chore: formatting

Author: phernandez

Makefile

@@ -42,4 +42,13 @@ installer-win:
 update-deps:
 	uv lock f--upgrade
 
-check: lint  format type-check test
+check: lint  format type-check test
+
+
+# Target for generating Alembic migrations with a message from command line
+migration:
+	@if [ -z "$(m)" ]; then \
+		echo "Usage: make migration m=\"Your migration message\""; \
+		exit 1; \
+	fi; \
+	cd src/basic_memory/alembic && alembic revision --autogenerate -m "$(m)"

src/basic_memory/alembic/env.py

@@ -1,5 +1,6 @@
 """Alembic environment configuration."""
 
+import os
 from logging.config import fileConfig
 
 from sqlalchemy import engine_from_config
@@ -8,6 +9,10 @@
 from alembic import context
 
 from basic_memory.models import Base
+
+# set config.env to "test" for pytest to prevent logging to file in utils.setup_logging()
+os.environ["BASIC_MEMORY_ENV"] = "test"
+
 from basic_memory.config import config as app_config
 
 # this is the Alembic Config object, which provides
@@ -18,7 +23,7 @@
 sqlalchemy_url = f"sqlite:///{app_config.database_path}"
 config.set_main_option("sqlalchemy.url", sqlalchemy_url)
 
-#print(f"Using SQLAlchemy URL: {sqlalchemy_url}")
+# print(f"Using SQLAlchemy URL: {sqlalchemy_url}")
 
 # Interpret the config file for Python logging.
 if config.config_file_name is not None:
@@ -29,6 +34,14 @@
 target_metadata = Base.metadata
 
 
+# Add this function to tell Alembic what to include/exclude
+def include_object(object, name, type_, reflected, compare_to):
+    # Ignore SQLite FTS tables
+    if type_ == "table" and name.startswith("search_index"):
+        return False
+    return True
+
+
 def run_migrations_offline() -> None:
     """Run migrations in 'offline' mode.
 
@@ -46,6 +59,8 @@ def run_migrations_offline() -> None:
         target_metadata=target_metadata,
         literal_binds=True,
         dialect_opts={"paramstyle": "named"},
+        include_object=include_object,
+        render_as_batch=True,
     )
 
     with context.begin_transaction():
@@ -65,7 +80,12 @@ def run_migrations_online() -> None:
     )
 
     with connectable.connect() as connection:
-        context.configure(connection=connection, target_metadata=target_metadata)
+        context.configure(
+            connection=connection,
+            target_metadata=target_metadata,
+            include_object=include_object,
+            render_as_batch=True,
+        )
 
         with context.begin_transaction():
             context.run_migrations()

src/basic_memory/alembic/versions/502b60eaa905_remove_required_from_entity_permalink.py

@@ -0,0 +1,51 @@
+"""remove required from entity.permalink
+
+Revision ID: 502b60eaa905
+Revises: b3c3938bacdb
+Create Date: 2025-02-24 13:33:09.790951
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "502b60eaa905"
+down_revision: Union[str, None] = "b3c3938bacdb"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("entity", schema=None) as batch_op:
+        batch_op.alter_column("permalink", existing_type=sa.VARCHAR(), nullable=True)
+        batch_op.drop_index("ix_entity_permalink")
+        batch_op.create_index(batch_op.f("ix_entity_permalink"), ["permalink"], unique=False)
+        batch_op.drop_constraint("uix_entity_permalink", type_="unique")
+        batch_op.create_index(
+            "uix_entity_permalink",
+            ["permalink"],
+            unique=True,
+            sqlite_where=sa.text("content_type = 'text/markdown' AND permalink IS NOT NULL"),
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("entity", schema=None) as batch_op:
+        batch_op.drop_index(
+            "uix_entity_permalink",
+            sqlite_where=sa.text("content_type = 'text/markdown' AND permalink IS NOT NULL"),
+        )
+        batch_op.create_unique_constraint("uix_entity_permalink", ["permalink"])
+        batch_op.drop_index(batch_op.f("ix_entity_permalink"))
+        batch_op.create_index("ix_entity_permalink", ["permalink"], unique=1)
+        batch_op.alter_column("permalink", existing_type=sa.VARCHAR(), nullable=False)
+
+    # ### end Alembic commands ###

src/basic_memory/alembic/versions/b3c3938bacdb_relation_to_name_unique_index.py

@@ -5,46 +5,40 @@
 Create Date: 2025-02-22 14:59:30.668466
 
 """
+
 from typing import Sequence, Union
 
 from alembic import op
-import sqlalchemy as sa
-from alembic.context import get_context
 
 
 # revision identifiers, used by Alembic.
-revision: str = 'b3c3938bacdb'
-down_revision: Union[str, None] = '3dae7c7b1564'
+revision: str = "b3c3938bacdb"
+down_revision: Union[str, None] = "3dae7c7b1564"
 branch_labels: Union[str, Sequence[str], None] = None
 depends_on: Union[str, Sequence[str], None] = None
 
 
 def upgrade() -> None:
     # SQLite doesn't support constraint changes through ALTER
     # Need to recreate table with desired constraints
-    with op.batch_alter_table('relation') as batch_op:
+    with op.batch_alter_table("relation") as batch_op:
         # Drop existing unique constraint
-        batch_op.drop_constraint('uix_relation', type_='unique')
-        
+        batch_op.drop_constraint("uix_relation", type_="unique")
+
         # Add new constraints
         batch_op.create_unique_constraint(
-            'uix_relation_from_id_to_id', 
-            ['from_id', 'to_id', 'relation_type']
+            "uix_relation_from_id_to_id", ["from_id", "to_id", "relation_type"]
         )
         batch_op.create_unique_constraint(
-            'uix_relation_from_id_to_name',
-            ['from_id', 'to_name', 'relation_type']
+            "uix_relation_from_id_to_name", ["from_id", "to_name", "relation_type"]
         )
 
 
 def downgrade() -> None:
-    with op.batch_alter_table('relation') as batch_op:
+    with op.batch_alter_table("relation") as batch_op:
         # Drop new constraints
-        batch_op.drop_constraint('uix_relation_from_id_to_name', type_='unique')
-        batch_op.drop_constraint('uix_relation_from_id_to_id', type_='unique')
-        
+        batch_op.drop_constraint("uix_relation_from_id_to_name", type_="unique")
+        batch_op.drop_constraint("uix_relation_from_id_to_id", type_="unique")
+
         # Restore original constraint
-        batch_op.create_unique_constraint(
-            'uix_relation',
-            ['from_id', 'to_id', 'relation_type']
-        )
+        batch_op.create_unique_constraint("uix_relation", ["from_id", "to_id", "relation_type"])

src/basic_memory/api/routers/knowledge_router.py

@@ -133,7 +133,7 @@ async def delete_entity(
         return DeleteEntitiesResponse(deleted=False)
 
     # Delete the entity
-    deleted = await entity_service.delete_entity(entity.permalink)
+    deleted = await entity_service.delete_entity(entity.permalink or entity.id)
 
     # Remove from search index
     background_tasks.add_task(search_service.delete_by_permalink, entity.permalink)

src/basic_memory/api/routers/memory_router.py

@@ -41,17 +41,19 @@ async def to_summary(item: SearchIndexRow | ContextResultRow):
             case SearchItemType.OBSERVATION:
                 assert item.category is not None
                 assert item.content is not None
+                assert item.permalink is not None
 
                 return ObservationSummary(
                     category=item.category, content=item.content, permalink=item.permalink
                 )
             case SearchItemType.RELATION:
                 assert item.from_id is not None
+                assert item.permalink is not None
                 from_entity = await entity_repository.find_by_id(item.from_id)
                 assert from_entity is not None
+                assert from_entity.permalink is not None
 
                 to_entity = await entity_repository.find_by_id(item.to_id) if item.to_id else None
-
                 return RelationSummary(
                     permalink=item.permalink,
                     relation_type=item.type,
@@ -104,9 +106,11 @@ async def recent(
     context = await context_service.build_context(
         types=types, depth=depth, since=since, limit=limit, offset=offset, max_related=max_related
     )
-    return await to_graph_context(
+    recent_context = await to_graph_context(
         context, entity_repository=entity_repository, page=page, page_size=page_size
     )
+    logger.debug(f"Recent context: {recent_context.model_dump_json()}")
+    return recent_context
 
 
 # get_memory_context needs to be declared last so other paths can match

src/basic_memory/cli/commands/mcp.py

@@ -17,4 +17,4 @@ def mcp():  # pragma: no cover
     home_dir = config.home
     logger.info(f"Starting Basic Memory MCP server {basic_memory.__version__}")
     logger.info(f"Home directory: {home_dir}")
-    mcp_server.run()
+    mcp_server.run()

src/basic_memory/cli/commands/status.py

@@ -141,4 +141,4 @@ def status(
         except Exception as e:
             logger.exception(f"Error checking status: {e}")
             typer.echo(f"Error checking status: {e}", err=True)
-            raise typer.Exit(code=1)  # pragma: no cover
+            raise typer.Exit(code=1)  # pragma: no cover

src/basic_memory/cli/commands/sync.py

@@ -160,8 +160,10 @@ async def run_sync(verbose: bool = False, watch: bool = False, console_status: b
             file_service=sync_service.entity_service.file_service,
             config=config,
         )
-        await watch_service.handle_changes(config.home)
-        await watch_service.run(console_status=console_status)  # pragma: no cover
+        # full sync
+        await sync_service.sync(config.home)
+        # watch changes
+        await watch_service.run()  # pragma: no cover
     else:
         # one time sync
         knowledge_changes = await sync_service.sync(config.home)
@@ -186,18 +188,15 @@ 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, console_status=console_status))
+        asyncio.run(run_sync(verbose=verbose, watch=watch))
 
     except Exception as e:  # pragma: no cover
         if not isinstance(e, typer.Exit):
             logger.exception("Sync failed")
             typer.echo(f"Error during sync: {e}", err=True)
             raise typer.Exit(1)
-        raise
+        raise

src/basic_memory/cli/commands/tools.py

@@ -9,7 +9,6 @@
 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_resource as mcp_read_resource
 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
@@ -156,14 +155,3 @@ def get_entity(identifier: str):
             typer.echo(f"Error during get_entity: {e}", err=True)
             raise typer.Exit(1)
         raise
-
-@tool_app.command()
-def read_resource(identifier: str):
-    try:
-        entity = asyncio.run(read_resource(identifier=identifier))
-        rprint(entity.model_dump_json(indent=2))
-    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