Issues

• Collection.get() and get_one() raise AttributeError instead of ValueError, with no identifier

  linkml/linkml-store#102 · Filter by author noelmcloughlin opened on Oct 9, 2026

• Web API: the fastapi extra misses two imports, and where returns 500"

  linkml/linkml-store#100 · Filter by author noelmcloughlin opened on Oct 9, 2026

• DuckDB delete() removes every row when the object has no inline-attribute key

  linkml/linkml-store#98 · Filter by author noelmcloughlin opened on Oct 9, 2026

• DuckDB delete_where returns None, so missing_ok=False never raises

  linkml/linkml-store#95 · Filter by author noelmcloughlin opened on Oct 9, 2026

• DuckDB delete_where, replace and store() fail under SQLAlchemy 2.1

  linkml/linkml-store#93 · Filter by author noelmcloughlin opened on Oct 9, 2026
  

• LLMIndexer.texts_to_vectors() crashes with raw tiktoken KeyError for any non-OpenAI embedding model

  linkml/linkml-store#92 · Filter by author mcallaway opened on Oct 7, 2026

• Compound groupby ("col1+col2") throws KeyError, despite being documented CLI syntax

  linkml/linkml-store#91 · Filter by author mcallaway opened on Oct 7, 2026

• query_facets() crashes with KeyError on schemas that use top-level slots: instead of inlined attributes:

  linkml/linkml-store#90 · Filter by author mcallaway opened on Oct 7, 2026

• Add a TypeDB adapter

  linkml/linkml-store#89 · Filter by author turbomam opened on Oct 7, 2026
  2

• Ibis store cannot connect to Postgres: ibis.postgres.connect() is given the whole URL as the host

  linkml/linkml-store#88 · Filter by author caufieldjh opened on Oct 1, 2026

• Neo4j: create_collection(recreate_if_exists=True) deletes every node in the database, not only the collection's

  linkml/linkml-store#87 · Filter by author caufieldjh opened on Oct 1, 2026

• DuckDB backend: float stored as 4-byte FLOAT, integer as INT32, boolean as text

  linkml/linkml-store#85 · Filter by author turbomam opened on Sep 28, 2026

• sqlite: handle silently returns no collections for semsql files (DuckDB cannot parse some views)

  linkml/linkml-store#82 · Filter by author turbomam opened on Sep 10, 2026

• find_iter(limit=...) raises TypeError: limit collides with the internal page_size argument

  linkml/linkml-store#81 · Filter by author turbomam opened on Sep 10, 2026

• MongoDBCollection.insert cannot be used for large writes: no iterator input, no batching, and it re-reads its input afterwards

  linkml/linkml-store#79 · Filter by author turbomam opened on Sep 9, 2026
  1

• Downstream applications show warning about use of deprecated Pydantic feature

  linkml/linkml-store#78 · Filter by author eecavanna opened on Jun 11, 2026

• MongoDBCollection.upsert does per-item round trips; switch to bulk_write

  linkml/linkml-store#77 · Filter by author turbomam opened on May 19, 2026
  1

• find_iter default page_size=100 is too small for large MongoDB collections

  linkml/linkml-store#75 · Filter by author turbomam opened on Apr 28, 2026
  1

• Bulk-fix 56 auto-fixable ruff violations

  linkml/linkml-store#74 · Filter by author turbomam opened on Apr 28, 2026
  1

• CI: add mypy type-checking (incremental / per-module)

  linkml/linkml-store#73 · Filter by author turbomam opened on Apr 28, 2026

• Fix 4 undefined-name (F821) errors caught by ruff

  linkml/linkml-store#72 · Filter by author turbomam opened on Apr 28, 2026

• CI: add ruff lint check

  linkml/linkml-store#71 · Filter by author turbomam opened on Apr 28, 2026

• Allow custom ValidationPlugins in iter_validate_collection()

  linkml/linkml-store#68 · Filter by author turbomam opened on Apr 10, 2026
  1

• CLI requires heavy optional dependencies (matplotlib, scipy) for basic operations

  linkml/linkml-store#65 · Filter by author turbomam opened on Jan 22, 2026

• Allow Client instantiation (in particular MongoClient instantiation), with an existing pymongo.MongoClient object

  linkml/linkml-store#55 · Filter by author sierra-moxon opened on Jun 11, 2025