hetmatpy

Python package for matrix storage and operations on hetnets

https://github.com/hetio/hetmatpy

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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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 (12.8%) to scientific vocabulary

Keywords

greenelab hetio hetmat hetnet-connectivity-search hetnets matrix numpy python scipy

Keywords from Contributors

edge-prediction heterogeneous-network hetnet rephetio dwpcs networks

Last synced: 6 months ago · JSON representation ·

Repository

Python package for matrix storage and operations on hetnets

Basic Info

Host: GitHub
Owner: hetio
License: other
Language: Python
Default Branch: main
Homepage:
Size: 1.36 MB

Statistics

Stars: 14
Watchers: 2
Forks: 9
Open Issues: 2
Releases: 2

Topics

greenelab hetio hetmat hetnet-connectivity-search hetnets matrix numpy python scipy

Created over 7 years ago · Last pushed almost 3 years ago

Metadata Files

Readme License Citation

hetmatpy: a Python 3 package for matrix operations of hetnets

This codebase enables identifying the relevant network connections between a set of query nodes. The method is designed to operate on hetnets (networks with multiple node or relationship types).

This project is still under development. Use with caution.

Environment

Install via pip from GitHub using:

```shell

install the latest release from PyPI

pip install hetmatpy

install latest version on GitHub

pip install git+https://github.com/hetio/hetmatpy

for local development, run the following inside the development environment:

pip install --editable . ```

Development

This repo uses pre-commit checks:

```shell

run once per local repo before committing

pre-commit install ```

Acknowledgments

This work is supported through a research collaboration with Pfizer Worldwide Research and Development. This work is funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grants GBMF4552 to Casey Greene and GBMF4560 to Blair Sullivan.

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/hetmatpy repository:
  Python package for matrix storage and operations on hetnets
message: >-
  This citation is for the source code of the hetmatpy Python library.
  The methods implemented by this software have been developed largely in
  <https://greenelab.github.io/connectivity-search-manuscript/>.
  See that manuscript for a more general citation to Hetnet Connectivity Search.
type: software
authors:
  - given-names: Daniel
    family-names: Himmelstein
    orcid: 'https://orcid.org/0000-0002-3012-7446'
  - given-names: Michael
    family-names: Zietz
    orcid: 'https://orcid.org/0000-0003-0539-630X'
  - given-names: Kyle
    family-names: Kloster
    orcid: 'https://orcid.org/0000-0001-5678-7197'
  - given-names: Benjamin
    family-names: Heil
    orcid: 'https://orcid.org/0000-0002-2811-1031'
  - given-names: Gregory
    family-names: Way
    orcid: 'https://orcid.org/0000-0002-0503-9348'
  - given-names: Blair
    family-names: Sullivan
    orcid: 'https://orcid.org/0000-0001-7720-6208'
  - given-names: Casey
    family-names: Greene
    orcid: 'https://orcid.org/0000-0001-8713-9213'
identifiers:
  - type: swh
    value: 'swh:1:dir:7a20d7c3a5a1b8e6ec0a455e22808dd61a987b02'
    description: Software Heritage Directory Snapshot
  - type: swh
    value: 'swh:1:rev:5ada9c37980296b2594c2fa69dc6a5d215218d0c'
    description: Software Heritage Revision Snapshot
  - type: other
    value: 'RRID:SCR_023409'
    description: Research Resource Identification CURIE
  - type: url
    value: 'https://bio.tools/hetmatpy'
    description: 'biotools:hetmatpy'
repository-code: 'https://github.com/hetio/hetmatpy'
url: 'https://hetio.github.io/hetmatpy/'
repository-artifact: 'https://pypi.org/project/hetmatpy/'
abstract: >-
  Python package for matrix storage and operations on
  hetnets.
keywords:
  - python
  - numpy
  - scipy
  - matrix
  - networks
  - hetmech
  - greenelab
  - hetmat
  - hetio
  - hetnets
  - hetnet-connectivity-search
license: BSD-2-Clause-Patent
commit: 3a426ccbcf63b27911e43be5ff305a3968224439
version: v0.1.0
date-released: '2022-04-05'

GitHub Events

Total

Issues event: 1
Watch event: 1
Fork event: 1

Last Year

Issues event: 1
Watch event: 1
Fork event: 1

Committers

Last synced: over 1 year ago

All Time

Total Commits: 127
Total Committers: 6
Avg Commits per committer: 21.167
Development Distribution Score (DDS): 0.291

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Daniel Himmelstein	d**n@g**m	90
Michael Zietz	m**z@g**m	23
Kyle Kloster	k****e	5
Kyle Kloster	k**r@g**m	4
Ben Heil	b**l@g**m	3
Greg Way	g**y@g**m	2

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 3
Total pull requests: 16
Average time to close issues: 12 days
Average time to close pull requests: 2 days
Total issue authors: 2
Total pull request authors: 3
Average comments per issue: 1.0
Average comments per pull request: 0.56
Merged pull requests: 16
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

dhimmel (2)
Travis-Barton (1)
dgoncalo (1)

Pull Request Authors

dhimmel (12)
ben-heil (3)
zietzm (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 49 last-month

Total dependent packages: 0
Total dependent repositories: 1
Total versions: 2
Total maintainers: 1

pypi.org: hetmatpy

Matrix implementations for hetnets and path-count-based measures

Homepage: https://het.io/software/
Documentation: https://hetio.github.io/hetmatpy
License: # BSD-2-Clause Plus Patent License _Copyright © 2016–2020, Contributors, the Greene Lab at the University of Pennsylvania, and the Sullivan Lab at North Carolina State University_<br> Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Subject to the terms and conditions of this license, each copyright holder and contributor hereby grants to those receiving rights under this license a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable (except for failure to satisfy the conditions of this license) patent license to make, have made, use, offer to sell, sell, import, and otherwise transfer this software, where such license applies only to those patent claims, already acquired or hereafter acquired, licensable by such copyright holder or contributor that are necessarily infringed by: (a) their Contribution(s) (the licensed copyrights of copyright holders and non-copyrightable additions of contributors, in source or binary form) alone; or (b) combination of their Contribution(s) with the work of authorship to which such Contribution(s) was added by such copyright holder or contributor, if, at the time the Contribution is added, such addition causes such combination to be necessarily infringed. The patent license shall not apply to any other combinations which include the Contribution. Except as expressly stated above, no rights or licenses from any copyright holder or contributor is granted under this license, whether expressly, by implication, estoppel or otherwise. DISCLAIMER THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Latest release: 0.1.0
published almost 4 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 49 Last month

Rankings

Dependent packages count: 10.1%

Forks count: 10.9%

Stargazers count: 16.0%

Dependent repos count: 21.6%

Average: 22.4%

Downloads: 53.3%

Maintainers (1)

dhimmel

Last synced: 6 months ago

Dependencies

.github/workflows/release.yaml actions

actions/checkout v2 composite
actions/setup-python v3 composite
pypa/gh-action-pypi-publish release/v1 composite

.github/workflows/test.yaml actions

actions/checkout v3 composite
actions/setup-python v2 composite
actions/setup-python v3 composite
peaceiris/actions-gh-pages v3 composite
pre-commit/action v2.0.3 composite

pyproject.toml pypi

hetnetpy >=0.3.0
numpy *
pandas *
scipy *

hetmatpy

Science Score: 44.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

hetmatpy: a Python 3 package for matrix operations of hetnets

Environment

install the latest release from PyPI

install latest version on GitHub

for local development, run the following inside the development environment:

Development

run once per local repo before committing

Acknowledgments

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: hetmatpy

Rankings

Maintainers (1)

Dependencies