Fix nexus parsing for NOMAD (#304)

* Fix nxdl_path construction for attributes

* Fix generating of duplicate attribute nodes in nxdl_path

* Ignore xml comments

* Use `ET._Element`

* Update definitions

* Update definitions file

* Update ref log

* Update definitions

* Update nexus-version.txt

* Update defs

* Update nexus version

pynxtools/nexus/nexus.py

@@ -9,30 +9,31 @@
 import click
 import h5py
 import lxml.etree as ET
+
 from pynxtools.definitions.dev_tools.utils.nxdl_utils import (
-    get_hdf_info_parent,
-    get_nxdl_child,
-    get_node_concept_path,
-    get_local_name_from_xml,
-    write_doc_string,
-    try_find_units,
+    NxdlAttributeNotFoundError,
+    add_base_classes,
     check_attr_name_nxdl,
-    get_required_string,
     get_best_child,
-    get_node_name,
-    add_base_classes,
-    walk_elist,
-    get_nx_class,
-    try_find_default,
-    other_attrs,
-    get_nexus_definitions_path,
-    NxdlAttributeNotFoundError,
-    get_node_at_nxdl_path,
     get_enums,
+    get_hdf_info_parent,
     get_inherited_nodes,
+    get_local_name_from_xml,
+    get_nexus_definitions_path,
+    get_node_at_nxdl_path,
+    get_node_concept_path,
+    get_node_name,
+    get_nx_attribute_type,
+    get_nx_class,
     get_nx_classes,
     get_nx_units,
-    get_nx_attribute_type,
+    get_nxdl_child,
+    get_required_string,
+    other_attrs,
+    try_find_default,
+    try_find_units,
+    walk_elist,
+    write_doc_string,
 )
 
 
@@ -151,6 +152,8 @@ def check_deprecation_enum_axis(variables, doc, elist, attr, hdf_node):
             if doc:
                 logger.debug("enumeration (" + get_node_concept_path(base_elem) + "):")
             for item in sdoc:
+                if isinstance(item, ET._Comment):
+                    continue
                 if get_local_name_from_xml(item) == "item":
                     if doc:
                         logger.debug("-> " + item.attrib["value"])
@@ -171,6 +174,7 @@ def get_nxdl_attr_doc(  # pylint: disable=too-many-arguments,too-many-locals
     """Get nxdl documentation for an attribute"""
     new_elem = []
     old_elem = elem
+    attr_inheritance_chain = []
     for elem_index, act_elem1 in enumerate(elist):
         act_elem = act_elem1
         # NX_class is a compulsory attribute for groups in a nexus file
@@ -187,13 +191,15 @@ def get_nxdl_attr_doc(  # pylint: disable=too-many-arguments,too-many-locals
         # units category is a compulsory attribute for any fields
         if attr == "units" and isinstance(hdf_node, h5py.Dataset):
             req_str = "<<REQUIRED>>"
-            logger, act_elem, nxdl_path, doc, attr = try_find_units(
-                logger, act_elem, nxdl_path, doc, attr
+            logger, act_elem, attr_inheritance_chain, doc, attr = try_find_units(
+                logger, act_elem, attr_inheritance_chain, doc, attr
             )
         # units for attributes can be given as ATTRIBUTENAME_units
         elif attr.endswith("_units"):
-            logger, act_elem, nxdl_path, doc, attr, req_str = check_attr_name_nxdl(
-                (logger, act_elem, nxdl_path, doc, attr, req_str)
+            logger, act_elem, attr_inheritance_chain, doc, attr, req_str = (
+                check_attr_name_nxdl(
+                    (logger, act_elem, attr_inheritance_chain, doc, attr, req_str)
+                )
             )
         # default is allowed for groups
         elif attr == "default" and not isinstance(hdf_node, h5py.Dataset):
@@ -202,16 +208,16 @@ def get_nxdl_attr_doc(  # pylint: disable=too-many-arguments,too-many-locals
             act_elem = get_nxdl_child(
                 act_elem, attr, nexus_type="attribute", go_base=False
             )
-            logger, act_elem, nxdl_path, doc, attr = try_find_default(
-                logger, act_elem1, act_elem, nxdl_path, doc, attr
+            logger, act_elem, attr_inheritance_chain, doc, attr = try_find_default(
+                logger, act_elem1, act_elem, attr_inheritance_chain, doc, attr
             )
         else:  # other attributes
             act_elem = get_nxdl_child(
                 act_elem, attr, nexus_type="attribute", go_base=False
             )
             if act_elem is not None:
-                logger, act_elem, nxdl_path, doc, attr = other_attrs(
-                    logger, act_elem1, act_elem, nxdl_path, doc, attr
+                logger, act_elem, attr_inheritance_chain, doc, attr = other_attrs(
+                    logger, act_elem1, act_elem, attr_inheritance_chain, doc, attr
                 )
         if act_elem is not None:
             new_elem.append(act_elem)
@@ -234,6 +240,10 @@ def get_nxdl_attr_doc(  # pylint: disable=too-many-arguments,too-many-locals
         if attr != "NX_class":
             logger.debug("@" + attr + " - IS NOT IN SCHEMA")
         logger.debug("")
+
+    # Add the lowest child element to the nxdl_path
+    if attr_inheritance_chain:
+        nxdl_path.append(attr_inheritance_chain[0])
     return (req_str, get_nxdl_entry(hdf_info), nxdl_path)
 
 
@@ -247,6 +257,8 @@ def get_nxdl_doc(hdf_info, logger, doc, attr=False):
         hdf_path=hdf_info["hdf_path"] if "hdf_path" in hdf_info else None,
         hdf_root=hdf_info["hdf_root"] if "hdf_root" in hdf_info else None,
     )
+    # Copy the nxdl_path, otherwise the cached object is altered
+    nxdl_path = nxdl_path.copy()
     elem = elist[0] if class_path and elist else None
     if doc:
         logger.debug("classpath: " + str(class_path))
@@ -310,7 +322,7 @@ def get_hdf_path(hdf_info):
 @lru_cache(maxsize=None)
 def get_inherited_hdf_nodes(
     nx_name: str = None,
-    elem: ET.Element = None,
+    elem: ET._Element = None,
     hdf_node=None,
     hdf_path=None,
     hdf_root=None,