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ci: add ruff linting and mypy type checking

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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>
This commit is contained in:
Justin Visser 2026-02-26 22:11:41 +01:00
parent 399276ea69
commit bf04c77aa9
137 changed files with 3066 additions and 1900 deletions
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214
app/db/models.py
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@ -62,18 +62,10 @@ class User(Base):
id: Mapped[int] = mapped_column(primary_key=True)
email: Mapped[str] = mapped_column(String(255), nullable=False, unique=True)
password_hash: Mapped[str] = mapped_column(String(255), nullable=False)
is_active: Mapped[bool] = mapped_column(
Boolean, nullable=False, server_default=text("true")
)
is_admin: Mapped[bool] = mapped_column(
Boolean, nullable=False, server_default=text("false")
)
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
is_active: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("true"))
is_admin: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class UserSetting(Base):
@ -89,18 +81,10 @@ class UserSetting(Base):
),
)
user_id: Mapped[int] = mapped_column(
ForeignKey("users.id", ondelete="CASCADE"), primary_key=True
)
auto_run_enabled: Mapped[bool] = mapped_column(
Boolean, nullable=False, server_default=text("false")
)
run_interval_minutes: Mapped[int] = mapped_column(
Integer, nullable=False, server_default=text("1440")
)
request_delay_seconds: Mapped[int] = mapped_column(
Integer, nullable=False, server_default=text("10")
)
user_id: Mapped[int] = mapped_column(ForeignKey("users.id", ondelete="CASCADE"), primary_key=True)
auto_run_enabled: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
run_interval_minutes: Mapped[int] = mapped_column(Integer, nullable=False, server_default=text("1440"))
request_delay_seconds: Mapped[int] = mapped_column(Integer, nullable=False, server_default=text("10"))
nav_visible_pages: Mapped[list[str]] = mapped_column(
JSONB,
nullable=False,
@ -115,17 +99,13 @@ class UserSetting(Base):
)
scrape_cooldown_until: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
scrape_cooldown_reason: Mapped[str | None] = mapped_column(String(64))
openalex_api_key: Mapped[str | None] = mapped_column(String(255))
crossref_api_token: Mapped[str | None] = mapped_column(String(255))
crossref_api_mailto: Mapped[str | None] = mapped_column(String(255))
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class ScholarProfile(Base):
@ -136,9 +116,7 @@ class ScholarProfile(Base):
)
id: Mapped[int] = mapped_column(primary_key=True)
user_id: Mapped[int] = mapped_column(
ForeignKey("users.id", ondelete="CASCADE"), nullable=False
)
user_id: Mapped[int] = mapped_column(ForeignKey("users.id", ondelete="CASCADE"), nullable=False)
scholar_id: Mapped[str] = mapped_column(String(64), nullable=False)
display_name: Mapped[str | None] = mapped_column(String(255))
profile_image_url: Mapped[str | None] = mapped_column(Text)
@ -146,22 +124,14 @@ class ScholarProfile(Base):
profile_image_upload_path: Mapped[str | None] = mapped_column(Text)
last_initial_page_fingerprint_sha256: Mapped[str | None] = mapped_column(String(64))
last_initial_page_checked_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
is_enabled: Mapped[bool] = mapped_column(
Boolean, nullable=False, server_default=text("true")
)
baseline_completed: Mapped[bool] = mapped_column(
Boolean, nullable=False, server_default=text("false")
)
is_enabled: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("true"))
baseline_completed: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
last_run_dt: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
last_run_status: Mapped[RunStatus | None] = mapped_column(
RUN_STATUS_DB_ENUM,
)
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class CrawlRun(Base):
@ -172,51 +142,29 @@ class CrawlRun(Base):
"uq_crawl_runs_user_active",
"user_id",
unique=True,
postgresql_where=text(
"status IN ('running'::run_status, 'resolving'::run_status)"
),
postgresql_where=text("status IN ('running'::run_status, 'resolving'::run_status)"),
),
Index(
"uq_crawl_runs_user_manual_idempotency_key",
"user_id",
"idempotency_key",
unique=True,
postgresql_where=text(
"idempotency_key IS NOT NULL AND trigger_type = 'manual'::run_trigger_type"
),
postgresql_where=text("idempotency_key IS NOT NULL AND trigger_type = 'manual'::run_trigger_type"),
),
)
id: Mapped[int] = mapped_column(primary_key=True)
user_id: Mapped[int] = mapped_column(
ForeignKey("users.id", ondelete="CASCADE"), nullable=False
)
trigger_type: Mapped[RunTriggerType] = mapped_column(
RUN_TRIGGER_TYPE_DB_ENUM, nullable=False
)
status: Mapped[RunStatus] = mapped_column(
RUN_STATUS_DB_ENUM, nullable=False
)
start_dt: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
user_id: Mapped[int] = mapped_column(ForeignKey("users.id", ondelete="CASCADE"), nullable=False)
trigger_type: Mapped[RunTriggerType] = mapped_column(RUN_TRIGGER_TYPE_DB_ENUM, nullable=False)
status: Mapped[RunStatus] = mapped_column(RUN_STATUS_DB_ENUM, nullable=False)
start_dt: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
end_dt: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
scholar_count: Mapped[int] = mapped_column(
Integer, nullable=False, server_default=text("0")
)
new_pub_count: Mapped[int] = mapped_column(
Integer, nullable=False, server_default=text("0")
)
scholar_count: Mapped[int] = mapped_column(Integer, nullable=False, server_default=text("0"))
new_pub_count: Mapped[int] = mapped_column(Integer, nullable=False, server_default=text("0"))
idempotency_key: Mapped[str | None] = mapped_column(String(128))
error_log: Mapped[dict] = mapped_column(
JSONB, nullable=False, server_default=text("'{}'::jsonb")
)
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
error_log: Mapped[dict] = mapped_column(JSONB, nullable=False, server_default=text("'{}'::jsonb"))
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class Publication(Base):
@ -237,28 +185,16 @@ class Publication(Base):
title_raw: Mapped[str] = mapped_column(Text, nullable=False)
title_normalized: Mapped[str] = mapped_column(Text, nullable=False)
year: Mapped[int | None] = mapped_column(Integer)
citation_count: Mapped[int] = mapped_column(
Integer, nullable=False, server_default=text("0")
)
citation_count: Mapped[int] = mapped_column(Integer, nullable=False, server_default=text("0"))
author_text: Mapped[str | None] = mapped_column(Text)
venue_text: Mapped[str | None] = mapped_column(Text)
pub_url: Mapped[str | None] = mapped_column(Text)
pdf_url: Mapped[str | None] = mapped_column(Text)
canonical_title_hash: Mapped[str | None] = mapped_column(
String(64), nullable=True, index=True
)
openalex_enriched: Mapped[bool] = mapped_column(
Boolean, nullable=False, server_default=text("false")
)
openalex_last_attempt_at: Mapped[datetime | None] = mapped_column(
DateTime(timezone=True), nullable=True
)
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
canonical_title_hash: Mapped[str | None] = mapped_column(String(64), nullable=True, index=True)
openalex_enriched: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
openalex_last_attempt_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True), nullable=True)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class PublicationIdentifier(Base):
@ -300,12 +236,8 @@ class PublicationIdentifier(Base):
server_default=text("0"),
)
evidence_url: Mapped[str | None] = mapped_column(Text)
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class PublicationPdfJob(Base):
@ -343,12 +275,8 @@ class PublicationPdfJob(Base):
last_requested_by_user_id: Mapped[int | None] = mapped_column(
ForeignKey("users.id", ondelete="SET NULL"),
)
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class PublicationPdfJobEvent(Base):
@ -372,9 +300,7 @@ class PublicationPdfJobEvent(Base):
source: Mapped[str | None] = mapped_column(String(32))
failure_reason: Mapped[str | None] = mapped_column(String(64))
message: Mapped[str | None] = mapped_column(Text)
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class ScholarPublication(Base):
@ -392,18 +318,10 @@ class ScholarPublication(Base):
ForeignKey("publications.id", ondelete="CASCADE"),
primary_key=True,
)
is_read: Mapped[bool] = mapped_column(
Boolean, nullable=False, server_default=text("false")
)
is_favorite: Mapped[bool] = mapped_column(
Boolean, nullable=False, server_default=text("false")
)
first_seen_run_id: Mapped[int | None] = mapped_column(
ForeignKey("crawl_runs.id", ondelete="SET NULL")
)
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
is_read: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
is_favorite: Mapped[bool] = mapped_column(Boolean, nullable=False, server_default=text("false"))
first_seen_run_id: Mapped[int | None] = mapped_column(ForeignKey("crawl_runs.id", ondelete="SET NULL"))
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class IngestionQueueItem(Base):
@ -458,12 +376,8 @@ class IngestionQueueItem(Base):
last_error: Mapped[str | None] = mapped_column(Text)
dropped_reason: Mapped[str | None] = mapped_column(String(128))
dropped_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class DataRepairJob(Base):
@ -503,12 +417,8 @@ class DataRepairJob(Base):
error_text: Mapped[str | None] = mapped_column(Text)
started_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
finished_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class AuthorSearchRuntimeState(Base):
@ -532,12 +442,8 @@ class AuthorSearchRuntimeState(Base):
nullable=False,
server_default=text("false"),
)
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class ArxivRuntimeState(Base):
@ -546,12 +452,8 @@ class ArxivRuntimeState(Base):
state_key: Mapped[str] = mapped_column(String(64), primary_key=True)
next_allowed_at: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
cooldown_until: Mapped[datetime | None] = mapped_column(DateTime(timezone=True))
created_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class ArxivQueryCacheEntry(Base):
@ -570,12 +472,8 @@ class ArxivQueryCacheEntry(Base):
DateTime(timezone=True),
nullable=False,
)
cached_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
cached_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
class AuthorSearchCacheEntry(Base):
@ -594,9 +492,5 @@ class AuthorSearchCacheEntry(Base):
DateTime(timezone=True),
nullable=False,
)
cached_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now()
)
cached_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())