ci: add ruff linting and mypy type checking

Add ruff and mypy to dev dependencies with configuration in pyproject.toml.
Add a lint CI job that runs ruff check, ruff format --check, and mypy.
Auto-fix import sorting and formatting across the codebase. Exclude
alembic/versions from linting (auto-generated migrations). Ignore B008
(FastAPI Depends pattern) and RUF001 (unicode in user-facing strings).

21 ruff lint errors and 50 mypy errors remain for manual review.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

tests/unit/services/domains/openalex/test_client.py

@@ -1,6 +1,6 @@
-import pytest
 from app.services.domains.openalex.types import OpenAlexWork
 
+
 def test_parse_openalex_work_from_api_dict() -> None:
     raw_api_response = {
         "id": "https://openalex.org/W2741809807",
@@ -13,28 +13,19 @@ def test_parse_openalex_work_from_api_dict() -> None:
             "doi": "https://doi.org/10.1038/s41586-020-0315-z",
             "mag": "2741809807",
             "pmid": "https://pubmed.ncbi.nlm.nih.gov/32040050",
-            "pmcid": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325852"
-        },
-        "open_access": {
-            "is_oa": True,
-            "oa_url": "https://example.com/pdf"
+            "pmcid": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325852",
         },
+        "open_access": {"is_oa": True, "oa_url": "https://example.com/pdf"},
         "authorships": [
             {
                 "author_position": "first",
-                "author": {
-                    "id": "https://openalex.org/A1969205032",
-                    "display_name": "Giuseppe Carleo"
-                }
+                "author": {"id": "https://openalex.org/A1969205032", "display_name": "Giuseppe Carleo"},
             },
             {
                 "author_position": "middle",
-                "author": {
-                    "id": "https://openalex.org/A4356881717",
-                    "display_name": "Ignacio Cirac"
-                }
-            }
-        ]
+                "author": {"id": "https://openalex.org/A4356881717", "display_name": "Ignacio Cirac"},
+            },
+        ],
     }
 
     work = OpenAlexWork.from_api_dict(raw_api_response)
@@ -52,6 +43,7 @@ def test_parse_openalex_work_from_api_dict() -> None:
     assert work.authors[0].display_name == "Giuseppe Carleo"
     assert work.authors[1].display_name == "Ignacio Cirac"
 
+
 def test_parse_openalex_work_empty() -> None:
     work = OpenAlexWork.from_api_dict({"id": "W123"})
     assert work.openalex_id == "W123"

tests/unit/services/domains/openalex/test_matching.py

@@ -1,54 +1,62 @@
-import pytest
-from app.services.domains.openalex.types import OpenAlexWork
 from app.services.domains.openalex.matching import find_best_match
+from app.services.domains.openalex.types import OpenAlexWork
+
 
 def test_find_best_match_exact_title():
     cand1 = OpenAlexWork.from_api_dict({"id": "W1", "title": "Exact Title of the Paper"})
     cand2 = OpenAlexWork.from_api_dict({"id": "W2", "title": "Totally Different Paper"})
-    
+
     match = find_best_match("Exact Title of the Paper", 2020, "Author A", [cand1, cand2])
     assert match is not None
     assert match.openalex_id == "W1"
 
+
 def test_find_best_match_fuzzy_title():
     # Only differences are punctuation or minor phrasing (e.g., matching a preprint title vs published)
     cand1 = OpenAlexWork.from_api_dict({"id": "W1", "title": "Fuzzier Title: A Study on OpenAlex"})
     cand2 = OpenAlexWork.from_api_dict({"id": "W2", "title": "Some completely unrelated work"})
-    
+
     match = find_best_match("Fuzzier Title A Study on OpenAlex", 2021, "Author B", [cand1, cand2])
     assert match is not None
     assert match.openalex_id == "W1"
 
+
 def test_find_best_match_rejects_low_score():
     cand1 = OpenAlexWork.from_api_dict({"id": "W1", "title": "Cats in hats"})
-    
+
     match = find_best_match("Dogs with logs", 2020, "Author A", [cand1])
     assert match is None
 
+
 def test_find_best_match_year_tiebreaker():
     # Both titles are very similar, one has exact year.
     cand1 = OpenAlexWork.from_api_dict({"id": "W1", "title": "The exact same title", "publication_year": 2018})
     cand2 = OpenAlexWork.from_api_dict({"id": "W2", "title": "The exact same title", "publication_year": 2020})
-    
+
     match = find_best_match("The exact same title", 2020, "Author A", [cand1, cand2])
     assert match is not None
     assert match.openalex_id == "W2"
 
+
 def test_find_best_match_author_tiebreaker():
     # Titles and years match exactly. Author overlap decides it.
-    cand1 = OpenAlexWork.from_api_dict({
-        "id": "W1", 
-        "title": "A popular title", 
-        "publication_year": 2020,
-        "authorships": [{"author": {"display_name": "Smith, J"}}]
-    })
-    cand2 = OpenAlexWork.from_api_dict({
-        "id": "W2", 
-        "title": "A popular title", 
-        "publication_year": 2020,
-        "authorships": [{"author": {"display_name": "Doe, J"}}]
-    })
-    
+    cand1 = OpenAlexWork.from_api_dict(
+        {
+            "id": "W1",
+            "title": "A popular title",
+            "publication_year": 2020,
+            "authorships": [{"author": {"display_name": "Smith, J"}}],
+        }
+    )
+    cand2 = OpenAlexWork.from_api_dict(
+        {
+            "id": "W2",
+            "title": "A popular title",
+            "publication_year": 2020,
+            "authorships": [{"author": {"display_name": "Doe, J"}}],
+        }
+    )
+
     # Target authors contains "Doe"
     match = find_best_match("A popular title", 2020, "A Einstein, J Doe", [cand1, cand2])
     assert match is not None