Use ruff format for code formatting

Makefile

@@ -198,8 +198,8 @@ lint-frontend:
 
 .PHONY: lint-backend
 lint-backend: 
-	$(RUN) ruff check --diff --exit-zero .
-	$(RUN) black --check --diff -l 120 src tests
+	-$(RUN) ruff check --diff .
+	-$(RUN) ruff format --diff .
 
 
 .PHONY: format
@@ -208,8 +208,8 @@ format: format-frontend format-backend
 
 .PHONY: format-backend
 format-backend: 
-	$(RUN) ruff check --fix --exit-zero .
-	$(RUN) black -l 120 src tests
+	-$(RUN) ruff check --fix .
+	-$(RUN) ruff format .
 
 
 .PHONY: format-frontend

backend/pyproject.toml

@@ -67,6 +67,10 @@ pythonpath = [".", "src"]
 
 [tool.ruff]
 line-length = 120
+exclude = ["tests/fixtures/*.py", "src/monarch_py/datamodels/model.py"]
+# per-file-ignores = {"" = ""}
+
+[tool.ruff.lint]
 ignore = [
     "F541", # f-strings with no placeholders
 ]

backend/src/monarch_py/api/config.py

@@ -16,7 +16,7 @@ class Settings(BaseModel):
 
     semsim_server_host: str = os.getenv("SEMSIM_SERVER_HOST", "127.0.0.1")
     semsim_server_port: str = os.getenv("SEMSIM_SERVER_PORT", 9999)
-    
+
     monarch_kg_version: str = os.getenv("MONARCH_KG_VERSION", "unknown")
     monarch_api_version: str = os.getenv("MONARCH_API_VERSION", "unknown")
     monarch_kg_source: str = os.getenv("MONARCH_KG_SOURCE", "unknown")

backend/src/monarch_py/api/search.py

@@ -55,7 +55,7 @@ async def autocomplete(
         default="*:*",
         title="Query string to autocomplete against",
         examples=["fanc", "ehler"],
-    )
+    ),
 ) -> SearchResults:
     """Autocomplete for entities by label
 

backend/src/monarch_py/api/semsim.py

@@ -61,8 +61,8 @@ def _compare(
     print(
         f"""
     Running semsim compare:
-        subjects: {subjects.split(',')}
-        objects: {objects.split(',')}
+        subjects: {subjects.split(",")}
+        objects: {objects.split(",")}
         metric: {metric}
     """
     )

backend/src/monarch_py/implementations/solr/solr_query_utils.py

@@ -30,7 +30,6 @@ def build_association_query(
     offset: int = 0,
     limit: int = 20,
 ) -> SolrQuery:
-
     entity_fields = ["subject", "object", "disease_context_qualifier"]
     """Populate a SolrQuery object with association filters"""
     query = SolrQuery(start=offset, rows=limit)

backend/src/monarch_py/utils/utils.py

@@ -131,4 +131,4 @@ def get_release_metadata(release: str, dev: bool = False):
 
 def print_release_info(release_info: Release):
     for key, value in release_info.model_dump().items():
-        console.print(f"{key+' ':—<12} {value}")
+        console.print(f"{key + ' ':—<12} {value}")

backend/tests/integration/test_solr_association.py

@@ -68,7 +68,6 @@ def test_entity():
     assert response
     assert response.total > 50
     for association in response.items:
-
         if (
             association.subject_closure is None or len(association.subject_closure) == 0
         ) and association.disease_context_qualifier is None:

backend/tests/unit/test_oak_semsim.py

@@ -5,7 +5,6 @@
 
 @pytest.mark.skip(reason="This is a long running test")
 def test_semsim_compare():
-
     subject_ids = ["MP:0010771"]
     object_ids = ["HP:0004325"]
 

backend/tests/unit/test_solr_entity_utils.py

@@ -49,9 +49,9 @@ def test_get_counterpart_entity(association, this_entity, other_entity):
     """Test that the get_counterpart_entity function returns the correct entity"""
     si = SolrImplementation()
     associated_entity = si._get_counterpart_entity(association, this_entity)
-    assert (
-        associated_entity == other_entity
-    ), f"Associated entity is not as expected. Expected: {other_entity}, got: {associated_entity}"
+    assert associated_entity == other_entity, (
+        f"Associated entity is not as expected. Expected: {other_entity}, got: {associated_entity}"
+    )
 
 
 def test_entity_boost_with_empty_calls_blank_search_boost():

backend/tests/unit/test_solr_parsers.py

@@ -24,27 +24,27 @@ def test_parse_associations_compact(association_response, associations_compact):
     association_response["response"]["numFound"] = association_response["response"].pop("num_found")
     solr_response = SolrQueryResult(**association_response)
     parsed = parse_associations(solr_response, compact=True).model_dump()
-    assert (
-        parsed == associations_compact
-    ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, associations_compact)}"
+    assert parsed == associations_compact, (
+        f"Parsed result is not as expected. Difference: {dict_diff(parsed, associations_compact)}"
+    )
 
 
 def test_parse_association_counts(association_counts_response, association_counts, node):
     association_counts_response["response"]["numFound"] = association_counts_response["response"].pop("num_found")
     solr_response = SolrQueryResult(**association_counts_response)
     parsed = parse_association_counts(solr_response, entity=Node(**node).id).model_dump()
-    assert (
-        parsed == association_counts
-    ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, association_counts)}"
+    assert parsed == association_counts, (
+        f"Parsed result is not as expected. Difference: {dict_diff(parsed, association_counts)}"
+    )
 
 
 def test_parse_association_table(association_table_response, association_table, node):
     association_table_response["response"]["numFound"] = association_table_response["response"].pop("num_found")
     solr_response = SolrQueryResult(**association_table_response)
     parsed = parse_association_table(solr_response, entity=[Node(**node).id], offset=0, limit=5).model_dump()
-    assert (
-        parsed == association_table
-    ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, association_table)}"
+    assert parsed == association_table, (
+        f"Parsed result is not as expected. Difference: {dict_diff(parsed, association_table)}"
+    )
 
 
 def test_parse_entity(entity_response, node):
@@ -64,9 +64,9 @@ def test_parse_search(search_response, search):
     solr_response = SolrQueryResult(**search_response)
     parsed = parse_search(solr_response).model_dump()
     # assert that top level keys are the same
-    assert set(parsed.keys()) == set(
-        search.keys()
-    ), f"Parsed result keys are not as expected. Difference: {dict_diff(parsed, search)}"
+    assert set(parsed.keys()) == set(search.keys()), (
+        f"Parsed result keys are not as expected. Difference: {dict_diff(parsed, search)}"
+    )
     # compare the first document (parsed.items[0]), assert that all of the keys in expected search (search.items[0])
     for key in search["items"][0].keys():
         assert key in parsed["items"][0], f"Key {key} not found in parsed result."
@@ -77,9 +77,9 @@ def test_parse_autocomplete(autocomplete_response, autocomplete):
     solr_response = SolrQueryResult(**autocomplete_response)
     parsed = parse_autocomplete(solr_response).model_dump()
     # assert that top level keys are the same
-    assert set(parsed.keys()) == set(
-        autocomplete.keys()
-    ), f"Parsed result keys are not as expected. Difference: {dict_diff(parsed, autocomplete)}"
+    assert set(parsed.keys()) == set(autocomplete.keys()), (
+        f"Parsed result keys are not as expected. Difference: {dict_diff(parsed, autocomplete)}"
+    )
     # compare the first document (parsed.items[0]), assert that all of the keys in expected autocomplete (autocomplete.items[0])
     for key in autocomplete["items"][0].keys():
         assert key in parsed["items"][0], f"Key {key} not found in parsed result."

backend/tests/unit/test_solr_queries.py

@@ -72,9 +72,9 @@ def test_build_association_multiple_predicates():
     )
     assert len(query.filter_queries) > 0, "filter_queries is empty"
     predicate_filter = [fq for fq in query.filter_queries if fq.startswith("predicate:")][0]
-    assert (
-        predicate_filter == "predicate:biolink\\:has_phenotype OR predicate:biolink\\:expressed_in"
-    ), "multiple predicate filter is not as expected"
+    assert predicate_filter == "predicate:biolink\\:has_phenotype OR predicate:biolink\\:expressed_in", (
+        "multiple predicate filter is not as expected"
+    )
 
 
 def test_build_association_multiple_entites():