Skills › Scientific Agent Skills › lamindb › sources.md

sources.md

45 lines · skills/lamindb/references/sources.md at 5f2bc03

1# Review sources and execution boundary

3Reviewed 2026-09-30. Current public documentation was checked alongside released

4source and installed runtime contracts; a successful page load alone was not

5used to validate examples.

Review sources and execution boundary

Reviewed 2026-09-30. Current public documentation was checked alongside released source and installed runtime contracts; a successful page load alone was not used to validate examples.

Raw lines 1 to 6

7## Versions inspected

9- `lamindb==2.10.0`, `lamindb-core==2.10.0`

10- `lamindb-setup==1.25.7`, `lamin-cli==1.19.3`

11- `bionty==2.5.0`, transitively installed `pertdb==2.2.0`

12- Python 3.12, pandas 3.0.6, AnnData 0.13.2, IPython 9.17.1

14Official metadata: [LaminDB](https://pypi.org/project/lamindb/2.10.0/),

15[Bionty](https://pypi.org/project/bionty/2.5.0/),

16[release tag](https://github.com/laminlabs/lamindb/tree/2.10.0).

17The release tag resolves to `ea00428098485bae94ea83a67b5b806918a78d9c`.

Versions inspected

lamindb==2.10.0, lamindb-core==2.10.0
lamindb-setup==1.25.7, lamin-cli==1.19.3
bionty==2.5.0, transitively installed pertdb==2.2.0
Python 3.12, pandas 3.0.6, AnnData 0.13.2, IPython 9.17.1

Official metadata: LaminDB, Bionty, release tag. The release tag resolves to ea00428098485bae94ea83a67b5b806918a78d9c.

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19## Sources by contract

21| Area | Primary source |

22| --- | --- |

23| Install, storage, settings, migrations | [Setup](https://docs.lamin.ai/setup), [CLI](https://docs.lamin.ai/cli), [dependencies](https://github.com/laminlabs/lamindb/blob/2.10.0/pyproject.toml) |

24| Artifact revisions and accessors | [Artifact source](https://github.com/laminlabs/lamindb/blob/2.10.0/lamindb/models/artifact.py), [arrays](https://docs.lamin.ai/arrays) |

25| Queries, result limits and get behavior | [QuerySet source](https://github.com/laminlabs/lamindb/blob/2.10.0/lamindb/models/query_set.py), [query guide](https://docs.lamin.ai/query-search) |

26| Schemas and curator methods | [Schema source](https://github.com/laminlabs/lamindb/blob/2.10.0/lamindb/models/schema.py), [curator source](https://github.com/laminlabs/lamindb/blob/2.10.0/lamindb/curators/core.py), [curation guide](https://docs.lamin.ai/curate) |

27| Lineage | [Tracking](https://docs.lamin.ai/track), [Run source](https://github.com/laminlabs/lamindb/blob/2.10.0/lamindb/models/run.py) |

28| Ontology operations | [Bionty](https://github.com/laminlabs/bionty), [ontology guide](https://docs.lamin.ai/manage-ontologies), [curation methods](https://github.com/laminlabs/lamindb/blob/2.10.0/lamindb/models/can_curate.py) |

29| Module provenance | [pertdb docs](https://docs.lamin.ai/pertdb), [Lamin Labs source](https://github.com/laminlabs/pertdb) |

30| Pipelines/integrations | [nf-lamin](https://docs.lamin.ai/nf-lamin), [integration API](https://docs.lamin.ai/lamindb.integrations), links in integrations.md |

Sources by contract

Area	Primary source
Install, storage, settings, migrations	Setup, CLI, dependencies
Artifact revisions and accessors	Artifact source, arrays
Queries, result limits and get behavior	QuerySet source, query guide
Schemas and curator methods	Schema source, curator source, curation guide
Lineage	Tracking, Run source
Ontology operations	Bionty, ontology guide, curation methods
Module provenance	pertdb docs, Lamin Labs source
Pipelines/integrations	nf-lamin, integration API, links in integrations.md

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32## Executed and not executed

34The repository's `tests/lamindb/` suite creates a disposable SQLite instance in

35a subprocess with fresh working directory, settings, cache, and storage. It

36exercises schema acceptance/rejection, data round trips, annotations, revisions,

37collections, local Bionty synonyms/hierarchies, and lineage. No existing user

38instance or remote service is mutated.

40Cloud providers, private Hub authentication, public ontology downloads, optional

41SOMA/SpatialData/MuData backends, Nextflow, external ML services, and live Vitessce

42serving were not tested end to end. Their retained examples are explicitly

43illustrative/source-verified and require environment-specific validation.

44No REST endpoints are called by this skill; the API audit covers the Python SDK

45and CLI contracts it actually teaches.

Executed and not executed

The repository's tests/lamindb/ suite creates a disposable SQLite instance in a subprocess with fresh working directory, settings, cache, and storage. It exercises schema acceptance/rejection, data round trips, annotations, revisions, collections, local Bionty synonyms/hierarchies, and lineage. No existing user instance or remote service is mutated.

Cloud providers, private Hub authentication, public ontology downloads, optional SOMA/SpatialData/MuData backends, Nextflow, external ML services, and live Vitessce serving were not tested end to end. Their retained examples are explicitly illustrative/source-verified and require environment-specific validation. No REST endpoints are called by this skill; the API audit covers the Python SDK and CLI contracts it actually teaches.

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