chore(main): release biocypher 0.13.3

[github-actions]

🤖 I have created a release beep boop

0.13.3 (2026-05-29)

⚠ BREAKING CHANGES

• write: file_format replaces rdf_format

Features

• Add AnnData KG in memory representation (#436) (6836001)
• add function for caching API requests and refine the args description (4af6257)
• add methods to generate the import script suitable for windows (c86ea56)
• core: allow head_ontology: null for headless builds (#523) (1bcda5d)
• dedicated graph class and simplified agent-usable API (#459) (56280ed)
• Extend NetworkX support (#403) (6cd7107)
• git_testing_pipeline: Include neo4j v5 and v4 (f4de5f9)
• mapping: accept 'namespace' as alias for 'preferred_id'; deprecate 'preferred_id' in schema config (#519) (87806c1)
• neo4j_v5_patch: Detect n4j ver.-adapt syntax (ef36f73)
• neo4j: allow several labels sorting methods (#410) (f0e5d56)
• neo4j: supports Neo4j 5+ (9534a5b)
• Networkx and csv output adapter (writing to disk) (cfc6523)
• select script name depending on host OS (4c47b91)
• test: Database name location in import call (38d6f85)
• test: Import call functionality test (2bb7258)
• tests: Test import call construction (03d4b25)
• write: OWL (#412) (2054ca5)

Bug Fixes

• _BatchWriter: write all labels for edges (#480) (455f62d)
• add newline to the powershell template based on pre-commit feedback (a8576e6)
• batch_writer: prevent schema mutation in strict-mode edge writes; fix f-string in translate error (#517) (9cd7c64)
• batch_writer: stringify list elements before joining in _write_array_string (#524) (9f2b153)
• batch_writer: write boolean properties as lowercase true/false for Neo4j (#510) (95e3021)
• CICD: Comment out MacOS Neo4j docker test (3332e68)
• config: properly merge all three config levels in read_config() (#515) (da251fd)
• core: _add_edges called non-existent method and wrong driver method (#538) (c58c75b)
• core/write_import_call: display an error message when no element is added (#464) (49c1ee1)
• core: allow pandas and tabular as dbms aliases in offline mode (#513) (7e3ee26)
• create: replace elif with if for reserved keyword checks in BioCypherEdge (#526) (06f75c1)
• create: skip .replace() for non-string items in list properties (#518) (49b5756)
• divide path in base and template paths (495e5d1)
• fix default import call bin prefix, now the writer script doesn't have a default path (6397f40)
• fix path to the powershell template in test_neo4j.py (9d00369)
• get: preserve query params in cache filenames; hash full URL when too long (#507) (538b8b3)
• get: treat lifetime=0 as permanent cache (never re-download) (#525) (fc6b092)
• handle empty iterables in write_nodes/write_edges without crashing (#504) (3b30e7b)
• import call: Add if-else statement (42e0e32)
• import call: Fix if-else statement (559aa0b)
• import call: Fix if-else statement (bafeae9)
• import_call: Database name after import prefix (4c12b9e)
• mapping: deprecate 'label_in_input' in favour of 'input_label' (#521) (26a1c1f)
• neo4j CSV output not escaping quote character and cause import error (#405) (9b02016)
• neo4j_v5_patch: Check neo4j v. - adapt syntax (ea026b9)
• neo4j: v4 only supports --version while v5 supports both (e6d6044)
• neo4j: version + shell handling in import (#490) (6f353a5)
• parse_label: guard against IndexError when label has no compliant characters (#529) (a8a4f8e)
• perform type checking to prevent import failure (#458) (b8a0fea)
• test-neo4j: use the right variable in asserts (c85e52f)
• translate: require 'version' and accept 'license' for edges in strict mode (#527) (e902ea3)
• writer: pass writer labels_order from config (#479) (5dffe6a)

Documentation

• add tutorial 'Hands-On Protein Graphs with BioCypher (offline mode) and Neo4j' (5387c71)
• address first round of reviewer feedback (9fd3f6d)
• clarify Neo4j import file prefix (#535) (b2ec20f)
• clarify Ruff development workflow (#536) (1c91dfc)
• config: add merge_nodes example to tail_ontologies in biocypher_config.yaml (#532) (f761fdb)
• create: fix BioCypherEdge docstring inaccuracies (#508) (e23c68c), closes #391
• document write_schema_info() workflow for BioChatter integration (#499) (9cb0042)
• fix wrong script filename (3b7c1ce)
• more llm instructions (027f890)

Miscellaneous

• override release version (154ec52)
• trigger patch release (#496) (741dd32)

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