Add GitHub Actions CI workflows for backend and frontend

Add mypy and tsc type checking to pre-commit hooks

Add Codecov upload to CI workflows with backend/frontend flags

Fix prettier version mismatch: use local npm run format hook instead of mirrors-prettier

Fix Prefect ephemeral server timeout in CI

Use prefect_test_harness in conftest so the server starts with in-memory
SQLite (avoiding slow file-based DB migration on first run). Also raise
PREFECT_SERVER_EPHEMERAL_STARTUP_TIMEOUT_SECONDS to 120s in both the
test session and the CI workflow env as a safety net.

Author: jat255

.github/workflows/backend.yml

@@ -0,0 +1,61 @@
+name: Backend CI
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'backend/**'
+      - '.github/workflows/backend.yml'
+  pull_request:
+    branches: [main]
+    paths:
+      - 'backend/**'
+      - '.github/workflows/backend.yml'
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: backend
+    env:
+      PREFECT_SERVER_EPHEMERAL_STARTUP_TIMEOUT_SECONDS: "120"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-caching: true
+          python-version: '3.12'
+
+      - name: Install dependencies
+        run: uv sync --all-groups
+
+      - name: Lint (ruff)
+        run: uv run ruff check .
+
+      - name: Format check (ruff)
+        run: uv run ruff format --check .
+
+      - name: Type check (ty)
+        run: uv run ty check app
+
+      - name: Test with coverage
+        run: uv run pytest
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: backend/coverage.lcov
+          flags: backend
+          fail_ci_if_error: true
+
+      - name: Upload coverage artifact
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: backend-coverage
+          path: backend/coverage.lcov

.github/workflows/frontend.yml

@@ -0,0 +1,58 @@
+name: Frontend CI
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'frontend/**'
+      - '.github/workflows/frontend.yml'
+  pull_request:
+    branches: [main]
+    paths:
+      - 'frontend/**'
+      - '.github/workflows/frontend.yml'
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: frontend
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-node@v4
+        with:
+          node-version: '22'
+
+      - name: Install dependencies
+        run: npm install
+
+      - name: Type check and build
+        run: npm run build
+
+      - name: Lint
+        run: npm run lint
+
+      - name: Format check
+        run: npm run format:check
+
+      - name: Test with coverage
+        run: npm run test:coverage
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: frontend/coverage/lcov.info
+          flags: frontend
+          fail_ci_if_error: true
+
+      - name: Upload coverage artifact
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: frontend-coverage
+          path: frontend/coverage/

.pre-commit-config.yaml

@@ -8,17 +8,32 @@ repos:
       - id: ruff-format
         files: ^backend/
 
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.1.0
+  - repo: local
     hooks:
       - id: prettier
+        name: prettier
+        entry: bash -c 'cd frontend && npm run format'
+        language: system
         files: ^frontend/src/.*\.(ts|tsx)$
+        pass_filenames: false
+
+      - id: ty
+        name: ty
+        entry: bash -c 'cd backend && uv run ty check app'
+        language: system
+        files: ^backend/.*\.py$
+        pass_filenames: false
 
-  - repo: local
-    hooks:
       - id: eslint
         name: eslint
         entry: bash -c 'cd frontend && npm run lint'
         language: system
         files: ^frontend/src/.*\.(ts|tsx)$
         pass_filenames: false
+
+      - id: tsc
+        name: tsc
+        entry: bash -c 'cd frontend && npm run build'
+        language: system
+        files: ^frontend/.*\.(ts|tsx)$
+        pass_filenames: false

backend/app/flows/harvest.py

@@ -39,7 +39,9 @@ async def _resolve_grantee(session, grantee_type: str, name: str) -> uuid.UUID |
     if grantee_type == "user":
         from app.models.user import User
 
-        result = await session.execute(select(User.id).where(User.email == name))
+        result = await session.execute(
+            select(User.id).where(User.email == name)  # ty: ignore[no-matching-overload]
+        )
     elif grantee_type == "group":
         from app.models.group import Group
 
@@ -332,10 +334,11 @@ async def harvest_instrument_flow(instrument_id: str, schedule_id: str) -> dict:
         from prefect.client.orchestration import get_client
 
         ctx = prefect.context.get_run_context()
-        if ctx and ctx.flow_run:
+        flow_run = getattr(ctx, "flow_run", None)
+        if flow_run:
             async with get_client() as client:
                 await client.update_flow_run(
-                    ctx.flow_run.id,
+                    flow_run.id,
                     name=f"harvest-{instrument_name}",
                 )
     except Exception:

backend/app/models/access.py

@@ -1,12 +1,18 @@
+from __future__ import annotations
+
 import enum
 import uuid
 from datetime import datetime
+from typing import TYPE_CHECKING
 
 from sqlalchemy import DateTime, Enum, ForeignKey, func
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from app.models.base import Base, UUIDPrimaryKey
 
+if TYPE_CHECKING:
+    from app.models.file import FileRecord
+
 
 class GranteeType(enum.StrEnum):
     user = "user"
@@ -22,4 +28,4 @@ class FileAccessGrant(UUIDPrimaryKey, Base):
     grantee_id: Mapped[uuid.UUID] = mapped_column()
     granted_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), server_default=func.now())
 
-    file: Mapped["FileRecord"] = relationship(back_populates="access_grants")  # noqa: F821
+    file: Mapped[FileRecord] = relationship(back_populates="access_grants")

backend/app/models/file.py

@@ -1,12 +1,20 @@
+from __future__ import annotations
+
 import enum
 import uuid
 from datetime import datetime
+from typing import TYPE_CHECKING
 
 from sqlalchemy import JSON, BigInteger, DateTime, Enum, ForeignKey, Index, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from app.models.base import Base, UUIDPrimaryKey
 
+if TYPE_CHECKING:
+    from app.models.access import FileAccessGrant
+    from app.models.instrument import Instrument
+    from app.models.transfer import FileTransfer
+
 
 class PersistentIdType(enum.StrEnum):
     ark = "ark"
@@ -34,10 +42,8 @@ class FileRecord(UUIDPrimaryKey, Base):
     metadata_: Mapped[dict | None] = mapped_column("metadata", JSON)
     owner_id: Mapped[uuid.UUID | None] = mapped_column(ForeignKey("users.id"), nullable=True)
 
-    instrument: Mapped["Instrument"] = relationship(back_populates="files")  # noqa: F821
-    transfers: Mapped[list["FileTransfer"]] = relationship(  # noqa: F821
-        back_populates="file"
-    )
-    access_grants: Mapped[list["FileAccessGrant"]] = relationship(  # noqa: F821
+    instrument: Mapped[Instrument] = relationship(back_populates="files")
+    transfers: Mapped[list[FileTransfer]] = relationship(back_populates="file")
+    access_grants: Mapped[list[FileAccessGrant]] = relationship(
         back_populates="file", cascade="all, delete-orphan"
     )

backend/app/models/hook.py

@@ -1,11 +1,17 @@
+from __future__ import annotations
+
 import enum
 import uuid
+from typing import TYPE_CHECKING
 
 from sqlalchemy import JSON, Boolean, Enum, ForeignKey, Integer, String, Text
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from app.models.base import Base, UUIDPrimaryKey
 
+if TYPE_CHECKING:
+    from app.models.instrument import Instrument
+
 
 class HookTrigger(enum.StrEnum):
     pre_transfer = "pre_transfer"
@@ -33,4 +39,4 @@ class HookConfig(UUIDPrimaryKey, Base):
     priority: Mapped[int] = mapped_column(Integer, default=0)
     enabled: Mapped[bool] = mapped_column(Boolean, default=True)
 
-    instrument: Mapped["Instrument | None"] = relationship(back_populates="hooks")  # noqa: F821
+    instrument: Mapped[Instrument | None] = relationship(back_populates="hooks")

backend/app/models/instrument.py

@@ -1,11 +1,19 @@
+from __future__ import annotations
+
 import enum
 import uuid
+from typing import TYPE_CHECKING
 
 from sqlalchemy import JSON, Boolean, Enum, ForeignKey, String, Text
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from app.models.base import Base, TimestampMixin, UUIDPrimaryKey
 
+if TYPE_CHECKING:
+    from app.models.file import FileRecord
+    from app.models.hook import HookConfig
+    from app.models.schedule import HarvestSchedule
+
 
 class TransferAdapterType(enum.StrEnum):
     rclone = "rclone"
@@ -21,7 +29,7 @@ class ServiceAccount(UUIDPrimaryKey, TimestampMixin, Base):
     username: Mapped[str] = mapped_column(String(255))
     password_encrypted: Mapped[str] = mapped_column(Text)
 
-    instruments: Mapped[list["Instrument"]] = relationship(back_populates="service_account")
+    instruments: Mapped[list[Instrument]] = relationship(back_populates="service_account")
 
 
 class Instrument(UUIDPrimaryKey, TimestampMixin, Base):
@@ -44,8 +52,6 @@ class Instrument(UUIDPrimaryKey, TimestampMixin, Base):
     enabled: Mapped[bool] = mapped_column(Boolean, default=True)
 
     service_account: Mapped[ServiceAccount | None] = relationship(back_populates="instruments")
-    schedules: Mapped[list["HarvestSchedule"]] = relationship(  # noqa: F821
-        back_populates="instrument"
-    )
-    files: Mapped[list["FileRecord"]] = relationship(back_populates="instrument")  # noqa: F821
-    hooks: Mapped[list["HookConfig"]] = relationship(back_populates="instrument")  # noqa: F821
+    schedules: Mapped[list[HarvestSchedule]] = relationship(back_populates="instrument")
+    files: Mapped[list[FileRecord]] = relationship(back_populates="instrument")
+    hooks: Mapped[list[HookConfig]] = relationship(back_populates="instrument")

backend/app/models/schedule.py

@@ -1,10 +1,17 @@
+from __future__ import annotations
+
 import uuid
+from typing import TYPE_CHECKING
 
 from sqlalchemy import Boolean, ForeignKey, String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from app.models.base import Base, TimestampMixin, UUIDPrimaryKey
 
+if TYPE_CHECKING:
+    from app.models.instrument import Instrument
+    from app.models.storage import StorageLocation
+
 
 class HarvestSchedule(UUIDPrimaryKey, TimestampMixin, Base):
     __tablename__ = "harvest_schedules"
@@ -17,5 +24,5 @@ class HarvestSchedule(UUIDPrimaryKey, TimestampMixin, Base):
     prefect_deployment_id: Mapped[str | None] = mapped_column(String(255))
     enabled: Mapped[bool] = mapped_column(Boolean, default=True)
 
-    instrument: Mapped["Instrument"] = relationship(back_populates="schedules")  # noqa: F821
-    default_storage_location: Mapped["StorageLocation"] = relationship()  # noqa: F821
+    instrument: Mapped[Instrument] = relationship(back_populates="schedules")
+    default_storage_location: Mapped[StorageLocation] = relationship()

backend/app/models/transfer.py

@@ -1,13 +1,20 @@
+from __future__ import annotations
+
 import enum
 import uuid
 from datetime import datetime
+from typing import TYPE_CHECKING
 
 from sqlalchemy import BigInteger, Boolean, DateTime, Enum, ForeignKey, String, Text
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from app.models.base import Base, UUIDPrimaryKey
 from app.models.instrument import TransferAdapterType
 
+if TYPE_CHECKING:
+    from app.models.file import FileRecord
+    from app.models.storage import StorageLocation
+
 
 class TransferStatus(enum.StrEnum):
     pending = "pending"
@@ -36,5 +43,5 @@ class FileTransfer(UUIDPrimaryKey, Base):
     error_message: Mapped[str | None] = mapped_column(Text)
     prefect_flow_run_id: Mapped[str | None] = mapped_column(String(255))
 
-    file: Mapped["FileRecord"] = relationship(back_populates="transfers")  # noqa: F821
-    storage_location: Mapped["StorageLocation"] = relationship()  # noqa: F821
+    file: Mapped[FileRecord] = relationship(back_populates="transfers")
+    storage_location: Mapped[StorageLocation] = relationship()