[pre-commit.ci] pre-commit autoupdate

.claude/agents/frontend-tester.md

@@ -109,5 +109,5 @@ After testing, provide a structured report:
 ```python
 from zndraw import ZnDraw
 
-vis = ZnDraw(room="<room_id>") # finds local server automatically
+vis = ZnDraw(room="<room_id>")  # finds local server automatically
 ```

.pre-commit-config.yaml

@@ -20,17 +20,17 @@ repos:
       - id: sort-simple-yaml
       - id: trailing-whitespace
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.2
+    rev: v2.4.3
     hooks:
       - id: codespell
         additional_dependencies: ["tomli"]
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.4.10  # Use the sha / tag you want to point at
+    rev: v2.5.15  # Use the sha / tag you want to point at
     hooks:
     -   id: biome-format # not using check becasue there are lots of things that need fixed
         additional_dependencies: ["@biomejs/biome@1.9.4"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.9
+    rev: v0.16.10
     hooks:
       - id: ruff
         args: [--fix]

README.md

@@ -57,7 +57,9 @@ ZnDraw supports multiple clients connecting to the same visualization. Each visu
 ```python
 from zndraw import ZnDraw
 
-vis = ZnDraw(url="http://localhost:1234", room="123e4567-e89b-12d3-a456-426614174000/my-room")
+vis = ZnDraw(
+    url="http://localhost:1234", room="123e4567-e89b-12d3-a456-426614174000/my-room"
+)
 ```
 
 > `room=` accepts the composed form `<owner_uuid>/<name>` returned by the server. Single-segment names are no longer supported.
@@ -71,7 +73,7 @@ vis = ZnDraw(
     url="http://localhost:1234",
     room="123e4567-e89b-12d3-a456-426614174000/my-room",
     user="username",
-    password="password"
+    password="password",
 )
 ```
 
@@ -106,12 +108,12 @@ subset = vis[10:20]
 Control various aspects of the visualization:
 
 ```python
-vis.selection   # Currently selected atoms
-vis.step        # Current frame index
-vis.figures     # Plotly figures
-vis.bookmarks   # Saved frame annotations
+vis.selection  # Currently selected atoms
+vis.step  # Current frame index
+vis.figures  # Plotly figures
+vis.bookmarks  # Saved frame annotations
 vis.geometries  # 3D geometry overlays (dict-like)
-vis.sessions    # Session configuration
+vis.sessions  # Session configuration
 ```
 
 ## Geometries
@@ -162,6 +164,7 @@ Create custom tools accessible via the ZnDraw UI:
 from molify import smiles2atoms
 from zndraw import ZnDraw, Extension, Category
 
+
 class AddMolecule(Extension):
     category = Category.MODIFIER
     smiles: str
@@ -170,6 +173,7 @@ class AddMolecule(Extension):
         vis.append(smiles2atoms(self.smiles))
         vis.step = len(vis) - 1
 
+
 vis = ZnDraw()
 vis.register_job(AddMolecule)  # room-scoped (default)
 vis.wait()
@@ -188,6 +192,7 @@ Register filesystem providers so users can load files from the UI:
 
 ```python
 import fsspec
+
 vis.register_fs(fsspec.filesystem("file"), name="local")
 ```
 

docs/superpowers/plans/2026-03-13-isosurface.md

@@ -272,7 +272,7 @@ Add to `geometries` dict (after the `"PropertyInspector": PropertyInspector,` li
 Add `"Isosurface"` to the `__all__` list (alphabetically, after `"InteractionSettings"`):
 
 ```python
-    "Isosurface",
+("Isosurface",)
 ```
 
 - [ ] **Step 5: Run tests to verify they pass**
@@ -824,9 +824,7 @@ async def test_isosurface_pyscf_h2(
         "cell": cc.box * bohr_to_ang,
     }
     frame = {
-        b"info.orbital_homo": msgpack.packb(
-            cube_data, default=msgpack_numpy.encode
-        ),
+        b"info.orbital_homo": msgpack.packb(cube_data, default=msgpack_numpy.encode),
     }
 
     user, token = await create_test_user_in_db(iso_session)
@@ -979,9 +977,7 @@ async def get_isosurface(
 
     _REQUIRED_KEYS = {"grid", "origin", "cell"}
     if not isinstance(cube_dict, dict):
-        raise UnprocessableContent.exception(
-            f"Key '{cube_key}' is not a dict"
-        )
+        raise UnprocessableContent.exception(f"Key '{cube_key}' is not a dict")
     missing = _REQUIRED_KEYS - cube_dict.keys()
     if missing:
         raise UnprocessableContent.exception(
@@ -990,9 +986,7 @@ async def get_isosurface(
 
     grid = np.asarray(cube_dict["grid"])
     if grid.ndim != 3:
-        raise UnprocessableContent.exception(
-            f"Grid must be 3D, got {grid.ndim}D"
-        )
+        raise UnprocessableContent.exception(f"Grid must be 3D, got {grid.ndim}D")
 
     origin = np.asarray(cube_dict["origin"], dtype=np.float64)
     cell = np.asarray(cube_dict["cell"], dtype=np.float64)

docs/superpowers/plans/2026-03-18-storage-refactor.md

@@ -189,9 +189,12 @@ class FrameStorage:
 
     async def has_mount(self, room_id: str) -> bool:
         """Check if a room has a provider-backed frame count."""
-        return await self._redis.exists(  # type: ignore[misc]
-            RedisKey.provider_frame_count(room_id)
-        ) > 0
+        return (
+            await self._redis.exists(  # type: ignore[misc]
+                RedisKey.provider_frame_count(room_id)
+            )
+            > 0
+        )
 
     async def set_frame_count(self, room_id: str, count: int) -> None:
         """Store provider frame count in Redis."""
@@ -266,6 +269,7 @@ The new dependency section (replacing lines 32-34 and 56-72):
 from zndraw.storage import FrameStorage
 # ... (remove AsebytesStorage and StorageRouter imports)
 
+
 def get_frame_storage(request: Request) -> FrameStorage:
     """Get frame storage registry from app.state."""
     return request.app.state.frame_storage
@@ -312,6 +316,7 @@ Find the section (around lines 239-248) that creates `AsebytesStorage` and `Stor
 ```python
 # Before:
 from zndraw.storage.router import StorageRouter
+
 default_storage = AsebytesStorage(uri=settings.storage)
 app.state.frame_storage = StorageRouter(
     default=default_storage,
@@ -320,6 +325,7 @@ app.state.frame_storage = StorageRouter(
 
 # After:
 from zndraw.storage import FrameStorage
+
 app.state.frame_storage = FrameStorage(
     uri=settings.storage,
     redis=app.state.redis,
@@ -355,9 +361,11 @@ Change the type annotation and all method bodies:
 # TYPE_CHECKING import changes:
 # Before:
 from zndraw.storage import AsebytesStorage
+
 # After:
 from zndraw.storage import FrameStorage
 
+
 # Class changes:
 class StorageResultBackend:
     """Adapt ``FrameStorage`` to the ``ResultBackend`` protocol.
@@ -545,7 +553,7 @@ Replace `storage: StorageDep` with `storage: FrameStorageDep`. Add `_: RequireWr
 await storage.delete_range(room_id, index, index + 1)
 
 # After:
-await storage[room_id][index:index + 1].delete()
+await storage[room_id][index : index + 1].delete()
 ```
 
 - [ ] **Step 9: Commit**
@@ -586,9 +594,7 @@ try:
 except (IndexError, KeyError):
     cube_raw = None
 if cube_raw is None:
-    raise UnprocessableContent.exception(
-        f"Key '{cube_key}' not found in frame {index}"
-    )
+    raise UnprocessableContent.exception(f"Key '{cube_key}' not found in frame {index}")
 cube_dict = msgpack.unpackb(cube_raw, ...)
 ```
 
@@ -889,6 +895,7 @@ app.dependency_overrides[get_frame_storage] = lambda: storage
 For tests without Redis fixture, create a minimal mock:
 ```python
 from unittest.mock import AsyncMock
+
 mock_redis = AsyncMock()
 mock_redis.get = AsyncMock(return_value=None)
 mock_redis.exists = AsyncMock(return_value=0)

docs/superpowers/plans/2026-03-19-cli-auth-consistency.md

@@ -444,9 +444,7 @@ Add at `src/zndraw/cli_agent/connection.py:39` after `RoomOpt`:
 ```python
 UserOpt = Annotated[
     str | None,
-    typer.Option(
-        "--user", envvar="ZNDRAW_USER", help="User email for authentication"
-    ),
+    typer.Option("--user", envvar="ZNDRAW_USER", help="User email for authentication"),
 ]
 PasswordOpt = Annotated[
     str | None,

docs/superpowers/plans/2026-03-20-global-extension-registration.md

@@ -94,45 +94,43 @@ Expected: FAIL — `register_job` passes `"@global"` to `_resolve_room` which tr
 In `src/zndraw/client/core.py`, replace the current `register_job` method (lines 592-603) with:
 
 ```python
-    def register_job(
-        self,
-        cls: type,
-        *,
-        room: Literal["@global"] | str | None = None,
-        public: Annotated[
-            bool | None,
-            typing_extensions.deprecated(
-                "Use room='@global' instead of public=True"
-            ),
-        ] = None,
-    ) -> None:
-        """Register an extension as a job. Connects the socket if needed.
-
-        Parameters
-        ----------
-        cls
-            Extension subclass to register.
-        room
-            Room scope. Use ``"@global"`` for global registration (admin-only).
-            Defaults to ``self.room``.
-        public
-            .. deprecated::
-                Use ``room='@global'`` instead.
-        """
-        if public and room is not None:
-            raise ValueError("Cannot specify both 'room' and 'public'")
-        if public:
-            warnings.warn(
-                "public=True is deprecated, use room='@global' instead",
-                DeprecationWarning,
-                stacklevel=2,
-            )
-            room = GLOBAL_ROOM
-        elif room != GLOBAL_ROOM:
-            room = self._resolve_room(room)
-
-        self._ensure_socket_connected()
-        self.jobs.register(cls, room=room)
+def register_job(
+    self,
+    cls: type,
+    *,
+    room: Literal["@global"] | str | None = None,
+    public: Annotated[
+        bool | None,
+        typing_extensions.deprecated("Use room='@global' instead of public=True"),
+    ] = None,
+) -> None:
+    """Register an extension as a job. Connects the socket if needed.
+
+    Parameters
+    ----------
+    cls
+        Extension subclass to register.
+    room
+        Room scope. Use ``"@global"`` for global registration (admin-only).
+        Defaults to ``self.room``.
+    public
+        .. deprecated::
+            Use ``room='@global'`` instead.
+    """
+    if public and room is not None:
+        raise ValueError("Cannot specify both 'room' and 'public'")
+    if public:
+        warnings.warn(
+            "public=True is deprecated, use room='@global' instead",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        room = GLOBAL_ROOM
+    elif room != GLOBAL_ROOM:
+        room = self._resolve_room(room)
+
+    self._ensure_socket_connected()
+    self.jobs.register(cls, room=room)
 ```
 
 Add necessary imports at the top of the file. `warnings` is already imported. Add:
@@ -201,20 +199,18 @@ Expected: FAIL — `AttributeError: 'ZnDraw' object has no attribute 'register_e
 In `src/zndraw/client/core.py`, add after the `register_job` method:
 
 ```python
-    @typing_extensions.deprecated(
-        "Use register_job(cls, room='@global') for global, "
-        "or register_job(cls) for room-scoped"
-    )
-    def register_extension(
-        self, cls: type, *, public: bool = False, **kwargs: Any
-    ) -> None:
-        """Register an extension.
-
-        .. deprecated::
-            Use :meth:`register_job` instead.
-        """
-        room = "@global" if public else kwargs.get("room")
-        self.register_job(cls, room=room)
+@typing_extensions.deprecated(
+    "Use register_job(cls, room='@global') for global, "
+    "or register_job(cls) for room-scoped"
+)
+def register_extension(self, cls: type, *, public: bool = False, **kwargs: Any) -> None:
+    """Register an extension.
+
+    .. deprecated::
+        Use :meth:`register_job` instead.
+    """
+    room = "@global" if public else kwargs.get("room")
+    self.register_job(cls, room=room)
 ```
 
 - [ ] **Step 4: Run test to verify it passes**

docs/superpowers/plans/2026-03-25-pydantic-settings-phase1.md

@@ -246,14 +246,17 @@ Read `tests/test_cli.py` focusing on tests that assert env var writes:
 
 ```python
 # Before:
-port: Annotated[int | None, typer.Option("--port", ..., envvar="ZNDRAW_PORT")] = None,
-host: Annotated[str, typer.Option(help="...", envvar="ZNDRAW_HOST")] = "127.0.0.1",
+port: Annotated[int | None, typer.Option("--port", ..., envvar="ZNDRAW_PORT")] = (None,)
+host: Annotated[str, typer.Option(help="...", envvar="ZNDRAW_HOST")] = ("127.0.0.1",)
 
 # After:
-port: Annotated[int | None, typer.Option("--port",
-    help="Server port [env: ZNDRAW_SERVER_PORT].")] = None,
-host: Annotated[str | None, typer.Option(
-    help="Server hostname or IP address [env: ZNDRAW_SERVER_HOST].")] = None,
+port: Annotated[
+    int | None, typer.Option("--port", help="Server port [env: ZNDRAW_SERVER_PORT].")
+] = (None,)
+host: Annotated[
+    str | None,
+    typer.Option(help="Server hostname or IP address [env: ZNDRAW_SERVER_HOST]."),
+] = (None,)
 ```
 
 **Behavioral change:** `host` default changes from `"127.0.0.1"` to `None`. When `None`, `Settings.host` default `"0.0.0.0"` takes over. This is intentional — Settings is the single source of truth.
@@ -277,9 +280,9 @@ settings = Settings(**overrides)
 
 ```python
 # Before:
-help="Database URL (overrides ZNDRAW_DATABASE_URL)"
+help = "Database URL (overrides ZNDRAW_DATABASE_URL)"
 # After:
-help="Database URL [env: ZNDRAW_SERVER_DATABASE_URL]."
+help = "Database URL [env: ZNDRAW_SERVER_DATABASE_URL]."
 ```
 
 - [ ] **Step 6: Rewrite `test_cli.py` tests that assert `os.environ` writes**