ipyvasp 0.9.87__tar.gz → 0.9.89__tar.gz

{ipyvasp-0.9.87 → ipyvasp-0.9.89}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.87
+Version: 0.9.89
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-0.9.87 → ipyvasp-0.9.89}/ipyvasp/__init__.py

@@ -18,7 +18,7 @@ __all__ = [  # For documentation purpose
     "webshow",
     "load_results",
     "parse_text",
-    "index",
+    "take",
     "summarize",
 ]
 

ipyvasp-0.9.89/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.9.89"

{ipyvasp-0.9.87 → ipyvasp-0.9.89}/ipyvasp/misc.py

@@ -3,6 +3,7 @@ __all__ = ["parse_text", "get_bib", "get_E0", "OUTCAR"]
 import requests
 from pathlib import Path
 from itertools import islice
+import numpy as np
 
 from .core import parser as vp
 from .utils import _sig_kwargs, _sub_doc
@@ -35,8 +36,8 @@ def get_bib(DOI):
     
     return response.status_code
 
-def get_E0(path: Path = 'OSZICAR'):
-    "Get the E0 from the last line of OSZICAR."
+def get_E0(path: Path = 'OSZICAR',nsteps=0):
+    "Get the E0 from the last line of OSZICAR. If `nsteps > 0`, returns as many available last steps ."
     fh = Path(path)
     if fh.is_file():
         lines = fh.read_text().splitlines()
@@ -51,6 +52,10 @@ def get_E0(path: Path = 'OSZICAR'):
     
     if not line.lstrip().startswith('1'):
         print(f"Calculation may not be converged for {path!r}\n{line}")
+    
+    if nsteps > 0: # not allow negative ones
+        lines = [float(line.split()[2]) for line in lines if (not 'dE' in line) and (not 'F=' in line)]
+        return np.array(lines[-nsteps:]) # as many last steps
         
     return float(line.split('=')[1].split()[0])
 

{ipyvasp-0.9.87 → ipyvasp-0.9.89}/ipyvasp/utils.py

@@ -15,6 +15,7 @@ import io
 from contextlib import contextmanager
 from pathlib import Path
 from inspect import signature, getdoc
+from itertools import islice
 
 
 import numpy as np
@@ -36,17 +37,22 @@ def get_file_size(path: str):
     else:
         return ""
     
-def take(f, rows, cols=None, dtype=str, sep=None):
-    """Read data from an opened file pointer `f` by indexing. Negative indexing is supported to read lines from end.
+def take(f, rows, cols=None, dtype=None, exclude=None,sep=None):
+    """Read data from an opened file pointer `f` by indexing. `rows=None` picks all lines. Negative indexing is supported to read lines from end.
     Negative indexing is not supported in cols because of variable length of each line.
     If `cols=None`, returns a single str of line if one integer given, otherwise a list of lines.
     If `cols` is int ot sequence of int, each line is splitted by `sep` (default all whitespaces) and `dtype` is applied over resulting fields.
+    `exclude` should be regex. It removes matching lines after selection by `rows`. Empty lines are also discarded if `cols` is given.
+
+    Returns list (nested or plain) or single value or None based on `rows` and `cols` selection.
 
     `take(f, -1, 1, float) == float(f.readlines()[-1].split()[1])` with advantage for consuming almost no memory as compared to `f.readlines()` on a huge file.
 
-    Note: For more robust reading of structured files like `PROCAR` use `ipyvasp.parse_text` function.
+    .. note::
+        For more robust reading of structured files like `PROCAR` use `ipyvasp.parse_text` function.
     
-    Tip: If your output is matrix-like, you can cast it to numpy array like `take(...)*np.array(1)`.
+    .. tip::
+        If your output is matrix-like, you can cast it to numpy array like `take(...)*np.array(1)`.
    
     >>> with open('some_file','r') as f:
     >>>     take(f, -1, 1, float) # read last line, second column as float
@@ -61,20 +67,27 @@ def take(f, rows, cols=None, dtype=str, sep=None):
         rows = [rows]
         return_line = True
 
-    if not isinstance(rows, (tuple,list, range)):
+    if rows and not isinstance(rows, (tuple,list, range)):
         raise TypeError(f"rows should int/list/tuple/range, got {type(rows)}")
     
     f.seek(0)
-    if min(rows) < 0:
+    if rows and min(rows) < 0:
         if not hasattr(f, '_nlines'): # do this once, assuming file is not changed while reading
             f._nlines = sum(1 for _ in enumerate(f))
             f.seek(0)
 
         rows = [i + (f._nlines if i < 0 else 0) for i in rows] # make all positive
     
-    lines = [l for i, l in enumerate(f) if i in rows]
+    if rows is None:
+        lines = islice(f, None)
+    else:
+        lines = (l for i, l in enumerate(f) if i in rows)
     
-    if cols:
+    if exclude:
+        lines = (l for l in lines if not re.search(exclude,l))
+    
+    if cols is not None:
+        conv = dtype if callable(dtype) else (lambda v: v)
         return_col = False
         if isinstance(cols, int):
             cols = [cols]
@@ -83,12 +96,16 @@ def take(f, rows, cols=None, dtype=str, sep=None):
         if not isinstance(cols, (list,tuple, range)):
             raise TypeError(f"cols should be a sequce of integers or single int, got {type(cols)}")
         
-        lines = [[dtype(v) for i, v in enumerate(l.split(sep)) if i in cols] for l in lines]
+        lines = (l for l in lines if l.strip()) # remove empty lines after indexing and only if cols are given
+        lines = ([conv(v) for i, v in enumerate(l.split(sep)) if i in cols] for l in lines)
         
         if return_col:
-            lines = [line[0] for line in lines]
+            lines = (line[0] if line else None for line in lines)
+    else:
+        return ''.join(lines) or None # just raw format as it is
 
-    return lines[0] if return_line else lines
+    # Try to return None where there is nothing
+    return next(lines,None) if return_line else (list(lines) or None)
 
 
 def _sig_kwargs(from_func, skip_params=()):

{ipyvasp-0.9.87 → ipyvasp-0.9.89}/ipyvasp/widgets.py

@@ -261,10 +261,10 @@ class Files:
             If you don't need to interpret the result of the function call, you can use the @self.interact decorator instead.
         """
         info = ipw.HTML().add_class("fprogess")
-        dd = Dropdown(description='File', options=['Select a File',*self._files]) # allows single file workable
+        dd = Dropdown(description='File', options=['',*self._files]) # allows single file workable
 
         def interact_func(fname, **kws):
-            if fname and str(fname) != 'Select a File':  # This would be None if no file is selected
+            if fname and str(fname) != '':  # This would be None if no file is selected
                 info.value = _progress_svg
                 try:
                     start = time()

{ipyvasp-0.9.87 → ipyvasp-0.9.89}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.87
+Version: 0.9.89
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

ipyvasp-0.9.87/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "0.9.87"