code quality updates

Author: Trojan-Dev-AFK

.github/workflows/ci.yml

@@ -0,0 +1,43 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  test-and-lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Install dependencies
+        run: uv sync --all-groups
+
+      - name: Ruff (Checking lint, imports, complexity, and commented-out code)
+        run: uv run ruff check .
+
+      - name: Black (Checking code formatting)
+        run: uv run black --check .
+
+      - name: Interrogate (Checking docstring coverage)
+        run: uv run interrogate app
+
+      - name: Vulture (Checking unused/dead production code)
+        run: uv run vulture app scripts --min-confidence 70
+
+      - name: Thin endpoint lint (Checking endpoint-layer boundaries)
+        run: uv run python scripts/lint_thin_endpoints.py
+
+      - name: Pytest (Checking unit and integration tests)
+        run: uv run pytest -q

README.md

@@ -56,7 +56,6 @@ Full setup guide: [docs/RUNBOOK.md](docs/RUNBOOK.md)
 | `GET` | `/v1/documents/` | Admin (own company) or Super Admin |
 | `GET` | `/v1/documents/{id}` | Admin (own company) or Super Admin |
 | `DELETE` | `/v1/documents/{id}` | Admin (own company) or Super Admin |
-| `POST` | `/v1/chat/warmup` | Authenticated |
 | `POST` | `/v1/chat/invoke` | Admin or Employee |
 
 ---
@@ -103,7 +102,6 @@ ACCESS_TOKEN_EXPIRE_MINUTES=60
 EMBEDDING_MODEL=all-MiniLM-L6-v2
 CHUNK_SIZE=1000
 CHUNK_OVERLAP=200
-AGENT_WARMUP_ON_STARTUP=true
 
 # Encoding
 ENCODING=utf-8
@@ -140,10 +138,12 @@ Full variable reference: [docs/RUNBOOK.md#environment-variables-reference](docs/
 
 ```bash
 # Linting and formatting
-ruff check app/        # lint
-ruff check app/ --fix  # auto-fix
-black app/             # format
-interrogate app/       # docstring coverage (min 80%)
+uv run ruff check .                             # lint + complexity + commented-out code checks
+uv run ruff check . --fix                       # auto-fix
+uv run black --check .                          # format verification
+uv run python scripts/lint_thin_endpoints.py   # endpoint thinness rule
+uv run interrogate app/                         # docstring coverage (min 80%)
+uv run vulture app scripts --min-confidence 70 # dead-code scan
 
 # Dependencies
 uv add <package>       # add a runtime dependency
@@ -161,5 +161,5 @@ export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES  # macOS only
 celery -A app.worker.celery_app worker --pool=solo --loglevel=info
 
 # Tests
-pytest
+uv run pytest -q
 ```

alembic/env.py

@@ -1,10 +1,10 @@
 import asyncio
 from logging.config import fileConfig
 
-from alembic import context
 from sqlalchemy import pool
 from sqlalchemy.ext.asyncio import async_engine_from_config
 
+from alembic import context
 from app.core.config import settings
 from app.db.models import Base
 

alembic/versions/0001_initial_schema.py

@@ -5,9 +5,11 @@
 Create Date: 2026-05-31
 """
 
-from typing import Sequence, Union
+from collections.abc import Sequence
+from typing import Union
 
 import sqlalchemy as sa
+
 from alembic import op
 
 revision: str = "0001"
@@ -72,9 +74,7 @@ def upgrade() -> None:
             PRIMARY KEY (id)
         )
     """))
-    op.execute(sa.text(
-        "CREATE UNIQUE INDEX IF NOT EXISTS ix_companies_name ON companies (name)"
-    ))
+    op.execute(sa.text("CREATE UNIQUE INDEX IF NOT EXISTS ix_companies_name ON companies (name)"))
 
     op.execute(sa.text("""
         CREATE TABLE IF NOT EXISTS users (
@@ -87,9 +87,7 @@ def upgrade() -> None:
             PRIMARY KEY (id)
         )
     """))
-    op.execute(sa.text(
-        "CREATE UNIQUE INDEX IF NOT EXISTS ix_users_username ON users (username)"
-    ))
+    op.execute(sa.text("CREATE UNIQUE INDEX IF NOT EXISTS ix_users_username ON users (username)"))
 
     op.execute(sa.text("""
         CREATE TABLE IF NOT EXISTS token_sessions (
@@ -105,9 +103,7 @@ def upgrade() -> None:
             PRIMARY KEY (id)
         )
     """))
-    op.execute(sa.text(
-        "CREATE UNIQUE INDEX IF NOT EXISTS ix_token_sessions_jti ON token_sessions (jti)"
-    ))
+    op.execute(sa.text("CREATE UNIQUE INDEX IF NOT EXISTS ix_token_sessions_jti ON token_sessions (jti)"))
 
     op.execute(sa.text("""
         CREATE TABLE IF NOT EXISTS documents (

alembic/versions/0002_add_user_role_constraint.py

@@ -5,9 +5,11 @@
 Create Date: 2026-05-31
 """
 
-from typing import Sequence, Union
+from collections.abc import Sequence
+from typing import Union
 
 import sqlalchemy as sa
+
 from alembic import op
 
 revision: str = "0002"

app/agent/graph.py

@@ -8,7 +8,6 @@
 from langgraph.graph.message import add_messages
 from langgraph.prebuilt import ToolNode, tools_condition
 
-from app.agent.tools.graph_generator import generate_graph
 from app.agent.tools.vector_search import search_documents
 from app.core.logger import get_logger
 
@@ -21,7 +20,7 @@ class GraphState(TypedDict):
     messages: Annotated[list[BaseMessage], add_messages]
 
 
-tools = [search_documents, generate_graph]
+tools = [search_documents]
 tool_node = ToolNode(tools)
 
 logger.info("Initialising LLM", extra={"model": "llama3.1", "temperature": 0})
@@ -37,27 +36,13 @@ def call_model(state: GraphState):
     system_instruction = SystemMessage(
         content=(
             "You are an expert financial and healthcare data assistant. "
-            "You have two tools available:\n"
-            "1. 'search_documents' — use this to look up factual information from uploaded documents.\n"
-            "2. 'generate_graph' — use this ONLY when the user explicitly asks for a chart, graph, plot, "
-            "or visual breakdown. This tool accepts a single JSON string parameter called 'data_json'.\n\n"
+            "You have one tool available:\n"
+            "1. 'search_documents' — use this to look up factual information from uploaded documents.\n\n"
             "CRITICAL RULES:\n"
-            "- If the user asks for a chart or graph, you MUST call 'generate_graph'."
-            " Do NOT just describe data in text.\n"
-            "- Never print JSON like {\"name\": \"generate_graph\", ...} in normal text."
-            " Use real tool-calling only.\n"
-            "- First use 'search_documents' to gather the numbers if needed,"
-            " then call 'generate_graph' with the data.\n"
-            "- Only chart numbers that are explicitly present in retrieved document evidence."
-            " Never invent placeholder values.\n"
-            "- For requests like monthly revenue for a specific year, include all 12 months"
-            " if the evidence supports it; otherwise clearly state the data is incomplete.\n"
+            "- Use 'search_documents' whenever factual document evidence is needed.\n"
             "- Never call 'search_documents' repeatedly with the same query in a loop."
             " If you already called it and have results, produce a final answer.\n"
-            "- If 'generate_graph' returns an error, do NOT call it again with the same payload."
-            " Return a concise failure message asking for a clearer chart request.\n"
-            "- After calling 'generate_graph', keep your final text response brief (e.g. 'Here is your chart.'). "
-            "Do NOT re-list all the data points in your text answer — the chart already shows them."
+            "- Do not fabricate data. If evidence is missing, say so clearly."
         )
     )