Merge branch 'main' into fix-issue-71-20250406012335

Author: phernandez

.github/workflows/test.yml

@@ -5,6 +5,12 @@ on:
     branches: [ "main" ]
   pull_request:
     branches: [ "main" ]
+  # pull_request_target runs on the BASE of the PR, not the merge result.
+  # It has write permissions and access to secrets.
+  # It's useful for PRs from forks or automated PRs but requires careful use for security reasons.
+  # See: https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows#pull_request_target
+  pull_request_target:
+    branches: [ "main" ]
 
 jobs:
   test:

README.md

@@ -13,8 +13,8 @@ Basic Memory lets you build persistent knowledge through natural conversations w
 Claude, while keeping everything in simple Markdown files on your computer. It uses the Model Context Protocol (MCP) to
 enable any compatible LLM to read and write to your local knowledge base.
 
-- Website: http://basicmachines.co
-- Documentation: http://memory.basicmachines.co
+- Website: https://basicmachines.co
+- Documentation: https://memory.basicmachines.co
 
 ## Pick up your conversation right where you left off
 
@@ -262,6 +262,43 @@ Examples of relations:
 - documented_in [[Coffee Journal]]
 ```
 
+## Using with VS Code
+For one-click installation, click one of the install buttons below...
+
+[![Install with UV in VS Code](https://img.shields.io/badge/VS_Code-UV-0098FF?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=basic-memory&config=%7B%22command%22%3A%22uvx%22%2C%22args%22%3A%5B%22basic-memory%22%2C%22mcp%22%5D%7D) [![Install with UV in VS Code Insiders](https://img.shields.io/badge/VS_Code_Insiders-UV-24bfa5?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=basic-memory&config=%7B%22command%22%3A%22uvx%22%2C%22args%22%3A%5B%22basic-memory%22%2C%22mcp%22%5D%7D&quality=insiders)
+
+You can use Basic Memory with VS Code to easily retrieve and store information while coding. Click the installation buttons above for one-click setup, or follow the manual installation instructions below.
+
+### Manual Installation
+
+Add the following JSON block to your User Settings (JSON) file in VS Code. You can do this by pressing `Ctrl + Shift + P` and typing `Preferences: Open User Settings (JSON)`.
+
+```json
+{
+  "mcp": {
+    "servers": {
+      "basic-memory": {
+        "command": "uvx",
+        "args": ["basic-memory", "mcp"]
+      }
+    }
+  }
+}
+```
+
+Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others.
+
+```json
+{
+  "servers": {
+    "basic-memory": {
+      "command": "uvx",
+      "args": ["basic-memory", "mcp"]
+    }
+  }
+}
+```
+
 ## Using with Claude Desktop
 
 Basic Memory is built using the MCP (Model Context Protocol) and works with the Claude desktop app (https://claude.ai/):

src/basic_memory/mcp/server.py

@@ -4,8 +4,8 @@
 from mcp.server.fastmcp.utilities.logging import configure_logging
 
 # mcp console logging
-configure_logging(level="INFO")
+configure_logging(level="ERROR")
 
 
 # Create the shared server instance
-mcp = FastMCP("Basic Memory")
+mcp = FastMCP("Basic Memory", log_level="ERROR")

src/basic_memory/sync/sync_service.py

@@ -362,18 +362,25 @@ async def sync_markdown_file(self, path: str, new: bool = True) -> Tuple[Optiona
         # Update relations and search index
         entity = await self.entity_service.update_entity_relations(path, entity_markdown)
 
+        # After updating relations, we need to compute the checksum again
+        # This is necessary for files with wikilinks to ensure consistent checksums
+        # after relation processing is complete
+        final_checksum = await self.file_service.compute_checksum(path)
+        
         # set checksum
-        await self.entity_repository.update(entity.id, {"checksum": checksum})
-
+        await self.entity_repository.update(entity.id, {"checksum": final_checksum})
+        
         logger.debug(
             "Markdown sync completed",
             path=path,
             entity_id=entity.id,
             observation_count=len(entity.observations),
             relation_count=len(entity.relations),
+            checksum=final_checksum,
         )
-
-        return entity, checksum
+        
+        # Return the final checksum to ensure everything is consistent
+        return entity, final_checksum
 
     async def sync_regular_file(self, path: str, new: bool = True) -> Tuple[Optional[Entity], str]:
         """Sync a non-markdown file with basic tracking.

tests/sync/test_sync_wikilink_issue.py

@@ -0,0 +1,62 @@
+"""Test for issue #72 - notes with wikilinks staying in modified status."""
+
+import pytest
+from pathlib import Path
+
+from basic_memory.sync.sync_service import SyncService
+
+
+async def create_test_file(path: Path, content: str) -> None:
+    """Create a test file with given content."""
+    path.parent.mkdir(parents=True, exist_ok=True)
+    path.write_text(content)
+
+
+@pytest.mark.asyncio
+async def test_wikilink_modified_status_issue(sync_service: SyncService, test_config):
+    """Test that files with wikilinks don't remain in modified status after sync."""
+    project_dir = test_config.home
+
+    # Create a file with a wikilink
+    content = """---
+title: Test Wikilink
+type: note
+---
+# Test File
+
+This file contains a wikilink to [[another-file]].
+"""
+    test_file_path = project_dir / "test_wikilink.md"
+    await create_test_file(test_file_path, content)
+
+    # Initial sync
+    report1 = await sync_service.sync(test_config.home, show_progress=False)
+    assert "test_wikilink.md" in report1.new
+    assert "test_wikilink.md" not in report1.modified
+
+    # Sync again without changing the file - should not be modified
+    report2 = await sync_service.sync(test_config.home, show_progress=False)
+    assert "test_wikilink.md" not in report2.new
+    assert "test_wikilink.md" not in report2.modified
+
+    # Create the target file
+    target_content = """---
+title: Another File
+type: note
+---
+# Another File
+
+This is the target file.
+"""
+    target_file_path = project_dir / "another_file.md"
+    await create_test_file(target_file_path, content)
+
+    # Sync again after adding target file
+    report3 = await sync_service.sync(test_config.home, show_progress=False)
+    assert "another_file.md" in report3.new
+    assert "test_wikilink.md" not in report3.modified
+
+    # Sync one more time - both files should now be stable
+    report4 = await sync_service.sync(test_config.home, show_progress=False)
+    assert "test_wikilink.md" not in report4.modified
+    assert "another_file.md" not in report4.modified