Skip to content

bug: linkml version 1.8.3 causes build-ingest-config to fail #274

Open
@Bento007

Description

@Bento007

first discovered on the branch: 23b714c

Error

$ make build-ingestion-config                                                          git:(tsmith/linkml|●1✚4-2…1 
rm -f core/v1.1.0/codegen/metadata_materialized.yaml
rm -f core/v1.1.0/codegen/metadata_models.py
rm -f ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml
rm -f ingestion_config/v1.0.0/codegen/ingestion_config_models.py
rm -f ingestion_config/v1.0.0/codegen/ingestion_config_models.schema.json
python3 schema.py materialize core/v1.1.0/metadata.yaml core/v1.1.0/common.yaml core/v1.1.0/codegen/metadata_materialized.yaml
python3 schema.py materialize ingestion_config/v1.0.0/ingestion_config_models.yaml core/v1.1.0/common.yaml ingestion_config/v1.0.0/codegen/ingestion_config_models_materialized.yaml
linkml generate pydantic --black core/v1.1.0/codegen/metadata_materialized.yaml > core/v1.1.0/codegen/metadata_models.py
ValueError: The ifabsent value `float(1)` of the `aligned_tiltseries_binning` slot could not be processed
make: *** [build-ingestion-config] Error 1

Steps to reproduce

  1. check out main
  2. run make build-ingest-config -C ./schema

Work around

Pin the linkml version to 1.8.2.

Note:

I suspect it's related to this recent change linkml/linkml#2175

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    bugSomething isn't working

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions