[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

misc/Sockets.md

@@ -3,15 +3,19 @@
 ## Main
 
 ### connect
-- WebClient has a `session[token]` from routing through `\`, therefore it will be send to join the room `app.config["ROOM_HOSTS"][session[token]]`
+
+- WebClient has a `session[token]` from routing through `\`, therefore it will
+  be send to join the room `app.config["ROOM_HOSTS"][session[token]]`
 
 ### disconnect
 
 ### join(token)
-- PyClient has no `session[token]`, therefore it provides a token to be sent to a room.
+
+- PyClient has no `session[token]`, therefore it provides a token to be sent to
+  a room.
 
 ### exit
 
 ## Scene
 
-### 
+###

zndraw/app.py

@@ -1,9 +1,8 @@
-import multiprocessing as mp
+import contextlib
 import uuid
 
 from flask import Flask, redirect, render_template, request, session
-from flask_socketio import SocketIO, emit, join_room, call
-import contextlib
+from flask_socketio import SocketIO, call, emit, join_room
 
 app = Flask(__name__)
 app.config["SECRET_KEY"] = str(uuid.uuid4())
@@ -257,7 +256,12 @@ def analysis_schema(data: dict):
     else:
         try:
             # emit to all webclients in the group, if no sid is provided
-            emit("analysis:schema", data["schema"], include_self=False, to=session["token"])
+            emit(
+                "analysis:schema",
+                data["schema"],
+                include_self=False,
+                to=session["token"],
+            )
         except KeyError:
             return "No host found."
 
@@ -269,7 +273,12 @@ def modifier_schema(data: dict):
     else:
         try:
             # emit to all webclients in the group, if no sid is provided
-            emit("modifier:schema", data["schema"], include_self=False, to=session["token"])
+            emit(
+                "modifier:schema",
+                data["schema"],
+                include_self=False,
+                to=session["token"],
+            )
         except KeyError:
             return "No host found."
 

zndraw/modify/__init__.py

@@ -1,8 +1,8 @@
 import abc
 import enum
 import logging
-import typing as t
 import time
+import typing as t
 
 import ase
 import numpy as np

zndraw/static/UI/json_editor.js

@@ -173,4 +173,4 @@ function modifier_editor(socket, cache, world) {
         }, 1000);
       });
   });
-}
+}

zndraw/static/World/World.js

@@ -225,23 +225,35 @@ class World {
     this.step = loop.step;
     this.socket = socket;
 
-    this.socket.on("scene:points", function(callback) {
-      const { points, segments } = this.getLineData();
-      callback(points);
-    }.bind(this));
-
-    this.socket.on("scene:segments", function(callback) {
-      const { points, segments } = this.getLineData();
-      callback(segments);
-    }.bind(this));
-
-    this.socket.on("scene:step", function(callback) {
-      callback(this.getStep());
-    }.bind(this));
-
-    this.socket.on("selection:get", function(callback) {
-      callback(this.getSelection());
-    }.bind(this));
+    this.socket.on(
+      "scene:points",
+      function (callback) {
+        const { points, segments } = this.getLineData();
+        callback(points);
+      }.bind(this),
+    );
+
+    this.socket.on(
+      "scene:segments",
+      function (callback) {
+        const { points, segments } = this.getLineData();
+        callback(segments);
+      }.bind(this),
+    );
+
+    this.socket.on(
+      "scene:step",
+      function (callback) {
+        callback(this.getStep());
+      }.bind(this),
+    );
+
+    this.socket.on(
+      "selection:get",
+      function (callback) {
+        callback(this.getSelection());
+      }.bind(this),
+    );
     // renderer.render(scene, camera);
   }
 

zndraw/static/World/systems/select.js

@@ -286,7 +286,7 @@ class Selection {
             const { points, segments } = this.world.getLineData();
             console.log(new Date().toISOString(), "running modifier");
             this.socket.emit("modifier:run", {
-              params: {"method": {"method": "Delete"}},
+              params: { method: { method: "Delete" } },
               url: window.location.href,
             });
             // particlesGroup.click();

zndraw/static/pycom/Cache.js

@@ -178,14 +178,17 @@ class Cache {
       ).innerHTML = `${slider.value} / ${slider.max}`;
     });
 
-    this._socket.on("atoms:download", function(ids, callback) {
-      // send all atoms at once
-      const data = {};
-      ids.forEach((x) => {
-        data[x] = this._cache[x];
-      });
-      callback(data);
-    }.bind(this));
+    this._socket.on(
+      "atoms:download",
+      function (ids, callback) {
+        // send all atoms at once
+        const data = {};
+        ids.forEach((x) => {
+          data[x] = this._cache[x];
+        });
+        callback(data);
+      }.bind(this),
+    );
 
     this._socket.on("atoms:clear", (start_index) => {
       // remove everything from the cache starting from start_index
@@ -196,9 +199,12 @@ class Cache {
       });
     });
 
-    this._socket.on("atoms:length", function(callback) {
-      callback(this.get_length());
-    }.bind(this));
+    this._socket.on(
+      "atoms:length",
+      function (callback) {
+        callback(this.get_length());
+      }.bind(this),
+    );
   }
 
   get(id) {

zndraw/view.py

@@ -1,10 +1,10 @@
 import logging
+import multiprocessing as mp
 import webbrowser
 
 from zndraw.app import app, io
 from zndraw.utils import ZnDrawLoggingHandler
-from zndraw.zndraw import ZnDrawDefault, FileIO
-import multiprocessing as mp
+from zndraw.zndraw import FileIO, ZnDrawDefault
 
 try:
     import urllib.request

zndraw/zndraw.py

@@ -1,30 +1,24 @@
-import collections.abc
 import contextlib
 import dataclasses
 import pathlib
 import threading
 import time
 import typing as t
-from io import StringIO
-import importlib
 
 import ase
 import ase.io
-import flask_socketio
-import networkx as nx
 import numpy as np
 import socketio
 import tqdm
 import znh5md
 
-from zndraw.bonds import ASEComputeBonds
-from zndraw.data import atoms_from_json, atoms_to_json
-from zndraw.select import get_selection_class
 from zndraw.analyse import get_analysis_class
-from zndraw.utils import ZnDrawLoggingHandler, get_port
+from zndraw.data import atoms_from_json, atoms_to_json
+from zndraw.draw import Geometry
 from zndraw.modify import get_modify_class
+from zndraw.select import get_selection_class
 from zndraw.settings import GlobalConfig
-from zndraw.draw import Geometry
+from zndraw.utils import ZnDrawLoggingHandler
 
 
 def _await_answer(socket, channel, data=None, timeout=5):
@@ -125,7 +119,7 @@ def __delitem__(self, index):
     def insert(self, index, value):
         """Insert atoms before index"""
         self.socket.emit("atoms:insert", {index: atoms_to_json(value)})
-    
+
     def append(self, value: ase.Atoms) -> None:
         """Append atoms to the end of the list"""
         self[len(self)] = value
@@ -179,7 +173,7 @@ def segments(self) -> np.ndarray:
     @property
     def step(self) -> int:
         if self._target_sid is not None:
-            step=  int(self.socket.call("scene:step", {"sid": self._target_sid}))
+            step = int(self.socket.call("scene:step", {"sid": self._target_sid}))
         else:
             step = int(self.socket.call("scene:step", {}))
         return step
@@ -262,18 +256,19 @@ def analysis_schema(self):
         cls = get_analysis_class(config.get_analysis_methods())
 
         self.socket.emit(
-                "analysis:schema",
-                {"schema": cls.model_json_schema_from_atoms(self[0]), "sid": self._target_sid},
-            )
-
+            "analysis:schema",
+            {
+                "schema": cls.model_json_schema_from_atoms(self[0]),
+                "sid": self._target_sid,
+            },
+        )
 
     def modifier_schema(self):
         config = GlobalConfig.load()
         cls = get_modify_class(config.get_modify_methods())
         data = {"schema": cls.model_json_schema(), "sid": self._target_sid}
         self.socket.emit("modifier:schema", data)
 
-
     def selection_schema(self):
         config = GlobalConfig.load()
         cls = get_selection_class(config.get_selection_methods())
@@ -343,16 +338,18 @@ def analysis_run(self, data):
             except ValueError as err:
                 print(err)
 
+
 @dataclasses.dataclass
 class ZnDraw(ZnDrawBase):
     """ZnDraw client.
-    
+
     Attributes
     ----------
     display_new : bool
         Display new atoms in the webclient, when they are added.
-    
+
     """
+
     jupyter: bool = False
     display_new: bool = True
 
@@ -433,7 +430,7 @@ def log(self, message: str) -> None:
 
     def get_logging_handler(self) -> ZnDrawLoggingHandler:
         return ZnDrawLoggingHandler(self.socket)
-    
+
     def __setitem__(self, index, value):
         super().__setitem__(index, value)
         if self.display_new: