from_file method allows to switch to pymatgen (#80)

Author: mikibonacci

docs/source/how_to/creation_mutation.md

@@ -224,12 +224,12 @@ Charges: [2. 0.]
 
 ### From Files
 
-Load structures from various file formats:
+Load structures from various file formats, via the `from_file` method. It is possible to specify the parser engine between "ase" and "pymatgen".If the file is not a .cif or .mcif, the default is ase. To change it, you can pass the `parser="pymatgen"` input parameters to the method.
 
 #### From CIF
 
 ```python
-# From CIF file
+# From CIF file ()
 structure = StructureData.from_file('path/to/your/structure.cif')
 print(f"Loaded from CIF: {structure.properties.formula}")
 ```
@@ -587,7 +587,7 @@ Total charge: -1.0
 
 ```python
 # Load existing structure
-original = StructureData.from_file('structure.cif')
+original = StructureData.from_file('structure.cif', parser='pymatgen')
 
 # Create mutable copy
 mutable = StructureBuilder(**original.to_dict())

src/aiida_atomistic/data/structure/getter_mixin.py

@@ -174,10 +174,14 @@ def from_file(
         cls,
         filename,
         format="cif",
+        parser:str="ase",
         **kwargs):
-        """Load the structure from a file."""
+        """Load the structure from a file.
 
-        if format == 'mcif' or '.mcif' in filename:
+        It is possible to specify the parser between ase or pymatgen, default is ase.
+        """
+
+        if format == 'mcif' or '.mcif' in filename or parser == "pymatgen":
             # in this case, we use pymatgen parser, because the ase one does not work properly for now.
             from pymatgen.io.cif import CifParser
             parser  = CifParser(filename)

src/aiida_atomistic/data/structure/structure.py

@@ -45,8 +45,8 @@ def properties(self):
             from aiida_atomistic.data.structure.utils import build_sites_from_expanded_properties
             if "kind_names" in self.base.attributes.all:
                 from aiida_atomistic.data.structure.utils_kinds import rebuild_site_lists_from_kind_lists
-                attribute_lists = rebuild_site_lists_from_kind_lists(self.base.attributes.all)
-                attributes = build_sites_from_expanded_properties(attribute_lists)
+                attribute_lists_dict = rebuild_site_lists_from_kind_lists(self.base.attributes.all)
+                attributes = build_sites_from_expanded_properties(attribute_lists_dict)
             else:
                 attributes = build_sites_from_expanded_properties(self.base.attributes.all)
 

src/aiida_atomistic/data/structure/utils.py

@@ -911,6 +911,9 @@ def order_k(k):
 def build_sites_from_expanded_properties(expanded):
     """
     Build the structure dictionary from expanded site-wise lists of properties.
+
+    Expanded is a dictionary where each key corresponds to a property and the value is a list of values for each site,
+    i.e. the format on which we store the properties in the database.
     """
 
     # Use all keys except positions if you want to exclude arrays, or specify your own