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Commits on Jan 23, 2026

• Merge pull request #86 from brain-bican/add_clauded

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Commits on Jan 22, 2026

• added CLAUDE.md file

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Commits on Nov 19, 2025

• Merge pull request #78 from brain-bican/nelson_cell_taxonomy_translator

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Commits on Nov 18, 2025

• Merge pull request #30 from djarecka/precommit

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• removing flake, and keeping just blake

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• adding all flag to pyproject setup

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• Merge branch 'main' into precommit

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• Merge pull request #71 from yarikoptic/enh-codespell

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Commits on Nov 16, 2025

• Merge pull request #83 from brain-bican/lib_gen_20251115

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• added option to serialize output to ttl

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Commits on Nov 15, 2025

• using linkml json_dumps to serialize objects (assigns @type).

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• id is now urn:bkbit. nimp id is assigned to xref. updated was_derived_from based off the id changes

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Commits on Nov 14, 2025

• Merge pull request #52 from brain-bican/fix_librarygen_trans_20241122

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• Merge pull request #80 from brain-bican/linkml_trimmer

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Commits on Nov 13, 2025

• Merge pull request #81 from brain-bican/generate_data_sfn_2025

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• changed key for gene_annotations dict to geneannotation.id for ENSMEL (was already done for NCBI).

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Commits on Oct 29, 2025

• added 'types' as part of the trimming. Switched from YamlGenerator to as_yaml for serialization (doesn't added extra 'types' and extra metadata that wasNOT included in input model.

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Commits on Oct 27, 2025

• added parsing for spatial_proportions and curated_markers

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• Merge branch 'main' of https://github.com/brain-bican/bkbit into nelson_cell_taxonomy_translator

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Commits on Oct 25, 2025

• Merge pull request #72 from brain-bican/v2.0.0

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• updated genome_annotation.py to match most update to date schema in brain-bican/models repo

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• updated docs for genome_annotation based off changes made to code

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• abstracted out serialization to ttl into module in utils dir

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• removed old out of date testing files

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• removed unused variables to clean up code

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• removed unused functions to clean up code

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• Merge branch 'main' of https://github.com/brain-bican/bkbit into v2.0.0

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• Merge pull request #79 from brain-bican/linkml_trimmer

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• updated generate_docs workflow: removed out of date branch from 'trigger' list

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• updated documentation for linkml-trimmer based off changes made to linkml-trimmer

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• added comments

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• changed --classes from required to optional

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Commits on Oct 24, 2025

• added cli options to modify the schema metadata i.e. id, title, name, version

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• removed requirement for input schema to be a local file in click.arguments

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• added .strip() to every element provided via cli

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