Merge pull request #30 from linkml/few-shot-inference

Adding variant of RAG inference engine for doing few-shot inference using schema as example

Author: cmungall

.github/workflows/qc.yml

@@ -40,4 +40,4 @@ jobs:
           mongodb-version: ${{ matrix.mongodb-version }}
 
       - name: Test with pytest and generate coverage file
-        run: poetry run pytest -m "not integration and not neo4j" --ignore=src/linkml_store/inference/implementations/rag_inference_engine.py
+        run: poetry run pytest -m "not integration and not neo4j" --ignore=src/linkml_store/inference/implementations/rag_inference_engine.py tests

Makefile

@@ -10,13 +10,13 @@ install:
 	poetry install --no-interaction --all-extras
 
 pytest:
-	$(RUN) pytest -m "not integration"
+	$(RUN) pytest -m "not integration"  tests
 
 pytest-neo4j:
 	$(RUN) pytest -k only_neo4j
 
 pytest-core:
-	$(RUN) pytest
+	$(RUN) pytest tests
 
 pytest-minimal:
 	$(RUN) pytest tests/test_api/test_filesystem_adapter.py
@@ -36,7 +36,7 @@ install-all:
 
 DOCTEST_DIR = docs src/linkml_store/api src/linkml_store/index src/linkml_store/utils
 doctest:
-	find $(DOCTEST_DIR) -type f \( -name "*.rst" -o -name "*.md" -o -name "*.py" \) -print0 | xargs -0 $(RUN) python -m doctest --option ELLIPSIS --option NORMALIZE_WHITESPACE
+	find $(DOCTEST_DIR) -type f \( -name "*.rst" -o -name "*.md" -o -name "*.py" \) ! -path "*/chromadb/*" -print0 | xargs -0 $(RUN) python -m doctest --option ELLIPSIS --option NORMALIZE_WHITESPACE
 
 NB_DIRS = tutorials how-to
 NB_DIRS_EXPANDED = $(patsubst %, docs/%/*.ipynb, $(NB_DIRS))