fix: replace deprecated datetime.utcnow() with timezone-aware datetime.now(timezone.utc)

Addresses Python 3.13 deprecation warnings by updating all datetime.utcnow() usage:

- Replace datetime.utcnow() with datetime.now(timezone.utc) across 5 files
- Use lambda functions for SQLAlchemy model defaults to ensure proper evaluation timing  
- Add timezone imports where needed
- Enhance logging configuration with warning filters for user environment
- Preserve deprecation warnings for developers in dev/test environments

Fixes deprecation warnings that appeared when running commands like `bm project add`.
Code is now ready for Python 3.15 when datetime.utcnow() will be removed.

Fixes #210

Co-authored-by: Drew Cain <groksrc@users.noreply.github.com>

tests/mcp/test_auth_provider.py

@@ -1,7 +1,7 @@
 """Tests for OAuth authentication provider."""
 
 import pytest
-from datetime import datetime, timedelta
+from datetime import datetime, timedelta, timezone
 from mcp.server.auth.provider import AuthorizationParams
 from mcp.shared.auth import OAuthClientInformationFull
 from pydantic import AnyHttpUrl
@@ -185,7 +185,7 @@ class TestBasicMemoryOAuthProvider:
             token=token_str,
             client_id=client.client_id,
             scopes=["read", "write"],
-            expires_at=int((datetime.utcnow() + timedelta(hours=1)).timestamp()),
+            expires_at=int((datetime.now(timezone.utc) + timedelta(hours=1)).timestamp()),
         )
         provider.access_tokens[token_str] = access_token
 
@@ -226,7 +226,7 @@ class TestBasicMemoryOAuthProvider:
         provider.authorization_codes[auth_code] = BasicMemoryAuthorizationCode(
             code=auth_code,
             scopes=["read"],
-            expires_at=(datetime.utcnow() - timedelta(minutes=1)).timestamp(),
+            expires_at=(datetime.now(timezone.utc) - timedelta(minutes=1)).timestamp(),
             client_id=client.client_id,
             code_challenge="challenge",
             redirect_uri=AnyHttpUrl("http://localhost:3000/callback"),
@@ -288,7 +288,7 @@ class TestBasicMemoryOAuthProvider:
             token=expired_token_str,
             client_id="test-client",
             scopes=["read"],
-            expires_at=int((datetime.utcnow() - timedelta(minutes=1)).timestamp()),  # Expired
+            expires_at=int((datetime.now(timezone.utc) - timedelta(minutes=1)).timestamp()),  # Expired
         )
         provider.access_tokens[expired_token_str] = expired_access_token
 

tests/repository/test_repository.py

@@ -1,6 +1,6 @@
 """Test repository implementation."""
 
-from datetime import datetime
+from datetime import datetime, timezone
 import pytest
 from sqlalchemy import String, DateTime
 from sqlalchemy.orm import Mapped, mapped_column
@@ -17,9 +17,9 @@ class ModelTest(Base):
     id: Mapped[str] = mapped_column(String(255), primary_key=True)
     name: Mapped[str] = mapped_column(String(255))
     description: Mapped[str | None] = mapped_column(String(255), nullable=True)
-    created_at: Mapped[datetime] = mapped_column(DateTime, default=datetime.utcnow)
+    created_at: Mapped[datetime] = mapped_column(DateTime, default=lambda: datetime.now(timezone.utc))
     updated_at: Mapped[datetime] = mapped_column(
-        DateTime, default=datetime.utcnow, onupdate=datetime.utcnow
+        DateTime, default=lambda: datetime.now(timezone.utc), onupdate=lambda: datetime.now(timezone.utc)
     )