Changelog

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

[Unreleased]

Added

refget.seqcolapi ships in the wheel. The service code moved from the top-level seqcolapi/ directory into refget/seqcolapi/, so a pip install 'refget[seqcolapi]' can serve the API with no repository checkout. Run it as uvicorn refget.seqcolapi.main:store_app (store-backed) or uvicorn refget.seqcolapi.main:app (PostgreSQL-backed).
refget.seqcolapi.create_seqcol_app: a store-backed app factory that returns a self-contained, mountable FastAPI app, so a host application can mount the seqcol API under a prefix and keep its own /service-info.
create_refget_router(mount_prefix=...): lets the compliance endpoints self-target the seqcol service rather than the server root when the router is included under a prefix.
db extra: pip install 'refget[db]' installs just the SQLModel layer (refget.models, refget.agents, refget admin) with no web server.
Importing a module without its extra now raises an error naming the extra to install, rather than a bare ModuleNotFoundError.

Changed

Distribution: sqlmodel is no longer a base dependency. It moved out of the base install into the new db extra, and out of the seqcolapi extra, which now installs fastapi and uvicorn only. If you import refget.models, refget.agents, or run refget admin, install refget[db]. The PostgreSQL-backed service now needs refget[seqcolapi-db] (equivalent to refget[seqcolapi,db]); the store-backed service needs only refget[seqcolapi] and pulls no ORM.
ubiquerg removed from the seqcolapi extra. Nothing under refget/ imports it.
refget store serve now builds its app with refget.seqcolapi.create_seqcol_app instead of hand-wiring FastAPI, so it serves the same routes the deployments do — notably /service-info, which it previously omitted — plus a permissive CORS middleware.
refget.seqcolapi.main.create_store_app was renamed to create_seqcolapi_store_app, so that it is not confused with the generic refget.seqcolapi.create_seqcol_app: it carries the seqcolapi.databio.org service identity (org.databio.seqcolapi.store) and the SCOM service-info block. The uvicorn refget.seqcolapi.main:store_app entry point is unchanged.
HTTP response models moved from refget.models (SQLModel) to refget.response_models (plain pydantic), so serving the API needs no ORM.

Removed

refget.router.compliance_router — the module-level router singleton is gone. It is replaced by create_refget_router(compliance=True) (the default), which builds the compliance routes per router so they can self-target a mounted prefix. No deprecation alias is provided on purpose: a module-level singleton can only be built with an empty mount_prefix, and would therefore silently reintroduce the root-targeting bug this replacement fixes. Nothing in-tree used the name.
python -m seqcolapi / python -m refget.seqcolapi — both __main__.py modules imported a main() that has never existed, so both raised ImportError on every invocation. Use the refget CLI, or uvicorn with one of the app paths above.

[0.11.0] - 2026-03-18

This is a major release with significant restructuring, new features, and improved tooling.

Added

CLI overhaul: New refget CLI built with Typer, including subcommands for store, seqcol, fasta, config, and admin
Local store: refget store pull command to pull sequence collections from remote servers to a local store
FASTA digesting: refget fasta digest CLI command for computing sequence collection digests from FASTA files
Sequence collection similarities: calc_similarities and calc_similarities_from_json functions with Jaccard similarity metrics and API endpoint
FASTA DRS objects: FastaDrsObject model for serving FASTA files via DRS endpoints
Comparison interpreter: Local sequence collection comparison interpretation module (SCIM)
Species filtering: Filter similarities endpoint by species
Human-readable names: human_readable_name field on SequenceCollection model
Pydantic API models: Structured response models for API endpoints (fixes #33)
Swagger documentation: API query parameter documentation
Frontend features: Strip plots, one-to-many comparison view, FASTA digest tool, species selector, SCIM integration, dynamic version display
Compliance testing: Comprehensive API compliance test suite
Integration test framework: New integration test infrastructure with ephemeral databases
CLI test suite: Extensive CLI tests covering store, seqcol, fasta, config, admin, and help commands
Service info: /service-info endpoints for fasta_drs and refget_store features
Attribute listing: /list/attributes endpoint per GA4GH paging guide
Bulk query: Preload and bulk query support for sequence collections
R package: First pass at refget-r R bindings (experimental)
New gtars features exposed in the refget Python API: compute_fai, digest_sequence, and SequenceCollection available via import refget
FHR metadata support: refget store metadata and refget store metadata-set commands for managing collection metadata
Seqcol CLI commands (show, compare, validate) look up collections in the local store before querying remote servers
Web UI compliance runner with real-time streaming results, a stop button, and per-test descriptions
gtars version displayed in service-info and frontend footer badges
Download collections in seqcol JSON format from the web UI

Changed

Switched to gtars: Replaced pyfaidx and henge with gtars for FASTA parsing and digest computation
Major code restructure: Consolidated schemas, reorganized modules, reduced code duplication
Improved error messages: Better dependency error messages (fixes #49), clearer import errors
Performance optimizations: Faster level 2 retrieval using get_many, optimized similarity calculations
Updated GA4GH compliance: Aligned with latest refget sequence collections specification
Schema consolidation: Single unified schema replacing multiple schema files
Collated attribute validation: Validation for collated attributes in sequence collections
Frontend overhaul: Updated comparison view, heatmap aliases, loading states, error handling
seqcolapi no longer has independent versioning; it now versions with refget

Removed

Henge dependency: Removed henge and biopython requirements
Legacy code: Removed old flags code, duplicate functions, unused yacman imports

Fixed

from_PySequenceCollection construction and associated tests
Circular dependency import issues in utilities
Level 1 model representation
Comparison links
Cancel handling in frontend
Various linting and type hint improvements

Security

Bumped frontend dependencies: vite, minimatch, rollup, esbuild, js-yaml, vega

[0.10.1] - 2026-01-27

Fix CLI store list JSON serialization error (was returning non-serializable metadata objects)
Fix CLI store get, store remove, and store pull commands that failed to find collections
Update CLI to use iter_collections() API instead of removed collections() method

[0.10.0] - 2026-01-26

Major restructure of the package with new comprehensive CLI (refget command)
New CLI subcommands: admin, config, fasta, seqcol, and store
Implement FASTA DRS objects for serving FASTA files via GA4GH DRS endpoints
Add RefgetStore integration for local sequence storage via gtars
Refactor to isolate gtars dependency, improving import performance
Add service-info capabilities for fasta_drs and refget_store features
New integration test framework with ephemeral Docker PostgreSQL
Comprehensive CLI test suite
API compliance tests against GA4GH seqcol specification
Fix endpoint path: /list/collection (was /list/collections in client)
New browser-based /digest feature for computing seqcol digests from FASTA files entirely client-side using @databio/gtars WASM module

[0.9.0] - 2025-08-13

performance fix for calculating jaccard similarties
add human_readable_name list as an attribute to SequenceCollection for displaying similarity results
adding SequenceCollections via PEP will now add associated sample_name as a human_readable_name
add wrapper for gtars RefgetStore so it can be called directly from refget

[0.8.3] - 2025-07-31

adds API endpoints for jaccard similarity calculations
some refactoring for newest gtars, v0.3.0
add class method from_PySequenceCollection for creating SequenceCollection from a gtars-created SequenceCollection
adds Similarity UI to frontend

[0.8.2] - 2025-03-26

updated add method to use boolean for updating SequenceCollection if already exists

[0.8.1] - 2025-03-21

addition of SCIM

[0.8.0] - 2025-03-05

Complete rewrite of the clients and agents.
New SequenceAgent class allows using the RefgetDBAgent class to store sequences. This is meant for testing purposes.
Completely refactored Clients work adds mature SequenceClient and SequenceCollectionClient classes.
Fix issues with rust digest calculations to improve flexibilty, using latest update to gtars interface.
Updates to latest ga4gh paging guidance
Add a beta CLI with digest-fasta and add-fasta functionality.
Remove some old stuff based on henge backend

[0.7.0] - 2025-01-11

Major revamp to RefGetClient object, which now works with either sequences or seqcol servers, and can handle any of the seqcol API endpoints.
Better integration of rust digest calculations built on gtars
switch back-end to use JSON instead of str
implement name_length_pairs and sorted_sequences attrs
improve some SeqCol object representations

[0.6.0] - 2024-08-08

Change paging style of list endpoints to match latest GA4GH pagination guide
Implement new /list/attribute endpoint on back-end, and add to demo
Update endpoint paths slightly after discussion for the /list and /attribute endpoints
Remove some of the duplicate endpoints to solidify to one API

[0.5.0] - 2024-07-06

Work on deployment, container building, configuration
Add some work toward pangenomes
Various misc improvements

[0.4.0] - 2024-06-26

Implement new sqlmodel and agent for new database backend
Add new React interface

[0.3.0] - 2024-02-23

Add seqcolapi router

[0.2.0] - 2024-02-03

Integrate seqcol into refget package.

[0.1.0] - 2021-06-17

First public version, backed by henge version 0.1.1.

[0.0.1] - 2020-06-25

Beta version for testing