetio, available at the following repositories:
- https://github.com/hetio/hetnetpy (current)
- https://github.com/hetio/hetio (former)
- https://github.com/dhimmel/hetio (former)
In July 2019, the package was renamed to hetnetpy to more clearly represent its functionality and disambiguate it from other products.
Background
Hetnets: Hetnets, also called heterogeneous information networks, are graphs with multiple node and edge types. Hetnets are both multipartite and multirelational. They provide a scalable, intuitive, and frictionless structure for data integration.
Purpose: This package provides data structures for hetnets and algorithms for edge prediction. It only supports hetnets, which is its primary advantage compared to other network software. Node/edge attributes and edge directionality are supported.
Impetus: Development originated with a study to predict disease-associated genes and continues with a successive study to repurpose drugs.
Caution: Documentation is currently spotty, testing coverage is moderate, and the API is not fully stable. Contributions are welcome. Please use GitHub Issues for feedback, questions, or troubleshooting.
Installation
To install the current PyPI version (recommended), run:
sh
pip install hetnetpy
For the latest GitHub version, run:
sh
pip install git+https://github.com/hetio/hetnetpy.git#egg=hetnetpy
For development, clone or download-and-extract the repository. Then run pip install --editable . from the repository's root directory. The --editable flag specifies editable mode, so updating the source updates your installation.
Once installed, tests can be executed by running py.test test/ from the repository's root directory.
Design
A Graph object stores a heterogeneous network and relies on the following classes:
- Graph
- MetaGraph
- Edge
- MetaEdge
Development
This repo uses pre-commit:
```sh
run once per local repo before committing
pre-commit install ```
This following is only relevant for maintainers. Create a new release at https://github.com/hetio/hetnetpy/releases/new. GitHub Actions will build the distribution and upload it to PyPI. The version information inferred from the Git tag using setuptools_scm.
License
This repository is dual licensed, available under either or both of the following licenses:
- BSD-2-Clause Plus Patent License at
LICENSE-BSD.md - CC0 1.0 Universal Public Domain Dedication at
LICENSE-CC0.md
Owner
- Name: Hetnets in Biomedicine
- Login: hetio
- Kind: organization
- Website: https://het.io
- Repositories: 9
- Profile: https://github.com/hetio
Repositories for hetnet-related research, tools, and datasets including Hetionet. By the teams of @dhimmel, @greenelab, & @sebaran
Citation (CITATION.cff)
cff-version: 1.2.0
title: >-
hetio/hetnetpy repository:
Hetnets in Python
message: >-
This citation is for the source code of the hetnetpy Python library.
The methods implemented by this software have been developed over the course of several studies:
<https://doi.org/10.1371/journal.pcbi.1004259>
<https://doi.org/10.7554/eLife.26726>
<https://greenelab.github.io/connectivity-search-manuscript/>
type: software
authors:
- given-names: Daniel
family-names: Himmelstein
orcid: 'https://orcid.org/0000-0002-3012-7446'
- given-names: Benjamin
family-names: Heil
orcid: 'https://orcid.org/0000-0002-2811-1031'
- given-names: Michael
family-names: Zietz
orcid: 'https://orcid.org/0000-0003-0539-630X'
- given-names: Tong Shu
family-names: Li
- given-names: Kyle
family-names: Kloster
orcid: 'https://orcid.org/0000-0001-5678-7197'
- given-names: Gregory
family-names: Way
orcid: 'https://orcid.org/0000-0002-0503-9348'
- given-names: Casey
family-names: Greene
orcid: 'https://orcid.org/0000-0001-8713-9213'
- given-names: Sergio
family-names: Baranzini
orcid: 'https://orcid.org/0000-0003-0067-194X'
identifiers:
- type: swh
value: 'swh:1:dir:2dc7b6e544b6502ace7be92a96536b41c80d6be0'
description: Software Heritage Directory
- type: swh
value: 'swh:1:rev:8bf8ccb620292757d96838c3139bbb14cbce60de'
description: Software Heritage Revision
- type: url
value: 'https://zenodo.org/record/3315264'
description: 'Zenodo Deposit'
repository-code: 'https://github.com/hetio/hetnetpy'
repository-artifact: 'https://pypi.org/project/hetnetpy/'
abstract: >-
Hetnets in Python (relocated from dhimmel/hetio)
keywords:
- python
- graph
- rephetio
- hetnet
- networks
- heterogeneous-network
- baranzini-lab
- greenelab
- hetio
- hetnets
license: BSD-2-Clause-Patent
commit: 42fd6d7d4c2dbfea5d21686b33626329048f8b1d
version: v0.3.1
date-released: '2021-06-13'
GitHub Events
Total
- Watch event: 4
- Issue comment event: 2
- Fork event: 1
- Create event: 1
Last Year
- Watch event: 4
- Issue comment event: 2
- Fork event: 1
- Create event: 1
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Daniel Himmelstein | d****n@g****m | 183 |
| ben-heil | b****l@g****m | 9 |
| Michael Zietz | m****z@g****m | 4 |
| Tong Shu Li | v****s | 2 |
| Kyle Kloster | k****e | 1 |
| Greg Way | g****y@g****m | 1 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 18
- Total pull requests: 34
- Average time to close issues: about 1 month
- Average time to close pull requests: 1 day
- Total issue authors: 10
- Total pull request authors: 7
- Average comments per issue: 3.11
- Average comments per pull request: 0.82
- Merged pull requests: 32
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 4.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dhimmel (5)
- veleritas (4)
- gwaybio (2)
- Tabatabaei1999 (1)
- vincerubinetti (1)
- zietzm (1)
- ben-heil (1)
- yuvaramsingh94 (1)
- Travis-Barton (1)
- ghost (1)
Pull Request Authors
- dhimmel (22)
- ben-heil (4)
- zietzm (3)
- veleritas (2)
- gwaybio (1)
- maggielee1111 (1)
- kkloste (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 1,809 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 2
- Total maintainers: 1
pypi.org: hetnetpy
Hetnets in Python
- Homepage: https://github.com/hetio/hetnetpy
- Documentation: https://hetnetpy.readthedocs.io/
- License: CC0 1.0
-
Latest release: 0.3.1
published over 4 years ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pre-commit/action v3.0.0 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish v1.5.1 composite