Changelog

This project adheres to Semantic Versioning and Keep a Changelog format.

[0.13.0] -- 2026-08-20

Added:

• /v1/objects/exports and /v1/objects/files endpoints listing published bulk-metadata exports and standalone analysis files [API]
• BEDHOST_INIT_ML environment variable to skip loading ML models [API]

Changed:

• Statistics cache moved to app state (thread safe), with a fallback for empty datasets [API]
• Blocking endpoints run in a threadpool instead of stalling the event loop [API]
• Missing markdown files return 404 instead of 500 [API]
• Logging configured once, in main.py

[0.12.7] -- 2026-04-22

Changed:

• UMAP page improvements and fixed link previews [UI]
• Migrated to Starlette 1.0 and yacman 1.0

[0.12.6] -- 2026-04-16

Fixed:

• Build fix

[0.12.5] -- 2026-04-15

Changed:

• UI updates and search improvements

[0.12.4] -- 2026-02-06

Fixed:

• Search by external id

Changed:

• Updated UMAP UI [UI]

[0.12.3] -- 2026-01-21

[0.12.2] -- 2026-01-21

Added:

• BED classifier and reference genome validator in the BED analyzer [UI]

Changed:

• Updated home page [UI]

[0.12.1] -- 2025-12-22

Added:

• Hybrid text search combining dense and sparse vector search [API]

Changed:

• Backend improvements that reduce container size

[0.12.0] -- 2025-12-01

Added:

• umap calculation [API]
• BED-analyzer (qc), which is backed by gtars-wasm package [UI]
• New improved home page [UI]
• Added visualization of the UMAP, and interactive [UI]

[0.11.0] -- 2025-09-11

Added:

• Added umap visualizations of bed embeddings
• Added bedbase-verse metrics
• Added filtering by assay and genome in the semantic search
• Added bed file qc check before running bed to bed search

Changed:

• Changed bivec search to text semantic search
• Multiple UI bug fix

[0.10.0] -- 2025-04-21

Added:

• Added usage statistics
• Added Bed file statistic page

Changed:

• Updated bed compliance and data formats

[0.9.0] -- 2025-01-03

Added:

• Added a new class CreateBEDsetRequest in bedhost/data_models.py to handle BEDset creation requests.
• Introduced a new API endpoint /v1/bed/{bed_id}/neighbours to get nearest neighbors for a BED record in bedhost/routers/bed_api.py.
• Implemented a new API endpoint /v1/bedset/create/ to create a new BEDset by providing a registry path to the PEPhub project in bedhost/routers/bedset_api.py.

Changed:

• Refactored text_to_bed_search function to include additional logic for handling specific queries in bedhost/routers/bed_api.py.

UI improvements:

• Added Most similar files table to bed page
• Improved Mobile friendly ui to both bed and bedset page
• Improved metadata tables on bed page
• Added Download pdf button for plots
• Improved search tables
• Added creation of bedset UI

[0.8.0] -- 2024-11-07

Added:

• Added endpoint showing available genomes
• Added endpoint listing bed_ids with missing plots

[0.7.0] -- 2024-10-23

Added:

• New text2bed search (bivec search)
• Added track_hub endpoints and pointing link
• Added pep generating endpoint for bedsets

[0.6.0] -- 2024-10-15

• Multiple ui improvements and fixes
• Updated bed metadata endpoint: added annotation to metadata return model, with standard schema
• Updated metadata in search endpoints.
• Added embed endpoint. #136

[0.5.0] -- 2024-06-11

• Improved Bed search (speed and quality)
• Added licenses
• UI tweaks
• Added universes and bed tokens to the database
• Added embedding endpoint

[0.4.0] -- 2024-04-08

• Support of new bbconf.
• Updated endpoints.

[0.3.0] -- 2023-03-01

• switch to pydantic2
• updated requirements
• updated docs

[0.2.0] -- 2023-10-17

• remove all graphql
• remove local static hosting of UI
• update to new pipestat-based bbconf (pending)
• major refactor of API that introduces backwards-incompatible changes

[0.1.3] -- 2023-09-01

• allow all origins

[0.1.2] -- 2023-02-06

change

• change /bedset/my_bedset/file_pathsendpoint from GET to POST

[0.1.1] -- 2021-10-30

change

• /bed/genomes and bedset/genomes: improve speed

[0.1.0] -- 2021-10-25

add

• GraphQL endpoints

change

• endpoints update due to bbconf and pipestat changes

[0.0.6] -- 2021-05-17

add

• Add endpoints that serve:
  • a list of genome assemblies in bedsets and bedfiles table
  • bed files by search term(s)
  • remote file path (http / s3)

[0.0.5] -- 2021-04-15

add

• Add examples of API endpoints

fix

• resolve /about page not found when typing/editing url in the address bar.

[0.0.4] -- 2021-04-01

add

• add endpoint for region-based query

fix

• construction of local file/img path

[0.0.3] -- 2021-02-22

• Initial project release