Implement HSD-wrappers to manipulate nested content

Author: aradi

.gitignore

@@ -1,5 +1,7 @@
 *~
 .idea
+.env
+.vscode
 *.pyc
 dist
 build

docs/conf.py

@@ -56,7 +56,7 @@
 # a list of builtin themes.
 #
 # html_theme = 'alabaster'
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'sphinx_book_theme'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/introduction.rst

@@ -36,6 +36,9 @@ or into the user space issueing ::
 Quick tutorial
 ==============
 
+The basics
+----------
+
 A typical, self-explaining input written in HSD looks like ::
 
   driver {
@@ -117,3 +120,81 @@ Python ::
 and then stored again in HSD format ::
 
     hsd.dump(hsdinput, "test2.hsd")
+
+
+   
+Accesing nested data structures via wrappers
+--------------------------------------------
+
+The hsd module contains lightweight wrappers (``HsdDict``, ``HsdList`` and
+``HsdValue``), which offer convenient access to entries in nested data
+structures.  With the help of these wrappers, nested nodes and values can be
+directly accessed using paths. When accessing nested content via wrappers, the
+resulting objects will be wrappers themself, wrapping the appropriate parts of
+the data structure (and inheriting certain properties of the original wrapper).
+
+For example, reading and wrapping the example above::
+
+  import hsd
+  hsdinp = hsd.wrap(hsd.load("test.hsd"))
+
+creates an ``HsdDict`` wrapper instance (``hsdinp``), which can be used to query
+encapsulated information in the structure::
+
+  # Reading out the value directly (100)
+  maxsteps = hsdinp["driver", "conjugate_gradients", "max_steps"].value
+
+  # Storing wrapper (HsdValue) instance and reading out value and the attribute
+  temp = hsdinp["hamiltonian / dftb / filling / fermi / temperature"]
+  temp_value = temp.value
+  temp_unit = temp.attrib
+
+  # Getting a default value, if a given path does not exists:
+  pot = hsdinp.get_item("hamiltonian / dftb / bias", default=hsd.HsdValue(100, attrib="V"))
+
+  # Setting a value for given path by creating missing parents
+  hsdinp.set_item("analysis / calculate_forces", True, parents=True)
+
+As demonstrated above, paths can be specified as tuples or as slash (``/``) joined strings.
+
+The wrappers also support case-insensitive access. Let's have a look at a
+mixed-case example file ``test2.hsd``::
+
+  Driver {
+  ConjugateGradients {
+    MovedAtoms = 1 2 "7:19"
+    MaxSteps = 100
+  }
+
+We now make copy of the data structure before wrapping it, and make sure that
+all keys are converted to lower case, but the original names are saved as
+HSD-attributes::
+
+  hsdinp = hsd.copy(hsd.load("test2.hsd"), lower_names=True, save_names=True)
+
+This way, paths passed to the Hsd-wrapper are treated in a case-insensitive
+way::
+
+  maxsteps = hsdinp["driver", "CONJUGATEGRADIENTS", "MAXSTEPS"].value
+
+When adding new items, the access is and remains case in-sensitive, but the
+actual form of the name of the new node will be saved. The code snippet::
+
+  hsdinp["driver", "conjugategradients", "MaxForce"] = hsd.HsdValue(1e-4, attrib="au")
+  maxforceval = hsdinp["driver", "conjugategradients", "maxforce"]
+  print(f"{maxforceval.value} {maxforceval.attrib}")
+  print(hsd.dump_string(hsdinp.value, use_hsd_attribs=True))
+
+will result in ::
+
+  0.0001 au
+  Driver {
+    ConjugateGradients {
+      MovedAtoms = 1 2 "7:19"
+      MaxSteps = 100
+      MaxForce [au] = 0.0001
+    }
+  }
+
+where the case-convention for ``MaxForce`` is identical to the one used when the
+item was created.

src/hsd/__init__.py

@@ -7,12 +7,12 @@
 """
 Toolbox for reading, writing and manipulating HSD-data.
 """
-from hsd.common import HSD_ATTRIB_LINE, HSD_ATTRIB_EQUAL, HSD_ATTRIB_SUFFIX,\
-     HSD_ATTRIB_NAME, HsdError
-from hsd.dict import HsdDictBuilder, HsdDictWalker
+from hsd.common import HSD_ATTRIB_LINE, HSD_ATTRIB_EQUAL, HSD_ATTRIB_NAME, HsdError
+from hsd.dict import ATTRIB_KEY_SUFFIX, HSD_ATTRIB_KEY_SUFFIX, HsdDictBuilder, HsdDictWalker
 from hsd.eventhandler import HsdEventHandler, HsdEventPrinter
 from hsd.formatter import HsdFormatter
 from hsd.io import load, load_string, dump, dump_string
 from hsd.parser import HsdParser
+from hsd.wrappers import HsdDict, HsdList, HsdValue, copy, wrap
 
 __version__ = '0.1'

src/hsd/common.py

@@ -28,12 +28,6 @@ def unquote(txt):
 # Name for default attribute (when attribute name is not specified)
 DEFAULT_ATTRIBUTE = "unit"
 
-# Suffix to mark attribute
-ATTRIB_SUFFIX = ".attrib"
-
-# Suffix to mark hsd processing attributes
-HSD_ATTRIB_SUFFIX = ".hsdattrib"
-
 # HSD attribute containing the original tag name
 HSD_ATTRIB_NAME = "name"
 

src/hsd/dict.py

@@ -9,10 +9,17 @@
 """
 import re
 from typing import List, Tuple, Union
-from hsd.common import HSD_ATTRIB_NAME, np, ATTRIB_SUFFIX, HSD_ATTRIB_SUFFIX, HsdError,\
-    QUOTING_CHARS, SPECIAL_CHARS
+from hsd.common import HSD_ATTRIB_NAME, np, HsdError, QUOTING_CHARS, SPECIAL_CHARS
 from hsd.eventhandler import HsdEventHandler, HsdEventPrinter
 
+
+# Dictionary key suffix to mark attribute
+ATTRIB_KEY_SUFFIX = ".attrib"
+
+# Dictionary keysuffix to mark hsd processing attributes
+HSD_ATTRIB_KEY_SUFFIX = ".hsdattrib"
+
+
 _ItemType = Union[float, complex, int, bool, str]
 
 _DataType = Union[_ItemType, List[_ItemType]]
@@ -130,26 +137,26 @@ def close_tag(self, tagname):
                 parentblock[key] = [{None: prevcont}, self._curblock]
 
         if attrib and prevcont is None:
-            parentblock[key + ATTRIB_SUFFIX] = attrib
+            parentblock[key + ATTRIB_KEY_SUFFIX] = attrib
         elif prevcont is not None:
-            prevattrib = parentblock.get(key + ATTRIB_SUFFIX)
+            prevattrib = parentblock.get(key + ATTRIB_KEY_SUFFIX)
             if isinstance(prevattrib, list):
                 prevattrib.append(attrib)
             else:
-                parentblock[key + ATTRIB_SUFFIX] = [prevattrib, attrib]
+                parentblock[key + ATTRIB_KEY_SUFFIX] = [prevattrib, attrib]
 
         if self._include_hsd_attribs:
             if self._lower_tag_names:
                 hsdattrib = {} if hsdattrib is None else hsdattrib
                 hsdattrib[HSD_ATTRIB_NAME] = tagname
             if prevcont is None:
-                parentblock[key + HSD_ATTRIB_SUFFIX] = hsdattrib
+                parentblock[key + HSD_ATTRIB_KEY_SUFFIX] = hsdattrib
             else:
-                prevhsdattrib = parentblock.get(key + HSD_ATTRIB_SUFFIX)
+                prevhsdattrib = parentblock.get(key + HSD_ATTRIB_KEY_SUFFIX)
                 if isinstance(prevhsdattrib, list):
                     prevhsdattrib.append(hsdattrib)
                 else:
-                    parentblock[key + HSD_ATTRIB_SUFFIX] = [prevhsdattrib, hsdattrib]
+                    parentblock[key + HSD_ATTRIB_KEY_SUFFIX] = [prevhsdattrib, hsdattrib]
         self._curblock = parentblock
         self._data = None
 
@@ -219,11 +226,11 @@ def walk(self, dictobj):
 
         for key, value in dictobj.items():
 
-            if key.endswith(ATTRIB_SUFFIX) or key.endswith(HSD_ATTRIB_SUFFIX):
+            if key.endswith(ATTRIB_KEY_SUFFIX) or key.endswith(HSD_ATTRIB_KEY_SUFFIX):
                 continue
 
-            hsdattrib = dictobj.get(key + HSD_ATTRIB_SUFFIX)
-            attrib = dictobj.get(key + ATTRIB_SUFFIX)
+            hsdattrib = dictobj.get(key + HSD_ATTRIB_KEY_SUFFIX)
+            attrib = dictobj.get(key + ATTRIB_KEY_SUFFIX)
 
             if isinstance(value, dict):
 

src/hsd/io.py

@@ -6,6 +6,7 @@
 """
 Provides functionality to dump Python structures to HSD
 """
+from collections.abc import Mapping
 import io
 from typing import Union, TextIO
 from hsd.dict import HsdDictWalker, HsdDictBuilder
@@ -155,7 +156,7 @@ def dump(data: dict, hsdfile: Union[TextIO, str],
 
         See :func:`hsd.load_string` for an example.
     """
-    if not isinstance(data, dict):
+    if not isinstance(data, Mapping):
         msg = "Invalid object type"
         raise TypeError(msg)
     if isinstance(hsdfile, str):