Merge pull request #68 from djarecka/new_library_gen

updates to the google sheet and the converter

.github/workflows/generate_other_formats.yaml

@@ -47,7 +47,7 @@ jobs:
               # generating jsonld context and removing generation_date field to avoid constant updates
               gen-jsonld-context ${file} > ../jsonld-context-autogen/${name}.context.jsonld;
               sed -i "/generation_date/d" ../jsonld-context-autogen/${name}.context.jsonld;
-              gen-pydantic --pydantic-version 2 ${file} > ../models_py-autogen/${name}.py;
+              gen-pydantic ${file} > ../models_py-autogen/${name}.py;
               if [ ${name} = "library_generation" ] || [ ${name} = "genome_annotation" ]; then
                 echo "Creating and Fixing diagrams for $name";
                 python ../utils/fix_and_create_erdiagram.py

.github/workflows/generate_yaml_model.yaml

@@ -26,6 +26,7 @@ jobs:
         run: |
           python -m pip install .[test]
           pip install git+https://github.com/brain-bican/bkbit.git
+          pip install git+https://github.com/linkml/schemasheets.git@649af7e1
 
       - name: Other installations
         run: |

.github/workflows/test_other_formats.yaml

@@ -39,7 +39,7 @@ jobs:
               # generating jsonld context
               gen-jsonld-context ${file};
               # generating pydantic schema
-              gen-pydantic --pydantic-version 2 ${file};
+              gen-pydantic ${file};
               if [ ${name} != "library_generation" ] && [ ${name} != "genome_annotation" ]; then
                 gen-erdiagram ${file};
               fi

linkml-schema/source_library_generation/README.md

@@ -2,4 +2,8 @@
 
 - Metadata from [Google Sheet](https://docs.google.com/spreadsheets/d/11OcQz1Vk3ofny3Ql7wN-XlHkZwub-hojt-fO094SxiI/edit?usp=sharing)
 - All the sheets will be saved as tsv files in `gsheet_output`
-- Current Google Sheet version: `bk_workshop_mit24`
+- Current Google Sheet version: `aug20_2024`
+- The generated LinkML schema will be saved in `bkbit/models/library_generation_model.yaml`
+- Additional information:
+  - currently using `no-inlined` due to some issues with pydantic generation
+  - currently using an older version of schemasheets due to issues with newer versions