ipyvasp 0.9.86__tar.gz → 0.9.88__tar.gz

{ipyvasp-0.9.86 → ipyvasp-0.9.88}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.86
+Version: 0.9.88
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

{ipyvasp-0.9.86 → ipyvasp-0.9.88}/ipyvasp/__init__.py

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

ipyvasp-0.9.88/ipyvasp/_version.py

@@ -0,0 +1 @@
+__version__ = "0.9.88"

{ipyvasp-0.9.86 → ipyvasp-0.9.88}/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-0.9.86 → ipyvasp-0.9.88}/ipyvasp/utils.py

@@ -1,6 +1,6 @@
 __all__ = [
     "get_file_size",
-    "get_lines",
+    "take",
     "set_dir",
     "interpolate_data",
     "rolling_mean",
@@ -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
@@ -36,37 +37,74 @@ def get_file_size(path: str):
     else:
         return ""
     
-def get_lines(f, indices):
-    """Read lines by indexing from an opened file pointer `f`. Negative indexing is supported to read lines from end.
-    Returns a single str of line if one integer given, otherwise a list of lines.
-    This consumes a lot less memory then indexing over `f.readlines()[index]`.
+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 lines after selection by `rows`.
 
+    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.
+    
+    .. 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:
-    >>>     get_lines(f, -1) # last line
-    >>>     get_lines(f, range(5)) # first 5 lines
-    >>>     get_lines(f, range(-5,0)) # last 5 lines
+    >>>     take(f, -1, 1, float) # read last line, second column as float
+    >>>     take(f, range(5)) # first 5 lines
+    >>>     take(f, range(-5,0)) # last 5 lines
     """
     if not isinstance(f, io.TextIOWrapper):
         raise TypeError(f"f should be file-like object. got {type(f)}")
     
     return_line = False
-    if isinstance(indices, int):
-        indices = [indices]
+    if isinstance(rows, int):
+        rows = [rows]
         return_line = True
 
-    if not isinstance(indices, (tuple,list, range)):
-        raise TypeError(f"indices should int/list/tuple/range, got {type(indices)}")
+    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(indices) < 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)
 
-        indices = [i + (f._nlines if i < 0 else 0) for i in indices] # make all positive
+        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 indices]
-    return lines[0] if return_line else lines
+    if rows is None:
+        lines = islice(f, None)
+    else:
+        lines = (l for i, l in enumerate(f) if i in rows)
+    
+    if exclude:
+        lines = (l for l in lines if not re.search(exclude,l))
+    
+    if cols:
+        conv = dtype if callable(dtype) else (lambda v: v)
+        return_col = False
+        if isinstance(cols, int):
+            cols = [cols]
+            return_col = True 
+
+        if not isinstance(cols, (list,tuple, range)):
+            raise TypeError(f"cols should be a sequce of integers or single int, got {type(cols)}")
+        
+        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] if line else None for line in lines)
+    else:
+        return ''.join(lines) or None # just raw format as it is
+
+    # 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-0.9.86 → ipyvasp-0.9.88}/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()
@@ -448,9 +448,9 @@ class Files:
         >>> import ipyvasp as ipv
         >>> files = ipv.Files(...)
         >>> files.mapf(lambda fp: json.load(fp,cls=ipv.DecodeToNumpy),to_df=True) # or use ipv.load(path) in map
-        >>> files.mapf(lambda fp: ipv.get_lines(fp, range(5)) # read first five lines
-        >>> files.mapf(lambda fp: ipv.get_lines(fp, range(-5,0)) # read last five lines
-        >>> files.mapf(lambda fp: ipv.get_lines(fp, -1) # read last line
+        >>> files.mapf(lambda fp: ipv.take(fp, range(5)) # read first five lines
+        >>> files.mapf(lambda fp: ipv.take(fp, range(-5,0)) # read last five lines
+        >>> files.mapf(lambda fp: ipv.take(fp, -1, 1, float) # read last line, second column as float
         """
         if not mode in 'rb':
             raise ValueError("Only 'r'/'rb' mode is allowed in this context!")

{ipyvasp-0.9.86 → ipyvasp-0.9.88}/ipyvasp.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ipyvasp
-Version: 0.9.86
+Version: 0.9.88
 Summary: A processing tool for VASP DFT input/output processing in Jupyter Notebook.
 Home-page: https://github.com/massgh/ipyvasp
 Author: Abdul Saboor

ipyvasp-0.9.86/ipyvasp/_version.py

@@ -1 +0,0 @@
-__version__ = "0.9.86"