Merge pull request #7 from nlesc-nano/devel

Bug fixes

CHANGELOG.rst

@@ -5,10 +5,22 @@ Change Log
 All notable changes to this project will be documented in this file.
 This project adheres to `Semantic Versioning <http://semver.org/>`_.
 
+1.0.1
+*****
+
+Changed
+-------
+* Trailing whitespaces are now removed from keys.
+* Content of the `&COORD`_ block is now converted into a
+  dictionary with ``"_1"`` as key and a list of atomic symbols + coordinates
+  as values.
+
+.. _`&COORD`: https://manual.cp2k.org/cp2k-6_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/COORD.html
+
+
 1.0.0
 *****
 
 Added
 -----
-
 * Release of CP2K-Parser

README.rst

@@ -1,18 +1,18 @@
 .. image:: https://travis-ci.org/nlesc-nano/CP2K-Parser.svg?branch=master
    :target: https://travis-ci.org/nlesc-nano/CP2K-Parser
-   
-| 
+
+|
 
 .. image:: https://img.shields.io/badge/python-3.5-blue.svg
    :target: https://www.python.org
-   
+
 .. image:: https://img.shields.io/badge/python-3.6-blue.svg
    :target: https://www.python.org
-   
+
 .. image:: https://img.shields.io/badge/python-3.7-blue.svg
    :target: https://www.python.org
 
-CP2K-Parser 1.0.0
+CP2K-Parser 1.0.1
 #################
 
 A package for converting CP2K_ input files into PLAMS_ compatible dictionaries.

cp2kparser/__version__.py

@@ -1 +1 @@
-__version__ = '1.0.0'
+__version__ = '1.0.1'

cp2kparser/parser.py

@@ -154,7 +154,7 @@ def split_str(item: str,
         The first string is decapitalized.
 
     """
-    sep = sep or ' '
+    sep = sep if sep is not None else ' '
     try:
         key, value = item.split(sep, maxsplit=1)
     except ValueError:
@@ -204,10 +204,10 @@ def parse_multi_keys(item: str,
         Raised if **item** does not contain any whitespaces.
 
     """
-    sep = sep or ' '
+    sep = sep if sep is not None else ' '
     i1, i2 = item.split(sep, maxsplit=1)
     i1 = i1.lstrip('&').lower()
-    return ''.join((i1, sep, i2))
+    return sep.join((i1, i2))
 
 
 def parse_header(input_gen: Generator[str, None, None],
@@ -238,7 +238,7 @@ def parse_header(input_gen: Generator[str, None, None],
         container[key].append({})
         recursive_update(input_gen, container[key][-1])
 
-    # A duplicate key; convert container[key] into a list of dictionaries
+    # container[key] already exists; convert container[key] into a list of dictionaries
     elif key in container:
         value_old = container[key]
         container[key] = [value_old, {}]
@@ -271,6 +271,28 @@ def parse_block(item: str,
     container[key] = value
 
 
+def parse_coord_block(input_gen: Generator[str, None, None],
+                      container: Union[dict, MutableSequence]) -> None:
+    """Parse ``"coord"`` blocks.
+
+    Parameters
+    ----------
+    item : :class:`str`
+        A string containing a key and value.
+
+    container : :class:`dict` or :class:`collections.abc.MutableSequence`
+        A to-be filled dictionary or mutable sequence.
+
+    """
+    item = next(input_gen)
+    container['coord'] = {}
+    container['coord']['_1'] = coord = []
+    while item.lower() != '&end':
+        coord.append(item)
+        item = next(input_gen)
+    return
+
+
 def recursive_update(input_gen: Generator[str, None, None],
                      container: Union[dict, MutableSequence]) -> None:
     r"""Update **container** an a recursive manner.
@@ -286,11 +308,13 @@ def recursive_update(input_gen: Generator[str, None, None],
 
     """
     for item in input_gen:
-        if item[0] == '&' and item[0:4].lower() != '&end':  # Beginning of a block
+        if item.lower() == '&coord':
+            parse_coord_block(input_gen, container)
+        elif item[0] == '&' and item[0:4].lower() != '&end':
             parse_header(input_gen, item, container)
-        elif item[0:4].lower() != '&end':  # End of a block
+        elif item[0:4].lower() != '&end':
             parse_block(item, container)
-        else:
+        else:  # End of a block
             return
 
 
@@ -403,7 +427,7 @@ def read_input(filename: Union[str, bytes, PurePath]) -> dict:
     """
     def _sanitize_line(item: str) -> str:
         """Sanitize and return a single line from **filename**."""
-        return item.rstrip('\n').replace('\t', '').lstrip(' ')
+        return item.rstrip('\n').rstrip().replace('\t', '').lstrip(' ')
 
     with open(filename, 'r') as f:
         input_list = [_sanitize_line(item) for item in f if item != '\n']

setup.py

@@ -37,7 +37,8 @@
         'python-3-7',
         'dictionary',
         'parsing',
-        'cp2k'
+        'cp2k',
+        'plams'
     ],
     classifiers=[
         'Development Status :: 5 - Production/Stable',