Bioversions

0.8.324 · active · verified Thu Apr 16

Bioversions is a Python library (current version 0.8.324) that provides programmatic access to the current version numbers for a wide array of biological databases. It aims to simplify the integration of up-to-date database versions into bioinformatics workflows and tools. The library actively maintains and daily updates a static listing of these versions, reflecting a frequent release cadence for its internal data, while the library itself sees regular patch updates.

Common errors

```
ModuleNotFoundError: No module named 'bioversions'
```
cause The `bioversions` package has not been installed in the current Python environment.

fix Run `pip install bioversions` to install the library.
```
AssertionError: This was true on Dec 5th, 2020!
```
cause This specific assertion, often found in older documentation or copied from examples, fails because the actual version of the biological database (e.g., BioGRID) has since been updated, as `bioversions` correctly reflects the current version.

fix Update your assertions to reflect the current expected version, or use `bioversions.get_version()` dynamically in your tests without hardcoding a specific version string, if appropriate for your test's intent.
```
KeyError: 'some_nonexistent_database'
```
cause Attempted to retrieve a version for a database name that `bioversions` does not recognize or that is misspelled.

fix Verify the correct spelling and availability of the database name by checking the `bioversions` documentation or by iterating through `bioversions.iter_versions()` to see supported names.

Warnings

gotcha The versions returned by `bioversions` are dynamic and reflect the current state of external biological databases. Hardcoding specific version strings in tests or logic will eventually lead to `AssertionError` or incorrect behavior as databases update.
Fix: Design code to be robust to version changes. For testing, consider using version comparison (e.g., `version >= 'expected_min_version'`) or mock results. Avoid direct equality checks with specific version strings unless explicitly testing for a historical state.
gotcha Results are cached locally (default: `~/.data/bioversions`) and refreshed only once per day. If you need immediate updates or are debugging, ensure to consider the cache's daily refresh cycle.
Fix: To bypass the cache for a specific call (if a method supports it, check documentation) or to force a refresh (e.g., by clearing the cache via `bioversions.clear_cache()`), or by manually deleting the cache directory. Note: `clear_cache()` refreshes for the next call.
gotcha The default cache location (`~/.data/bioversions`) can be inconvenient in some environments. While the library is generally stable, its dependence on external databases means their internal APIs or naming conventions might change, potentially affecting the accuracy of retrieved versions.
Fix: Override the cache location by setting the `BIOVERSIONS_HOME` environment variable to a desired path before running your application. For robust production systems, monitor the upstream databases' release notes for major structural changes.

Install

pip install bioversions Install from PyPI

Imports

bioversions
```
import bioversions
```

Quickstart

This quickstart demonstrates how to import the `bioversions` library and retrieve the current version of a biological database, such as BioGRID, using `get_version()` for a simple string or `resolve()` for more detailed metadata.

import bioversions

# Get the current version for a specific database (e.g., BioGRID)
biogrid_version = bioversions.get_version('biogrid')
print(f"Current BioGRID version: {biogrid_version}")

# Get more detailed information using resolve()
bioversion_obj = bioversions.resolve('biogrid')
print(f"BioGRID version object: {bioversion_obj.version} (updated {bioversion_obj.date})")

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