chore(release): 0.6.0 [skip ci]

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

CHANGELOG.md

@@ -1,6 +1,37 @@
 # CHANGELOG
 
 
+## v0.6.0 (2025-02-18)
+
+### 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

@@ -4,7 +4,7 @@ install:
 	pip install -e ".[dev]"
 
 test:
-	pytest -p pytest_mock -v
+	uv run pytest -p pytest_mock -v
 
 lint:
 	ruff check . --fix
@@ -40,4 +40,4 @@ installer-win:
 
 
 update-deps:
-	uv lock f--upgrade
+	uv lock f--upgrade

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 = "0.6.0"
 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,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__ = "0.6.0"

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/resource_router.py

@@ -1,34 +1,118 @@
 """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) -> list[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,
 ) -> 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}",
+    # 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)
+        if not search_results:
+            raise HTTPException(status_code=404, detail=f"Resource not found: {identifier}")
+
+        # get the 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(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/cli/commands/import_chatgpt.py

@@ -69,7 +69,11 @@ 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."""
 

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
@@ -16,8 +15,5 @@ from basic_memory.cli.commands import (  # noqa: F401  # pragma: no cover
 )
 
 
-# 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", "prod"]
+
 
 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

@@ -140,11 +140,15 @@ 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 +157,4 @@ 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/mcp/tools/notes.py

@@ -17,42 +17,62 @@ 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
+        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
 
     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"]
+            title="Search Implementation",
+            content="# Search Component\\n\\n"
+                   "Implementation of the search feature, building on [[Core Search]].\\n\\n"
+                   "## Observations\\n"
+                   "- [tech] Using FTS5 for full-text search #implementation\\n"
+                   "- [design] Need pagination support #todo\\n\\n"
+                   "## Relations\\n"
+                   "- implements [[Search Spec]]\\n"
+                   "- depends_on [[Database Schema]]",
+            folder="docs/components"
         )
     """
     logger.info(f"Writing note folder:'{folder}' title: '{title}'")
@@ -68,34 +88,97 @@ async def write_note(
         entity_metadata=metadata,
     )
 
-    # Use existing knowledge tool
+    # 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())
-    return result if verbose else result.permalink
+
+    # 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")
+@mcp.tool(description="Read note content by title, permalink, relation, or pattern")
 async def read_note(identifier: str) -> str:
-    """Get the markdown content of a note.
-    Uses the resource router to return the actual file content.
+    """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")
 
     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)

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(
@@ -106,14 +122,14 @@ 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 +139,15 @@ 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:
@@ -173,7 +196,7 @@ class SearchRepository:
             LIMIT :limit
         """
 
-        # 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 +222,11 @@ 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 +259,7 @@ 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/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/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

@@ -75,7 +75,7 @@ class SearchService:
             else None
         )
 
-        # permalink search
+        # search
         results = await self.repository.search(
             search_text=query.text,
             permalink=query.permalink,

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 +64,45 @@ 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
+) -> 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
     """
 
     # 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,
+        )
+        logger.configure(handlers=[logfire.loguru_handler()])
+
+        # instrument code spans
+        logfire.instrument_sqlite3()
+        logfire.instrument_pydantic()
+
+        from basic_memory.db import _engine as engine
+
+        if engine:
+            logfire.instrument_sqlalchemy(engine=engine)
+
+        # 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 +114,5 @@ 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_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):
@@ -67,7 +69,7 @@ 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 +91,138 @@ 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_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/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 +22,10 @@ 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"
@@ -36,40 +37,40 @@ 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_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 +78,7 @@ 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

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 +194,32 @@ 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
@@ -172,16 +231,16 @@ 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 +266,7 @@ 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 +277,27 @@ 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 +310,14 @@ 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 +26,7 @@ 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

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/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]
 
@@ -80,6 +104,7 @@ async def test_fuzzy_title_match_misspelling(link_resolver):
 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 +139,3 @@ 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

@@ -32,21 +32,24 @@ 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 +71,27 @@ 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 +101,20 @@ 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 = "0.5.0"
 source = { editable = "." }
 dependencies = [
     { name = "aiosqlite" },
@@ -79,6 +88,7 @@ dependencies = [
     { name = "fastapi", extra = ["standard"] },
     { name = "greenlet" },
     { name = "icecream" },
+    { name = "logfire", extra = ["fastapi", "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", "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 },
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