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-0.5.32.tar.gz (188.7 kB view details)

Uploaded Source

Built Distribution

bioversions-0.5.32-py3-none-any.whl (50.8 kB view details)

Uploaded Python 3

File details

Details for the file bioversions-0.5.32.tar.gz.

File metadata

  • Download URL: bioversions-0.5.32.tar.gz
  • Upload date:
  • Size: 188.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.10.5

File hashes

Hashes for bioversions-0.5.32.tar.gz
Algorithm Hash digest
SHA256 fab42fd3128106c671f80457b3013e7ace39d6bb1238539bf91146c6b0c66a7c
MD5 d77b219a839ac601bbf014c25c14eca4
BLAKE2b-256 fa16ff38c46996239c1be0f4b3cf7a48052051bf3d4c2e4d8cd3e114f6e7d2ea

See more details on using hashes here.

Provenance

File details

Details for the file bioversions-0.5.32-py3-none-any.whl.

File metadata

  • Download URL: bioversions-0.5.32-py3-none-any.whl
  • Upload date:
  • Size: 50.8 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.10.5

File hashes

Hashes for bioversions-0.5.32-py3-none-any.whl
Algorithm Hash digest
SHA256 57c7ae58ea899142e44fde64e17d805dc0f86fe017342fbcd54be5b9e089d14d
MD5 de424fbd860433c590a14dbe68833d79
BLAKE2b-256 bb456c05faa39ae1160a42a3ecec7b34a2a5e0b2ba6950fa8411a6225c102699

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