Skip to main content

What's the current version for each biological database?

Project description

Bioversions

PyPI PyPI - Python Version PyPI - License DOI Code style: black Powered by the Bioregistry

What's the current version for each biological database?

A daily updated static listing of all current versions (that are incorporated) can be found at https://biopragmatics.github.io/bioversions.

🚀 Installation

$ pip install bioversions

💪 Usage

import bioversions

assert bioversions.get_version('biogrid') == '4.2.192', 'This was true on Dec 5th, 2020!'

# If you want more information, use the resolve() function
bioversion = bioversions.resolve('biogrid')
assert bioversion.version == '4.2.192'

By default, the results are cached and only refreshed once per day with the help of cachier. The cache is stored in ~/.data/bioversions. The cache location can be overridden by setting the BIOVERSIONS_HOME environment variable via pystow.

🌐 Web Application

While https://biopragmatics.github.io/bioversions provides a daily updated static listing of the database, you can run a dynamic version with an API from your shell with:

$ bioversions web

Options can be listed with bioversions web --help.

You can navigate to http://localhost:5000 to see all versions as HTML or programmatically resolve given databases with the http://localhost:5000/database/<name> endpoint like in the following:

import requests

res = requests.get('http://localhost:5000/database/biogrid').json()
assert res['success']
assert res['result']['name'] == 'BioGRID'
assert res['result']['version'] == '4.2.192', 'This was true on Dec 5th, 2020!'

CLI Usage

You can use bioversions get to incorporate the latest versions in your shell scripts or REPL usage like in:

$ wget "https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-$(bioversions get biogrid)/BIOGRID-ALL-$(bioversions get biogrid).mitab.zip"

🙏 Contributing

To add more databases to the list, you can create a new submodule of bioversions.sources and extend the bioversions.utils.Getter class to identify the most recent version for your target database. See bioversions.sources.biogrid as an example.

👋 Attribution

⚖️ License

Code is licensed under the MIT License.

🎁 Support

The Bioversions service was developed by the INDRA Lab, a part of the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.

💰 Funding

The development of the Bioregistry is funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).

Project details


Release history Release notifications | RSS feed

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

bioversions-0.4.24.tar.gz (182.4 kB view details)

Uploaded Source

Built Distribution

bioversions-0.4.24-py3-none-any.whl (49.3 kB view details)

Uploaded Python 3

File details

Details for the file bioversions-0.4.24.tar.gz.

File metadata

  • Download URL: bioversions-0.4.24.tar.gz
  • Upload date:
  • Size: 182.4 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.8.0 pkginfo/1.8.2 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/0.9.1 urllib3/1.26.9 tqdm/4.63.0 importlib-metadata/4.11.3 keyring/23.5.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.10.2

File hashes

Hashes for bioversions-0.4.24.tar.gz
Algorithm Hash digest
SHA256 735090bed6a2039022f14afd94565bb1a925ee4ec6febc0805a7c4e7be8f0d20
MD5 dd97becfa6c2dec72b05b212f4cf20d3
BLAKE2b-256 b406eaa8c95ee069546b12ed7918a4ae866b7684026b683c83d9d394bb4077db

See more details on using hashes here.

Provenance

File details

Details for the file bioversions-0.4.24-py3-none-any.whl.

File metadata

  • Download URL: bioversions-0.4.24-py3-none-any.whl
  • Upload date:
  • Size: 49.3 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.8.0 pkginfo/1.8.2 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/0.9.1 urllib3/1.26.9 tqdm/4.63.0 importlib-metadata/4.11.3 keyring/23.5.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.10.2

File hashes

Hashes for bioversions-0.4.24-py3-none-any.whl
Algorithm Hash digest
SHA256 142a202bcaf6ceebd6f21b0a6427575a5de1319a400a1538a0f2f6cd2b6b3313
MD5 12799a8c4620a19a2cd01b651d16797d
BLAKE2b-256 631319dcba18002687acca41d1ad6fb5cd2980bfe9dac0b33aa56a893658264a

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page