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nglviewer · Nov 22, 2024 · a3cc1b2 · a3cc1b2
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commit a3cc1b2
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Showing 24 changed files with 188 additions and 143 deletions.
diff --git a/.style.yapf b/.style.yapf
@@ -0,0 +1,2 @@
+[style]
+based_on_style = google
diff --git a/nglview/__init__.py b/nglview/__init__.py
@@ -21,6 +21,7 @@
 with warnings.catch_warnings():
     warnings.simplefilter("ignore")
 
+
 # Register nbextension
 # FIXME: do we still need this?
 def _jupyter_nbextension_paths():
@@ -33,4 +34,4 @@ def _jupyter_nbextension_paths():
 
 
 __all__ = ['NGLWidget', 'write_html'
-           ] + widget.__all__ + adaptor.__all__ + show.__all__
+          ] + widget.__all__ + adaptor.__all__ + show.__all__
diff --git a/nglview/adaptor.py b/nglview/adaptor.py
@@ -62,6 +62,7 @@ def _get_structure_string(write_method, suffix='.pdb'):
 
 
 class register_backend:
+
     def __init__(self, package_name):
         # package_name must match exactly to your Python package
         self.package_name = package_name
@@ -72,6 +73,7 @@ def __call__(self, cls):
 
 
 class FileStructure(Structure):
+
     def __init__(self, path):
         super().__init__()
         self.fm = FileManager(path)
@@ -84,6 +86,7 @@ def get_structure_string(self):
 
 
 class TextStructure(Structure):
+
     def __init__(self, text, ext='pdb', params={}):
         super().__init__()
         self.path = ''
@@ -97,6 +100,7 @@ def get_structure_string(self):
 
 @register_backend('rdkit')
 class RdkitStructure(Structure):
+
     def __init__(self, rdkit_mol, ext="pdb", conf_id=-1):
         super().__init__()
         self.path = ''
@@ -114,6 +118,7 @@ def get_structure_string(self):
 
 
 class PdbIdStructure(Structure):
+
     def __init__(self, pdbid):
         super().__init__()
         self.pdbid = pdbid
@@ -126,6 +131,7 @@ def get_structure_string(self):
 
 
 class ASEStructure(Structure):
+
     def __init__(self, ase_atoms, ext='pdb', params={}):
         super().__init__()
         self.path = ''
@@ -138,6 +144,7 @@ def get_structure_string(self):
 
 
 class IODataStructure(Structure):
+
     def __init__(self, obj):
         super().__init__()
         self._obj = obj
@@ -152,6 +159,7 @@ def get_structure_string(self):
 
 
 class QCElementalStructure(Structure):
+
     def __init__(self, obj):
         super().__init__()
         self._obj = obj
@@ -166,6 +174,7 @@ class Psi4Structure(QCElementalStructure):
 
 
 class OpenbabelStructure(Structure):
+
     def __init__(self, obj):
         super().__init__()
         self._obj = obj
@@ -183,6 +192,7 @@ def get_structure_string(self):
 
 
 class BiopythonStructure(Structure):
+
     def __init__(self, entity, ext='pdb', params={}):
         super().__init__()
         self.path = ''
@@ -201,6 +211,7 @@ def get_structure_string(self):
 
 
 class IOTBXStructure(Structure):
+
     def __init__(self, obj, ext='pdb', params={}):
         """
         obj must have as_pdb_string method
@@ -216,6 +227,7 @@ def get_structure_string(self):
 
 
 class RosettaStructure(Structure):
+
     def __init__(self, pose, ext='pdb', params={}):
         # type: (pyrosetta.rosetta.core.pose.Pose, str, Dict) -> None
         super().__init__()
@@ -230,6 +242,7 @@ def get_structure_string(self):
 
 @register_backend('prody')
 class ProdyStructure(Structure):
+
     def __init__(self, obj):
         super().__init__()
         self._obj = obj
@@ -251,6 +264,7 @@ def write(fname):
 
 @register_backend('prody')
 class ProdyTrajectory(Trajectory, ProdyStructure):
+
     def __init__(self, obj):
         ProdyStructure.__init__(self, obj)
 
@@ -370,6 +384,7 @@ def get_structure_string(self, index=0):
 
 @register_backend('parmed')
 class ParmEdStructure(Structure):
+
     def __init__(self, structure):
         self._structure = structure
         self.only_save_1st_model = True

diff --git a/nglview/base.py b/nglview/base.py
@@ -5,10 +5,12 @@
 def _singleton(cls):
     # https://www.python.org/dev/peps/pep-0318/#examples
     instances = {}
+
     def getinstance():
         if cls not in instances:
             instances[cls] = cls()
         return instances[cls]
+
     return getinstance
 
 
@@ -21,17 +23,20 @@ def _js(self, code):
         self._call("executeCode", code)
 
     def _call(self, method_name, *args, **kwargs):
-        msg = {"type": "callMethod",
-               "methodName": method_name,
-                "args": args, "kwargs": kwargs}
+        msg = {
+            "type": "callMethod",
+            "methodName": method_name,
+            "args": args,
+            "kwargs": kwargs
+        }
         if not self._ready:
             # fire later
             self._msg_q.append(msg)
         else:
             self.send(msg)
         msg_ar = self._msg_ar[:]
         msg_ar.append(msg)
-        self._msg_ar = msg_ar # trigger sync
+        self._msg_ar = msg_ar  # trigger sync
 
     @observe("_ready")
     def _on_ready(self, change):

diff --git a/nglview/color.py b/nglview/color.py
@@ -5,7 +5,6 @@
 from IPython.display import display
 import time
 
-
 COLOR_SCHEMES = [
     " ", "picking", "random", "uniform", "atomindex", "residueindex",
     "chainindex", "modelindex", "sstruc", "element", "resname", "bfactor",
@@ -15,7 +14,6 @@
 _USER_COLOR_DICT = {}
 
 
-
 class _ColorScheme:
     _color_dict = {}
 
@@ -38,12 +36,14 @@ class _ColormakerRegistry(BaseWidget):
     _model_name = Unicode("ColormakerRegistryModel").tag(sync=True)
     _model_module = Unicode("nglview-js-widgets").tag(sync=True)
     _model_module_version = Unicode(__frontend_version__).tag(sync=True)
-    _msg_q = List().tag(sync=True) # overwrite BaseWidget's trait to avoid caling base method in frontend
+    _msg_q = List().tag(
+        sync=True
+    )  # overwrite BaseWidget's trait to avoid caling base method in frontend
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         try:
-            get_ipython() # only display in notebook
+            get_ipython()  # only display in notebook
             self._ipython_display_()
         except NameError:
             pass

diff --git a/nglview/component.py b/nglview/component.py
@@ -21,8 +21,8 @@ def __init__(self, view, id):
         widget_utils._add_repr_method_shortcut(self, self._view)
         self._borrow_attribute(self._view, [
             'clear_representations', '_remove_representations_by_name',
-            '_update_representations_by_name', 'center_view', 'center',
-            'clear', 'set_representations'
+            '_update_representations_by_name', 'center_view', 'center', 'clear',
+            'set_representations'
         ], ['get_structure_string', 'get_coordinates', 'n_frames'])
 
     @property

diff --git a/nglview/contrib/movie.py b/nglview/contrib/movie.py
@@ -132,8 +132,8 @@ def sleep(self):
 
     def make_old_impl(self, in_memory=False):
         # TODO : make base class so we can reuse this with sandbox/base.py
-        progress = IntProgress(
-            description='Rendering...', max=len(self._time_range) - 1)
+        progress = IntProgress(description='Rendering...',
+                               max=len(self._time_range) - 1)
         self._event = threading.Event()
 
         def _make(event):
@@ -156,18 +156,16 @@ def _make(event):
                             iw = self.view.render_image(**self.render_params)
                         self.sleep()
                         if self.in_memory:
-                            rgb = self._base64_to_ndarray(
-                                self.view._image_data)
+                            rgb = self._base64_to_ndarray(self.view._image_data)
                             self._image_array.append(rgb)
                             if iw:
                                 iw.close()  # free memory
                 if not self.in_memory:
                     template = "{}/{}.{}.png"
                     image_files = [
-                        image_dir
-                        for image_dir in (template.format(
+                        image_dir for image_dir in (template.format(
                             self.download_folder, self.prefix, str(i))
-                                          for i in self._time_range)
+                                                    for i in self._time_range)
                         if os.path.exists(image_dir)
                     ]
                 else:
@@ -177,20 +175,20 @@ def _make(event):
                 clip = mpy.ImageSequenceClip(image_files, fps=self.fps)
                 with Output():
                     if self.output.endswith('.gif'):
-                        clip.write_gif(
-                            self.output,
-                            fps=self.fps,
-                            verbose=False,
-                            **self.moviepy_params)
+                        clip.write_gif(self.output,
+                                       fps=self.fps,
+                                       verbose=False,
+                                       **self.moviepy_params)
                     else:
-                        clip.write_videofile(
-                            self.output, fps=self.fps, **self.moviepy_params)
+                        clip.write_videofile(self.output,
+                                             fps=self.fps,
+                                             **self.moviepy_params)
                 self._image_array = []
                 progress.description = 'Done'
                 time.sleep(1)
                 progress.close()
 
-        self.thread = threading.Thread(target=_make, args=(self._event, ))
+        self.thread = threading.Thread(target=_make, args=(self._event,))
         self.thread.daemon = True
         self.thread.start()
         return progress
@@ -219,8 +217,9 @@ def hook(frame):
 
         # trigger movie making communication between backend and frontend
         self.perframe_hook and hook(frame)
-        self.view._set_coordinates(
-            frame, movie_making=True, render_params=self.render_params)
+        self.view._set_coordinates(frame,
+                                   movie_making=True,
+                                   render_params=self.render_params)
         self._progress.description = 'Rendering ...'
 
         def on_msg(widget, msg, buffers):
@@ -229,10 +228,9 @@ def on_msg(widget, msg, buffers):
                 try:
                     frame = next(iframe)
                     self.perframe_hook and hook(frame)
-                    self.view._set_coordinates(
-                        frame,
-                        movie_making=True,
-                        render_params=self.render_params)
+                    self.view._set_coordinates(frame,
+                                               movie_making=True,
+                                               render_params=self.render_params)
                     self._progress.value = frame
                 except StopIteration:
                     if movie:
@@ -262,15 +260,15 @@ def _make_from_array(self, image_array: List[str]):
         clip = mpy.ImageSequenceClip(image_files, fps=self.fps)
         with self._woutput:
             if self.output.endswith('.gif'):
-                clip.write_gif(
-                    self.output,
-                    fps=self.fps,
-                    verbose=False,
-                    **self.moviepy_params)
+                clip.write_gif(self.output,
+                               fps=self.fps,
+                               verbose=False,
+                               **self.moviepy_params)
             else:
 
-                clip.write_videofile(
-                    self.output, fps=self.fps, **self.moviepy_params)
+                clip.write_videofile(self.output,
+                                     fps=self.fps,
+                                     **self.moviepy_params)
 
     def interupt(self):
         """ Stop making process """
@@ -287,4 +285,3 @@ def _base64_to_ndarray(cls, value):
         im_bytes = io.BytesIO(im_bytes)
         # convert to numpy RGB value (for moviepy.editor.VideoClip)
         return np.array(Image.open(im_bytes))
-
diff --git a/nglview/layout.py b/nglview/layout.py
@@ -34,8 +34,7 @@ def _relayout(box, form_item_layout):
                 kid,
             ], layout=form_item_layout)
         else:
-            box2 = Box([Label(value=label_value), kid],
-                       layout=form_item_layout)
+            box2 = Box([Label(value=label_value), kid], layout=form_item_layout)
         form_items.append(box2)
 
     return form_items

diff --git a/nglview/parameters.py b/nglview/parameters.py
@@ -25,5 +25,4 @@
 ]
 
 REPRESENTATION_NAMES = list(
-    sorted({name
-            for pairs in REPRESENTATION_NAME_PAIRS for name in pairs}))
+    sorted({name for pairs in REPRESENTATION_NAME_PAIRS for name in pairs}))
diff --git a/nglview/remote_thread.py b/nglview/remote_thread.py
@@ -3,6 +3,7 @@
 
 
 class RemoteCallThread(threading.Thread):
+
     def __init__(self, view, timeout=0.1, registered_funcs=['loadFile']):
         '''
 

diff --git a/nglview/sandbox/amber.py b/nglview/sandbox/amber.py
@@ -65,7 +65,7 @@ def _update(event):
                 self._update_coordinates(traj[0].xyz)
 
         # non-blocking so we can use other Jupyter's cells
-        self.thread = threading.Thread(target=_update, args=(self.event, ))
+        self.thread = threading.Thread(target=_update, args=(self.event,))
         self.thread.daemon = True
         self.thread.start()
 

diff --git a/nglview/sandbox/grid_view.py b/nglview/sandbox/grid_view.py
@@ -43,6 +43,7 @@
 
 
 class GridBoxNGL(GridBox):
+
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self._ngl_class_id = None
@@ -69,6 +70,7 @@ def fullscreen(self, js_code=None):
 
 
 class GridBoxViewAndPlayer(GridBoxNGL):
+
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self._view = self.children[0]
Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,6 +3,7 @@


		class RemoteCallThread(threading.Thread):

		def __init__(self, view, timeout=0.1, registered_funcs=['loadFile']):
		'''

Expand Down