Merge pull request #52 from puja-trivedi/change_gars_to_ga_20240529

Change GARS to Genome Annotation

.github/workflows/generate_docs.yaml

@@ -34,14 +34,14 @@ jobs:
           cp -r src/docs/* docs/
           touch docs/.nojekyll
           cp erdiagram-autogen/ansrs.md docs/ansrs.md
-          cp erdiagram-autogen/gars.md docs/gars.md
+          cp erdiagram-autogen/genome_annotation.md docs/genome_annotation.md
           cp erdiagram-autogen/library_generation.md docs/library_generation.md
           gen-doc -d docs linkml-schema/library_generation.yaml
           mv docs/index.md docs/index_library_generation.md
           gen-doc -d docs linkml-schema/ansrs.yaml
           mv docs/index.md docs/index_ansrs.md
-          gen-doc -d docs linkml-schema/gars.yaml
-          mv docs/index.md docs/index_gars.md
+          gen-doc -d docs linkml-schema/genome_annotation.yaml
+          mv docs/index.md docs/index_genome_annotation.md
           mv docs/index_main.md docs/index.md
           
 

.github/workflows/generate_other_formats.yaml

@@ -40,7 +40,7 @@ jobs:
               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;
-              if [ ${name} = "library_generation" ] || [ ${name} = "gars" ]; then
+              if [ ${name} = "library_generation" ] || [ ${name} = "genome_annotation" ]; then
                 echo "Creating and Fixing diagrams for $name";
                 python ../utils/fix_and_create_erdiagram.py
               else

.github/workflows/push_gars_to_bkbit.yaml

@@ -1,15 +1,15 @@
-name: push pydantic gars to bkbit
+name: push pydantic genome_annotation to bkbit
 
 on:
   push:
-    paths: 'models_py-autogen/gars.py'
+    paths: 'models_py-autogen/genome_annotation.py'
   workflow_run:
     workflows: [generating other formats]
     types:
       - completed
 
 jobs:
-  update_gars:
+  update_genome_annotation:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout this repository
@@ -21,9 +21,9 @@ jobs:
         env: 
           API_TOKEN_GITHUB: ${{ secrets.API_TOKEN_GITHUB }}
         with:
-          source_file: 'models_py-autogen/gars.py'
+          source_file: 'models_py-autogen/genome_annotation.py'
           destination_repo: 'brain-bican/bkbit'
           destination_folder: 'bkbit/models/'
           user_email: '[email protected]' # the GitHub user email associated with the API token secret.
           user_name: 'puja-trivedi' # the GitHub username associated with the API token secret.
-          commit_message: "pydantic version of gars model (gars.py) was updated. Pushed from brain-bican/model repository"
+          commit_message: "pydantic version of genome_annotation model (genome_annotation.py) was updated. Pushed from brain-bican/model repository"

.github/workflows/test_other_formats.yaml

@@ -40,7 +40,7 @@ jobs:
               gen-jsonld-context ${file};
               # generating pydantic schema
               gen-pydantic --pydantic-version 2 ${file};
-              if [ ${name} != "library_generation" ] && [ ${name} != "gars" ]; then
+              if [ ${name} != "library_generation" ] && [ ${name} != "genome_annotation" ]; then
                 gen-erdiagram ${file};
               fi
             fi