fix: resolve mypy errors, fix arxiv test session isolation, and add premerge script

- Remove unused type:ignore comment in scholars.py
- Fix 51 mypy errors across test files (Any return types, cast(), protocol stubs)
- Fix arxiv unit test failures caused by session isolation (patch_session_factory fixture)
- Fix integration test rate-limit bleed between search and create
- Add scripts/premerge.sh for local CI verification
- Add docs/website/.docusaurus/ to .gitignore

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

.gitignore

@@ -18,3 +18,5 @@ frontend/dist/
 frontend/.vite/
 docs/website/node_modules/
 docs/website/build/
+docs/website/.docusaurus/
+.claude/settings.json

app/api/schemas/scholars.py

@@ -136,7 +136,7 @@ class DataImportRequest(BaseModel):
 
     @model_validator(mode="before")
     @classmethod
-    def unwrap_export_envelope(cls, values: dict) -> dict:  # type: ignore[override]
+    def unwrap_export_envelope(cls, values: dict) -> dict:
         """Accept the full export envelope format (with data/meta wrapper)."""
         if isinstance(values, dict) and "data" in values and isinstance(values["data"], dict):
             return values["data"]

scripts/premerge.sh

@@ -0,0 +1,58 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+DC="docker compose -f docker-compose.yml -f docker-compose.dev.yml"
+
+passed=0
+failed=0
+failures=()
+
+step() {
+  local label="$1"
+  shift
+  printf '\n\033[1;34m── %s\033[0m\n' "$label"
+  if "$@"; then
+    printf '\033[1;32m   PASS\033[0m  %s\n' "$label"
+    ((passed++)) || true
+  else
+    printf '\033[1;31m   FAIL\033[0m  %s\n' "$label"
+    ((failed++)) || true
+    failures+=("$label")
+  fi
+}
+
+# ── repo hygiene (host-side, no runtime deps) ────────────────────────────────
+step "No generated artifacts"        ./scripts/check_no_generated_artifacts.sh
+step "Env contract parity"           python3 scripts/check_env_contract.py
+step "API contract drift"            python3 scripts/check_frontend_api_contract.py
+
+# ── backend lint + typecheck ─────────────────────────────────────────────────
+step "Ruff check"                    $DC run --rm app ruff check .
+step "Ruff format"                   $DC run --rm app ruff format --check .
+step "Mypy"                          $DC run --rm app mypy app/ --ignore-missing-imports
+
+# ── backend tests ────────────────────────────────────────────────────────────
+step "Unit tests"                    $DC run --rm app python -m pytest tests/unit
+step "Integration tests"             $DC run --rm app python -m pytest -m integration
+
+# ── frontend ─────────────────────────────────────────────────────────────────
+step "Frontend theme tokens"         $DC run --rm frontend npm run check:theme-tokens
+step "Frontend typecheck"            $DC run --rm frontend npm run typecheck
+step "Frontend unit tests"           $DC run --rm frontend npm run test:run
+step "Frontend build"                $DC run --rm frontend npm run build
+
+# ── docs ─────────────────────────────────────────────────────────────────────
+step "Docs build"                    npm --prefix docs/website run build
+
+# ── summary ──────────────────────────────────────────────────────────────────
+printf '\n\033[1;34m── Summary ─────────────────────────────────────────────\033[0m\n'
+printf '   %s passed, %s failed\n' "$passed" "$failed"
+if ((failed > 0)); then
+  printf '\n\033[1;31m   Failed steps:\033[0m\n'
+  for f in "${failures[@]}"; do
+    printf '     - %s\n' "$f"
+  done
+  exit 1
+else
+  printf '\n\033[1;32m   All checks passed.\033[0m\n'
+fi

tests/integration/test_api_scholars.py

@@ -9,6 +9,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
 
 from app.api.runtime_deps import get_scholar_source
 from app.main import app
+from app.services.scholar.rate_limit import reset_scholar_rate_limit_state_for_tests
 from app.services.scholar.source import FetchResult
 from app.settings import settings
 from tests.integration.helpers import (
@@ -141,6 +142,7 @@ async def test_api_scholars_search_and_profile_image_management(
         assert candidate["scholar_id"] == "abcDEF123456"
         assert candidate["profile_image_url"] == "https://scholar.google.com/citations/images/avatar_scholar_256.png"
 
+        reset_scholar_rate_limit_state_for_tests()
         create_response = client.post(
             "/api/v1/scholars",
             json={

tests/integration/test_fixture_probe_runs.py

@@ -76,6 +76,9 @@ class FixtureScholarSource:
     async def fetch_profile_html(self, scholar_id: str) -> FetchResult:
         return await self.fetch_profile_page_html(scholar_id, cstart=0, pagesize=100)
 
+    async def fetch_author_search_html(self, query: str, *, start: int = 0) -> FetchResult:
+        raise NotImplementedError
+
 
 @pytest.mark.integration
 @pytest.mark.db

tests/integration/test_run_lifecycle_consistency.py

@@ -33,6 +33,9 @@ class _PassthroughSource:
     async def fetch_profile_page_html(self, scholar_id: str, *, cstart: int, pagesize: int) -> FetchResult:
         return await self.fetch_profile_html(scholar_id)
 
+    async def fetch_author_search_html(self, query: str, *, start: int = 0) -> FetchResult:
+        raise NotImplementedError
+
 
 def _csrf_headers(client: TestClient) -> dict[str, str]:
     response = client.get("/api/v1/auth/me")

tests/unit/services/domains/arxiv/conftest.py

@@ -0,0 +1,17 @@
+from __future__ import annotations
+
+import pytest
+from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
+
+
+@pytest.fixture
+def patch_session_factory(db_session: AsyncSession, monkeypatch: pytest.MonkeyPatch):
+    """Patch get_session_factory in arxiv modules to use the test's DB engine.
+
+    Without this, the implementation creates its own engine via get_session_factory()
+    which may not share transaction visibility with the test's db_session fixture.
+    """
+    factory = async_sessionmaker(db_session.bind, expire_on_commit=False)
+    monkeypatch.setattr("app.services.arxiv.rate_limit.get_session_factory", lambda: factory)
+    monkeypatch.setattr("app.services.arxiv.cache.get_session_factory", lambda: factory)
+    return factory

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

@@ -147,8 +147,8 @@ async def test_client_coalesces_concurrent_identical_search_requests() -> None:
 async def test_client_logs_cache_hit_and_miss(
     db_session: AsyncSession,
     monkeypatch: pytest.MonkeyPatch,
+    patch_session_factory,
 ) -> None:
-    _ = db_session
     calls = {"count": 0}
     logged: list[dict[str, object]] = []
 

tests/unit/services/domains/arxiv/test_gateway.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from types import SimpleNamespace
+from typing import Any
 
 import pytest
 
@@ -10,7 +10,9 @@ from app.services.arxiv.types import ArxivEntry, ArxivFeed, ArxivOpenSearchMeta
 from app.settings import settings
 
 
-def _item(*, title: str = "A Test Paper", scholar_label: str = "Ada Lovelace") -> SimpleNamespace:
+def _item(*, title: str = "A Test Paper", scholar_label: str = "Ada Lovelace") -> Any:
+    from types import SimpleNamespace
+
     return SimpleNamespace(title=title, scholar_label=scholar_label)
 
 
@@ -71,7 +73,7 @@ async def test_http_gateway_returns_none_when_disabled(monkeypatch: pytest.Monke
     fake_client = FakeClient()
     object.__setattr__(settings, "arxiv_enabled", False)
     try:
-        gateway = arxiv_gateway.HttpArxivGateway(client=fake_client)
+        gateway = arxiv_gateway.HttpArxivGateway(client=fake_client)  # type: ignore[arg-type]
         result = await gateway.discover_arxiv_id_for_publication(item=_item())
         assert result is None
         assert fake_client.calls == 0
@@ -102,7 +104,7 @@ async def test_http_gateway_uses_client_search_for_discovery() -> None:
             )
 
     fake_client = FakeClient()
-    gateway = arxiv_gateway.HttpArxivGateway(client=fake_client)
+    gateway = arxiv_gateway.HttpArxivGateway(client=fake_client)  # type: ignore[arg-type]
     result = await gateway.discover_arxiv_id_for_publication(
         item=_item(title="My Paper", scholar_label="Ada Lovelace"),
         request_email="user@example.com",

tests/unit/services/domains/arxiv/test_rate_limit.py

@@ -16,7 +16,7 @@ from app.settings import settings
 
 
 @pytest.mark.asyncio
-async def test_arxiv_rate_limit_respects_cooldown(db_session: AsyncSession) -> None:
+async def test_arxiv_rate_limit_respects_cooldown(db_session: AsyncSession, patch_session_factory) -> None:
     db_session.add(
         ArxivRuntimeState(
             state_key=ARXIV_RUNTIME_STATE_KEY,
@@ -37,7 +37,7 @@ async def test_arxiv_rate_limit_respects_cooldown(db_session: AsyncSession) -> N
 
 
 @pytest.mark.asyncio
-async def test_arxiv_rate_limit_persists_cooldown_after_429(db_session: AsyncSession) -> None:
+async def test_arxiv_rate_limit_persists_cooldown_after_429(db_session: AsyncSession, patch_session_factory) -> None:
     previous_interval = settings.arxiv_min_interval_seconds
     previous_cooldown = settings.arxiv_rate_limit_cooldown_seconds
     object.__setattr__(settings, "arxiv_min_interval_seconds", 0.0)
@@ -62,7 +62,7 @@ async def test_arxiv_rate_limit_persists_cooldown_after_429(db_session: AsyncSes
 
 
 @pytest.mark.asyncio
-async def test_arxiv_rate_limit_serializes_concurrent_calls(db_session: AsyncSession) -> None:
+async def test_arxiv_rate_limit_serializes_concurrent_calls(db_session: AsyncSession, patch_session_factory) -> None:
     previous_interval = settings.arxiv_min_interval_seconds
     previous_cooldown = settings.arxiv_rate_limit_cooldown_seconds
     object.__setattr__(settings, "arxiv_min_interval_seconds", 0.2)
@@ -90,6 +90,7 @@ async def test_arxiv_rate_limit_serializes_concurrent_calls(db_session: AsyncSes
 async def test_arxiv_rate_limit_logs_request_scheduled_and_completed(
     db_session: AsyncSession,
     monkeypatch: pytest.MonkeyPatch,
+    patch_session_factory,
 ) -> None:
     logged: list[dict[str, object]] = []
 
@@ -107,8 +108,8 @@ async def test_arxiv_rate_limit_logs_request_scheduled_and_completed(
 
     assert scheduled
     assert completed
-    assert float(scheduled[0]["wait_seconds"]) >= 0.0
+    assert float(str(scheduled[0]["wait_seconds"])) >= 0.0
-    assert int(completed[0]["status_code"]) == 200
+    assert int(str(completed[0]["status_code"])) == 200
     assert completed[0]["source_path"] == "search"
 
 
@@ -116,6 +117,7 @@ async def test_arxiv_rate_limit_logs_request_scheduled_and_completed(
 async def test_arxiv_rate_limit_logs_cooldown_activation(
     db_session: AsyncSession,
     monkeypatch: pytest.MonkeyPatch,
+    patch_session_factory,
 ) -> None:
     logged_warning: list[dict[str, object]] = []
     previous_interval = settings.arxiv_min_interval_seconds
@@ -140,11 +142,11 @@ async def test_arxiv_rate_limit_logs_cooldown_activation(
     cooldown_events = [entry for entry in logged_warning if entry.get("event") == "arxiv.cooldown_activated"]
     assert cooldown_events
     assert cooldown_events[0]["source_path"] == "lookup_ids"
-    assert float(cooldown_events[0]["cooldown_remaining_seconds"]) > 0.0
+    assert float(str(cooldown_events[0]["cooldown_remaining_seconds"])) > 0.0
 
 
 @pytest.mark.asyncio
-async def test_get_arxiv_cooldown_status_reads_active_cooldown(db_session: AsyncSession) -> None:
+async def test_get_arxiv_cooldown_status_reads_active_cooldown(db_session: AsyncSession, patch_session_factory) -> None:
     now_utc = datetime(2026, 2, 26, 13, 0, tzinfo=UTC)
     existing = await db_session.get(ArxivRuntimeState, ARXIV_RUNTIME_STATE_KEY)
     if existing is None:

tests/unit/test_ingestion_arxiv_rate_limit.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from types import SimpleNamespace
+from typing import Any, cast
 
 import pytest
 
@@ -38,8 +39,8 @@ async def test_discover_identifiers_for_enrichment_disables_arxiv_on_rate_limit(
     monkeypatch.setattr(runner, "_publish_identifier_update_event", _publish_noop)
 
     result = await runner._discover_identifiers_for_enrichment(
-        object(),
+        cast(Any, object()),
-        publication=publication,
+        publication=cast(Any, publication),
         run_id=321,
         allow_arxiv_lookup=True,
     )

tests/unit/test_portability_import.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from typing import Any
 from unittest.mock import MagicMock
 
 from app.services.portability.publication_import import (
@@ -9,14 +10,14 @@ from app.services.portability.publication_import import (
 )
 
 
-def _mock_profile(scholar_id: str = "ABC123DEF456") -> MagicMock:
+def _mock_profile(scholar_id: str = "ABC123DEF456") -> Any:
     profile = MagicMock()
     profile.id = 1
     profile.scholar_id = scholar_id
     return profile
 
 
-def _scholar_map(scholar_id: str = "ABC123DEF456") -> dict[str, MagicMock]:
+def _scholar_map(scholar_id: str = "ABC123DEF456") -> dict[str, Any]:
     return {scholar_id: _mock_profile(scholar_id)}
 
 

tests/unit/test_portability_normalize.py

@@ -111,8 +111,9 @@ class TestBuildFingerprint:
         assert all(c in "0123456789abcdef" for c in fp)
 
     def test_deterministic(self) -> None:
-        kwargs = {"title": "Test Title", "year": 2024, "author_text": "Smith", "venue_text": "ICML"}
+        fp_a = _build_fingerprint(title="Test Title", year=2024, author_text="Smith", venue_text="ICML")
-        assert _build_fingerprint(**kwargs) == _build_fingerprint(**kwargs)
+        fp_b = _build_fingerprint(title="Test Title", year=2024, author_text="Smith", venue_text="ICML")
+        assert fp_a == fp_b
 
     def test_different_titles_produce_different_fingerprints(self) -> None:
         fp1 = _build_fingerprint(title="Title A", year=2024, author_text=None, venue_text=None)

tests/unit/test_publication_pdf_queue_policy.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 from datetime import UTC, datetime, timedelta
 from types import SimpleNamespace
+from typing import Any
 
 import pytest
 
@@ -27,7 +28,7 @@ def _job(
 
 def _row(
     *, pub_url: str | None = "https://scholar.google.com/citations?view_op=view_citation&citation_for_view=abc:xyz"
-) -> SimpleNamespace:
+) -> Any:
     return SimpleNamespace(
         publication_id=1,
         scholar_profile_id=1,
@@ -235,7 +236,7 @@ async def test_run_resolution_task_disables_arxiv_for_remaining_batch(
 ) -> None:
     calls: list[tuple[int, bool]] = []
     first = _row()
-    second = SimpleNamespace(**{**first.__dict__, "publication_id": 2})
+    second: Any = SimpleNamespace(**{**first.__dict__, "publication_id": 2})
 
     def _raise_session_factory_error():
         raise RuntimeError("skip user settings lookup in test")

tests/unit/test_publication_pdf_resolution_pipeline.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 from datetime import UTC, datetime
 from types import SimpleNamespace
+from typing import Any
 
 import pytest
 
@@ -11,7 +12,7 @@ from app.services.publications import pdf_resolution_pipeline as pipeline
 from app.services.unpaywall.application import OaResolutionOutcome
 
 
-def _row(*, display_identifier: DisplayIdentifier | None = None) -> SimpleNamespace:
+def _row(*, display_identifier: DisplayIdentifier | None = None) -> Any:
     return SimpleNamespace(
         publication_id=1,
         scholar_profile_id=1,

tests/unit/test_scholar_search_safety.py

@@ -23,6 +23,12 @@ class StubScholarSource:
         index = min(self.calls - 1, len(self._fetch_results) - 1)
         return self._fetch_results[index]
 
+    async def fetch_profile_html(self, scholar_id: str) -> FetchResult:
+        raise NotImplementedError
+
+    async def fetch_profile_page_html(self, scholar_id: str, *, cstart: int, pagesize: int) -> FetchResult:
+        raise NotImplementedError
+
 
 def _ok_author_search_fetch() -> FetchResult:
     body = (

tests/unit/test_scholars_create_hydration.py

@@ -1,4 +1,5 @@
 from types import SimpleNamespace
+from typing import Any, cast
 
 import pytest
 
@@ -42,9 +43,9 @@ async def test_create_hydration_skips_when_global_throttle_active(
     )
 
     result = await scholar_helpers.hydrate_scholar_metadata_if_needed(
-        db_session=None,
+        db_session=cast(Any, None),
         profile=profile,
-        source=object(),
+        source=cast(Any, object()),
         user_id=7,
     )
 
@@ -77,9 +78,9 @@ async def test_create_hydration_runs_when_throttle_is_clear(
     )
 
     result = await scholar_helpers.hydrate_scholar_metadata_if_needed(
-        db_session=None,
+        db_session=cast(Any, None),
         profile=profile,
-        source=object(),
+        source=cast(Any, object()),
         user_id=8,
     )
 
@@ -109,7 +110,7 @@ async def test_initial_scrape_job_enqueued_on_create(
     )
 
     queued = await scholar_helpers.enqueue_initial_scrape_job_for_scholar(
-        session,
+        cast(Any, session),
         profile=profile,
         user_id=9,
     )
@@ -134,7 +135,7 @@ async def test_initial_scrape_job_not_enqueued_when_disabled(
     )
 
     queued = await scholar_helpers.enqueue_initial_scrape_job_for_scholar(
-        session,
+        cast(Any, session),
         profile=profile,
         user_id=11,
     )