Sebastian Lobentanzer

Mock downloads in _get module tests

1

CI fails regularly, often on macOS runner, because of a timeout of the folder download test. We should mock all downloads to remove reliance on connectivity / external servers.

Introduces a benchmark dataset for safety-related KG query generation Fixes internal handling of labels (sentence case vs PascalCase)

Ubuntu 24: Python 3.12 leads to package incompatibility

1

Getting errors from `grpcio`, `xoscar`, and `pkgutil` (`ImpImporter` not found). Using python3.11 fixes the problem. For some reason, CI does not have this issue on the linux runners.

Switch from Sphinx to mkdocs material. The resulting page is already live at https://biocypher.org. Allow combination of individual repos under one monorepo (`documentation`), using mkdocs.nav.yaml (which is a separate navigation...

[FEAT]: Harmonise re-labelling: edges should also be subject to the synonym process

5

### Feature Type Add new functionality to BioCypher ### 🚀 The feature and motivation For nodes, we currently have the "synonym" feature to translate labels (e.g., because of readability issues)...

We don't maintain these comments, and contributors do not add themselves to the list of names. I think it makes more sense to remove these comments from all modules that...

The RDF/OWL branch of output adapters is sufficiently different from the CSV way of writing things to justify detaching the base classes of the two approaches. Since OWL is a...

Prevent misspellings in configuration or make the user aware of potential problems. For instance, #420 Aligned with GUI developments (https://github.com/biocypher/biochatter-light/issues/61)

This issue is to define a minimum viable product for automating the grounding of a knowledge graph in a condensed ontology built from a more extensive source (e.g., ubergraph). `As...