⚙️ Upgrade dependencies and synchronize documentation

CLAUDE.md

@@ -24,8 +24,8 @@ make test_nondeterministic # Run nondeterministic tests only
 make fmt            # Run ruff formatter + JSON formatting
 make ruff           # Run ruff linter
 make vulture        # Find dead code
-make ty             # Run typer type checker
-make ci             # Run all CI checks (ruff, vulture, ty)
+make ty             # Run type checker
+make ci             # Run all CI checks (ruff, vulture, ty, import_lint, docs_lint, check_deps)
 
 # Dependencies
 uv sync             # Install dependencies (not pip install)
@@ -46,11 +46,10 @@ uv run pytest path/to/test.py  # Run specific test
   - `<name>.yaml` - Optional split configs (loaded as root key `<name>`)
   - `global_config.py` - Config class (access via `from common import global_config`)
   - `.env` - Secrets/API keys (git-ignored)
-- **src/** - Source code (api/, db/, utils/, stripe/)
+- **src/** - Source code (utils/)
 - **utils/llm/** - LLM inference with DSPY (`dspy_inference.py`) and LangFuse observability
 - **tests/** - pytest tests inheriting from `TestTemplate` in `test_template.py`
 - **init/** - Initialization scripts (banner generation)
-- **alembic/** - Database migrations
 
 ## Code Style
 

README.md

@@ -57,7 +57,8 @@ Opinionated Python stack for fast development. The `saas` branch extends `main`
 - `make all` - runs `main.py`
 - `make fmt` - runs `ruff format` + JSON formatting
 - `make banner` - create a new banner that makes the README nice 😊
-- `make test` - runs all tests defined by `TEST_TARGETS = tests/folder1 tests/folder2`
+- `make test` - runs all tests in `tests/`
+- `make ci` - runs all CI checks (ruff, vulture, ty, etc.)
 
 
 

pyproject.toml

@@ -6,32 +6,32 @@ authors = [
     { name = "Miyamura80", email = "eitomiyamura@gmail.com" }
 ]
 dependencies = [
-    "pyyaml>=6.0.2",
-    "python-dotenv>=1.0.1",
+    "pyyaml>=6.0.3",
+    "python-dotenv>=1.2.1",
     "human-id>=0.2.0",
-    "import-linter>=2.0.0",
-    "pytest>=8.3.3",
+    "import-linter>=2.1.1",
+    "pytest>=8.3.4",
     "pytest-xdist>=3.6.1",
-    "termcolor>=2.4.0",
+    "termcolor>=2.5.0",
     "loguru>=0.7.3",
     "vulture>=2.14",
-    "dspy>=2.6.24",
-    "langfuse>=2.60.5",
-    "litellm>=1.70.0",
-    "tenacity>=9.1.2",
-    "pillow>=11.2.1",
-    "google-genai>=1.15.0",
-    "ty>=0.0.1a9",
-    "pytest-env>=1.1.5",
-    "pydantic-settings>=2.12.0",
+    "dspy>=3.1.2",
+    "langfuse>=3.12.1",
+    "litellm>=1.59.8",
+    "tenacity>=9.0.0",
+    "pillow>=12.1.0",
+    "google-genai>=1.60.0",
+    "ty>=0.0.14",
+    "pytest-env>=1.2.0",
+    "pydantic-settings>=2.7.1",
     "pytest-cov>=7.0.0",
-    "pytest-repeat>=0.9.4",
-    "pylint>=3.3.0",
-    "deptry>=0.24.0",
-    "openfeature-sdk>=0.8.4",
+    "pytest-repeat>=0.9.3",
+    "pylint>=3.3.3",
+    "deptry>=0.23.0",
+    "openfeature-sdk>=0.7.1",
     "scrubadub>=2.0.1",
-    "pydantic>=2.0.0",
-    "numpy>=1.26.0",
+    "pydantic>=2.10.6",
+    "numpy>=2.2.2",
 ]
 readme = "README.md"
 requires-python = ">= 3.12"
@@ -44,7 +44,7 @@ build-backend = "hatchling.build"
 allow-direct-references = true
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/python_template"]
+packages = ["src", "common", "utils"]
 
 [tool.ruff]
 line-length = 88

tests/healthcheck/test_env_var_loading.py

@@ -37,7 +37,7 @@ def test_env_var_loading_precedence(monkeypatch):
 
         # 3. Reload the common module to pick up the new .env file
         importlib.reload(common_module)
-        reloaded_config = common_module.global_config  # type: ignore
+        reloaded_config = common_module.global_config
 
         # 4. Assert that the variables are loaded with the correct precedence
         assert reloaded_config.DEV_ENV == "dotenv", "Should load from .env first"

tests/healthcheck/test_pydantic_type_coercion.py

@@ -36,7 +36,7 @@ def test_pydantic_type_coercion(monkeypatch):
 
     # Reload the config module to pick up the new environment variables
     importlib.reload(common_module)
-    config = common_module.global_config  # type: ignore[attr-defined]
+    config = common_module.global_config
 
     # Verify integer coercion
     assert isinstance(config.default_llm.default_max_tokens, int), (

tests/test_logging_security.py

@@ -14,23 +14,29 @@ def test_email_redaction(self):
         """Test that email addresses are redacted from log messages."""
         record = {"message": "User email is test@example.com", "exception": None}
         scrub_sensitive_data(record)
-        assert "test@example.com" not in record["message"]
-        assert "{{EMAIL}}" in record["message"]
+        message = record["message"]
+        assert isinstance(message, str)
+        assert "test@example.com" not in message
+        assert "{{EMAIL}}" in message
 
     def test_phone_redaction(self):
         """Test that phone numbers are redacted (new capability via scrubadub)."""
         record = {"message": "Call me at 1-800-555-0199", "exception": None}
         scrub_sensitive_data(record)
-        assert "1-800-555-0199" not in record["message"]
-        assert "{{PHONE}}" in record["message"]
+        message = record["message"]
+        assert isinstance(message, str)
+        assert "1-800-555-0199" not in message
+        assert "{{PHONE}}" in message
 
     def test_api_key_redaction(self):
         """Test that OpenAI API keys are redacted from log messages."""
         api_key = "sk-abc123def456ghi789jkl012mno345pqr678stu901"
         record = {"message": f"Using key: {api_key}", "exception": None}
         scrub_sensitive_data(record)
-        assert api_key not in record["message"]
-        assert "[REDACTED_API_KEY]" in record["message"]
+        message = record["message"]
+        assert isinstance(message, str)
+        assert api_key not in message
+        assert "[REDACTED_API_KEY]" in message
 
     def test_multiple_redactions(self):
         """Test redacting multiple sensitive items in a single message."""
@@ -39,10 +45,12 @@ def test_multiple_redactions(self):
             "exception": None,
         }
         scrub_sensitive_data(record)
-        assert "{{EMAIL}}" in record["message"]
-        assert "[REDACTED_API_KEY]" in record["message"]
-        assert "test@example.com" not in record["message"]
-        assert "sk-123456789012345678901234" not in record["message"]
+        message = record["message"]
+        assert isinstance(message, str)
+        assert "{{EMAIL}}" in message
+        assert "[REDACTED_API_KEY]" in message
+        assert "test@example.com" not in message
+        assert "sk-123456789012345678901234" not in message
 
     def test_exception_message_redaction(self):
         """Test that PII is redacted from exception messages."""
@@ -87,8 +95,10 @@ def test_anthropic_api_key_redaction(self):
         api_key = "sk-ant-api03-abc123def456ghi789jkl012mno345pqr678"
         record = {"message": f"Using Anthropic key: {api_key}", "exception": None}
         scrub_sensitive_data(record)
-        assert api_key not in record["message"]
-        assert "[REDACTED_API_KEY]" in record["message"]
+        message = record["message"]
+        assert isinstance(message, str)
+        assert api_key not in message
+        assert "[REDACTED_API_KEY]" in message
 
     def test_stripe_api_key_redaction(self):
         """Test that Stripe API keys are redacted."""
@@ -100,16 +110,20 @@ def test_stripe_api_key_redaction(self):
             key = prefix + suffix
             record = {"message": f"Stripe key: {key}", "exception": None}
             scrub_sensitive_data(record)
-            assert key not in record["message"]
-            assert "[REDACTED_API_KEY]" in record["message"]
+            message = record["message"]
+            assert isinstance(message, str)
+            assert key not in message
+            assert "[REDACTED_API_KEY]" in message
 
     def test_bearer_token_redaction(self):
         """Test that Authorization Bearer tokens are redacted."""
         token = "Bearer eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkw"
         record = {"message": f"Authorization: {token}", "exception": None}
         scrub_sensitive_data(record)
-        assert "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9" not in record["message"]
-        assert "[REDACTED_BEARER_TOKEN]" in record["message"]
+        message = record["message"]
+        assert isinstance(message, str)
+        assert "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9" not in message
+        assert "[REDACTED_BEARER_TOKEN]" in message
 
     def test_generic_api_key_redaction(self):
         """Test that generic api_key patterns are redacted."""
@@ -123,5 +137,7 @@ def test_generic_api_key_redaction(self):
         for pattern in patterns:
             record = {"message": f"Config: {pattern}", "exception": None}
             scrub_sensitive_data(record)
-            assert "abc123def456ghi789jkl012" not in record["message"]
-            assert "[REDACTED_KEY]" in record["message"]
+            message = record["message"]
+            assert isinstance(message, str)
+            assert "abc123def456ghi789jkl012" not in message
+            assert "[REDACTED_KEY]" in message

utils/llm/dspy_langfuse.py

@@ -6,7 +6,7 @@
 from dspy.utils.callback import BaseCallback
 from langfuse.client import Langfuse, StatefulGenerationClient  # type: ignore
 from langfuse.decorators import langfuse_context  # type: ignore
-from litellm.cost_calculator import completion_cost  # type: ignore
+from litellm.cost_calculator import completion_cost
 from loguru import logger as log
 from pydantic import BaseModel, Field, ValidationError
 
@@ -138,7 +138,7 @@ def on_lm_start(  # noqa
         parent_observation_id = langfuse_context.get_current_observation_id()
         span_obj: StatefulGenerationClient | None = None
         if trace_id:
-            span_obj = self.langfuse.generation(  # type: ignore (Langfuse fails the type check in this function, grr...)
+            span_obj = self.langfuse.generation(
                 input=user_input,
                 name=model_name,
                 trace_id=trace_id,
@@ -314,7 +314,7 @@ def on_lm_end(  # noqa
                         "total": total_cost,
                         # "cache_read_input_tokens": 0.0, # Optional
                     }
-                    span.update(  # type: ignore[call-arg] # Langfuse typing for update can be tricky
+                    span.update(
                         usage_details=usage_details_update,
                         cost_details=cost_details_update,
                     )
@@ -355,7 +355,7 @@ def on_lm_end(  # noqa
                 "status_message": status_message,
             }
             # Langfuse client's `end` method handles None for these specific optional parameters.
-            span.end(**end_args)  # type: ignore[call-arg] # Langfuse typing for end can be tricky
+            span.end(**end_args)
             self.current_span.set(None)
 
         if level == "DEFAULT" and completion_content is not None: