fix: #118 (#120)

* using toml lib+configs instead of dotenv stuff
* feat: secrets.toml is used
* chore: docs update - toml stuff added

Author: HardMax71

.github/workflows/docs.yml

@@ -42,6 +42,9 @@ jobs:
       - name: Install backend dependencies
         run: cd backend && uv sync --frozen
 
+      - name: Set up config for OpenAPI generation
+        run: cp backend/secrets.example.toml backend/secrets.toml
+
       - name: Generate OpenAPI spec
         run: ./deploy.sh openapi
 

.github/workflows/stack-tests.yml

@@ -48,6 +48,9 @@ jobs:
           uv python install 3.12
           uv sync --frozen
 
+      - name: Set up config
+        run: cp backend/secrets.example.toml backend/secrets.toml
+
       - name: Run unit tests
         timeout-minutes: 5
         run: |
@@ -211,7 +214,9 @@ jobs:
         uses: ./.github/actions/k3s-setup
 
       - name: Use test environment config
-        run: cp backend/.env.test backend/.env
+        run: |
+          cp backend/config.test.toml backend/config.toml
+          cp backend/secrets.example.toml backend/secrets.toml
 
       - name: Start stack
         run: ./deploy.sh dev --wait
@@ -322,7 +327,9 @@ jobs:
         uses: ./.github/actions/k3s-setup
 
       - name: Use test environment config
-        run: cp backend/.env.test backend/.env
+        run: |
+          cp backend/config.test.toml backend/config.toml
+          cp backend/secrets.example.toml backend/secrets.toml
 
       - name: Start stack
         run: ./deploy.sh dev --wait

.gitignore

@@ -64,6 +64,9 @@ dmypy.json
 .env.*.local
 *.local.env
 
+# TOML secrets (dev values — production mounts from K8s Secret)
+secrets.toml
+
 # Certificates (generated locally)
 certs/
 *.pem

backend/.env

@@ -5,7 +5,7 @@ FROM base
 COPY ./app /app/app
 COPY ./workers /app/workers
 COPY ./scripts /app/scripts
-COPY .env /app/.env
+COPY config.toml /app/config.toml
 COPY openssl.cnf /app/openssl.cnf
 
 # Ensure the certs directory exists
@@ -25,17 +25,16 @@ while [ ! -f /app/certs/server.key ]; do
 done
 
 echo "Starting application..."
-[ -f /app/kubeconfig.yaml ] && export KUBECONFIG=/app/kubeconfig.yaml
 
 exec gunicorn 'app.main:create_app()' \
   -k uvicorn.workers.UvicornWorker \
   --bind 0.0.0.0:443 \
-  --workers ${WEB_CONCURRENCY:-4} \
-  --threads ${WEB_THREADS:-1} \
-  --timeout ${WEB_TIMEOUT:-60} \
+  --workers 4 \
+  --threads 4 \
+  --timeout 60 \
   --graceful-timeout 30 \
   --keep-alive 2 \
-  --backlog ${WEB_BACKLOG:-2048} \
+  --backlog 2048 \
   --log-level info \
   --access-logfile - \
   --error-logfile - \

backend/.env.test

@@ -24,3 +24,4 @@ RUN uv sync --locked --no-dev --no-install-project
 # Set paths: PYTHONPATH for imports, PATH for venv binaries (no uv run needed at runtime)
 ENV PYTHONPATH=/app
 ENV PATH="/app/.venv/bin:$PATH"
+ENV KUBECONFIG=/app/kubeconfig.yaml

backend/Dockerfile

@@ -48,7 +48,7 @@ def create_app(settings: Settings | None = None) -> FastAPI:
 
     Args:
         settings: Optional pre-configured settings (e.g., TestSettings for testing).
-                 If None, creates Settings() which reads from env vars then .env file.
+                 If None, loads from config.toml.
     """
     settings = settings or Settings()
     logger = setup_logger(settings.LOG_LEVEL)

backend/Dockerfile.base

@@ -1,19 +1,53 @@
+import tomllib
+from pathlib import Path
 from typing import Literal
 
-from pydantic import Field
-from pydantic_settings import BaseSettings, SettingsConfigDict
+from pydantic import BaseModel, ConfigDict, Field
 
 from app.domain.execution import LanguageInfoDomain
 from app.runtime_registry import EXAMPLE_SCRIPTS as EXEC_EXAMPLE_SCRIPTS
 from app.runtime_registry import SUPPORTED_RUNTIMES as RUNTIME_MATRIX
 
 
-class Settings(BaseSettings):
+class Settings(BaseModel):
+    """Application settings loaded from TOML configuration files.
+
+    All config is read from TOML — no environment variables, no .env files.
+
+    Load order (each layer overrides the previous):
+        1. config_path    — base settings (committed to git)
+        2. secrets_path   — sensitive overrides (gitignored, mounted from K8s Secret in prod)
+        3. override_path  — per-worker service overrides (TRACING_SERVICE_NAME, etc.)
+
+    Usage:
+        Settings()                                                       # config.toml + secrets
+        Settings(config_path="config.test.toml")                         # test config (has own secrets)
+        Settings(override_path="config.coordinator.toml")                # base + secrets + worker
+    """
+
+    model_config = ConfigDict(extra="forbid")
+
+    def __init__(
+        self,
+        config_path: str = "config.toml",
+        override_path: str | None = None,
+        secrets_path: str = "secrets.toml",
+    ) -> None:
+        with open(config_path, "rb") as f:
+            data = tomllib.load(f)
+        if Path(secrets_path).is_file():
+            with open(secrets_path, "rb") as f:
+                data |= tomllib.load(f)
+        if override_path:
+            with open(override_path, "rb") as f:
+                data |= tomllib.load(f)
+        super().__init__(**data)
+
     PROJECT_NAME: str = "integr8scode"
     DATABASE_NAME: str = "integr8scode_db"
     API_V1_STR: str = "/api/v1"
     SECRET_KEY: str = Field(
-        ...,  # Actual key be loaded from .env file
+        ...,
         min_length=32,
         description="Secret key for JWT token signing. Must be at least 32 characters.",
     )
@@ -145,27 +179,14 @@ class Settings(BaseSettings):
     OTEL_RESOURCE_ATTRIBUTES: str | None = None
 
     # Web server (Gunicorn/Uvicorn) concurrency settings
-    # These are read from environment and used by the runtime entrypoint
-    # and by app.main when started directly via uvicorn.
     WEB_CONCURRENCY: int = 4
     WEB_THREADS: int = 1
     WEB_TIMEOUT: int = 60
     WEB_BACKLOG: int = 2048
 
-    # Additional MongoDB settings (for docker-compose compatibility)
-    MONGO_ROOT_USER: str | None = None
-    MONGO_ROOT_PASSWORD: str | None = None
-
     # Development mode detection
     DEVELOPMENT_MODE: bool = False
-    SECURE_COOKIES: bool = True  # Can be overridden in .env for development
+    SECURE_COOKIES: bool = True
 
     # Logging configuration
     LOG_LEVEL: str = Field(default="DEBUG", description="Logging level (DEBUG, INFO, WARNING, ERROR, CRITICAL)")
-
-    model_config = SettingsConfigDict(
-        env_file=".env",
-        env_file_encoding="utf-8",
-        case_sensitive=True,
-        extra="forbid",  # Raise error on extra fields
-    )

backend/app/main.py

@@ -0,0 +1,2 @@
+TRACING_SERVICE_NAME = "execution-coordinator"
+KAFKA_CONSUMER_GROUP_ID = "execution-coordinator"