chore(release): 0.7.0 [skip ci]

Co-authored-by: phernandez <phernandez@basicmachines.co>

CHANGELOG.md

@@ -1,6 +1,78 @@
 # CHANGELOG
 
 
+## v0.7.0 (2025-02-19)
+
+### Bug Fixes
+
+- Add logfire instrumentation to tools
+  ([`3e8e3e8`](https://github.com/basicmachines-co/basic-memory/commit/3e8e3e8961eae2e82839746e28963191b0aef0a0))
+
+- Add logfire spans to cli
+  ([`00d23a5`](https://github.com/basicmachines-co/basic-memory/commit/00d23a5ee15ddac4ea45e702dcd02ab9f0509276))
+
+- Add logfire spans to cli
+  ([`812136c`](https://github.com/basicmachines-co/basic-memory/commit/812136c8c22ad191d14ff32dcad91aae076d4120))
+
+- Search query pagination params
+  ([`bc9ca07`](https://github.com/basicmachines-co/basic-memory/commit/bc9ca0744ffe4296d7d597b4dd9b7c73c2d63f3f))
+
+### Chores
+
+- Fix tests
+  ([`57984aa`](https://github.com/basicmachines-co/basic-memory/commit/57984aa912625dcde7877afb96d874c164af2896))
+
+- Remove unused tests
+  ([`2c8ed17`](https://github.com/basicmachines-co/basic-memory/commit/2c8ed1737d6769fe1ef5c96f8a2bd75b9899316a))
+
+### Features
+
+- Add cli commands for mcp tools
+  ([`f5a7541`](https://github.com/basicmachines-co/basic-memory/commit/f5a7541da17e97403b7a702720a05710f68b223a))
+
+- Add pagination to build_context and recent_activity
+  ([`0123544`](https://github.com/basicmachines-co/basic-memory/commit/0123544556513af943d399d70b849b142b834b15))
+
+- Add pagination to read_notes
+  ([`02f8e86`](https://github.com/basicmachines-co/basic-memory/commit/02f8e866923d5793d2620076c709c920d99f2c4f))
+
+
+## v0.6.0 (2025-02-18)
+
+### Chores
+
+- Re-add sync status console on watch
+  ([`66b57e6`](https://github.com/basicmachines-co/basic-memory/commit/66b57e682f2e9c432bffd4af293b0d1db1d3469b))
+
+### Features
+
+- Configure logfire telemetry ([#12](https://github.com/basicmachines-co/basic-memory/pull/12),
+  [`6da1438`](https://github.com/basicmachines-co/basic-memory/commit/6da143898bd45cdab8db95b5f2b75810fbb741ba))
+
+Co-authored-by: phernandez <phernandez@basicmachines.co>
+
+
+## v0.5.0 (2025-02-18)
+
+### Features
+
+- Return semantic info in markdown after write_note
+  ([#11](https://github.com/basicmachines-co/basic-memory/pull/11),
+  [`0689e7a`](https://github.com/basicmachines-co/basic-memory/commit/0689e7a730497827bf4e16156ae402ddc5949077))
+
+Co-authored-by: phernandez <phernandez@basicmachines.co>
+
+
+## v0.4.3 (2025-02-18)
+
+### Bug Fixes
+
+- Re do enhanced read note format ([#10](https://github.com/basicmachines-co/basic-memory/pull/10),
+  [`39bd5ca`](https://github.com/basicmachines-co/basic-memory/commit/39bd5ca08fd057220b95a8b5d82c5e73a1f5722b))
+
+Co-authored-by: phernandez <phernandez@basicmachines.co>
+
+
 ## v0.4.2 (2025-02-17)
 
 

Makefile

@@ -1,10 +1,10 @@
-.PHONY: install test lint clean format type-check installer-mac installer-win
+.PHONY: install test lint clean format type-check installer-mac installer-win check
 
 install:
 	pip install -e ".[dev]"
 
 test:
-	pytest -p pytest_mock -v
+	uv run pytest -p pytest_mock -v
 
 lint:
 	ruff check . --fix
@@ -41,3 +41,5 @@ installer-win:
 
 update-deps:
 	uv lock f--upgrade
+
+check: lint  format type-check test

installer/installer.py

@@ -49,7 +49,14 @@ def update_claude_config():
         config = {"mcpServers": {}}
 
     # Add/update basic-memory config
-    config["mcpServers"]["basic-memory"] = {"command": "uvx", "args": ["basic-memory", "mcp"]}
+    config["mcpServers"]["basic-memory"] = {
+        "command": "uvx",
+        "args": ["basic-memory@latest", "mcp"],
+        "env": {
+            "BASIC_MEMORY_ENV": "user",
+            "LOGFIRE_TOKEN": "n2Fpvn34LjKYq8TdF1ZrXMgdBPXGn4HfXy6tYghZ55dB",
+        },
+    }
 
     # Write back config
     config_path.write_text(json.dumps(config, indent=2))

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "basic-memory"
-version = "0.4.2"
+version = "0.7.0"
 description = "Local-first knowledge management combining Zettelkasten with knowledge graphs"
 readme = "README.md"
 requires-python = ">=3.12.1"
@@ -29,6 +29,7 @@ dependencies = [
     "fastapi[standard]>=0.115.8",
     "alembic>=1.14.1",
     "qasync>=0.27.1",
+    "logfire[fastapi,httpx,sqlalchemy,sqlite3]>=3.6.0",
 ]
 
 

src/basic_memory/__init__.py

@@ -1,3 +1,3 @@
 """basic-memory - Local-first knowledge management combining Zettelkasten with knowledge graphs"""
 
-__version__ = "0.4.2"
+__version__ = "0.7.0"

src/basic_memory/api/app.py

@@ -2,6 +2,7 @@
 
 from contextlib import asynccontextmanager
 
+import logfire
 from fastapi import FastAPI, HTTPException
 from fastapi.exception_handlers import http_exception_handler
 from loguru import logger
@@ -10,11 +11,13 @@ import basic_memory
 from basic_memory import db
 from basic_memory.config import config as app_config
 from basic_memory.api.routers import knowledge, search, memory, resource
+from basic_memory.utils import setup_logging
 
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):  # pragma: no cover
     """Lifecycle manager for the FastAPI app."""
+    setup_logging(log_file=".basic-memory/basic-memory.log")
     logger.info(f"Starting Basic Memory API {basic_memory.__version__}")
     await db.run_migrations(app_config)
     yield
@@ -30,6 +33,10 @@ app = FastAPI(
     lifespan=lifespan,
 )
 
+if app_config != "test":
+    logfire.instrument_fastapi(app)
+
+
 # Include routers
 app.include_router(knowledge.router)
 app.include_router(search.router)

src/basic_memory/api/routers/knowledge_router.py

@@ -94,11 +94,8 @@ async def get_entity(
     try:
         entity = await entity_service.get_by_permalink(permalink)
         result = EntityResponse.model_validate(entity)
-
-        logger.info(f"response: get_entity with result={result}")
         return result
     except EntityNotFoundError:
-        logger.error(f"Error: Entity with {permalink} not found")
         raise HTTPException(status_code=404, detail=f"Entity with {permalink} not found")
 
 
@@ -114,8 +111,6 @@ async def get_entities(
     result = EntityListResponse(
         entities=[EntityResponse.model_validate(entity) for entity in entities]
     )
-
-    logger.info(f"response: get_entities with result={result}")
     return result
 
 
@@ -135,7 +130,6 @@ async def delete_entity(
 
     entity = await link_resolver.resolve_link(identifier)
     if entity is None:
-        logger.info("response: delete_entity with result=DeleteEntitiesResponse(deleted=False)")
         return DeleteEntitiesResponse(deleted=False)
 
     # Delete the entity
@@ -145,7 +139,6 @@ async def delete_entity(
     background_tasks.add_task(search_service.delete_by_permalink, entity.permalink)
 
     result = DeleteEntitiesResponse(deleted=deleted)
-    logger.info(f"response: delete_entity with result={result}")
     return result
 
 
@@ -166,5 +159,4 @@ async def delete_entities(
         background_tasks.add_task(search_service.delete_by_permalink, permalink)
 
     result = DeleteEntitiesResponse(deleted=deleted)
-    logger.info(f"response: delete_entities with result={result}")
     return result

src/basic_memory/api/routers/memory_router.py

@@ -24,7 +24,7 @@ from basic_memory.services.context_service import ContextResultRow
 router = APIRouter(prefix="/memory", tags=["memory"])
 
 
-async def to_graph_context(context, entity_repository: EntityRepository):
+async def to_graph_context(context, entity_repository: EntityRepository, page: int, page_size: int):
     # return results
     async def to_summary(item: SearchIndexRow | ContextResultRow):
         match item.type:
@@ -66,7 +66,11 @@ async def to_graph_context(context, entity_repository: EntityRepository):
     metadata = MemoryMetadata.model_validate(context["metadata"])
     # Transform to GraphContext
     return GraphContext(
-        primary_results=primary_results, related_results=related_results, metadata=metadata
+        primary_results=primary_results,
+        related_results=related_results,
+        metadata=metadata,
+        page=page,
+        page_size=page_size,
     )
 
 
@@ -77,7 +81,9 @@ async def recent(
     type: Annotated[list[SearchItemType] | None, Query()] = None,
     depth: int = 1,
     timeframe: TimeFrame = "7d",
-    max_results: int = 10,
+    page: int = 1,
+    page_size: int = 10,
+    max_related: int = 10,
 ) -> GraphContext:
     # return all types by default
     types = (
@@ -87,16 +93,20 @@ async def recent(
     )
 
     logger.debug(
-        f"Getting recent context: `{types}` depth: `{depth}` timeframe: `{timeframe}` max_results: `{max_results}`"
+        f"Getting recent context: `{types}` depth: `{depth}` timeframe: `{timeframe}` page: `{page}` page_size: `{page_size}` max_related: `{max_related}`"
     )
     # Parse timeframe
     since = parse(timeframe)
+    limit = page_size
+    offset = (page - 1) * page_size
 
     # Build context
     context = await context_service.build_context(
-        types=types, depth=depth, since=since, max_results=max_results
+        types=types, depth=depth, since=since, limit=limit, offset=offset, max_related=max_related
+    )
+    return await to_graph_context(
+        context, entity_repository=entity_repository, page=page, page_size=page_size
     )
-    return await to_graph_context(context, entity_repository=entity_repository)
 
 
 # get_memory_context needs to be declared last so other paths can match
@@ -109,21 +119,27 @@ async def get_memory_context(
     uri: str,
     depth: int = 1,
     timeframe: TimeFrame = "7d",
-    max_results: int = 10,
+    page: int = 1,
+    page_size: int = 10,
+    max_related: int = 10,
 ) -> GraphContext:
     """Get rich context from memory:// URI."""
     # add the project name from the config to the url as the "host
     # Parse URI
     logger.debug(
-        f"Getting context for URI: `{uri}` depth: `{depth}` timeframe: `{timeframe}` max_results: `{max_results}`"
+        f"Getting context for URI: `{uri}` depth: `{depth}` timeframe: `{timeframe}` page: `{page}` page_size: `{page_size}` max_related: `{max_related}`"
     )
     memory_url = normalize_memory_url(uri)
 
     # Parse timeframe
     since = parse(timeframe)
+    limit = page_size
+    offset = (page - 1) * page_size
 
     # Build context
     context = await context_service.build_context(
-        memory_url, depth=depth, since=since, max_results=max_results
+        memory_url, depth=depth, since=since, limit=limit, offset=offset, max_related=max_related
+    )
+    return await to_graph_context(
+        context, entity_repository=entity_repository, page=page, page_size=page_size
     )
-    return await to_graph_context(context, entity_repository=entity_repository)

src/basic_memory/api/routers/resource_router.py

@@ -1,34 +1,124 @@
 """Routes for getting entity content."""
 
+import tempfile
 from pathlib import Path
 
-from fastapi import APIRouter, HTTPException
+from fastapi import APIRouter, HTTPException, BackgroundTasks
 from fastapi.responses import FileResponse
 from loguru import logger
 
-from basic_memory.deps import ProjectConfigDep, LinkResolverDep
+from basic_memory.deps import (
+    ProjectConfigDep,
+    LinkResolverDep,
+    SearchServiceDep,
+    EntityServiceDep,
+    FileServiceDep,
+)
+from basic_memory.repository.search_repository import SearchIndexRow
+from basic_memory.schemas.memory import normalize_memory_url
+from basic_memory.schemas.search import SearchQuery, SearchItemType
 
 router = APIRouter(prefix="/resource", tags=["resources"])
 
 
+def get_entity_ids(item: SearchIndexRow) -> set[int]:
+    match item.type:
+        case SearchItemType.ENTITY:
+            return {item.id}
+        case SearchItemType.OBSERVATION:
+            return {item.entity_id}  # pyright: ignore [reportReturnType]
+        case SearchItemType.RELATION:
+            from_entity = item.from_id
+            to_entity = item.to_id  # pyright: ignore [reportReturnType]
+            return {from_entity, to_entity} if to_entity else {from_entity}  # pyright: ignore [reportReturnType]
+        case _:  # pragma: no cover
+            raise ValueError(f"Unexpected type: {item.type}")
+
+
 @router.get("/{identifier:path}")
 async def get_resource_content(
     config: ProjectConfigDep,
     link_resolver: LinkResolverDep,
+    search_service: SearchServiceDep,
+    entity_service: EntityServiceDep,
+    file_service: FileServiceDep,
+    background_tasks: BackgroundTasks,
     identifier: str,
+    page: int = 1,
+    page_size: int = 10,
 ) -> FileResponse:
     """Get resource content by identifier: name or permalink."""
-    logger.debug(f"Getting content for permalink: {identifier}")
+    logger.debug(f"Getting content for: {identifier}")
 
-    # Find entity by permalink
+    # Find single entity by permalink
     entity = await link_resolver.resolve_link(identifier)
-    if not entity:
-        raise HTTPException(status_code=404, detail=f"Entity not found: {identifier}")
+    results = [entity] if entity else []
 
-    file_path = Path(f"{config.home}/{entity.file_path}")
-    if not file_path.exists():
-        raise HTTPException(
-            status_code=404,
-            detail=f"File not found: {file_path}",
+    # pagination for multiple results
+    limit = page_size
+    offset = (page - 1) * page_size
+
+    # search using the identifier as a permalink
+    if not results:
+        # if the identifier contains a wildcard, use GLOB search
+        query = (
+            SearchQuery(permalink_match=identifier)
+            if "*" in identifier
+            else SearchQuery(permalink=identifier)
         )
-    return FileResponse(path=file_path)
+        search_results = await search_service.search(query, limit, offset)
+        if not search_results:
+            raise HTTPException(status_code=404, detail=f"Resource not found: {identifier}")
+
+        # get the deduplicated entities related to the search results
+        entity_ids = {id for result in search_results for id in get_entity_ids(result)}
+        results = await entity_service.get_entities_by_id(list(entity_ids))
+
+    # return single response
+    if len(results) == 1:
+        entity = results[0]
+        file_path = Path(f"{config.home}/{entity.file_path}")
+        if not file_path.exists():
+            raise HTTPException(
+                status_code=404,
+                detail=f"File not found: {file_path}",
+            )
+        return FileResponse(path=file_path)
+
+    # for multiple files, initialize a temporary file for writing the results
+    with tempfile.NamedTemporaryFile(delete=False, mode="w", suffix=".md") as tmp_file:
+        temp_file_path = tmp_file.name
+
+        for result in results:
+            # Read content for each entity
+            content = await file_service.read_entity_content(result)
+            memory_url = normalize_memory_url(result.permalink)
+            modified_date = result.updated_at.isoformat()
+            assert result.checksum
+            checksum = result.checksum[:8]
+
+            # Prepare the delimited content
+            response_content = f"--- {memory_url} {modified_date} {checksum}\n"
+            response_content += f"\n{content}\n"
+            response_content += "\n"
+
+            # Write content directly to the temporary file in append mode
+            tmp_file.write(response_content)
+
+        # Ensure all content is written to disk
+        tmp_file.flush()
+
+    # Schedule the temporary file to be deleted after the response
+    background_tasks.add_task(cleanup_temp_file, temp_file_path)
+
+    # Return the file response
+    return FileResponse(path=temp_file_path)
+
+
+def cleanup_temp_file(file_path: str):
+    """Delete the temporary file."""
+    try:
+        Path(file_path).unlink()  # Deletes the file
+        logger.debug(f"Temporary file deleted: {file_path}")
+    except Exception as e:  # pragma: no cover
+        logger.error(f"Error deleting temporary file {file_path}: {e}")

src/basic_memory/api/routers/search_router.py

@@ -2,27 +2,35 @@
 
 from dataclasses import asdict
 
-from fastapi import APIRouter, Depends, BackgroundTasks
+from fastapi import APIRouter, BackgroundTasks
 
-from basic_memory.services.search_service import SearchService
 from basic_memory.schemas.search import SearchQuery, SearchResult, SearchResponse
-from basic_memory.deps import get_search_service
+from basic_memory.deps import SearchServiceDep
 
 router = APIRouter(prefix="/search", tags=["search"])
 
 
 @router.post("/", response_model=SearchResponse)
-async def search(query: SearchQuery, search_service: SearchService = Depends(get_search_service)):
+async def search(
+    query: SearchQuery,
+    search_service: SearchServiceDep,
+    page: int = 1,
+    page_size: int = 10,
+):
     """Search across all knowledge and documents."""
-    results = await search_service.search(query)
+    limit = page_size
+    offset = (page - 1) * page_size
+    results = await search_service.search(query, limit=limit, offset=offset)
     search_results = [SearchResult.model_validate(asdict(r)) for r in results]
-    return SearchResponse(results=search_results)
+    return SearchResponse(
+        results=search_results,
+        current_page=page,
+        page_size=page_size,
+    )
 
 
 @router.post("/reindex")
-async def reindex(
-    background_tasks: BackgroundTasks, search_service: SearchService = Depends(get_search_service)
-):
+async def reindex(background_tasks: BackgroundTasks, search_service: SearchServiceDep):
     """Recreate and populate the search index."""
     await search_service.reindex_all(background_tasks=background_tasks)
     return {"status": "ok", "message": "Reindex initiated"}

src/basic_memory/cli/app.py

@@ -6,7 +6,7 @@ from basic_memory import db
 from basic_memory.config import config
 from basic_memory.utils import setup_logging
 
-setup_logging(log_file=".basic-memory/basic-memory-cli.log")  # pragma: no cover
+setup_logging(log_file=".basic-memory/basic-memory-cli.log", console=False)  # pragma: no cover
 
 asyncio.run(db.run_migrations(config))
 

src/basic_memory/cli/commands/db.py

@@ -1,6 +1,8 @@
 """Database management commands."""
 
 import asyncio
+
+import logfire
 import typer
 from loguru import logger
 
@@ -13,13 +15,14 @@ def reset(
     reindex: bool = typer.Option(False, "--reindex", help="Rebuild indices from filesystem"),
 ):  # pragma: no cover
     """Reset database (drop all tables and recreate)."""
-    if typer.confirm("This will delete all data. Are you sure?"):
-        logger.info("Resetting database...")
-        asyncio.run(migrations.reset_database())
+    with logfire.span("reset"):  # pyright: ignore [reportGeneralTypeIssues]
+        if typer.confirm("This will delete all data in your db. Are you sure?"):
+            logger.info("Resetting database...")
+            asyncio.run(migrations.reset_database())
 
-        if reindex:
-            # Import and run sync
-            from basic_memory.cli.commands.sync import sync
+            if reindex:
+                # Import and run sync
+                from basic_memory.cli.commands.sync import sync
 
-            logger.info("Rebuilding search index from filesystem...")
-            sync(watch=False)  # pyright: ignore
+                logger.info("Rebuilding search index from filesystem...")
+                sync(watch=False)  # pyright: ignore

src/basic_memory/cli/commands/import_chatgpt.py

@@ -6,6 +6,7 @@ from datetime import datetime
 from pathlib import Path
 from typing import Dict, Any, List, Annotated, Set, Optional
 
+import logfire
 import typer
 from loguru import logger
 from rich.console import Console
@@ -69,7 +70,11 @@ def traverse_messages(
 
 
 def format_chat_markdown(
-    title: str, mapping: Dict[str, Any], root_id: Optional[str], created_at: float, modified_at: float
+    title: str,
+    mapping: Dict[str, Any],
+    root_id: Optional[str],
+    created_at: float,
+    modified_at: float,
 ) -> str:
     """Format chat as clean markdown."""
 
@@ -205,7 +210,7 @@ async def get_markdown_processor() -> MarkdownProcessor:
 @import_app.command(name="chatgpt", help="Import conversations from ChatGPT JSON export.")
 def import_chatgpt(
     conversations_json: Annotated[
-        Path, typer.Option(..., help="Path to ChatGPT conversations.json file")
+        Path, typer.Argument(help="Path to ChatGPT conversations.json file")
     ] = Path("conversations.json"),
     folder: Annotated[
         str, typer.Option(help="The folder to place the files in.")
@@ -221,35 +226,38 @@ def import_chatgpt(
     After importing, run 'basic-memory sync' to index the new files.
     """
 
-    try:
-        if conversations_json:
-            if not conversations_json.exists():
-                typer.echo(f"Error: File not found: {conversations_json}", err=True)
-                raise typer.Exit(1)
+    with logfire.span("import chatgpt"):  # pyright: ignore [reportGeneralTypeIssues]
+        try:
+            if conversations_json:
+                if not conversations_json.exists():
+                    typer.echo(f"Error: File not found: {conversations_json}", err=True)
+                    raise typer.Exit(1)
 
-            # Get markdown processor
-            markdown_processor = asyncio.run(get_markdown_processor())
+                # Get markdown processor
+                markdown_processor = asyncio.run(get_markdown_processor())
 
-            # Process the file
-            base_path = config.home / folder
-            console.print(f"\nImporting chats from {conversations_json}...writing to {base_path}")
-            results = asyncio.run(
-                process_chatgpt_json(conversations_json, folder, markdown_processor)
-            )
-
-            # Show results
-            console.print(
-                Panel(
-                    f"[green]Import complete![/green]\n\n"
-                    f"Imported {results['conversations']} conversations\n"
-                    f"Containing {results['messages']} messages",
-                    expand=False,
+                # Process the file
+                base_path = config.home / folder
+                console.print(
+                    f"\nImporting chats from {conversations_json}...writing to {base_path}"
+                )
+                results = asyncio.run(
+                    process_chatgpt_json(conversations_json, folder, markdown_processor)
                 )
-            )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+                # Show results
+                console.print(
+                    Panel(
+                        f"[green]Import complete![/green]\n\n"
+                        f"Imported {results['conversations']} conversations\n"
+                        f"Containing {results['messages']} messages",
+                        expand=False,
+                    )
+                )
 
-    except Exception as e:
-        logger.error("Import failed")
-        typer.echo(f"Error during import: {e}", err=True)
-        raise typer.Exit(1)
+            console.print("\nRun 'basic-memory sync' to index the new files.")
+
+        except Exception as e:
+            logger.error("Import failed")
+            typer.echo(f"Error during import: {e}", err=True)
+            raise typer.Exit(1)

src/basic_memory/cli/commands/import_claude_conversations.py

@@ -6,6 +6,7 @@ from datetime import datetime
 from pathlib import Path
 from typing import Dict, Any, List, Annotated
 
+import logfire
 import typer
 from loguru import logger
 from rich.console import Console
@@ -178,34 +179,35 @@ def import_claude(
     After importing, run 'basic-memory sync' to index the new files.
     """
 
-    try:
-        if not conversations_json.exists():
-            typer.echo(f"Error: File not found: {conversations_json}", err=True)
-            raise typer.Exit(1)
+    with logfire.span("import claude conversations"):  # pyright: ignore [reportGeneralTypeIssues]
+        try:
+            if not conversations_json.exists():
+                typer.echo(f"Error: File not found: {conversations_json}", err=True)
+                raise typer.Exit(1)
 
-        # Get markdown processor
-        markdown_processor = asyncio.run(get_markdown_processor())
+            # Get markdown processor
+            markdown_processor = asyncio.run(get_markdown_processor())
 
-        # Process the file
-        base_path = config.home / folder
-        console.print(f"\nImporting chats from {conversations_json}...writing to {base_path}")
-        results = asyncio.run(
-            process_conversations_json(conversations_json, base_path, markdown_processor)
-        )
-
-        # Show results
-        console.print(
-            Panel(
-                f"[green]Import complete![/green]\n\n"
-                f"Imported {results['conversations']} conversations\n"
-                f"Containing {results['messages']} messages",
-                expand=False,
+            # Process the file
+            base_path = config.home / folder
+            console.print(f"\nImporting chats from {conversations_json}...writing to {base_path}")
+            results = asyncio.run(
+                process_conversations_json(conversations_json, base_path, markdown_processor)
             )
-        )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+            # Show results
+            console.print(
+                Panel(
+                    f"[green]Import complete![/green]\n\n"
+                    f"Imported {results['conversations']} conversations\n"
+                    f"Containing {results['messages']} messages",
+                    expand=False,
+                )
+            )
 
-    except Exception as e:
-        logger.error("Import failed")
-        typer.echo(f"Error during import: {e}", err=True)
-        raise typer.Exit(1)
+            console.print("\nRun 'basic-memory sync' to index the new files.")
+
+        except Exception as e:
+            logger.error("Import failed")
+            typer.echo(f"Error during import: {e}", err=True)
+            raise typer.Exit(1)

src/basic_memory/cli/commands/import_claude_projects.py

@@ -5,6 +5,7 @@ import json
 from pathlib import Path
 from typing import Dict, Any, Annotated, Optional
 
+import logfire
 import typer
 from loguru import logger
 from rich.console import Console
@@ -160,36 +161,36 @@ def import_projects(
 
     After importing, run 'basic-memory sync' to index the new files.
     """
+    with logfire.span("import claude projects"):  # pyright: ignore [reportGeneralTypeIssues]
+        try:
+            if projects_json:
+                if not projects_json.exists():
+                    typer.echo(f"Error: File not found: {projects_json}", err=True)
+                    raise typer.Exit(1)
 
-    try:
-        if projects_json:
-            if not projects_json.exists():
-                typer.echo(f"Error: File not found: {projects_json}", err=True)
-                raise typer.Exit(1)
+                # Get markdown processor
+                markdown_processor = asyncio.run(get_markdown_processor())
 
-            # Get markdown processor
-            markdown_processor = asyncio.run(get_markdown_processor())
-
-            # Process the file
-            base_path = config.home / base_folder if base_folder else config.home
-            console.print(f"\nImporting projects from {projects_json}...writing to {base_path}")
-            results = asyncio.run(
-                process_projects_json(projects_json, base_path, markdown_processor)
-            )
-
-            # Show results
-            console.print(
-                Panel(
-                    f"[green]Import complete![/green]\n\n"
-                    f"Imported {results['documents']} project documents\n"
-                    f"Imported {results['prompts']} prompt templates",
-                    expand=False,
+                # Process the file
+                base_path = config.home / base_folder if base_folder else config.home
+                console.print(f"\nImporting projects from {projects_json}...writing to {base_path}")
+                results = asyncio.run(
+                    process_projects_json(projects_json, base_path, markdown_processor)
                 )
-            )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+                # Show results
+                console.print(
+                    Panel(
+                        f"[green]Import complete![/green]\n\n"
+                        f"Imported {results['documents']} project documents\n"
+                        f"Imported {results['prompts']} prompt templates",
+                        expand=False,
+                    )
+                )
 
-    except Exception as e:
-        logger.error("Import failed")
-        typer.echo(f"Error during import: {e}", err=True)
-        raise typer.Exit(1)
+            console.print("\nRun 'basic-memory sync' to index the new files.")
+
+        except Exception as e:
+            logger.error("Import failed")
+            typer.echo(f"Error during import: {e}", err=True)
+            raise typer.Exit(1)

src/basic_memory/cli/commands/import_memory_json.py

@@ -5,6 +5,7 @@ import json
 from pathlib import Path
 from typing import Dict, Any, List, Annotated
 
+import logfire
 import typer
 from loguru import logger
 from rich.console import Console
@@ -113,32 +114,33 @@ def memory_json(
     After importing, run 'basic-memory sync' to index the new files.
     """
 
-    if not json_path.exists():
-        typer.echo(f"Error: File not found: {json_path}", err=True)
-        raise typer.Exit(1)
+    with logfire.span("import memory_json"):  # pyright: ignore [reportGeneralTypeIssues]
+        if not json_path.exists():
+            typer.echo(f"Error: File not found: {json_path}", err=True)
+            raise typer.Exit(1)
 
-    try:
-        # Get markdown processor
-        markdown_processor = asyncio.run(get_markdown_processor())
+        try:
+            # Get markdown processor
+            markdown_processor = asyncio.run(get_markdown_processor())
 
-        # Process the file
-        base_path = config.home
-        console.print(f"\nImporting from {json_path}...writing to {base_path}")
-        results = asyncio.run(process_memory_json(json_path, base_path, markdown_processor))
+            # Process the file
+            base_path = config.home
+            console.print(f"\nImporting from {json_path}...writing to {base_path}")
+            results = asyncio.run(process_memory_json(json_path, base_path, markdown_processor))
 
-        # Show results
-        console.print(
-            Panel(
-                f"[green]Import complete![/green]\n\n"
-                f"Created {results['entities']} entities\n"
-                f"Added {results['relations']} relations",
-                expand=False,
+            # Show results
+            console.print(
+                Panel(
+                    f"[green]Import complete![/green]\n\n"
+                    f"Created {results['entities']} entities\n"
+                    f"Added {results['relations']} relations",
+                    expand=False,
+                )
             )
-        )
 
-        console.print("\nRun 'basic-memory sync' to index the new files.")
+            console.print("\nRun 'basic-memory sync' to index the new files.")
 
-    except Exception as e:
-        logger.error("Import failed")
-        typer.echo(f"Error during import: {e}", err=True)
-        raise typer.Exit(1)
+        except Exception as e:
+            logger.error("Import failed")
+            typer.echo(f"Error during import: {e}", err=True)
+            raise typer.Exit(1)

src/basic_memory/cli/commands/status.py

@@ -3,6 +3,7 @@
 import asyncio
 from typing import Set, Dict
 
+import logfire
 import typer
 from loguru import logger
 from rich.console import Console
@@ -146,9 +147,10 @@ def status(
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed file information"),
 ):
     """Show sync status between files and database."""
-    try:
-        sync_service = asyncio.run(get_file_change_scanner())
-        asyncio.run(run_status(sync_service, verbose))  # pragma: no cover
-    except Exception as e:
-        logger.exception(f"Error checking status: {e}")
-        raise typer.Exit(code=1)  # pragma: no cover
+    with logfire.span("status"):  # pyright: ignore [reportGeneralTypeIssues]
+        try:
+            sync_service = asyncio.run(get_file_change_scanner())
+            asyncio.run(run_status(sync_service, verbose))  # pragma: no cover
+        except Exception as e:
+            logger.exception(f"Error checking status: {e}")
+            raise typer.Exit(code=1)  # pragma: no cover

src/basic_memory/cli/commands/sync.py

@@ -151,7 +151,7 @@ def display_detailed_sync_results(knowledge: SyncReport):
         console.print(knowledge_tree)
 
 
-async def run_sync(verbose: bool = False, watch: bool = False):
+async def run_sync(verbose: bool = False, watch: bool = False, console_status: bool = False):
     """Run sync operation."""
 
     sync_service = await get_sync_service()
@@ -164,7 +164,7 @@ async def run_sync(verbose: bool = False, watch: bool = False):
             config=config,
         )
         await watch_service.handle_changes(config.home)
-        await watch_service.run()  # pragma: no cover
+        await watch_service.run(console_status=console_status)  # pragma: no cover
     else:
         # one time sync
         knowledge_changes = await sync_service.sync(config.home)
@@ -189,11 +189,14 @@ def sync(
         "-w",
         help="Start watching for changes after sync.",
     ),
+    console_status: bool = typer.Option(
+        False, "--console-status", "-c", help="Show live console status"
+    ),
 ) -> None:
     """Sync knowledge files with the database."""
     try:
         # Run sync
-        asyncio.run(run_sync(verbose=verbose, watch=watch))
+        asyncio.run(run_sync(verbose=verbose, watch=watch, console_status=console_status))
 
     except Exception as e:  # pragma: no cover
         if not isinstance(e, typer.Exit):

src/basic_memory/cli/commands/tools.py

@@ -0,0 +1,157 @@
+"""Database management commands."""
+
+import asyncio
+from typing import Optional, List, Annotated
+
+import typer
+from rich import print as rprint
+
+from basic_memory.cli.app import app
+from basic_memory.mcp.tools import build_context as mcp_build_context
+from basic_memory.mcp.tools import get_entity as mcp_get_entity
+from basic_memory.mcp.tools import read_note as mcp_read_note
+from basic_memory.mcp.tools import recent_activity as mcp_recent_activity
+from basic_memory.mcp.tools import search as mcp_search
+from basic_memory.mcp.tools import write_note as mcp_write_note
+from basic_memory.schemas.base import TimeFrame
+from basic_memory.schemas.memory import MemoryUrl
+from basic_memory.schemas.search import SearchQuery
+
+tool_app = typer.Typer()
+app.add_typer(tool_app, name="tools", help="cli versions mcp tools")
+
+
+@tool_app.command()
+def write_note(
+    title: Annotated[str, typer.Option(help="The title of the note")],
+    content: Annotated[str, typer.Option(help="The content of the note")],
+    folder: Annotated[str, typer.Option(help="The folder to create the note in")],
+    tags: Annotated[
+        Optional[List[str]], typer.Option(help="A list of tags to apply to the note")
+    ] = None,
+):
+    try:
+        note = asyncio.run(mcp_write_note(title, content, folder, tags))
+        rprint(note)
+    except Exception as e:  # pragma: no cover
+        if not isinstance(e, typer.Exit):
+            typer.echo(f"Error during write_note: {e}", err=True)
+            raise typer.Exit(1)
+        raise
+
+
+@tool_app.command()
+def read_note(identifier: str, page: int = 1, page_size: int = 10):
+    try:
+        note = asyncio.run(mcp_read_note(identifier, page, page_size))
+        rprint(note)
+    except Exception as e:  # pragma: no cover
+        if not isinstance(e, typer.Exit):
+            typer.echo(f"Error during read_note: {e}", err=True)
+            raise typer.Exit(1)
+        raise
+
+
+@tool_app.command()
+def build_context(
+    url: MemoryUrl,
+    depth: Optional[int] = 1,
+    timeframe: Optional[TimeFrame] = "7d",
+    page: int = 1,
+    page_size: int = 10,
+    max_related: int = 10,
+):
+    try:
+        context = asyncio.run(
+            mcp_build_context(
+                url=url,
+                depth=depth,
+                timeframe=timeframe,
+                page=page,
+                page_size=page_size,
+                max_related=max_related,
+            )
+        )
+        rprint(context.model_dump())
+    except Exception as e:  # pragma: no cover
+        if not isinstance(e, typer.Exit):
+            typer.echo(f"Error during build_context: {e}", err=True)
+            raise typer.Exit(1)
+        raise
+
+
+@tool_app.command()
+def recent_activity(
+    type: Annotated[Optional[List[str]], typer.Option()] = ["entity", "observation", "relation"],
+    depth: Optional[int] = 1,
+    timeframe: Optional[TimeFrame] = "7d",
+    page: int = 1,
+    page_size: int = 10,
+    max_related: int = 10,
+):
+    assert type is not None, "type is required"
+    if any(t not in ["entity", "observation", "relation"] for t in type):  # pragma: no cover
+        print("type must be one of ['entity', 'observation', 'relation']")
+        raise typer.Abort()
+
+    try:
+        context = asyncio.run(
+            mcp_recent_activity(
+                type=type,  # pyright: ignore [reportArgumentType]
+                depth=depth,
+                timeframe=timeframe,
+                page=page,
+                page_size=page_size,
+                max_related=max_related,
+            )
+        )
+        rprint(context.model_dump())
+    except Exception as e:  # pragma: no cover
+        if not isinstance(e, typer.Exit):
+            typer.echo(f"Error during build_context: {e}", err=True)
+            raise typer.Exit(1)
+        raise
+
+
+@tool_app.command()
+def search(
+    query: str,
+    permalink: Annotated[bool, typer.Option("--permalink", help="Search permalink values")] = False,
+    title: Annotated[bool, typer.Option("--title", help="Search title values")] = False,
+    after_date: Annotated[
+        Optional[str],
+        typer.Option("--after_date", help="Search results after date, eg. '2d', '1 week'"),
+    ] = None,
+    page: int = 1,
+    page_size: int = 10,
+):
+    if permalink and title:  # pragma: no cover
+        print("Cannot search both permalink and title")
+        raise typer.Abort()
+
+    try:
+        search_query = SearchQuery(
+            permalink_match=query if permalink else None,
+            text=query if query else None,
+            title=query if title else None,
+            after_date=after_date,
+        )
+        results = asyncio.run(mcp_search(query=search_query, page=page, page_size=page_size))
+        rprint(results.model_dump())
+    except Exception as e:  # pragma: no cover
+        if not isinstance(e, typer.Exit):
+            typer.echo(f"Error during search: {e}", err=True)
+            raise typer.Exit(1)
+        raise
+
+
+@tool_app.command()
+def get_entity(identifier: str):
+    try:
+        entity = asyncio.run(mcp_get_entity(identifier=identifier))
+        rprint(entity.model_dump())
+    except Exception as e:  # pragma: no cover
+        if not isinstance(e, typer.Exit):
+            typer.echo(f"Error during get_entity: {e}", err=True)
+            raise typer.Exit(1)
+        raise

src/basic_memory/cli/main.py

@@ -1,7 +1,6 @@
 """Main CLI entry point for basic-memory."""  # pragma: no cover
 
 from basic_memory.cli.app import app  # pragma: no cover
-from basic_memory.utils import setup_logging  # pragma: no cover
 
 # Register commands
 from basic_memory.cli.commands import (  # noqa: F401  # pragma: no cover
@@ -13,11 +12,9 @@ from basic_memory.cli.commands import (  # noqa: F401  # pragma: no cover
     import_claude_conversations,
     import_claude_projects,
     import_chatgpt,
+    tools,
 )
 
 
-# Set up logging when module is imported
-setup_logging(log_file=".basic-memory/basic-memory-cli.log")  # pragma: no cover
-
 if __name__ == "__main__":  # pragma: no cover
     app()

src/basic_memory/config.py

@@ -1,6 +1,7 @@
 """Configuration management for basic-memory."""
 
 from pathlib import Path
+from typing import Literal
 
 from pydantic import Field, field_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
@@ -8,10 +9,14 @@ from pydantic_settings import BaseSettings, SettingsConfigDict
 DATABASE_NAME = "memory.db"
 DATA_DIR_NAME = ".basic-memory"
 
+Environment = Literal["test", "dev", "user"]
+
 
 class ProjectConfig(BaseSettings):
     """Configuration for a specific basic-memory project."""
 
+    env: Environment = Field(default="dev", description="Environment name")
+
     # Default to ~/basic-memory but allow override with env var: BASIC_MEMORY_HOME
     home: Path = Field(
         default_factory=lambda: Path.home() / "basic-memory",

src/basic_memory/db.py

@@ -4,6 +4,7 @@ from enum import Enum, auto
 from pathlib import Path
 from typing import AsyncGenerator, Optional
 
+
 from basic_memory.config import ProjectConfig
 from alembic import command
 from alembic.config import Config
@@ -140,11 +141,15 @@ async def run_migrations(app_config: ProjectConfig, database_type=DatabaseType.F
 
         # Set required Alembic config options programmatically
         config.set_main_option("script_location", str(alembic_dir))
-        config.set_main_option("file_template",
-                               "%%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d%%(minute).2d-%%(rev)s_%%(slug)s")
+        config.set_main_option(
+            "file_template",
+            "%%(year)d_%%(month).2d_%%(day).2d_%%(hour).2d%%(minute).2d-%%(rev)s_%%(slug)s",
+        )
         config.set_main_option("timezone", "UTC")
         config.set_main_option("revision_environment", "false")
-        config.set_main_option("sqlalchemy.url", DatabaseType.get_db_url(app_config.database_path, database_type))
+        config.set_main_option(
+            "sqlalchemy.url", DatabaseType.get_db_url(app_config.database_path, database_type)
+        )
 
         command.upgrade(config, "head")
         logger.info("Migrations completed successfully")
@@ -153,4 +158,4 @@ async def run_migrations(app_config: ProjectConfig, database_type=DatabaseType.F
         await SearchRepository(session_maker).init_search_index()
     except Exception as e:  # pragma: no cover
         logger.error(f"Error running migrations: {e}")
-        raise
+        raise

src/basic_memory/deps.py

@@ -2,6 +2,7 @@
 
 from typing import Annotated
 
+import logfire
 from fastapi import Depends
 from sqlalchemy.ext.asyncio import (
     AsyncSession,
@@ -43,7 +44,10 @@ async def get_engine_factory(
     project_config: ProjectConfigDep,
 ) -> tuple[AsyncEngine, async_sessionmaker[AsyncSession]]:  # pragma: no cover
     """Get engine and session maker."""
-    return await db.get_or_create_db(project_config.database_path)
+    engine, session_maker = await db.get_or_create_db(project_config.database_path)
+    if project_config.env != "test":
+        logfire.instrument_sqlalchemy(engine=engine)
+    return engine, session_maker
 
 
 EngineFactoryDep = Annotated[

src/basic_memory/mcp/tools/knowledge.py

@@ -1,8 +1,10 @@
 """Knowledge graph management tools for Basic Memory MCP server."""
 
+import logfire
+
 from basic_memory.mcp.server import mcp
 from basic_memory.mcp.tools.utils import call_get, call_post
-from basic_memory.schemas.base import Permalink
+from basic_memory.schemas.memory import memory_url_path
 from basic_memory.schemas.request import (
     GetEntitiesRequest,
 )
@@ -16,15 +18,17 @@ from basic_memory.mcp.async_client import client
 @mcp.tool(
     description="Get complete information about a specific entity including observations and relations",
 )
-async def get_entity(permalink: Permalink) -> EntityResponse:
+async def get_entity(identifier: str) -> EntityResponse:
     """Get a specific entity info by its permalink.
 
     Args:
-        permalink: Path identifier for the entity
+        identifier: Path identifier for the entity
     """
-    url = f"/knowledge/entities/{permalink}"
-    response = await call_get(client, url)
-    return EntityResponse.model_validate(response.json())
+    with logfire.span("Getting entity", permalink=identifier):  # pyright: ignore [reportGeneralTypeIssues]
+        permalink = memory_url_path(identifier)
+        url = f"/knowledge/entities/{permalink}"
+        response = await call_get(client, url)
+        return EntityResponse.model_validate(response.json())
 
 
 @mcp.tool(
@@ -39,11 +43,16 @@ async def get_entities(request: GetEntitiesRequest) -> EntityListResponse:
     Returns:
         EntityListResponse containing complete details for each requested entity
     """
-    url = "/knowledge/entities"
-    response = await call_get(
-        client, url, params=[("permalink", permalink) for permalink in request.permalinks]
-    )
-    return EntityListResponse.model_validate(response.json())
+    with logfire.span("Getting multiple entities", permalink_count=len(request.permalinks)):  # pyright: ignore [reportGeneralTypeIssues]
+        url = "/knowledge/entities"
+        response = await call_get(
+            client,
+            url,
+            params=[
+                ("permalink", memory_url_path(identifier)) for identifier in request.permalinks
+            ],
+        )
+        return EntityListResponse.model_validate(response.json())
 
 
 @mcp.tool(
@@ -51,6 +60,9 @@ async def get_entities(request: GetEntitiesRequest) -> EntityListResponse:
 )
 async def delete_entities(request: DeleteEntitiesRequest) -> DeleteEntitiesResponse:
     """Delete entities from the knowledge graph."""
-    url = "/knowledge/entities/delete"
-    response = await call_post(client, url, json=request.model_dump())
-    return DeleteEntitiesResponse.model_validate(response.json())
+    with logfire.span("Deleting entities", permalink_count=len(request.permalinks)):  # pyright: ignore [reportGeneralTypeIssues]
+        url = "/knowledge/entities/delete"
+
+        request.permalinks = [memory_url_path(permlink) for permlink in request.permalinks]
+        response = await call_post(client, url, json=request.model_dump())
+        return DeleteEntitiesResponse.model_validate(response.json())

src/basic_memory/mcp/tools/memory.py

@@ -3,6 +3,7 @@
 from typing import Optional, Literal, List
 
 from loguru import logger
+import logfire
 
 from basic_memory.mcp.async_client import client
 from basic_memory.mcp.server import mcp
@@ -32,7 +33,9 @@ async def build_context(
     url: MemoryUrl,
     depth: Optional[int] = 1,
     timeframe: Optional[TimeFrame] = "7d",
-    max_results: int = 10,
+    page: int = 1,
+    page_size: int = 10,
+    max_related: int = 10,
 ) -> GraphContext:
     """Get context needed to continue a discussion.
 
@@ -44,7 +47,9 @@ async def build_context(
         url: memory:// URI pointing to discussion content (e.g. memory://specs/search)
         depth: How many relation hops to traverse (1-3 recommended for performance)
         timeframe: How far back to look. Supports natural language like "2 days ago", "last week"
-        max_results: Maximum number of results to return (default: 10)
+        page: Page number of results to return (default: 1)
+        page_size: Number of results to return per page (default: 10)
+        max_related: Maximum number of related results to return (default: 10)
 
     Returns:
         GraphContext containing:
@@ -65,14 +70,21 @@ async def build_context(
         # Research the history of a feature
         build_context("memory://features/knowledge-graph", timeframe="3 months ago")
     """
-    logger.info(f"Building context from {url}")
-    url = normalize_memory_url(url)
-    response = await call_get(
-        client,
-        f"/memory/{memory_url_path(url)}",
-        params={"depth": depth, "timeframe": timeframe, "max_results": max_results},
-    )
-    return GraphContext.model_validate(response.json())
+    with logfire.span("Building context", url=url, depth=depth, timeframe=timeframe):  # pyright: ignore [reportGeneralTypeIssues]
+        logger.info(f"Building context from {url}")
+        url = normalize_memory_url(url)
+        response = await call_get(
+            client,
+            f"/memory/{memory_url_path(url)}",
+            params={
+                "depth": depth,
+                "timeframe": timeframe,
+                "page": page,
+                "page_size": page_size,
+                "max_related": max_related,
+            },
+        )
+        return GraphContext.model_validate(response.json())
 
 
 @mcp.tool(
@@ -91,7 +103,9 @@ async def recent_activity(
     type: List[Literal["entity", "observation", "relation"]] = [],
     depth: Optional[int] = 1,
     timeframe: Optional[TimeFrame] = "7d",
-    max_results: int = 10,
+    page: int = 1,
+    page_size: int = 10,
+    max_related: int = 10,
 ) -> GraphContext:
     """Get recent activity across the knowledge base.
 
@@ -106,7 +120,9 @@ async def recent_activity(
             - Relative: "2 days ago", "last week", "yesterday"
             - Points in time: "2024-01-01", "January 1st"
             - Standard format: "7d", "24h"
-        max_results: Maximum number of results to return (default: 10)
+        page: Page number of results to return (default: 1)
+        page_size: Number of results to return per page (default: 10)
+        max_related: Maximum number of related results to return (default: 10)
 
     Returns:
         GraphContext containing:
@@ -132,20 +148,23 @@ async def recent_activity(
         - For focused queries, consider using build_context with a specific URI
         - Max timeframe is 1 year in the past
     """
-    logger.info(
-        f"Getting recent activity from {type}, depth={depth}, timeframe={timeframe}, max_results={max_results}"
-    )
-    params = {
-        "depth": depth,
-        "timeframe": timeframe,
-        "max_results": max_results,
-    }
-    if type:
-        params["type"] = type
+    with logfire.span("Getting recent activity", type=type, depth=depth, timeframe=timeframe):  # pyright: ignore [reportGeneralTypeIssues]
+        logger.info(
+            f"Getting recent activity from {type}, depth={depth}, timeframe={timeframe}, page={page}, page_size={page_size}, max_related={max_related}"
+        )
+        params = {
+            "depth": depth,
+            "timeframe": timeframe,
+            "page": page,
+            "page_size": page_size,
+            "max_related": max_related,
+        }
+        if type:
+            params["type"] = type
 
-    response = await call_get(
-        client,
-        "/memory/recent",
-        params=params,
-    )
-    return GraphContext.model_validate(response.json())
+        response = await call_get(
+            client,
+            "/memory/recent",
+            params=params,
+        )
+        return GraphContext.model_validate(response.json())

src/basic_memory/mcp/tools/notes.py

@@ -7,6 +7,7 @@ while leveraging the underlying knowledge graph structure.
 from typing import Optional, List
 
 from loguru import logger
+import logfire
 
 from basic_memory.mcp.server import mcp
 from basic_memory.mcp.async_client import client
@@ -17,90 +18,165 @@ from basic_memory.schemas.memory import memory_url_path
 
 
 @mcp.tool(
-    description="Create or update a markdown note. Returns the permalink for referencing.",
+    description="Create or update a markdown note. Returns a markdown formatted summary of the semantic content.",
 )
 async def write_note(
     title: str,
     content: str,
     folder: str,
     tags: Optional[List[str]] = None,
-    verbose: bool = False,
-) -> EntityResponse | str:
+) -> str:
     """Write a markdown note to the knowledge base.
 
+    The content can include semantic observations and relations using markdown syntax.
+    Relations can be specified either explicitly or through inline wiki-style links:
+
+    Observations format:
+        `- [category] Observation text #tag1 #tag2 (optional context)`
+
+        Examples:
+        `- [design] Files are the source of truth #architecture (All state comes from files)`
+        `- [tech] Using SQLite for storage #implementation`
+        `- [note] Need to add error handling #todo`
+
+    Relations format:
+        - Explicit: `- relation_type [[Entity]] (optional context)`
+        - Inline: Any `[[Entity]]` reference creates a relation
+
+        Examples:
+        `- depends_on [[Content Parser]] (Need for semantic extraction)`
+        `- implements [[Search Spec]] (Initial implementation)`
+        `- This feature extends [[Base Design]] and uses [[Core Utils]]`
+
     Args:
         title: The title of the note
-        content: Markdown content for the note
+        content: Markdown content for the note, can include observations and relations
         folder: the folder where the file should be saved
         tags: Optional list of tags to categorize the note
-        verbose: If True, returns full EntityResponse with semantic info
 
     Returns:
-        If verbose=False: Permalink that can be used to reference the note
-        If verbose=True: EntityResponse with full semantic details
-
-    Examples:
-        # Create a simple note
-        write_note(
-            tile="Meeting Notes: Project Planning.md",
-            content="# Key Points\\n\\n- Discussed timeline\\n- Set priorities"
-            folder="notes"
-        )
-
-        # Create note with tags
-        write_note(
-            title="Security Review",
-            content="# Findings\\n\\n1. Updated auth flow\\n2. Added rate limiting",
-            folder="security",
-            tags=["security", "development"]
-        )
+        A markdown formatted summary of the semantic content, including:
+        - Creation/update status
+        - File path and checksum
+        - Observation counts by category
+        - Relation counts (resolved/unresolved)
+        - Tags if present
     """
-    logger.info(f"Writing note folder:'{folder}' title: '{title}'")
+    with logfire.span("Writing note", title=title, folder=folder):  # pyright: ignore [reportGeneralTypeIssues]
+        logger.info(f"Writing note folder:'{folder}' title: '{title}'")
 
-    # Create the entity request
-    metadata = {"tags": [f"#{tag}" for tag in tags]} if tags else None
-    entity = Entity(
-        title=title,
-        folder=folder,
-        entity_type="note",
-        content_type="text/markdown",
-        content=content,
-        entity_metadata=metadata,
-    )
+        # Create the entity request
+        metadata = {"tags": [f"#{tag}" for tag in tags]} if tags else None
+        entity = Entity(
+            title=title,
+            folder=folder,
+            entity_type="note",
+            content_type="text/markdown",
+            content=content,
+            entity_metadata=metadata,
+        )
 
-    # Use existing knowledge tool
-    logger.info(f"Creating {entity.permalink}")
-    url = f"/knowledge/entities/{entity.permalink}"
-    response = await call_put(client, url, json=entity.model_dump())
-    result = EntityResponse.model_validate(response.json())
-    return result if verbose else result.permalink
+        # Create or update via knowledge API
+        logger.info(f"Creating {entity.permalink}")
+        url = f"/knowledge/entities/{entity.permalink}"
+        response = await call_put(client, url, json=entity.model_dump())
+        result = EntityResponse.model_validate(response.json())
+
+        # Format semantic summary based on status code
+        action = "Created" if response.status_code == 201 else "Updated"
+        assert result.checksum is not None
+        summary = [
+            f"# {action} {result.file_path} ({result.checksum[:8]})",
+            f"permalink: {result.permalink}",
+        ]
+
+        if result.observations:
+            categories = {}
+            for obs in result.observations:
+                categories[obs.category] = categories.get(obs.category, 0) + 1
+
+            summary.append("\n## Observations")
+            for category, count in sorted(categories.items()):
+                summary.append(f"- {category}: {count}")
+
+        if result.relations:
+            unresolved = sum(1 for r in result.relations if not r.to_id)
+            resolved = len(result.relations) - unresolved
+
+            summary.append("\n## Relations")
+            summary.append(f"- Resolved: {resolved}")
+            if unresolved:
+                summary.append(f"- Unresolved: {unresolved}")
+                summary.append("\nUnresolved relations will be retried on next sync.")
+
+        if tags:
+            summary.append(f"\n## Tags\n- {', '.join(tags)}")
+
+        return "\n".join(summary)
 
 
-@mcp.tool(description="Read a note's content by its title or permalink")
-async def read_note(identifier: str) -> str:
-    """Get the markdown content of a note.
-    Uses the resource router to return the actual file content.
+@mcp.tool(description="Read note content by title, permalink, relation, or pattern")
+async def read_note(identifier: str, page: int = 1, page_size: int = 10) -> str:
+    """Get note content in unified diff format.
+
+    The content is returned in a unified diff inspired format:
+    ```
+    --- memory://docs/example 2025-01-31T19:32:49 7d9f1c8b
+    <document content>
+    ```
+
+    Multiple documents (from relations or pattern matches) are separated by
+    additional headers.
 
     Args:
-        identifier: Note title or permalink
+        identifier: Can be one of:
+            - Note title ("Project Planning")
+            - Note permalink ("docs/example")
+            - Relation path ("docs/example/depends-on/other-doc")
+            - Pattern match ("docs/*-architecture")
+        page: the page number of results to return (default 1)
+        page_size: the number of results to return per page (default 10)
 
     Returns:
-        The note's markdown content
+        Document content in unified diff format. For single documents, returns
+        just that document's content. For relations or pattern matches, returns
+        multiple documents separated by unified diff headers.
 
     Examples:
-        # Read by title
-        read_note("Meeting Notes: Project Planning")
+        # Single document
+        content = await read_note("Project Planning")
 
         # Read by permalink
-        read_note("notes/project-planning")
+        content = await read_note("docs/architecture/file-first")
 
-    Raises:
-        ValueError: If the note cannot be found
+        # Follow relation
+        content = await read_note("docs/architecture/depends-on/docs/content-parser")
+
+        # Pattern matching
+        content = await read_note("docs/*-architecture")  # All architecture docs
+        content = await read_note("docs/*/implements/*")  # Find implementations
+
+    Output format:
+        ```
+        --- memory://docs/example 2025-01-31T19:32:49 7d9f1c8b
+        <first document content>
+
+        --- memory://docs/other 2025-01-30T15:45:22 a1b2c3d4
+        <second document content>
+        ```
+
+    The headers include:
+    - Full memory:// URI for the document
+    - Last modified timestamp
+    - Content checksum
     """
-    logger.info(f"Reading note {identifier}")
-    url = memory_url_path(identifier)
-    response = await call_get(client, f"/resource/{url}")
-    return response.text
+    with logfire.span("Reading note", identifier=identifier):  # pyright: ignore [reportGeneralTypeIssues]
+        logger.info(f"Reading note {identifier}")
+        url = memory_url_path(identifier)
+        response = await call_get(
+            client, f"/resource/{url}", params={"page": page, "page_size": page_size}
+        )
+        return response.text
 
 
 @mcp.tool(description="Delete a note by title or permalink")
@@ -120,6 +196,7 @@ async def delete_note(identifier: str) -> bool:
         # Delete by permalink
         delete_note("notes/project-planning")
     """
-    response = await call_delete(client, f"/knowledge/entities/{identifier}")
-    result = DeleteEntitiesResponse.model_validate(response.json())
-    return result.deleted
+    with logfire.span("Deleting note", identifier=identifier):  # pyright: ignore [reportGeneralTypeIssues]
+        response = await call_delete(client, f"/knowledge/entities/{identifier}")
+        result = DeleteEntitiesResponse.model_validate(response.json())
+        return result.deleted

src/basic_memory/mcp/tools/search.py

@@ -1,5 +1,6 @@
 """Search tools for Basic Memory MCP server."""
 
+import logfire
 from loguru import logger
 
 from basic_memory.mcp.server import mcp
@@ -11,7 +12,7 @@ from basic_memory.mcp.async_client import client
 @mcp.tool(
     description="Search across all content in basic-memory, including documents and entities",
 )
-async def search(query: SearchQuery) -> SearchResponse:
+async def search(query: SearchQuery, page: int = 1, page_size: int = 10) -> SearchResponse:
     """Search across all content in basic-memory.
 
     Args:
@@ -20,10 +21,18 @@ async def search(query: SearchQuery) -> SearchResponse:
             - types: Optional list of content types to search ("document" or "entity")
             - entity_types: Optional list of entity types to filter by
             - after_date: Optional date filter for recent content
+        page: the page number of results to return (default 1)
+        page_size: the number of results to return per page (default 10)
 
     Returns:
         SearchResponse with search results and metadata
     """
-    logger.info(f"Searching for {query.text}")
-    response = await call_post(client, "/search/", json=query.model_dump())
-    return SearchResponse.model_validate(response.json())
+    with logfire.span("Searching for {query}", query=query):  # pyright: ignore [reportGeneralTypeIssues]
+        logger.info(f"Searching for {query}")
+        response = await call_post(
+            client,
+            "/search/",
+            json=query.model_dump(),
+            params={"page": page, "page_size": page_size},
+        )
+        return SearchResponse.model_validate(response.json())

src/basic_memory/repository/search_repository.py

@@ -68,24 +68,40 @@ class SearchRepository:
 
     async def init_search_index(self):
         """Create or recreate the search index."""
-
         logger.info("Initializing search index")
-        async with db.scoped_session(self.session_maker) as session:
-            await session.execute(CREATE_SEARCH_INDEX)
-            await session.commit()
+        try:
+            async with db.scoped_session(self.session_maker) as session:
+                await session.execute(CREATE_SEARCH_INDEX)
+                await session.commit()
+        except Exception as e:  # pragma: no cover
+            logger.error(f"Error initializing search index: {e}")
+            raise e
 
-    def _quote_search_term(self, term: str) -> str:
-        """Add quotes if term contains special characters.
-        For FTS5, special characters and phrases need to be quoted to be treated as a single token.
+    def _prepare_search_term(self, term: str, is_prefix: bool = True) -> str:
+        """Prepare a search term for FTS5 query.
+
+        Args:
+            term: The search term to prepare
+            is_prefix: Whether to add prefix search capability (* suffix)
+
+        For FTS5:
+        - Special characters and phrases need to be quoted
+        - Terms with spaces or special chars need quotes
         """
-        # List of special characters that need quoting
-        special_chars = ["/", "*", "-", ".", " ", "(", ")", "[", "]", '"', "'"]
+        if "*" in term:
+            return term
+
+        # List of special characters that need quoting (excluding *)
+        special_chars = ["/", "-", ".", " ", "(", ")", "[", "]", '"', "'"]
 
         # Check if term contains any special characters
-        if any(c in term for c in special_chars):
-            # If the term already contains quotes, escape them
+        needs_quotes = any(c in term for c in special_chars)
+
+        if needs_quotes:
+            # If the term already contains quotes, escape them and add a wildcard
             term = term.replace('"', '""')
-            return f'"{term}"'
+            term = f'"{term}"*'
+
         return term
 
     async def search(
@@ -98,6 +114,7 @@ class SearchRepository:
         after_date: Optional[datetime] = None,
         entity_types: Optional[List[str]] = None,
         limit: int = 10,
+        offset: int = 0,
     ) -> List[SearchIndexRow]:
         """Search across all indexed content with fuzzy matching."""
         conditions = []
@@ -106,14 +123,14 @@ class SearchRepository:
 
         # Handle text search for title and content
         if search_text:
-            search_text = self._quote_search_term(search_text.lower().strip())
-            params["text"] = f"{search_text}*"
+            search_text = self._prepare_search_term(search_text.strip())
+            params["text"] = search_text
             conditions.append("(title MATCH :text OR content MATCH :text)")
 
         # Handle title match search
         if title:
-            title_text = self._quote_search_term(title.lower().strip())
-            params["text"] = f"{title_text}*"
+            title_text = self._prepare_search_term(title.strip())
+            params["text"] = title_text
             conditions.append("title MATCH :text")
 
         # Handle permalink exact search
@@ -123,8 +140,15 @@ class SearchRepository:
 
         # Handle permalink match search, supports *
         if permalink_match:
-            params["permalink"] = self._quote_search_term(permalink_match)
-            conditions.append("permalink MATCH :permalink")
+            # Clean and prepare permalink for FTS5 GLOB match
+            permalink_text = self._prepare_search_term(
+                permalink_match.lower().strip(), is_prefix=False
+            )
+            params["permalink"] = permalink_text
+            if "*" in permalink_match:
+                conditions.append("permalink GLOB :permalink")
+            else:
+                conditions.append("permalink MATCH :permalink")
 
         # Handle type filter
         if types:
@@ -146,6 +170,7 @@ class SearchRepository:
 
         # set limit on search query
         params["limit"] = limit
+        params["offset"] = offset
 
         # Build WHERE clause
         where_clause = " AND ".join(conditions) if conditions else "1=1"
@@ -171,9 +196,10 @@ class SearchRepository:
             WHERE {where_clause}
             ORDER BY score ASC {order_by_clause}
             LIMIT :limit
+            OFFSET :offset
         """
 
-        # logger.debug(f"Search {sql} params: {params}")
+        logger.debug(f"Search {sql} params: {params}")
         async with db.scoped_session(self.session_maker) as session:
             result = await session.execute(text(sql), params)
             rows = result.fetchall()
@@ -199,8 +225,11 @@ class SearchRepository:
             for row in rows
         ]
 
-        # for r in results:
-        #    logger.debug(f"Search result: type:{r.type} title: {r.title} permalink: {r.permalink} score: {r.score}")
+        logger.debug(f"Found {len(results)} search results")
+        for r in results:
+            logger.debug(
+                f"Search result: type:{r.type} title: {r.title} permalink: {r.permalink} score: {r.score}"
+            )
 
         return results
 
@@ -233,7 +262,7 @@ class SearchRepository:
                 """),
                 search_index_row.to_insert(),
             )
-            logger.debug(f"indexed permalink {search_index_row.permalink}")
+            logger.debug(f"indexed row {search_index_row}")
             await session.commit()
 
     async def delete_by_permalink(self, permalink: str):

src/basic_memory/schemas/memory.py

@@ -111,3 +111,6 @@ class GraphContext(BaseModel):
 
     # Context metadata
     metadata: MemoryMetadata
+
+    page: int = 1
+    page_size: int = 1

src/basic_memory/schemas/request.py

@@ -51,7 +51,7 @@ class GetEntitiesRequest(BaseModel):
     discovered through search.
     """
 
-    permalinks: Annotated[List[Permalink], MinLen(1)]
+    permalinks: Annotated[List[Permalink], MinLen(1), MaxLen(10)]
 
 
 class CreateRelationsRequest(BaseModel):

src/basic_memory/schemas/response.py

@@ -11,6 +11,7 @@ Key Features:
 4. Bulk operations return all affected items
 """
 
+from datetime import datetime
 from typing import List, Optional, Dict
 
 from pydantic import BaseModel, ConfigDict, Field, AliasPath, AliasChoices
@@ -43,6 +44,8 @@ class ObservationResponse(Observation, SQLAlchemyModel):
     }
     """
 
+    permalink: Permalink
+
 
 class RelationResponse(Relation, SQLAlchemyModel):
     """Response schema for relation operations.
@@ -59,6 +62,8 @@ class RelationResponse(Relation, SQLAlchemyModel):
     }
     """
 
+    permalink: Permalink
+
     from_id: Permalink = Field(
         # use the permalink from the associated Entity
         # or the from_id value
@@ -131,9 +136,12 @@ class EntityResponse(SQLAlchemyModel):
     file_path: str
     entity_type: EntityType
     entity_metadata: Optional[Dict] = None
+    checksum: Optional[str] = None
     content_type: ContentType
     observations: List[ObservationResponse] = []
     relations: List[RelationResponse] = []
+    created_at: datetime
+    updated_at: datetime
 
 
 class EntityListResponse(SQLAlchemyModel):

src/basic_memory/schemas/search.py

@@ -102,6 +102,8 @@ class SearchResponse(BaseModel):
     """Wrapper for search results."""
 
     results: List[SearchResult]
+    current_page: int
+    page_size: int
 
 
 # Schema for future advanced search endpoint

src/basic_memory/services/context_service.py

@@ -54,11 +54,13 @@ class ContextService:
         types: Optional[List[SearchItemType]] = None,
         depth: int = 1,
         since: Optional[datetime] = None,
-        max_results: int = 10,
+        limit=10,
+        offset=0,
+        max_related: int = 10,
     ):
         """Build rich context from a memory:// URI."""
         logger.debug(
-            f"Building context for URI: '{memory_url}' depth: '{depth}' since: '{since}' max_results: '{max_results}'"
+            f"Building context for URI: '{memory_url}' depth: '{depth}' since: '{since}' limit: '{limit}' offset: '{offset}'  max_related: '{max_related}'"
         )
 
         if memory_url:
@@ -66,15 +68,21 @@ class ContextService:
             # Pattern matching - use search
             if "*" in path:
                 logger.debug(f"Pattern search for '{path}'")
-                primary = await self.search_repository.search(permalink_match=path)
+                primary = await self.search_repository.search(
+                    permalink_match=path, limit=limit, offset=offset
+                )
 
             # Direct lookup for exact path
             else:
                 logger.debug(f"Direct lookup for '{path}'")
-                primary = await self.search_repository.search(permalink=path)
+                primary = await self.search_repository.search(
+                    permalink=path, limit=limit, offset=offset
+                )
         else:
             logger.debug(f"Build context for '{types}'")
-            primary = await self.search_repository.search(types=types, after_date=since)
+            primary = await self.search_repository.search(
+                types=types, after_date=since, limit=limit, offset=offset
+            )
 
         # Get type_id pairs for traversal
 
@@ -83,7 +91,7 @@ class ContextService:
 
         # Find related content
         related = await self.find_related(
-            type_id_pairs, max_depth=depth, since=since, max_results=max_results
+            type_id_pairs, max_depth=depth, since=since, max_results=max_related
         )
         logger.debug(f"Found {len(related)} related results")
         for r in related:

src/basic_memory/services/entity_service.py

@@ -185,6 +185,11 @@ class EntityService(BaseService[EntityModel]):
             raise EntityNotFoundError(f"Entity not found: {permalink}")
         return db_entity
 
+    async def get_entities_by_id(self, ids: List[int]) -> Sequence[EntityModel]:
+        """Get specific entities and their relationships."""
+        logger.debug(f"Getting entities: {ids}")
+        return await self.repository.find_by_ids(ids)
+
     async def get_entities_by_permalinks(self, permalinks: List[str]) -> Sequence[EntityModel]:
         """Get specific nodes and their relationships."""
         logger.debug(f"Getting entities permalinks: {permalinks}")

src/basic_memory/services/link_resolver.py

@@ -16,9 +16,10 @@ class LinkResolver:
 
     Uses a combination of exact matching and search-based resolution:
     1. Try exact permalink match (fastest)
-    2. Try exact title match
-    3. Fall back to search for fuzzy matching
-    4. Generate new permalink if no match found
+    2. Try permalink pattern match (for wildcards)
+    3. Try exact title match
+    4. Fall back to search for fuzzy matching
+    5. Generate new permalink if no match found
     """
 
     def __init__(self, entity_repository: EntityRepository, search_service: SearchService):
@@ -45,8 +46,8 @@ class LinkResolver:
             logger.debug(f"Found title match: {entity.title}")
             return entity
 
-        if use_search:
-            # 3. Fall back to search for fuzzy matching on title if specified
+        if use_search and "*" not in clean_text:
+            # 3. Fall back to search for fuzzy matching on title
             results = await self.search_service.search(
                 query=SearchQuery(title=clean_text, types=[SearchItemType.ENTITY]),
             )
@@ -59,7 +60,7 @@ class LinkResolver:
                 )
                 return await self.entity_repository.get_by_permalink(best_match.permalink)
 
-            # if we couldn't find anything then return None
+        # if we couldn't find anything then return None
         return None
 
     def _normalize_link_text(self, link_text: str) -> Tuple[str, Optional[str]]:
@@ -87,7 +88,7 @@ class LinkResolver:
 
         return text, alias
 
-    def _select_best_match(self, search_text: str, results: List[SearchIndexRow]) -> Entity:
+    def _select_best_match(self, search_text: str, results: List[SearchIndexRow]) -> SearchIndexRow:
         """Select best match from search results.
 
         Uses multiple criteria:

src/basic_memory/services/search_service.py

@@ -51,7 +51,7 @@ class SearchService:
 
         logger.info("Reindex complete")
 
-    async def search(self, query: SearchQuery) -> List[SearchIndexRow]:
+    async def search(self, query: SearchQuery, limit=10, offset=0) -> List[SearchIndexRow]:
         """Search across all indexed content.
 
         Supports three modes:
@@ -75,7 +75,7 @@ class SearchService:
             else None
         )
 
-        # permalink search
+        # search
         results = await self.repository.search(
             search_text=query.text,
             permalink=query.permalink,
@@ -84,6 +84,8 @@ class SearchService:
             types=query.types,
             entity_types=query.entity_types,
             after_date=after_date,
+            limit=limit,
+            offset=offset,
         )
 
         return results

src/basic_memory/sync/sync_service.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 from typing import Dict
 
+import logfire
 from loguru import logger
 from sqlalchemy.exc import IntegrityError
 
@@ -61,105 +62,113 @@ class SyncService:
 
     async def sync(self, directory: Path) -> SyncReport:
         """Sync knowledge files with database."""
-        changes = await self.scanner.find_knowledge_changes(directory)
-        logger.info(f"Found {changes.total_changes} knowledge changes")
 
-        # Handle moves first
-        for old_path, new_path in changes.moves.items():
-            logger.debug(f"Moving entity: {old_path} -> {new_path}")
-            entity = await self.entity_repository.get_by_file_path(old_path)
-            if entity:
-                # Update file_path but keep the same permalink for link stability
-                updated = await self.entity_repository.update(
-                    entity.id, {"file_path": new_path, "checksum": changes.checksums[new_path]}
-                )
-                # update search index
-                if updated:
-                    await self.search_service.index_entity(updated)
+        with logfire.span("sync", directory=directory):  # pyright: ignore [reportGeneralTypeIssues]
+            changes = await self.scanner.find_knowledge_changes(directory)
+            logger.info(f"Found {changes.total_changes} knowledge changes")
 
-        # Handle deletions next
-        # remove rows from db for files no longer present
-        for path in changes.deleted:
-            await self.handle_entity_deletion(path)
+            # Handle moves first
+            for old_path, new_path in changes.moves.items():
+                logger.debug(f"Moving entity: {old_path} -> {new_path}")
+                entity = await self.entity_repository.get_by_file_path(old_path)
+                if entity:
+                    # Update file_path but keep the same permalink for link stability
+                    updated = await self.entity_repository.update(
+                        entity.id, {"file_path": new_path, "checksum": changes.checksums[new_path]}
+                    )
+                    # update search index
+                    if updated:
+                        await self.search_service.index_entity(updated)
 
-        # Parse files that need updating
-        parsed_entities: Dict[str, EntityMarkdown] = {}
+            # Handle deletions next
+            # remove rows from db for files no longer present
+            for path in changes.deleted:
+                await self.handle_entity_deletion(path)
 
-        for path in [*changes.new, *changes.modified]:
-            entity_markdown = await self.entity_parser.parse_file(directory / path)
-            parsed_entities[path] = entity_markdown
+            # Parse files that need updating
+            parsed_entities: Dict[str, EntityMarkdown] = {}
 
-        # First pass: Create/update entities
-        # entities will have a null checksum to indicate they are not complete
-        for path, entity_markdown in parsed_entities.items():
-            # Get unique permalink and update markdown if needed
-            permalink = await self.entity_service.resolve_permalink(
-                Path(path), markdown=entity_markdown
-            )
+            for path in [*changes.new, *changes.modified]:
+                entity_markdown = await self.entity_parser.parse_file(directory / path)
+                parsed_entities[path] = entity_markdown
 
-            if permalink != entity_markdown.frontmatter.permalink:
-                # Add/update permalink in frontmatter
-                logger.info(f"Adding permalink '{permalink}' to file: {path}")
-
-                # update markdown
-                entity_markdown.frontmatter.metadata["permalink"] = permalink
-
-                # update file frontmatter
-                updated_checksum = await file_utils.update_frontmatter(
-                    directory / path, {"permalink": permalink}
+            # First pass: Create/update entities
+            # entities will have a null checksum to indicate they are not complete
+            for path, entity_markdown in parsed_entities.items():
+                # Get unique permalink and update markdown if needed
+                permalink = await self.entity_service.resolve_permalink(
+                    Path(path), markdown=entity_markdown
                 )
 
-                # Update checksum in changes report since file was modified
-                changes.checksums[path] = updated_checksum
+                if permalink != entity_markdown.frontmatter.permalink:
+                    # Add/update permalink in frontmatter
+                    logger.info(f"Adding permalink '{permalink}' to file: {path}")
 
-            # if the file is new, create an entity
-            if path in changes.new:
-                # Create entity with final permalink
-                logger.debug(f"Creating new entity_markdown: {path}")
-                await self.entity_service.create_entity_from_markdown(Path(path), entity_markdown)
-            # otherwise we need to update the entity and observations
-            else:
-                logger.debug(f"Updating entity_markdown: {path}")
-                await self.entity_service.update_entity_and_observations(
+                    # update markdown
+                    entity_markdown.frontmatter.metadata["permalink"] = permalink
+
+                    # update file frontmatter
+                    updated_checksum = await file_utils.update_frontmatter(
+                        directory / path, {"permalink": permalink}
+                    )
+
+                    # Update checksum in changes report since file was modified
+                    changes.checksums[path] = updated_checksum
+
+                # if the file is new, create an entity
+                if path in changes.new:
+                    # Create entity with final permalink
+                    logger.debug(f"Creating new entity_markdown: {path}")
+                    await self.entity_service.create_entity_from_markdown(
+                        Path(path), entity_markdown
+                    )
+                # otherwise we need to update the entity and observations
+                else:
+                    logger.debug(f"Updating entity_markdown: {path}")
+                    await self.entity_service.update_entity_and_observations(
+                        Path(path), entity_markdown
+                    )
+
+            # Second pass
+            for path, entity_markdown in parsed_entities.items():
+                logger.debug(f"Updating relations for: {path}")
+
+                # Process relations
+                checksum = changes.checksums[path]
+                entity = await self.entity_service.update_entity_relations(
                     Path(path), entity_markdown
                 )
 
-        # Second pass
-        for path, entity_markdown in parsed_entities.items():
-            logger.debug(f"Updating relations for: {path}")
+                # add to search index
+                await self.search_service.index_entity(entity)
 
-            # Process relations
-            checksum = changes.checksums[path]
-            entity = await self.entity_service.update_entity_relations(Path(path), entity_markdown)
+                # Set final checksum to mark sync complete
+                await self.entity_repository.update(entity.id, {"checksum": checksum})
 
-            # add to search index
-            await self.search_service.index_entity(entity)
-
-            # Set final checksum to mark sync complete
-            await self.entity_repository.update(entity.id, {"checksum": checksum})
-
-        # Third pass: Try to resolve any forward references
-        logger.debug("Attempting to resolve forward references")
-        for relation in await self.relation_repository.find_unresolved_relations():
-            target_entity = await self.entity_service.link_resolver.resolve_link(relation.to_name)
-            # check we found a link that is not the source
-            if target_entity and target_entity.id != relation.from_id:
-                logger.debug(
-                    f"Resolved forward reference: {relation.to_name} -> {target_entity.permalink}"
+            # Third pass: Try to resolve any forward references
+            logger.debug("Attempting to resolve forward references")
+            for relation in await self.relation_repository.find_unresolved_relations():
+                target_entity = await self.entity_service.link_resolver.resolve_link(
+                    relation.to_name
                 )
-
-                try:
-                    await self.relation_repository.update(
-                        relation.id,
-                        {
-                            "to_id": target_entity.id,
-                            "to_name": target_entity.title,  # Update to actual title
-                        },
+                # check we found a link that is not the source
+                if target_entity and target_entity.id != relation.from_id:
+                    logger.debug(
+                        f"Resolved forward reference: {relation.to_name} -> {target_entity.permalink}"
                     )
-                except IntegrityError:
-                    logger.debug(f"Ignoring duplicate relation {relation}")
 
-                # update search index
-                await self.search_service.index_entity(target_entity)
+                    try:
+                        await self.relation_repository.update(
+                            relation.id,
+                            {
+                                "to_id": target_entity.id,
+                                "to_name": target_entity.title,  # Update to actual title
+                            },
+                        )
+                    except IntegrityError:
+                        logger.debug(f"Ignoring duplicate relation {relation}")
 
-        return changes
+                    # update search index
+                    await self.search_service.index_entity(target_entity)
+
+            return changes

src/basic_memory/utils.py

@@ -9,8 +9,11 @@ from typing import Optional, Union
 from loguru import logger
 from unidecode import unidecode
 
+import basic_memory
 from basic_memory.config import config
 
+import logfire
+
 
 def generate_permalink(file_path: Union[Path, str]) -> str:
     """Generate a stable permalink from a file path.
@@ -61,19 +64,42 @@ def generate_permalink(file_path: Union[Path, str]) -> str:
     return "/".join(clean_segments)
 
 
-def setup_logging(home_dir: Path = config.home, log_file: Optional[str] = None) -> None:
+def setup_logging(
+    home_dir: Path = config.home, log_file: Optional[str] = None, console: bool = True
+) -> None:  # pragma: no cover
     """
     Configure logging for the application.
+    :param home_dir: the root directory for the application
+    :param log_file: the name of the log file to write to
+    :param app: the fastapi application instance
+    :param console: whether to log to the console
     """
 
     # Remove default handler and any existing handlers
     logger.remove()
 
-    # Add file handler
-    if log_file:
+    # Add file handler if we are not running tests
+    if log_file and config.env != "test":
+        # enable pydantic logfire
+        logfire.configure(
+            code_source=logfire.CodeSource(
+                repository="https://github.com/basicmachines-co/basic-memory",
+                revision=basic_memory.__version__,
+                root_path="/src/basic_memory",
+            ),
+            environment=config.env,
+            console=False,
+        )
+        logger.configure(handlers=[logfire.loguru_handler()])
+
+        # instrument code spans
+        logfire.instrument_sqlite3()
+        logfire.instrument_httpx()
+
+        # setup logger
         log_path = home_dir / log_file
         logger.add(
-            str(log_path),  # loguru expects a string path
+            str(log_path),
             level=config.log_level,
             rotation="100 MB",
             retention="10 days",
@@ -85,3 +111,5 @@ def setup_logging(home_dir: Path = config.home, log_file: Optional[str] = None)
 
     # Add stderr handler
     logger.add(sys.stderr, level=config.log_level, backtrace=True, diagnose=True, colorize=True)
+
+    logger.info(f"ENV: '{config.env}' Log level: '{config.log_level}' Logging to {log_file}")

tests/__init__.py

@@ -0,0 +1,4 @@
+from basic_memory.config import config
+
+# set config.env to "test" for pytest to prevent logging to file in utils.setup_logging()
+config.env = "test"

tests/api/test_memory_router.py

@@ -26,6 +26,25 @@ async def test_get_memory_context(client, test_graph):
     assert context.metadata.total_results == 3
 
 
+@pytest.mark.asyncio
+async def test_get_memory_context_pagination(client, test_graph):
+    """Test getting context from memory URL."""
+    response = await client.get("/memory/test/root?page=1&page_size=1")
+    assert response.status_code == 200
+
+    context = GraphContext(**response.json())
+    assert len(context.primary_results) == 1
+    assert context.primary_results[0].permalink == "test/root"
+    assert len(context.related_results) > 0
+
+    # Verify metadata
+    assert context.metadata.uri == "test/root"
+    assert context.metadata.depth == 1  # default depth
+    # assert context.metadata["timeframe"] == "7d"  # default timeframe
+    assert isinstance(context.metadata.generated_at, datetime)
+    assert context.metadata.total_results == 3
+
+
 @pytest.mark.asyncio
 async def test_get_memory_context_pattern(client, test_graph):
     """Test getting context with pattern matching."""
@@ -91,6 +110,17 @@ async def test_recent_activity(client, test_graph):
     assert len(context.related_results) > 0
 
 
+@pytest.mark.asyncio
+async def test_recent_activity_pagination(client, test_graph):
+    """Test handling of paths."""
+    response = await client.get("/memory/recent?page=1&page_size=1")
+    assert response.status_code == 200
+
+    context = GraphContext(**response.json())
+    assert len(context.primary_results) == 1
+    assert len(context.related_results) > 0
+
+
 @pytest.mark.asyncio
 async def test_recent_activity_by_type(client, test_graph):
     """Test handling of non-existent paths."""

tests/api/test_resource_router.py

@@ -5,6 +5,8 @@ from datetime import datetime, timezone
 import pytest
 from pathlib import Path
 
+from basic_memory.schemas import EntityResponse
+
 
 @pytest.mark.asyncio
 async def test_get_resource_content(client, test_config, entity_repository):
@@ -35,6 +37,35 @@ async def test_get_resource_content(client, test_config, entity_repository):
     assert response.text == content
 
 
+@pytest.mark.asyncio
+async def test_get_resource_pagination(client, test_config, entity_repository):
+    """Test getting content by permalink with pagination."""
+    # Create a test file
+    content = "# Test Content\n\nThis is a test file."
+    test_file = Path(test_config.home) / "test" / "test.md"
+    test_file.parent.mkdir(parents=True, exist_ok=True)
+    test_file.write_text(content)
+
+    # Create entity referencing the file
+    entity = await entity_repository.create(
+        {
+            "title": "Test Entity",
+            "entity_type": "test",
+            "permalink": "test/test",
+            "file_path": "test/test.md",  # Relative to config.home
+            "content_type": "text/markdown",
+            "created_at": datetime.now(timezone.utc),
+            "updated_at": datetime.now(timezone.utc),
+        }
+    )
+
+    # Test getting the content
+    response = await client.get(f"/resource/{entity.permalink}", params={"page": 1, "page_size": 1})
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "text/markdown; charset=utf-8"
+    assert response.text == content
+
+
 @pytest.mark.asyncio
 async def test_get_resource_by_title(client, test_config, entity_repository):
     """Test getting content by permalink."""
@@ -67,7 +98,7 @@ async def test_get_resource_missing_entity(client):
     """Test 404 when entity doesn't exist."""
     response = await client.get("/resource/does/not/exist")
     assert response.status_code == 404
-    assert "Entity not found" in response.json()["detail"]
+    assert "Resource not found" in response.json()["detail"]
 
 
 @pytest.mark.asyncio
@@ -89,3 +120,186 @@ async def test_get_resource_missing_file(client, test_config, entity_repository)
     response = await client.get(f"/resource/{entity.permalink}")
     assert response.status_code == 404
     assert "File not found" in response.json()["detail"]
+
+
+@pytest.mark.asyncio
+async def test_get_resource_observation(client, test_config, entity_repository):
+    """Test getting content by observation permalink."""
+    # Create entity
+    content = "# Test Content\n\n- [note] an observation."
+    data = {
+        "title": "Test Entity",
+        "folder": "test",
+        "entity_type": "test",
+        "content": f"{content}",
+    }
+    response = await client.post("/knowledge/entities", json=data)
+    entity_response = response.json()
+    entity = EntityResponse(**entity_response)
+
+    assert len(entity.observations) == 1
+    observation = entity.observations[0]
+
+    # Test getting the content via the observation
+    response = await client.get(f"/resource/{observation.permalink}")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "text/markdown; charset=utf-8"
+    assert (
+        """
+---
+title: Test Entity
+type: test
+permalink: test/test-entity
+---
+
+# Test Content
+
+- [note] an observation.
+    """.strip()
+        in response.text
+    )
+
+
+@pytest.mark.asyncio
+async def test_get_resource_entities(client, test_config, entity_repository):
+    """Test getting content by permalink match."""
+    # Create entity
+    content1 = "# Test Content\n"
+    data = {
+        "title": "Test Entity",
+        "folder": "test",
+        "entity_type": "test",
+        "content": f"{content1}",
+    }
+    response = await client.post("/knowledge/entities", json=data)
+    entity_response = response.json()
+    entity1 = EntityResponse(**entity_response)
+
+    content2 = "# Related Content\n- links to [[Test Entity]]"
+    data = {
+        "title": "Related Entity",
+        "folder": "test",
+        "entity_type": "test",
+        "content": f"{content2}",
+    }
+    response = await client.post("/knowledge/entities", json=data)
+    entity_response = response.json()
+    entity2 = EntityResponse(**entity_response)
+
+    assert len(entity2.relations) == 1
+
+    # Test getting the content via the relation
+    response = await client.get("/resource/test/*")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "text/markdown; charset=utf-8"
+    assert (
+        f"""
+--- memory://test/test-entity {entity1.updated_at.isoformat()} {entity1.checksum[:8]}
+
+# Test Content
+
+--- memory://test/related-entity {entity2.updated_at.isoformat()} {entity2.checksum[:8]}
+
+# Related Content
+- links to [[Test Entity]]
+
+    """.strip()
+        in response.text
+    )
+
+
+@pytest.mark.asyncio
+async def test_get_resource_entities_pagination(client, test_config, entity_repository):
+    """Test getting content by permalink match."""
+    # Create entity
+    content1 = "# Test Content\n"
+    data = {
+        "title": "Test Entity",
+        "folder": "test",
+        "entity_type": "test",
+        "content": f"{content1}",
+    }
+    response = await client.post("/knowledge/entities", json=data)
+    entity_response = response.json()
+    entity1 = EntityResponse(**entity_response)
+    assert entity1
+
+    content2 = "# Related Content\n- links to [[Test Entity]]"
+    data = {
+        "title": "Related Entity",
+        "folder": "test",
+        "entity_type": "test",
+        "content": f"{content2}",
+    }
+    response = await client.post("/knowledge/entities", json=data)
+    entity_response = response.json()
+    entity2 = EntityResponse(**entity_response)
+
+    assert len(entity2.relations) == 1
+
+    # Test getting second result
+    response = await client.get("/resource/test/*", params={"page": 2, "page_size": 1})
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "text/markdown; charset=utf-8"
+    assert (
+        """
+---
+title: Related Entity
+type: test
+permalink: test/related-entity
+---
+
+# Related Content
+- links to [[Test Entity]]
+""".strip()
+        in response.text
+    )
+
+
+@pytest.mark.asyncio
+async def test_get_resource_relation(client, test_config, entity_repository):
+    """Test getting content by relation permalink."""
+    # Create entity
+    content1 = "# Test Content\n"
+    data = {
+        "title": "Test Entity",
+        "folder": "test",
+        "entity_type": "test",
+        "content": f"{content1}",
+    }
+    response = await client.post("/knowledge/entities", json=data)
+    entity_response = response.json()
+    entity1 = EntityResponse(**entity_response)
+
+    content2 = "# Related Content\n- links to [[Test Entity]]"
+    data = {
+        "title": "Related Entity",
+        "folder": "test",
+        "entity_type": "test",
+        "content": f"{content2}",
+    }
+    response = await client.post("/knowledge/entities", json=data)
+    entity_response = response.json()
+    entity2 = EntityResponse(**entity_response)
+
+    assert len(entity2.relations) == 1
+    relation = entity2.relations[0]
+
+    # Test getting the content via the relation
+    response = await client.get(f"/resource/{relation.permalink}")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "text/markdown; charset=utf-8"
+    assert (
+        f"""
+--- memory://test/test-entity {entity1.updated_at.isoformat()} {entity1.checksum[:8]}
+
+# Test Content
+
+--- memory://test/related-entity {entity2.updated_at.isoformat()} {entity2.checksum[:8]}
+
+# Related Content
+- links to [[Test Entity]]
+    
+    """.strip()
+        in response.text
+    )

tests/api/test_search_router.py

@@ -35,6 +35,18 @@ async def test_search_basic(client, indexed_entity):
     assert found, "Expected to find indexed entity in results"
 
 
+@pytest.mark.asyncio
+async def test_search_basic_pagination(client, indexed_entity):
+    """Test basic text search."""
+    response = await client.post("/search/?page=3&page_size=1", json={"text": "search"})
+    assert response.status_code == 200
+    search_results = SearchResponse.model_validate(response.json())
+    assert len(search_results.results) == 1
+
+    assert search_results.current_page == 3
+    assert search_results.page_size == 1
+
+
 @pytest.mark.asyncio
 async def test_search_with_type_filter(client, indexed_entity):
     """Test search with type filter."""
@@ -92,28 +104,6 @@ async def test_search_with_date_filter(client, indexed_entity):
     assert len(search_results.results) == 0
 
 
-@pytest.mark.skip("search scoring is not implemented yet")
-@pytest.mark.asyncio
-async def test_search_scoring(client, indexed_entity):
-    """Test search result scoring."""
-    # Exact match should score higher
-    exact_response = await client.post("/search/", json={"text": "TestComponent"})
-
-    # Partial match should score lower
-    partial_response = await client.post("/search/", json={"text": "test"})
-
-    assert exact_response.status_code == 200
-    assert partial_response.status_code == 200
-
-    exact_result = SearchResponse.model_validate(exact_response.json())
-    partial_result = SearchResponse.model_validate(partial_response.json())
-
-    exact_score = exact_result.results[0].score
-    partial_score = partial_result.results[0].score
-
-    assert exact_score > partial_score
-
-
 @pytest.mark.asyncio
 async def test_search_empty(search_service, client):
     """Test search with no matches."""

tests/cli/test_cli_tools.py

@@ -0,0 +1,294 @@
+"""Tests for the Basic Memory CLI tools."""
+
+from datetime import datetime, timezone
+import pytest
+from typer.testing import CliRunner
+from unittest.mock import patch, AsyncMock
+
+from basic_memory.cli.commands.tools import tool_app
+from basic_memory.schemas.response import EntityResponse
+from basic_memory.schemas.search import SearchResponse
+from basic_memory.schemas.memory import GraphContext
+
+runner = CliRunner()
+
+
+@pytest.fixture
+def mock_write_note():
+    with patch("basic_memory.cli.commands.tools.mcp_write_note", new_callable=AsyncMock) as mock:
+        mock.return_value = "Created test/note.md (abc123)\npermalink: test/note"
+        yield mock
+
+
+@pytest.fixture
+def mock_read_note():
+    with patch("basic_memory.cli.commands.tools.mcp_read_note", new_callable=AsyncMock) as mock:
+        mock.return_value = "--- memory://test/note 2025-01 abc123\nTest content"
+        yield mock
+
+
+@pytest.fixture
+def mock_search():
+    with patch("basic_memory.cli.commands.tools.mcp_search", new_callable=AsyncMock) as mock:
+        mock.return_value = SearchResponse(results=[], current_page=1, page_size=10)
+        yield mock
+
+
+@pytest.fixture
+def mock_build_context():
+    with patch("basic_memory.cli.commands.tools.mcp_build_context", new_callable=AsyncMock) as mock:
+        now = datetime.now(timezone.utc)
+        mock.return_value = GraphContext(
+            primary_results=[],
+            related_results=[],
+            metadata={
+                "uri": "test/*",
+                "depth": 1,
+                "timeframe": "7d",
+                "generated_at": now,
+                "total_results": 0,
+                "total_relations": 0,
+            },
+        )
+        yield mock
+
+
+@pytest.fixture
+def mock_recent_activity():
+    with patch(
+        "basic_memory.cli.commands.tools.mcp_recent_activity", new_callable=AsyncMock
+    ) as mock:
+        now = datetime.now(timezone.utc)
+        mock.return_value = GraphContext(
+            primary_results=[],
+            related_results=[],
+            metadata={
+                "uri": None,
+                "types": ["entity", "observation"],
+                "depth": 1,
+                "timeframe": "7d",
+                "generated_at": now,
+                "total_results": 0,
+                "total_relations": 0,
+            },
+        )
+        yield mock
+
+
+@pytest.fixture
+def mock_get_entity():
+    with patch("basic_memory.cli.commands.tools.mcp_get_entity", new_callable=AsyncMock) as mock:
+        now = datetime.now(timezone.utc)
+        mock.return_value = EntityResponse(
+            permalink="test/entity",
+            title="Test Entity",
+            file_path="test/entity.md",
+            entity_type="note",
+            content_type="text/markdown",
+            observations=[],
+            relations=[],
+            created_at=now,
+            updated_at=now,
+        )
+        yield mock
+
+
+def test_write_note(mock_write_note):
+    """Test write_note command with basic arguments."""
+    result = runner.invoke(
+        tool_app,
+        [
+            "write-note",
+            "--title",
+            "Test Note",
+            "--content",
+            "Test content",
+            "--folder",
+            "test",
+        ],
+    )
+    assert result.exit_code == 0
+    mock_write_note.assert_awaited_once_with("Test Note", "Test content", "test", None)
+
+
+def test_write_note_with_tags(mock_write_note):
+    """Test write_note command with tags."""
+    result = runner.invoke(
+        tool_app,
+        [
+            "write-note",
+            "--title",
+            "Test Note",
+            "--content",
+            "Test content",
+            "--folder",
+            "test",
+            "--tags",
+            "tag1",
+            "--tags",
+            "tag2",
+        ],
+    )
+    assert result.exit_code == 0
+    mock_write_note.assert_awaited_once_with("Test Note", "Test content", "test", ["tag1", "tag2"])
+
+
+def test_read_note(mock_read_note):
+    """Test read_note command."""
+    result = runner.invoke(
+        tool_app,
+        ["read-note", "test/note"],
+    )
+    assert result.exit_code == 0
+    mock_read_note.assert_awaited_once_with("test/note", 1, 10)
+
+
+def test_read_note_with_pagination(mock_read_note):
+    """Test read_note command with pagination."""
+    result = runner.invoke(
+        tool_app,
+        ["read-note", "test/note", "--page", "2", "--page-size", "5"],
+    )
+    assert result.exit_code == 0
+    mock_read_note.assert_awaited_once_with("test/note", 2, 5)
+
+
+def test_search_basic(mock_search):
+    """Test basic search command."""
+    result = runner.invoke(
+        tool_app,
+        ["search", "test query"],
+    )
+    assert result.exit_code == 0
+    mock_search.assert_awaited_once()
+    args = mock_search.await_args[1]
+    assert args["query"].text == "test query"
+
+
+def test_search_permalink(mock_search):
+    """Test search with permalink flag."""
+    result = runner.invoke(
+        tool_app,
+        ["search", "test/*", "--permalink"],
+    )
+    assert result.exit_code == 0
+    mock_search.assert_awaited_once()
+    args = mock_search.await_args[1]
+    assert args["query"].permalink_match == "test/*"
+
+
+def test_search_title(mock_search):
+    """Test search with title flag."""
+    result = runner.invoke(
+        tool_app,
+        ["search", "test", "--title"],
+    )
+    assert result.exit_code == 0
+    mock_search.assert_awaited_once()
+    args = mock_search.await_args[1]
+    assert args["query"].title == "test"
+
+
+def test_search_with_pagination(mock_search):
+    """Test search with pagination."""
+    result = runner.invoke(
+        tool_app,
+        ["search", "test", "--page", "2", "--page-size", "5"],
+    )
+    assert result.exit_code == 0
+    mock_search.assert_awaited_once()
+    args = mock_search.await_args[1]
+    assert args["page"] == 2
+    assert args["page_size"] == 5
+
+
+def test_build_context(mock_build_context):
+    """Test build_context command."""
+    result = runner.invoke(
+        tool_app,
+        ["build-context", "memory://test/*"],
+    )
+    assert result.exit_code == 0
+    mock_build_context.assert_awaited_once_with(
+        url="memory://test/*", depth=1, timeframe="7d", page=1, page_size=10, max_related=10
+    )
+
+
+def test_build_context_with_options(mock_build_context):
+    """Test build_context command with all options."""
+    result = runner.invoke(
+        tool_app,
+        [
+            "build-context",
+            "memory://test/*",
+            "--depth",
+            "2",
+            "--timeframe",
+            "1d",
+            "--page",
+            "2",
+            "--page-size",
+            "5",
+            "--max-related",
+            "20",
+        ],
+    )
+    assert result.exit_code == 0
+    mock_build_context.assert_awaited_once_with(
+        url="memory://test/*", depth=2, timeframe="1d", page=2, page_size=5, max_related=20
+    )
+
+
+def test_get_entity(mock_get_entity):
+    """Test get_entity command."""
+    result = runner.invoke(
+        tool_app,
+        ["get-entity", "test/entity"],
+    )
+    assert result.exit_code == 0
+    mock_get_entity.assert_awaited_once_with(identifier="test/entity")
+
+
+def test_recent_activity(mock_recent_activity):
+    """Test recent_activity command with defaults."""
+    result = runner.invoke(
+        tool_app,
+        ["recent-activity"],
+    )
+    assert result.exit_code == 0
+    mock_recent_activity.assert_awaited_once_with(
+        type=["entity", "observation", "relation"],
+        depth=1,
+        timeframe="7d",
+        page=1,
+        page_size=10,
+        max_related=10,
+    )
+
+
+def test_recent_activity_with_options(mock_recent_activity):
+    """Test recent_activity command with options."""
+    result = runner.invoke(
+        tool_app,
+        [
+            "recent-activity",
+            "--type",
+            "entity",
+            "--type",
+            "observation",
+            "--depth",
+            "2",
+            "--timeframe",
+            "1d",
+            "--page",
+            "2",
+            "--page-size",
+            "5",
+            "--max-related",
+            "20",
+        ],
+    )
+    assert result.exit_code == 0
+    mock_recent_activity.assert_awaited_once_with(
+        type=["entity", "observation"], depth=2, timeframe="1d", page=2, page_size=5, max_related=20
+    )

tests/cli/test_import_chatgpt.py

@@ -220,7 +220,7 @@ async def test_hidden_messages(tmp_path, sample_conversation_with_hidden):
 def test_import_chatgpt_command_file_not_found(tmp_path):
     """Test error handling for nonexistent file."""
     nonexistent = tmp_path / "nonexistent.json"
-    result = runner.invoke(app, ["import", "chatgpt", "--conversations-json", str(nonexistent)])
+    result = runner.invoke(app, ["import", "chatgpt", str(nonexistent)])
     assert result.exit_code == 1
     assert "File not found" in result.output
 
@@ -231,9 +231,7 @@ def test_import_chatgpt_command_success(tmp_path, sample_chatgpt_json, monkeypat
     monkeypatch.setenv("HOME", str(tmp_path))
 
     # Run import
-    result = runner.invoke(
-        import_app, ["chatgpt", "--conversations-json", str(sample_chatgpt_json)]
-    )
+    result = runner.invoke(import_app, ["chatgpt", str(sample_chatgpt_json)])
     assert result.exit_code == 0
     assert "Import complete" in result.output
     assert "Imported 1 conversations" in result.output
@@ -246,7 +244,7 @@ def test_import_chatgpt_command_invalid_json(tmp_path):
     invalid_file = tmp_path / "invalid.json"
     invalid_file.write_text("not json")
 
-    result = runner.invoke(import_app, ["chatgpt", "--conversations-json", str(invalid_file)])
+    result = runner.invoke(import_app, ["chatgpt", str(invalid_file)])
     assert result.exit_code == 1
     assert "Error during import" in result.output
 
@@ -263,7 +261,6 @@ def test_import_chatgpt_with_custom_folder(tmp_path, sample_chatgpt_json, monkey
         [
             "import",
             "chatgpt",
-            "--conversations-json",
             str(sample_chatgpt_json),
             "--folder",
             conversations_folder,

tests/conftest.py

@@ -308,27 +308,6 @@ async def test_graph(
     for entity in entities:
         await search_service.index_entity(entity)
 
-    # search_content = await entity_repository.execute_query(text("select * from search_index"),
-    #                                                        use_query_options=False)
-    # for row in search_content:
-    #     print(row)
-    # print("relation:")
-    # search_content = await entity_repository.execute_query(text("select * from search_index where type = 'relation'"),
-    #                                                        use_query_options=False)
-    # for row in search_content:
-    #     print(row)
-    #
-    # # In test_graph fixture after creating everything:
-    # print("Entities:")
-    # entities = await entity_repository.find_all()
-    # for e in entities:
-    #     print(f"- {e.title} (id={e.id})")
-    #
-    # print("\nRelations:")
-    # relations = await relation_repository.find_all()
-    # for r in relations:
-    #     print(f"- {r.from_id} -> {r.to_id} ({r.relation_type})")
-
     return {
         "root": root,
         "connected1": connected_1,

tests/mcp/test_tool_get_entity.py

@@ -1,45 +0,0 @@
-"""Tests for get_entity MCP tool."""
-
-import pytest
-from mcp.server.fastmcp.exceptions import ToolError
-
-from basic_memory.mcp.tools import notes
-from basic_memory.mcp.tools.knowledge import get_entity
-
-
-@pytest.mark.asyncio
-async def test_get_basic_entity(client):
-    """Test retrieving a basic entity."""
-    # First create an entity
-    permalink = await notes.write_note(
-        title="Test Note",
-        folder="test",
-        content="""
-# Test\nThis is a test note
-- [note] First observation
-""",
-        tags=["test", "documentation"],
-    )
-
-    assert permalink  # Got a valid permalink
-
-    # Get the entity without content
-    entity = await get_entity(permalink)
-
-    # Verify entity details
-    assert entity.file_path == "test/Test Note.md"
-    assert entity.entity_type == "note"
-    assert entity.permalink == "test/test-note"
-
-    # Check observations
-    assert len(entity.observations) == 1
-    obs = entity.observations[0]
-    assert obs.content == "First observation"
-    assert obs.category == "note"
-
-
-@pytest.mark.asyncio
-async def test_get_nonexistent_entity(client):
-    """Test attempting to get a non-existent entity."""
-    with pytest.raises(ToolError):
-        await get_entity("test/nonexistent")

tests/mcp/test_tool_knowledge.py

@@ -13,7 +13,7 @@ from basic_memory.schemas.delete import DeleteEntitiesRequest
 async def test_get_single_entity(client):
     """Test retrieving a single entity."""
     # First create an entity
-    permalink = await notes.write_note(
+    result = await notes.write_note(
         title="Test Note",
         folder="test",
         content="""
@@ -22,9 +22,34 @@ async def test_get_single_entity(client):
 """,
         tags=["test", "documentation"],
     )
+    assert result
 
     # Get the entity
-    entity = await get_entity(permalink)
+    entity = await get_entity("test/test-note")
+
+    # Verify entity details
+    assert entity.title == "Test Note"
+    assert entity.permalink == "test/test-note"
+    assert len(entity.observations) == 1
+
+
+@pytest.mark.asyncio
+async def test_get_single_entity_memory_url(client):
+    """Test retrieving a single entity."""
+    # First create an entity
+    result = await notes.write_note(
+        title="Test Note",
+        folder="test",
+        content="""
+# Test\nThis is a test note
+- [note] First observation
+""",
+        tags=["test", "documentation"],
+    )
+    assert result
+
+    # Get the entity
+    entity = await get_entity("memory://test/test-note")
 
     # Verify entity details
     assert entity.title == "Test Note"
@@ -36,40 +61,68 @@ async def test_get_single_entity(client):
 async def test_get_multiple_entities(client):
     """Test retrieving multiple entities."""
     # Create two test entities
-    permalink1 = await notes.write_note(
+    await notes.write_note(
         title="Test Note 1",
         folder="test",
         content="# Test 1",
     )
-    permalink2 = await notes.write_note(
+    await notes.write_note(
         title="Test Note 2",
         folder="test",
         content="# Test 2",
     )
 
     # Get both entities
-    request = GetEntitiesRequest(permalinks=[permalink1, permalink2])
+    request = GetEntitiesRequest(permalinks=["test/test-note-1", "test/test-note-2"])
     response = await get_entities(request)
 
     # Verify we got both entities
     assert len(response.entities) == 2
     permalinks = {e.permalink for e in response.entities}
-    assert permalink1 in permalinks
-    assert permalink2 in permalinks
+    assert "test/test-note-1" in permalinks
+    assert "test/test-note-2" in permalinks
+
+
+@pytest.mark.asyncio
+async def test_get_multiple_entities_memory_ur(client):
+    """Test retrieving multiple entities."""
+    # Create two test entities
+    await notes.write_note(
+        title="Test Note 1",
+        folder="test",
+        content="# Test 1",
+    )
+    await notes.write_note(
+        title="Test Note 2",
+        folder="test",
+        content="# Test 2",
+    )
+
+    # Get both entities
+    request = GetEntitiesRequest(
+        permalinks=["memory://test/test-note-1", "memory://test/test-note-2"]
+    )
+    response = await get_entities(request)
+
+    # Verify we got both entities
+    assert len(response.entities) == 2
+    permalinks = {e.permalink for e in response.entities}
+    assert "test/test-note-1" in permalinks
+    assert "test/test-note-2" in permalinks
 
 
 @pytest.mark.asyncio
 async def test_delete_entities(client):
     """Test deleting entities."""
     # Create a test entity
-    permalink = await notes.write_note(
+    await notes.write_note(
         title="Test Note",
         folder="test",
         content="# Test Note to Delete",
     )
 
     # Delete the entity
-    request = DeleteEntitiesRequest(permalinks=[permalink])
+    request = DeleteEntitiesRequest(permalinks=["test/test-note"])
     response = await delete_entities(request)
 
     # Verify deletion
@@ -77,7 +130,29 @@ async def test_delete_entities(client):
 
     # Verify entity no longer exists
     with pytest.raises(ToolError):
-        await get_entity(permalink)
+        await get_entity("test/test-note")
+
+
+@pytest.mark.asyncio
+async def test_delete_entities_memory_url(client):
+    """Test deleting entities."""
+    # Create a test entity
+    await notes.write_note(
+        title="Test Note",
+        folder="test",
+        content="# Test Note to Delete",
+    )
+
+    # Delete the entity
+    request = DeleteEntitiesRequest(permalinks=["memory://test/test-note"])
+    response = await delete_entities(request)
+
+    # Verify deletion
+    assert response.deleted is True
+
+    # Verify entity no longer exists
+    with pytest.raises(ToolError):
+        await get_entity("test/test-note")
 
 
 @pytest.mark.asyncio

tests/mcp/test_tool_memory.py

@@ -89,7 +89,9 @@ async def test_recent_activity_timeframe_formats(client, test_graph):
     # Test each valid timeframe
     for timeframe in valid_timeframes:
         try:
-            result = await recent_activity(type=["entity"], timeframe=timeframe, max_results=1)
+            result = await recent_activity(
+                type=["entity"], timeframe=timeframe, page=1, page_size=10, max_related=10
+            )
             assert result is not None
         except Exception as e:
             pytest.fail(f"Failed with valid timeframe '{timeframe}': {str(e)}")
@@ -136,7 +138,9 @@ async def test_build_context_timeframe_formats(client, test_graph):
     # Test each valid timeframe
     for timeframe in valid_timeframes:
         try:
-            result = await build_context(url=test_url, timeframe=timeframe, max_results=1)
+            result = await build_context(
+                url=test_url, timeframe=timeframe, page=1, page_size=10, max_related=10
+            )
             assert result is not None
         except Exception as e:
             pytest.fail(f"Failed with valid timeframe '{timeframe}': {str(e)}")

tests/mcp/test_tool_notes.py

@@ -1,10 +1,11 @@
 """Tests for note tools that exercise the full stack with SQLite."""
 
+from textwrap import dedent
+
 import pytest
 from mcp.server.fastmcp.exceptions import ToolError
 
 from basic_memory.mcp.tools import notes
-from basic_memory.schemas import EntityResponse
 
 
 @pytest.mark.asyncio
@@ -17,31 +18,41 @@ async def test_write_note(app):
     - Handle tags correctly
     - Return valid permalink
     """
-    permalink = await notes.write_note(
+    result = await notes.write_note(
         title="Test Note",
         folder="test",
         content="# Test\nThis is a test note",
         tags=["test", "documentation"],
     )
 
-    assert permalink  # Got a valid permalink
+    assert result
+    assert (
+        dedent("""
+        # Created test/Test Note.md (159f2168)
+        permalink: test/test-note
+        
+        ## Tags
+        - test, documentation
+        """).strip()
+        in result
+    )
 
     # Try reading it back via permalink
-    content = await notes.read_note(permalink)
+    content = await notes.read_note("test/test-note")
     assert (
-        """
----
-title: Test Note
-type: note
-permalink: test/test-note
-tags:
-- '#test'
-- '#documentation'
----
-
-# Test
-This is a test note
-""".strip()
+        dedent("""
+        ---
+        title: Test Note
+        type: note
+        permalink: test/test-note
+        tags:
+        - '#test'
+        - '#documentation'
+        ---
+        
+        # Test
+        This is a test note
+        """).strip()
         in content
     )
 
@@ -49,20 +60,28 @@ This is a test note
 @pytest.mark.asyncio
 async def test_write_note_no_tags(app):
     """Test creating a note without tags."""
-    permalink = await notes.write_note(title="Simple Note", folder="test", content="Just some text")
+    result = await notes.write_note(title="Simple Note", folder="test", content="Just some text")
 
-    # Should be able to read it back
-    content = await notes.read_note(permalink)
+    assert result
     assert (
-        """
---
-title: Simple Note
-type: note
-permalink: test/simple-note
----
-
-Just some text
-""".strip()
+        dedent("""
+        # Created test/Simple Note.md (9a1ff079)
+        permalink: test/simple-note
+        """).strip()
+        in result
+    )
+    # Should be able to read it back
+    content = await notes.read_note("test/simple-note")
+    assert (
+        dedent("""
+        --
+        title: Simple Note
+        type: note
+        permalink: test/simple-note
+        ---
+        
+        Just some text
+        """).strip()
         in content
     )
 
@@ -84,24 +103,44 @@ async def test_write_note_update_existing(app):
     - Handle tags correctly
     - Return valid permalink
     """
-    permalink = await notes.write_note(
+    result = await notes.write_note(
         title="Test Note",
         folder="test",
         content="# Test\nThis is a test note",
         tags=["test", "documentation"],
     )
 
-    assert permalink  # Got a valid permalink
+    assert result  # Got a valid permalink
+    assert (
+        dedent("""
+        # Created test/Test Note.md (159f2168)
+        permalink: test/test-note
+        
+        ## Tags
+        - test, documentation
+        """).strip()
+        in result
+    )
 
-    permalink = await notes.write_note(
+    result = await notes.write_note(
         title="Test Note",
         folder="test",
         content="# Test\nThis is an updated note",
         tags=["test", "documentation"],
     )
+    assert (
+        dedent("""
+        # Updated test/Test Note.md (131b5662)
+        permalink: test/test-note
+        
+        ## Tags
+        - test, documentation
+        """).strip()
+        in result
+    )
 
     # Try reading it back
-    content = await notes.read_note(permalink)
+    content = await notes.read_note("test/test-note")
     assert (
         """
 ---
@@ -135,10 +174,18 @@ async def test_read_note_by_title(app):
 async def test_note_unicode_content(app):
     """Test handling of unicode content in notes."""
     content = "# Test 🚀\nThis note has emoji 🎉 and unicode ♠♣♥♦"
-    permalink = await notes.write_note(title="Unicode Test", folder="test", content=content)
+    result = await notes.write_note(title="Unicode Test", folder="test", content=content)
+
+    assert (
+        dedent("""
+        # Created test/Unicode Test.md (272389cd)
+        permalink: test/unicode-test
+        """).strip()
+        in result
+    )
 
     # Read back should preserve unicode
-    result = await notes.read_note(permalink)
+    result = await notes.read_note("test/unicode-test")
     assert content in result
 
 
@@ -147,20 +194,61 @@ async def test_multiple_notes(app):
     """Test creating and managing multiple notes."""
     # Create several notes
     notes_data = [
-        ("Note 1", "test", "Content 1", ["tag1"]),
-        ("Note 2", "test", "Content 2", ["tag1", "tag2"]),
-        ("Note 3", "test", "Content 3", []),
+        ("test/note-1", "Note 1", "test", "Content 1", ["tag1"]),
+        ("test/note-2", "Note 2", "test", "Content 2", ["tag1", "tag2"]),
+        ("test/note-3", "Note 3", "test", "Content 3", []),
     ]
 
-    permalinks = []
-    for title, folder, content, tags in notes_data:
-        permalink = await notes.write_note(title=title, folder=folder, content=content, tags=tags)
-        permalinks.append(permalink)
+    for _, title, folder, content, tags in notes_data:
+        await notes.write_note(title=title, folder=folder, content=content, tags=tags)
 
     # Should be able to read each one
-    for i, permalink in enumerate(permalinks):
-        content = await notes.read_note(permalink)
-        assert f"Content {i + 1}" in content
+    for permalink, title, folder, content, _ in notes_data:
+        note = await notes.read_note(permalink)
+        assert content in note
+
+    # read multiple notes at once
+
+    result = await notes.read_note("test/*")
+
+    # note we can't compare times
+    assert "--- memory://test/note-1" in result
+    assert "Content 1" in result
+
+    assert "--- memory://test/note-2" in result
+    assert "Content 2" in result
+
+    assert "--- memory://test/note-3" in result
+    assert "Content 3" in result
+
+
+@pytest.mark.asyncio
+async def test_multiple_notes_pagination(app):
+    """Test creating and managing multiple notes."""
+    # Create several notes
+    notes_data = [
+        ("test/note-1", "Note 1", "test", "Content 1", ["tag1"]),
+        ("test/note-2", "Note 2", "test", "Content 2", ["tag1", "tag2"]),
+        ("test/note-3", "Note 3", "test", "Content 3", []),
+    ]
+
+    for _, title, folder, content, tags in notes_data:
+        await notes.write_note(title=title, folder=folder, content=content, tags=tags)
+
+    # Should be able to read each one
+    for permalink, title, folder, content, _ in notes_data:
+        note = await notes.read_note(permalink)
+        assert content in note
+
+    # read multiple notes at once with pagination
+    result = await notes.read_note("test/*", page=1, page_size=2)
+
+    # note we can't compare times
+    assert "--- memory://test/note-1" in result
+    assert "Content 1" in result
+
+    assert "--- memory://test/note-2" in result
+    assert "Content 2" in result
 
 
 @pytest.mark.asyncio
@@ -172,16 +260,16 @@ async def test_delete_note_existing(app):
     - Return valid permalink
     - Delete the note
     """
-    permalink = await notes.write_note(
+    result = await notes.write_note(
         title="Test Note",
         folder="test",
         content="# Test\nThis is a test note",
         tags=["test", "documentation"],
     )
 
-    assert permalink  # Got a valid permalink
+    assert result
 
-    deleted = await notes.delete_note(permalink)
+    deleted = await notes.delete_note("test/test-note")
     assert deleted is True
 
 
@@ -207,7 +295,7 @@ async def test_write_note_verbose(app):
     - Handle tags correctly
     - Return valid permalink
     """
-    entity = await notes.write_note(
+    result = await notes.write_note(
         title="Test Note",
         folder="test",
         content="""
@@ -218,24 +306,27 @@ async def test_write_note_verbose(app):
 
 """,
         tags=["test", "documentation"],
-        verbose=True,
     )
 
-    assert isinstance(entity, EntityResponse)
-
-    assert entity.title == "Test Note"
-    assert entity.file_path == "test/Test Note.md"
-    assert entity.entity_type == "note"
-    assert entity.permalink == "test/test-note"
-
-    assert len(entity.observations) == 1
-    assert entity.observations[0].content == "First observation"
-
-    assert len(entity.relations) == 1
-    assert entity.relations[0].relation_type == "relates to"
-    assert entity.relations[0].from_id == "test/test-note"
-    assert entity.relations[0].to_id is None
-    assert entity.relations[0].to_name == "Knowledge"
+    assert (
+        dedent("""
+        # Created test/Test Note.md (06873a7a)
+        permalink: test/test-note
+        
+        ## Observations
+        - note: 1
+        
+        ## Relations
+        - Resolved: 0
+        - Unresolved: 1
+        
+        Unresolved relations will be retried on next sync.
+        
+        ## Tags
+        - test, documentation
+        """).strip()
+        in result
+    )
 
 
 @pytest.mark.asyncio
@@ -248,13 +339,14 @@ async def test_read_note_memory_url(app):
     - Return the note content
     """
     # First create a note
-    permalink = await notes.write_note(
+    result = await notes.write_note(
         title="Memory URL Test",
         folder="test",
         content="Testing memory:// URL handling",
     )
+    assert result
 
     # Should be able to read it with a memory:// URL
-    memory_url = f"memory://{permalink}"
+    memory_url = "memory://test/memory-url-test"
     content = await notes.read_note(memory_url)
     assert "Testing memory:// URL handling" in content

tests/mcp/test_tool_search.py

@@ -12,12 +12,13 @@ from basic_memory.schemas.search import SearchQuery, SearchItemType
 async def test_search_basic(client):
     """Test basic search functionality."""
     # Create a test note
-    permalink = await notes.write_note(
+    result = await notes.write_note(
         title="Test Search Note",
         folder="test",
         content="# Test\nThis is a searchable test note",
         tags=["test", "search"],
     )
+    assert result
 
     # Search for it
     query = SearchQuery(text="searchable")
@@ -25,7 +26,28 @@ async def test_search_basic(client):
 
     # Verify results
     assert len(response.results) > 0
-    assert any(r.permalink == permalink for r in response.results)
+    assert any(r.permalink == "test/test-search-note" for r in response.results)
+
+
+@pytest.mark.asyncio
+async def test_search_pagination(client):
+    """Test basic search functionality."""
+    # Create a test note
+    result = await notes.write_note(
+        title="Test Search Note",
+        folder="test",
+        content="# Test\nThis is a searchable test note",
+        tags=["test", "search"],
+    )
+    assert result
+
+    # Search for it
+    query = SearchQuery(text="searchable")
+    response = await search(query, page=1, page_size=1)
+
+    # Verify results
+    assert len(response.results) == 1
+    assert any(r.permalink == "test/test-search-note" for r in response.results)
 
 
 @pytest.mark.asyncio

tests/schemas/test_schemas.py

@@ -51,16 +51,17 @@ def test_relation_in_validation():
 def test_relation_response():
     """Test RelationResponse validation."""
     data = {
+        "permalink": "test/123/relates_to/test/456",
         "from_id": "test/123",
         "to_id": "test/456",
-        "relation_type": "test",
+        "relation_type": "relates_to",
         "from_entity": {"permalink": "test/123"},
         "to_entity": {"permalink": "test/456"},
     }
     relation = RelationResponse.model_validate(data)
     assert relation.from_id == "test/123"
     assert relation.to_id == "test/456"
-    assert relation.relation_type == "test"
+    assert relation.relation_type == "relates_to"
     assert relation.context is None
 
 
@@ -73,16 +74,27 @@ def test_entity_out_from_attributes():
         "file_path": "test",
         "entity_type": "knowledge",
         "content_type": "text/markdown",
-        "observations": [{"id": 1, "category": "note", "content": "test obs", "context": None}],
-        "relations": [
+        "observations": [
             {
                 "id": 1,
-                "from_id": "test/test",
-                "to_id": "test/test",
-                "relation_type": "test",
+                "permalink": "permalink",
+                "category": "note",
+                "content": "test obs",
                 "context": None,
             }
         ],
+        "relations": [
+            {
+                "id": 1,
+                "permalink": "test/test/relates_to/test/test",
+                "from_id": "test/test",
+                "to_id": "test/test",
+                "relation_type": "relates_to",
+                "context": None,
+            }
+        ],
+        "created_at": "2023-01-01T00:00:00",
+        "updated_at": "2023-01-01T00:00:00",
     }
     entity = EntityResponse.model_validate(db_data)
     assert entity.permalink == "test/test"

tests/schemas/test_search.py

@@ -112,7 +112,7 @@ def test_search_response():
             metadata={},
         ),
     ]
-    response = SearchResponse(results=results)
+    response = SearchResponse(results=results, current_page=1, page_size=1)
     assert len(response.results) == 2
     assert response.results[0].score > response.results[1].score
 

tests/services/test_context_service.py

@@ -128,18 +128,6 @@ async def test_build_context(context_service, test_graph):
     assert total_results == len(primary_results) + len(related_results)
 
 
-@pytest.mark.skip("search prefix see:'https://sqlite.org/fts5.html#FTS5 Prefix Queries'")
-@pytest.mark.asyncio
-async def test_build_context_pattern(context_service, test_graph):
-    """Test permalink wildcard lookup."""
-    # url = memory_url.validate_strings("memory://test/connected*")
-    # results = await context_service.build_context(url)
-    # matched_results = results["metadata"]["matched_results"]
-    # primary_results = results["primary_results"]
-    # related_results = results["related_results"]
-    # total_results = results["metadata"]["total_results"]
-
-
 @pytest.mark.asyncio
 async def test_build_context_not_found(context_service):
     """Test handling non-existent permalinks."""

tests/services/test_link_resolver.py

@@ -10,7 +10,17 @@ from basic_memory.services.link_resolver import LinkResolver
 
 @pytest_asyncio.fixture
 async def test_entities(entity_service, file_service):
-    """Create a set of test entities."""
+    """Create a set of test entities.
+
+    ├── components
+    │   ├── Auth Service.md
+    │   └── Core Service.md
+    ├── config
+    │   └── Service Config.md
+    └── specs
+        └── Core Features.md
+
+    """
 
     e1, _ = await entity_service.create_or_update_entity(
         EntitySchema(
@@ -40,6 +50,20 @@ async def test_entities(entity_service, file_service):
             folder="specs",
         )
     )
+    e5, _ = await entity_service.create_or_update_entity(
+        EntitySchema(
+            title="Sub Features 1",
+            entity_type="specs",
+            folder="specs/subspec",
+        )
+    )
+    e6, _ = await entity_service.create_or_update_entity(
+        EntitySchema(
+            title="Sub Features 2",
+            entity_type="specs",
+            folder="specs/subspec",
+        )
+    )
 
     return [e1, e2, e3, e4]
 
@@ -68,18 +92,11 @@ async def test_exact_title_match(link_resolver, test_entities):
     assert entity.permalink == "components/core-service"
 
 
-@pytest.mark.skip(reason="Fuzzy misspelling not yet implemented")
-@pytest.mark.asyncio
-async def test_fuzzy_title_match_misspelling(link_resolver):
-    # Test slight misspelling
-    result = await link_resolver.resolve_link("Core Servise")
-    assert result.permalink == "components/core-service"
-
-
 @pytest.mark.asyncio
 async def test_fuzzy_title_partial_match(link_resolver):
     # Test partial match
     result = await link_resolver.resolve_link("Auth Serv")
+    assert result is not None, "Did not find partial match"
     assert result.permalink == "components/auth-service"
 
 
@@ -114,31 +131,3 @@ async def test_resolve_none(link_resolver):
     """Test resolving non-existent entity."""
     # Basic new entity
     assert await link_resolver.resolve_link("New Feature") is None
-
-
-@pytest.mark.skip("Advanced relevance scoring not yet implemented")
-@pytest.mark.asyncio
-async def test_multiple_matches_resolution(link_resolver):
-    """Test resolution when multiple potential matches exist."""
-    # Add some similar entities
-    test_cases = [
-        {
-            "link": "Service",  # Ambiguous
-            "expected_prefix": "components/",  # Should prefer component directory match
-        },
-        {
-            "link": "Core",  # Ambiguous
-            "expected_prefix": "specs/",  # Should prefer specs directory match
-        },
-        {
-            "link": "Service",
-            "expected": "components/core-service",  # Should pick shortest/highest scored
-        },
-    ]
-
-    for case in test_cases:
-        result = await link_resolver.resolve_link(case["link"])
-        if "expected_prefix" in case:
-            assert result.startswith(case["expected_prefix"])
-        else:
-            assert result == case["expected"]

tests/services/test_search_service.py

@@ -19,6 +19,25 @@ async def test_search_permalink(search_service, test_graph):
         assert "test/root" in r.permalink
 
 
+@pytest.mark.asyncio
+async def test_search_limit_offset(search_service, test_graph):
+    """Exact permalink"""
+    results = await search_service.search(SearchQuery(permalink_match="test/*"))
+    assert len(results) > 1
+
+    results = await search_service.search(SearchQuery(permalink_match="test/*"), limit=1)
+    assert len(results) == 1
+
+    results = await search_service.search(SearchQuery(permalink_match="test/*"), limit=100)
+    num_results = len(results)
+
+    # assert offset
+    offset_results = await search_service.search(
+        SearchQuery(permalink_match="test/*"), limit=100, offset=1
+    )
+    assert len(offset_results) == num_results - 1
+
+
 @pytest.mark.asyncio
 async def test_search_permalink_observations_wildcard(search_service, test_graph):
     """Pattern matching"""
@@ -32,21 +51,24 @@ async def test_search_permalink_observations_wildcard(search_service, test_graph
 @pytest.mark.asyncio
 async def test_search_permalink_relation_wildcard(search_service, test_graph):
     """Pattern matching"""
-    results = await search_service.search(SearchQuery(permalink_match="test/root/connects_to/*"))
+    results = await search_service.search(SearchQuery(permalink_match="test/root/connects-to/*"))
     assert len(results) == 1
     permalinks = {r.permalink for r in results}
     assert "test/root/connects-to/test/connected-entity-1" in permalinks
 
 
-@pytest.mark.skip("search prefix see:'https://sqlite.org/fts5.html#FTS5 Prefix Queries'")
 @pytest.mark.asyncio
 async def test_search_permalink_wildcard2(search_service, test_graph):
     """Pattern matching"""
-    results = await search_service.search(SearchQuery(permalink_match="test/connected*"))
-    assert len(results) == 2
+    results = await search_service.search(
+        SearchQuery(
+            permalink_match="test/connected*",
+        )
+    )
+    assert len(results) >= 2
     permalinks = {r.permalink for r in results}
-    assert "test/connected1" in permalinks
-    assert "test/connected2" in permalinks
+    assert "test/connected-entity-1" in permalinks
+    assert "test/connected-entity-2" in permalinks
 
 
 @pytest.mark.asyncio
@@ -68,17 +90,27 @@ async def test_search_title(search_service, test_graph):
 
 
 @pytest.mark.asyncio
-async def test_text_search_features(search_service, test_graph):
+async def test_text_search_case_insensitive(search_service, test_graph):
     """Test text search functionality."""
     # Case insensitive
     results = await search_service.search(SearchQuery(text="ENTITY"))
     assert any("test/root" in r.permalink for r in results)
 
-    # Partial word match
-    results = await search_service.search(SearchQuery(text="Connect"))
+
+@pytest.mark.asyncio
+async def test_text_search_content_word_match(search_service, test_graph):
+    """Test text search functionality."""
+
+    # content word match
+    results = await search_service.search(SearchQuery(text="Connected"))
     assert len(results) > 0
     assert any(r.file_path == "test/Connected Entity 2.md" for r in results)
 
+
+@pytest.mark.asyncio
+async def test_text_search_multiple_terms(search_service, test_graph):
+    """Test text search functionality."""
+
     # Multiple terms
     results = await search_service.search(SearchQuery(text="root note"))
     assert any("test/root" in r.permalink for r in results)
@@ -88,15 +120,20 @@ async def test_text_search_features(search_service, test_graph):
 async def test_pattern_matching(search_service, test_graph):
     """Test pattern matching with various wildcards."""
     # Test wildcards
-    results = await search_service.search(SearchQuery(permalink="test/*"))
+    results = await search_service.search(SearchQuery(permalink_match="test/*"))
     for r in results:
         assert "test/" in r.permalink
 
     # Test start wildcards
-    results = await search_service.search(SearchQuery(permalink="*/observations"))
+    results = await search_service.search(SearchQuery(permalink_match="*/observations"))
     for r in results:
         assert "/observations" in r.permalink
 
+    # Test permalink partial match
+    results = await search_service.search(SearchQuery(permalink_match="test"))
+    for r in results:
+        assert "test/" in r.permalink
+
 
 @pytest.mark.asyncio
 async def test_filters(search_service, test_graph):

tests/test_basic_memory.py

@@ -1,8 +1,47 @@
 """Tests for basic-memory package"""
 
+import sys
+import tomllib
+
+import pytest
+from frontmatter.default_handlers import toml
+
 from basic_memory import __version__
+from basic_memory.config import config
+
+
+def read_toml_version(file_path):
+    try:
+        with open(file_path, "rb") as f:
+            if sys.version_info >= (3, 11):
+                data = tomllib.load(f)
+            else:
+                data = toml.load(f)
+        if "project" in data and "version" in data["project"]:
+            return data["project"]["version"]
+        else:
+            return None
+    except FileNotFoundError:
+        return None
+    except (toml.TomlDecodeError, tomllib.TOMLDecodeError):
+        return None
+
+
+file_path = "pyproject.toml"
+version = read_toml_version(file_path)
 
 
 def test_version():
-    """Test version is set"""
-    assert __version__ is not None
+    """Test version is set in project src code and pyproject.toml"""
+    assert __version__ == version
+
+
+def test_config_env():
+    """Test the config env is set to test for pytest"""
+    assert config.env == "test"
+
+
+@pytest.mark.asyncio
+async def test_config_env_async():
+    """Test the config env is set to test for async pytest"""
+    assert config.env == "test"

uv.lock

@@ -59,6 +59,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/46/eb/e7f063ad1fec6b3178a3cd82d1a3c4de82cccf283fc42746168188e1cdd5/anyio-4.8.0-py3-none-any.whl", hash = "sha256:b5011f270ab5eb0abf13385f851315585cc37ef330dd88e27ec3d34d651fd47a", size = 96041 },
 ]
 
+[[package]]
+name = "asgiref"
+version = "3.8.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/29/38/b3395cc9ad1b56d2ddac9970bc8f4141312dbaec28bc7c218b0dfafd0f42/asgiref-3.8.1.tar.gz", hash = "sha256:c343bd80a0bec947a9860adb4c432ffa7db769836c64238fc34bdc3fec84d590", size = 35186 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/39/e3/893e8757be2612e6c266d9bb58ad2e3651524b5b40cf56761e985a28b13e/asgiref-3.8.1-py3-none-any.whl", hash = "sha256:3e1e3ecc849832fe52ccf2cb6686b7a55f82bb1d6aee72a58826471390335e47", size = 23828 },
+]
+
 [[package]]
 name = "asttokens"
 version = "3.0.0"
@@ -70,7 +79,7 @@ wheels = [
 
 [[package]]
 name = "basic-memory"
-version = "0.3.0"
+version = "0.6.0"
 source = { editable = "." }
 dependencies = [
     { name = "aiosqlite" },
@@ -79,6 +88,7 @@ dependencies = [
     { name = "fastapi", extra = ["standard"] },
     { name = "greenlet" },
     { name = "icecream" },
+    { name = "logfire", extra = ["fastapi", "httpx", "sqlalchemy", "sqlite3"] },
     { name = "loguru" },
     { name = "markdown-it-py" },
     { name = "mcp" },
@@ -116,6 +126,7 @@ requires-dist = [
     { name = "fastapi", extras = ["standard"], specifier = ">=0.115.8" },
     { name = "greenlet", specifier = ">=3.1.1" },
     { name = "icecream", specifier = ">=2.1.3" },
+    { name = "logfire", extras = ["fastapi", "httpx", "sqlalchemy", "sqlite3"], specifier = ">=3.6.0" },
     { name = "loguru", specifier = ">=0.7.3" },
     { name = "markdown-it-py", specifier = ">=3.0.0" },
     { name = "mcp", specifier = ">=1.2.0" },
@@ -169,6 +180,41 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/7c/fc/6a8cb64e5f0324877d503c854da15d76c1e50eb722e320b15345c4d0c6de/cffi-1.17.1-cp313-cp313-win_amd64.whl", hash = "sha256:f6a16c31041f09ead72d69f583767292f750d24913dadacf5756b966aacb3f1a", size = 182009 },
 ]
 
+[[package]]
+name = "charset-normalizer"
+version = "3.4.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/16/b0/572805e227f01586461c80e0fd25d65a2115599cc9dad142fee4b747c357/charset_normalizer-3.4.1.tar.gz", hash = "sha256:44251f18cd68a75b56585dd00dae26183e102cd5e0f9f1466e6df5da2ed64ea3", size = 123188 }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/0a/9a/dd1e1cdceb841925b7798369a09279bd1cf183cef0f9ddf15a3a6502ee45/charset_normalizer-3.4.1-cp312-cp312-macosx_10_13_universal2.whl", hash = "sha256:73d94b58ec7fecbc7366247d3b0b10a21681004153238750bb67bd9012414545", size = 196105 },
+    { url = "https://files.pythonhosted.org/packages/d3/8c/90bfabf8c4809ecb648f39794cf2a84ff2e7d2a6cf159fe68d9a26160467/charset_normalizer-3.4.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:dad3e487649f498dd991eeb901125411559b22e8d7ab25d3aeb1af367df5efd7", size = 140404 },
+    { url = "https://files.pythonhosted.org/packages/ad/8f/e410d57c721945ea3b4f1a04b74f70ce8fa800d393d72899f0a40526401f/charset_normalizer-3.4.1-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:c30197aa96e8eed02200a83fba2657b4c3acd0f0aa4bdc9f6c1af8e8962e0757", size = 150423 },
+    { url = "https://files.pythonhosted.org/packages/f0/b8/e6825e25deb691ff98cf5c9072ee0605dc2acfca98af70c2d1b1bc75190d/charset_normalizer-3.4.1-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:2369eea1ee4a7610a860d88f268eb39b95cb588acd7235e02fd5a5601773d4fa", size = 143184 },
+    { url = "https://files.pythonhosted.org/packages/3e/a2/513f6cbe752421f16d969e32f3583762bfd583848b763913ddab8d9bfd4f/charset_normalizer-3.4.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc2722592d8998c870fa4e290c2eec2c1569b87fe58618e67d38b4665dfa680d", size = 145268 },
+    { url = "https://files.pythonhosted.org/packages/74/94/8a5277664f27c3c438546f3eb53b33f5b19568eb7424736bdc440a88a31f/charset_normalizer-3.4.1-cp312-cp312-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:ffc9202a29ab3920fa812879e95a9e78b2465fd10be7fcbd042899695d75e616", size = 147601 },
+    { url = "https://files.pythonhosted.org/packages/7c/5f/6d352c51ee763623a98e31194823518e09bfa48be2a7e8383cf691bbb3d0/charset_normalizer-3.4.1-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:804a4d582ba6e5b747c625bf1255e6b1507465494a40a2130978bda7b932c90b", size = 141098 },
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