ipyvasp 1.0.8__tar.gz → 1.1.0__tar.gz

{ipyvasp-1.0.8 → ipyvasp-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 1.0.8
+Version: 1.1.0
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-1.0.8 → ipyvasp-1.1.0}/ipyvasp/_lattice.py

@@ -231,6 +231,21 @@ def periodic_table(selection=None):
     ax.set(xlim=[-0.6,17.6],ylim=[9.6,-0.6]) # to show borders correctly
     return ax
 
+def _write_text(dest, text: str, *, encoding: str = "utf-8") -> None:
+    "Write unicode text either to a path-like destination or to a writable text stream."
+    # Treat file-like objects (streams) first (avoid Path("CON") / weird Windows devices, etc.)
+    if hasattr(dest, "write") and callable(getattr(dest, "write")):
+        dest.write(text)
+        # Best-effort flush (sys.stdout has it, StringIO doesn't need it)
+        flush = getattr(dest, "flush", None)
+        if callable(flush):
+            flush()
+        return
+
+    # Otherwise treat as a filesystem path
+    path = Path(dest)
+    with path.open("w", encoding=encoding) as f:
+        f.write(text)
 
 def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=False, comment="", scale=None, system=None):
     """Writes POSCAR data to a file or returns string
@@ -285,19 +300,18 @@ def write_poscar(poscar_data, outfile=None, selective_dynamics=None, overwrite=F
         pos_list = [f"{p}   {s}" for p, s in zip(pos_list, sd)]
 
     out_str += "\n".join(pos_list)
-    if outfile:
-        path = Path(outfile)
-        if not path.is_file():
-            with path.open("w", encoding="utf-8") as f:
-                f.write(out_str)
-
-        elif overwrite and path.is_file():
-            with path.open("w", encoding="utf-8") as f:
-                f.write(out_str)
+    if outfile is not None:
+        # If it's a writable stream (sys.stdout, StringIO, open file handle), write directly.
+        if hasattr(outfile, "write") and callable(getattr(outfile, "write")):
+            _write_text(outfile, out_str)
         else:
-            raise FileExistsError(
-                f"{outfile!r} exists, can not overwrite, \nuse overwrite=True if you want to change."
-            )
+            # Otherwise treat as path-like with overwrite protection.
+            path = Path(outfile)
+            if path.exists() and not overwrite:
+                raise FileExistsError(
+                    f"{str(path)!r} exists, can not overwrite; use overwrite=True."
+                )
+            _write_text(path, out_str)
     else:
         print(out_str)
 
@@ -555,9 +569,8 @@ class InvokeMaterialsProject:
                 return f"Structure(unit={self.unit},mp_id={self.mp_id!r},symbol={self.symbol!r},crystal={self.crystal!r},cif='{self._cif[:10]}...')"
 
             def write_cif(self, outfile=None):
-                if isinstance(outfile, str):
-                    with open(outfile, "w") as f:
-                        f.write(self._cif)
+                if outfile is not None:
+                    _write_text(outfile, self._cif)
                 else:
                     print(self._cif)
 
@@ -640,12 +653,12 @@ def get_kpath(
     ibzkpt : PathLike
         Path to ibzkpt file, required for HSE calculations.
     outfile : PathLike
-        Path/to/file to write kpoints.
+        Path/to/file to write kpoints. Use sys.stdout to print to console.
     rec_basis : array_like
         Reciprocal basis 3x3 array to use for calculating uniform points.
 
 
-    If `outfile = None`, KPONITS file content is printed.
+    If `outfile = None`, kpoints array (Nx3) is returned.
     """
     if isinstance(kpoints, str):
         kpoints = _str2kpoints(kpoints)
@@ -766,10 +779,9 @@ def get_kpath(
     )
     out_str = "{}\n{}".format(top_str, out_str)
     if outfile != None:
-        with open(outfile, "w", encoding="utf-8") as f:  # allow unicode
-            f.write(out_str)
+        _write_text(outfile, out_str)
     else:
-        print(out_str)
+        return points  # return points for any processing by user.
 
 
 # Cell
@@ -799,12 +811,12 @@ def get_kmesh(
     ibzkpt : PathLike
         Path to ibzkpt file, required for HSE calculations.
     outfile : PathLike
-        Path/to/file to write kpoints.
+        Path/to/file to write kpoints. Use sys.stdout to print to console.
     endpoint : bool
         Default True, include endpoints in mesh at edges away from origin.
 
 
-    If `outfile = None`, KPOINTS file content is printed.
+    If `outfile = None`, kpoints array (Nx3) is returned.
 
     """
     if len(args) not in [1, 3]:
@@ -879,10 +891,9 @@ def get_kmesh(
     )
     out_str = "{}\n{}".format(top_str, out_str)
     if outfile != None:
-        with open(outfile, "w", encoding="utf-8") as f:
-            f.write(out_str)
+        _write_text(outfile, out_str)
     else:
-        print(out_str)
+        return points # return points for any processing by user.
 
 
 # Cell

ipyvasp-1.1.0/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "1.1.0"

{ipyvasp-1.0.8 → ipyvasp-1.1.0}/ipyvasp/bsdos.py

@@ -270,7 +270,7 @@ class Bands(_BandsDosBase):
 
     Parameters
     ----------
-    source : instance of `ipyvasp.DataSource` such as `ipyvasp.Vasprun` or `ipyvasp.Vaspout`. 
+    source : instance of `ipyvasp.DataSource` such as `ipyvasp.Vasprun` or a user defined subclass. 
     You can define your own class to parse data with same attributes and methods by subclassing `ipyvasp.DataSource`.
     """
 
@@ -627,7 +627,7 @@ class DOS(_BandsDosBase):
 
     Parameters
     ----------
-    source : instance of `ipyvasp.DataSource` such as `ipyvasp.Vasprun` or `ipyvasp.Vaspout`. 
+    source : instance of `ipyvasp.DataSource` such as `ipyvasp.Vasprun` or a user defined subclass. 
     You can define your own class to parse data with same attributes and methods by subclassing `ipyvasp.DataSource`.
     """
 

{ipyvasp-1.0.8 → ipyvasp-1.1.0}/ipyvasp/core/parser.py

@@ -1,4 +1,4 @@
-__all__ = ["Vasprun", "Vaspout", "minify_vasprun", "xml2dict","read"]
+__all__ = ["Vasprun", "minify_vasprun", "xml2dict","read"]
 
 import re
 from io import StringIO
@@ -14,7 +14,8 @@ from . import serializer
 
 class DataSource:
     """Base class for all data sources. It provides a common interface to access data from different sources.
-    Subclass it to get data from a source and implement the abstract methods."""
+    Subclass it to get data from a source such as recently implemented `vaspout.h5` file and implement the required 
+    methods with same output as done in Vasprun class."""
 
     def __init__(self, path, skipk=None):
         self._path = Path(path).absolute()
@@ -122,18 +123,6 @@ class DataSource:
         )
 
 
-class Vaspout(DataSource):
-    "Read data from vaspout.h5 file on demand."
-    # These methods are accessible from parent class, but need here for including in sphinx documentation
-    get_evals_dataframe = DataSource.get_evals_dataframe
-    poscar = DataSource.poscar
-    dos = DataSource.dos
-    bands = DataSource.bands
-
-    def __init__(self, path, skipk=None):
-        # super().__init__(path, skipk)
-        raise NotImplementedError("Vaspout is not implemented yet.")
-
 def read(file, start_match, stop_match=r'\n', nth_match=1, skip_last=False,apply=None):
     """Reads a part of the file between start_match and stop_match and returns a generator. It is lazy and fast.
     `start_match` and `stop_match`(default is end of same line) are regular expressions. `nth_match` is the number of occurence of start_match to start reading.

{ipyvasp-1.0.8 → ipyvasp-1.1.0}/ipyvasp/core/plot_toolkit.py

@@ -937,7 +937,7 @@ def plt2text(
             print(out_str)
 
 
-def plt2html(plt_fig=None, transparent=True):
+def plt2html(plt_fig=None, transparent=False):
     """Returns ``ipython.display.HTML(<svg of figure>)``. It clears figure after use. So ``plt.show()`` will not work after this.
 
     Parameters

{ipyvasp-1.0.8 → ipyvasp-1.1.0}/ipyvasp/evals_dataframe.py

@@ -64,7 +64,7 @@ class EvalsDataFrame(pd.DataFrame):
     Parameters
     ----------
     source : DataSource
-        Data source to collect data from. Could be ``ipyvasp.Vasprun`` or ``ipyvasp.Vaspout``.  Alternatively you can use ``DataSource.get_dataframe`` method to get dataframe directly.
+        Data source to collect data from. Could be ``ipyvasp.Vasprun`` or a user defined subclass of ``ipyvasp.DataSource``.  Alternatively you can use ``DataSource.get_dataframe`` method to get dataframe directly.
     spins : list
         of spin indices [zero based here], In output data frame you will see corresponding spin number based on full data.
     bands : list

{ipyvasp-1.0.8 → ipyvasp-1.1.0}/ipyvasp/widgets.py

@@ -275,9 +275,9 @@ class Files:
         "Get KPathWidget instance with these files."
         return KPathWidget(files = self.with_name('POSCAR'), height = height)
 
-    def bands_widget(self, height='450px'):
+    def bands_widget(self, height='450px',store_clicks=None):
         "Get BandsWidget instance with these files."
-        return BandsWidget(files=self._files, height=height)
+        return BandsWidget(files=self._files, height=height, store_clicks=store_clicks)
     
     def map(self,func, to_df=False):
         """Map files to a function that takes path as argument. 
@@ -438,7 +438,7 @@ class PropsPicker(VBox): # NOTE: remove New Later
 
     Parameters
     ----------
-    system_summary : (Vasprun,Vaspout).summary
+    system_summary : DataSource.summary such as impelemented in Vasprun.
     N : int, default is 3, number of projections to pick.
     
     You can observe `projections` trait.
@@ -764,9 +764,7 @@ class BandsWidget(_ThemedFigureInteract):
     @dl.callback('out-data')
     def _load_data(self, file):
         if not file: return  # First time not available
-        self._bands = (
-            vp.Vasprun(file) if file.parts[-1].endswith('xml') else vp.Vaspout(file)
-        ).bands
+        self._bands = vp.Vasprun(file).bands
         self.params.ppicks.update(self.bands.source.summary)
         self.params.krange.max = self.bands.source.summary.NKPTS - 1
         self.params.krange.tooltip = f"Includes {self.bands.source.get_skipk()} non-zero weight kpoints"
@@ -912,7 +910,7 @@ class BandsWidget(_ThemedFigureInteract):
     
     @property
     def source(self):
-        "Returns data source object such as Vasprun or Vaspout."
+        "Returns data source object such as Vasprun or user defined subclass of DataSource."
         return self.bands.source
 
     @property

{ipyvasp-1.0.8 → ipyvasp-1.1.0}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 1.0.8
+Version: 1.1.0
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

ipyvasp-1.0.8/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "1.0.8"