ipyvasp 0.8.7__tar.gz → 0.8.9__tar.gz

{ipyvasp-0.8.7 → ipyvasp-0.8.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.7
+Version: 0.8.9
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor
@@ -68,7 +68,7 @@ Interactively select bandstructure path by clicking on high symmetry points on p
 
 ![KP](KP.png)
 
-Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` or `WeasWidget` in Jupyterlab side by side.
+Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` in Jupyterlab side by side.
 
 ![snip](op.png)
 

{ipyvasp-0.8.7 → ipyvasp-0.8.9}/README.md

@@ -36,7 +36,7 @@ Interactively select bandstructure path by clicking on high symmetry points on p
 
 ![KP](KP.png)
 
-Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` or `WeasWidget` in Jupyterlab side by side.
+Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` in Jupyterlab side by side.
 
 ![snip](op.png)
 

{ipyvasp-0.8.7 → ipyvasp-0.8.9}/ipyvasp/_lattice.py

@@ -1867,10 +1867,10 @@ def _fix_color_size(types, colors, sizes, default_size, backend=None):
     if isinstance(colors,dict):
         for k,v in colors.items():
             cs[k]['color'] = v 
-    elif colors is not None and isinstance(colors,(str,list,tuple,np.ndarray)):
+    elif isinstance(colors,(str,list,tuple,np.ndarray)):
         for k in cs:
             cs[k]['color'] = colors
-    else:
+    elif colors is not None:
         raise TypeError("colors should be a single valid color or dict as {'Ga':'red','As':'blue',...}")
     return cs
 

ipyvasp-0.8.9/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.8.9"

{ipyvasp-0.8.7 → ipyvasp-0.8.9}/ipyvasp/core/plot_toolkit.py

@@ -1015,14 +1015,18 @@ def iplot2widget(fig, fig_widget=None, template=None):
 
     if fig_widget is None:
         fig_widget = go.FigureWidget()
+        scene = fig.layout.scene # need to copy scane form given fig
     elif not isinstance(fig_widget, go.FigureWidget):
         raise ValueError("fig_widget must be FigureWidget")
+    else:
+        scene = fig_widget.layout.scene # keep scene from widget
 
     fig_widget.data = []  # Clear previous data
     if template is not None:
-        fig.layout.template = template  # will make white flash if not done before
-
+        fig.layout.template = template  # will make white flash if not done before 
+    
     fig_widget.layout = fig.layout
+    fig_widget.layout.scene = scene # reset scene back
 
     with fig_widget.batch_update():
         for data in fig.data:

{ipyvasp-0.8.7 → ipyvasp-0.8.9}/ipyvasp/core/serializer.py

@@ -422,7 +422,9 @@ class PoscarData(Dict2Data):
     
 
     def get_bond_data(self, site_indices, k = 5):
-        "Returns a DataFrame with bonds angle, bond length, vector positions etc. that can be used for plotting."
+        """Returns a DataFrame with bonds angle, bond length, vector positions etc. that can be used for plotting.
+        t_a and t_b are translation vectors to get them near selected sites. You can use `POSCAR.translate` if somehow need nearest coordinates.
+        """
         if k < 3:
             raise ValueError("k >= 3 is required!")
     
@@ -434,16 +436,18 @@ class PoscarData(Dict2Data):
             for j in js:
                 bs = np.array([self.to_cartesian(self.positions[j] + p) for p in product([-1,0,1],[-1,0,1],[-1,0,1])])
                 ds = np.array([np.linalg.norm(a-b) for b in bs])
-                nears.append((j, bs[ds.argsort()][0]))
+                b = bs[ds.argsort()][0]
+                t = tuple((self.to_fractional(b) - self.positions[j]).astype(int)) # keep track of translation vector
+                nears.append((j, b, t))
             
-            for (m,b),(n, c) in combinations(nears,2):
-                v1, v2 = b-a, c-a
+            for (m,b,t1),(n, c,t2) in combinations(nears,2):
+                v1, v2 = b - a, c - a
                 n1, n2 = np.linalg.norm(v1), np.linalg.norm(v2)
                 name = '-'.join(self.symbols[[m,i,n]])
                 angle = np.degrees(np.arccos(v1.dot(v2)/(n1*n2)))
-                out.append([name, m,i,n, angle, n1, n2, *b, *a,  *c])
+                out.append([name, m,i,n, angle, n1, n2, t1,t2])
                 
-        columns = 'bond a o b angle d_ao d_bo ax ay az ox oy oz bx by bz'.split()
+        columns = 'bond a o b angle d_ao d_bo t_a t_b'.split()
         return DataFrame(out, columns=columns)
     
     def to_fractional(self, coords):

{ipyvasp-0.8.7 → ipyvasp-0.8.9}/ipyvasp/lattice.py

@@ -250,11 +250,54 @@ def weas_viewer(poscar,
     return w
 
 
+class _AutoRenderer:
+    _figw = None
+    _kws = {} 
+
+    def __init__(self, pc_instance):
+        self._pc = pc_instance
+
+    def on(self, template=None):
+        "Enable auto rendering. In Jupyterlab, you can use `Create New View for Output` to drag a view on side."
+        self.off()
+        type(self)._figw = iplot2widget(self._pc.iplot_lattice(**self._kws), fig_widget=self._figw,template=template)
+        
+        def ip_display(that):
+            iplot2widget(that.iplot_lattice(**self._kws), fig_widget=self._figw, template=template)
+        
+        type(self._pc)._ipython_display_ = ip_display
+        
+        from ipywidgets import Button, VBox
+        btn = Button(description='Disable Auto Rendering',icon='close',layout={'width': 'max-content'})
+        btn.on_click(lambda btn: self.off())
+        type(self)._box = VBox([btn, self._figw])
+        return display(self._box)
+
+    def off(self):
+        "Disable auto rendering."
+        if hasattr(self, '_box'):
+            self._box.close()
+            type(self)._figw = None # no need to close figw, it raise warning, but now garbage collected
+        
+        if hasattr(type(self._pc), '_ipython_display_'):
+            del type(self._pc)._ipython_display_
+
+    @_sig_kwargs(plat.iplot_lattice,('poscar_data',))
+    def update_params(self, **kwargs):
+        type(self)._kws = kwargs
+        if hasattr(type(self._pc), '_ipython_display_'):
+            self._pc._ipython_display_()
+    
+    @property
+    def params(self):
+        return self._kws.copy() # avoid messing original
+    
+    def __repr__(self):
+        return f"AutoRenderer(params = {self._kws})"
+
 class POSCAR:
     _cb_instance = {}  # Loads last clipboard data if not changed
     _mp_instance = {}  # Loads last mp data if not changed
-    _plotly_kws = {}  # kwargs to pass to auto update figurewidget
-    _weas_kws = {}
 
     def __init__(self, path=None, content=None, data=None):
         """
@@ -268,10 +311,16 @@ class POSCAR:
         data : PoscarData object. This assumes positions are in fractional coordinates.
 
         Prefrence order: data > content > path
+
+        Tip: You can use `self.auto_renderer.on()` to keep doing opertions and visualize while last line of any cell is a POSCAR object.
         """
         self._path = Path(path or "POSCAR")  # Path to file
         self._content = content
 
+        if not hasattr(self, '_renderer'): # Only once
+            type(self)._renderer = _AutoRenderer(self) # assign to class
+        self._renderer._pc = self # keep latest refrence there too, for update_params on right one
+
         if data:
             self._data = serializer.PoscarData.validated(data)
         else:
@@ -295,6 +344,19 @@ class POSCAR:
     @property
     def path(self):
         return self._path
+    
+    @property
+    def auto_renderer(self):
+        """A renderer for auto viewing POSCAR when at last line of cell.
+
+        Use `auto_renderer.on()` to enable it.
+        Use `auto_renderer.off()` to disable it.
+        Use `auto_renderer.[params, update_params()]` to view and update parameters.
+        
+        In Jupyterlab, you can use `Create New View for Output` to drag a view on side.
+        In VS Code, you can open another view of Notebook to see it on side while doing operations.
+        """
+        return self._renderer
 
     def to_ase(self):
         """Convert to ase.Atoms format. You need to have ase installed.
@@ -327,6 +389,8 @@ class POSCAR:
             return plat.view_poscar(self.data, **kwargs)
         elif viewer in "weas":
             return weas_viewer(self, **kwargs)
+        elif viewer in "plotly":
+            return self.view_plotly(**kwargs)
         elif viewer in "nglview":
             return print(
                 f"Use `self.view_ngl()` for better customization in case of viewer={viewer!r}"
@@ -344,9 +408,7 @@ class POSCAR:
     @_sub_doc(weas_viewer)
     @_sig_kwargs(weas_viewer, ("poscar",))
     def view_weas(self, **kwargs):
-        self.__class__._weas_kws = kwargs  # attach to class, not self
         return weas_viewer(self, **kwargs)
-    
 
     def view_kpath(self):
         "Initialize a KpathWidget instance to view kpath for current POSCAR, and you can select others too."
@@ -357,13 +419,8 @@ class POSCAR:
     @_sub_doc(plat.iplot_lattice)
     @_sig_kwargs(plat.iplot_lattice, ("poscar_data",))
     def view_plotly(self, **kwargs):
-        self.__class__._plotly_kws = kwargs  # attach to class, not self
         return iplot2widget(self.iplot_lattice(**kwargs))
 
-    def update_plotly(self, handle):
-        "Update plotly widget (already shown in notebook) after some operation on POSCAR with `handle` returned by `view_plotly`."
-        iplot2widget(self.iplot_lattice(**self._plotly_kws), fig_widget=handle)
-
     @classmethod
     def from_file(cls, path):
         "Load data from POSCAR file"
@@ -504,12 +561,6 @@ class POSCAR:
         "Writes POSCAR to clipboard (as implemented by pandas library) for copy in other programs such as vim."
         clipboard_set(self.content)  # write to clipboard
 
-
-    def update_weas(self, handle):
-        """Send result of any operation to view on opened weas widget handle.
-        Useful in Jupyterlab side panel to look operations results on POSCAR."""
-        handle.children = weas_viewer(self, **self._weas_kws).children # does not work properly otherwise
-
     @property
     def data(self):
         "Data object in POSCAR."

{ipyvasp-0.8.7 → ipyvasp-0.8.9}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.8.7
+Version: 0.8.9
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor
@@ -68,7 +68,7 @@ Interactively select bandstructure path by clicking on high symmetry points on p
 
 ![KP](KP.png)
 
-Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` or `WeasWidget` in Jupyterlab side by side.
+Apply operations on POSCAR and simultaneously view using plotly's `FigureWidget` in Jupyterlab side by side.
 
 ![snip](op.png)
 

ipyvasp-0.8.7/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "0.8.7"