https://github.com/biopragmatics/bioversions

🪝 What's the latest version for each database?
https://github.com/biopragmatics/bioversions

biopragmatics

Last synced: about 20 hours ago
JSON representation

🪝 What's the latest version for each database?

• Host: GitHub
• URL: https://github.com/biopragmatics/bioversions
• Owner: biopragmatics
• License: mit
• Created: 2020-12-05T17:48:54.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2024-10-30T01:02:36.000Z (16 days ago)
• Last Synced: 2024-10-30T03:51:15.722Z (16 days ago)
• Topics: biopragmatics
• Language: Python
• Homepage: https://biopragmatics.github.io/bioversions
• Size: 4.46 MB
• Stars: 26
• Watchers: 3
• Forks: 7
• Open Issues: 12
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        


  





    Bioversions





    

        

    

    

        

    

    

        

    

    

        

    

    

        

    

    

        

    



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

```bash

$ pip install bioversions

```

## 💪 Usage

```python

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`](https://github.com/shaypal5/cachier). The cache is stored in `~/.data/bioversions`. The cache location

can be overridden by setting the

`BIOVERSIONS_HOME` environment variable via [`pystow`](https://github.com/cthoyt/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:

```bash

$ 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/` endpoint like in the following:

```python

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:

```bash

$ 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](https://indralab.github.io), a part of the

[Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/)

and the [Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu)

at [Harvard Medical School](https://hms.harvard.edu/).

### 💰 Funding

The development of the Bioregistry is funded by the DARPA Young Faculty Award W911NF2010255 (PI:

Benjamin M. Gyori).