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-0.5.473.tar.gz (221.6 kB view details)

Uploaded Source

Built Distribution

bioversions-0.5.473-py3-none-any.whl (55.6 kB view details)

Uploaded Python 3

File details

Details for the file bioversions-0.5.473.tar.gz.

File metadata

  • Download URL: bioversions-0.5.473.tar.gz
  • Upload date:
  • Size: 221.6 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.1.1 CPython/3.10.14

File hashes

Hashes for bioversions-0.5.473.tar.gz
Algorithm Hash digest
SHA256 a9710fe1b57535050b22820adf393ed0bb3787021153812f6c4965f13f441565
MD5 37b7a06eaeb324cfe26a7c4f1a3b5eed
BLAKE2b-256 9f6d5926818123ce84ea65e8cc93793c250c525e5bf91e2922398da26ad127ed

See more details on using hashes here.

Provenance

File details

Details for the file bioversions-0.5.473-py3-none-any.whl.

File metadata

File hashes

Hashes for bioversions-0.5.473-py3-none-any.whl
Algorithm Hash digest
SHA256 6b9e27e793a8779dd34e2939268069d71cc834bc25b985dd50edd36f1fbc6468
MD5 acfcce269fe7e21961b7983d38b763be
BLAKE2b-256 5581aa5002e3f259dc53a8b0129a6114e39e4cb19ec2ceb08ee8df47c548beb6

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