bbconf

Run pytests

BEDBASE project configuration package (agent)

What is this?

bbconf is a configuration and data management library for the BEDbase platform. It serves as the central backbone for all BEDbase tools and pipelines by:

Reading and validating YAML configuration files
Setting up and managing connections to PostgreSQL, Qdrant, S3, and PEPHub
Loading ML models (Region2Vec, text embedders, sparse encoders, UMAP) used for BED file search
Providing high-level Python interfaces for querying and managing BED files and BED sets
Exposing a unified BedBaseAgent object that all downstream tools use to interact with the platform

Documentation: https://docs.bedbase.org/bedboss

Source Code: https://github.com/databio/bbconf

Installation

To install bbclient use this command:

pip install bbconf

or install the latest version from the GitHub repository:

pip install git+https://github.com/databio/bbconf.git

Quick start

from bbconf import BedBaseAgent

agent = BedBaseAgent(config="config.yaml")

# Access submodules
agent.bed  # BED file operations
agent.bedset  # BED set operations
agent.objects  # Generic object/file operations

# Get platform statistics
stats = agent.get_stats()
print(stats.bedfiles_number, stats.bedsets_number)

Database migrations

bbconf uses Alembic to version the database schema. The migration scripts live in bbconf/alembic, and alembic.ini (repo root) is used for local CLI work. The first (baseline) revision is 8b0b706d0827; it reproduces exactly the schema that Base.metadata.create_all() builds, including the pg_trgm extension and the trigram / partial / expression indexes.

To update schema for desirable database, use different database url in alembic.ini, otherwise run test database

Creating a new revision

After changing the models in bbconf/db_utils.py:

alembic revision --autogenerate -m "Describe your change"

Review the generated file. Alembic cannot autogenerate a few constructs used by bbconf — the pg_trgm extension and expression-based indexes may need a manual op.execute(...) — so always check the diff before committing.

Applying migrations

alembic upgrade head      # upgrade to the latest revision
alembic downgrade -1      # roll back one revision
alembic current           # show the DB's current revision

Running migrations automatically

To upgrade the database to head automatically when bbconf starts, set run_migrations: true under the database section of the config file:

database:
  host: localhost
  port: 5432
  user: postgres
  password: docker
  database: bedbase
  run_migrations: true

Note: enable this only after the database has been stamped/upgraded to a known revision. Turning it on against an un-stamped existing database will fail on startup, because the baseline revision creates tables that already exist.

Release files for bbconf 0.15.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for bbconf 0.15.0
File	Size	Uploaded
bbconf-0.15.0.tar.gz	423.9 kB	Aug 18, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for bbconf 0.15.0
File	Interpreter	ABI	Platform	Reset
bbconf-0.15.0-py3-none-any.whl 66.2 kB Aug 18, 2026	Python 3	none	any	Details

Total release size: 490.1 kB

Release files / bbconf-0.15.0.tar.gz

Download URL	bbconf-0.15.0.tar.gz
Size	423.9 kB
Tags	Source
SHA-256 checksum How to use checksums	`c99540782ceddb570704f631f934b5676d7495219fb4e6a344b25f57b18c7dae`
BLAKE2b-256 checksum How to use checksums	`0be70bce07372e58b1f5ae356e4658e57431b275807556473abe7201da24173e`
Upload date	Aug 18, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/databio/bbconf
Publishing commit: github.com/databio/bbconf/tree/c8ece776d959111dca5c36f1f44343c711c5723b

Workflow

Publishing configuration: github.com/databio/bbconf/blob/c8ece776d959111dca5c36f1f44343c711c5723b/.github/workflows/python-publish.yml
Publishing logs: github.com/databio/bbconf/actions/runs/32175653262/attempts/1

Artifact

Subject: bbconf-0.15.0.tar.gz
SHA-256 checksum: c99540782ceddb570704f631f934b5676d7495219fb4e6a344b25f57b18c7dae Verifying attestations

Release files / bbconf-0.15.0-py3-none-any.whl

Download URL	bbconf-0.15.0-py3-none-any.whl
Size	66.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`97a46586fcce42693e9ce0011e1fef4ee9545729c270149a6ecb4f7c49eaa4aa`
BLAKE2b-256 checksum How to use checksums	`54b6ce1c9293cc5efa8ec6fb0c443d7a1fef9d7be4c28d5b2d3bdad0b6c4aae8`
Upload date	Aug 18, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/databio/bbconf
Publishing commit: github.com/databio/bbconf/tree/c8ece776d959111dca5c36f1f44343c711c5723b

Workflow

Publishing configuration: github.com/databio/bbconf/blob/c8ece776d959111dca5c36f1f44343c711c5723b/.github/workflows/python-publish.yml
Publishing logs: github.com/databio/bbconf/actions/runs/32175653262/attempts/1

Artifact

Subject: bbconf-0.15.0-py3-none-any.whl
SHA-256 checksum: 97a46586fcce42693e9ce0011e1fef4ee9545729c270149a6ecb4f7c49eaa4aa Verifying attestations