Merge pull request #47 from QEF/develop

Update dependencies and fix XPath selection on document schema

.github/workflows/test.yml

@@ -15,11 +15,11 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
@@ -29,7 +29,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r requirements-dev.txt
       - name: Lint with flake8
-        if: ${{ matrix.python-version != '3.7' }}
         run: |
           flake8 qeschema --max-line-length=100 --statistics
       - name: Run tests

docs/conf.py

@@ -18,11 +18,11 @@
 # -- Project information -----------------------------------------------------
 
 project = 'qeschema'
-copyright = '2015-2023, Quantum Espresso Foundation and SISSA'
+copyright = '2015-2024, Quantum Espresso Foundation and SISSA'
 author = 'Davide Brunato, Pietro Delugas'
 
 # The full version, including alpha/beta/rc tags
-release = '1.5.1'
+release = '1.5.2'
 
 
 # -- General configuration ---------------------------------------------------

qeschema/__init__.py

@@ -15,7 +15,7 @@
 from .exceptions import QESchemaError, XmlDocumentError
 from .utils import set_logger
 
-__version__ = '1.5.1'
+__version__ = '1.5.2'
 
 __all__ = [
     'XmlDocument', 'QeDocument', 'PwDocument', 'PhononDocument', 'NebDocument',

qeschema/cards.py

@@ -249,7 +249,7 @@ def labnl(nnum, lnum):
 
                     label = labnl(value['n2_number'], value['l2_number'])
                     if 'two' in background:
-                        label = f"{label}-{labnl(value['n3_number'],value['l3_number'])}"
+                        label = f"{label}-{labnl(value['n3_number'], value['l3_number'])}"
                     lines.append(f"U {specie}-{label}  {value['$']:8.3f}")
             elif tag == 'V':
                 speclab1 = f"{value['@specie1']}-{value['@label1']}"

qeschema/documents.py

@@ -16,7 +16,6 @@
 import xmlschema
 from xmlschema import etree_tostring
 
-
 try:
     import yaml
 except ImportError:
@@ -27,7 +26,7 @@
     NebInputConverter, TdInputConverter, TdSpectrumInputConverter, \
     XSpectraInputConverter, EPWInputConverter
 from .exceptions import XmlDocumentError
-from .utils import etree_iter_path
+from .utils import etree_iter_path, get_target_prefix
 
 logger = logging.getLogger('qeschema')
 
@@ -48,7 +47,7 @@ def removeprefix(s, prefix):
     return s[len(prefix):] if s.startswith(prefix) else s
 
 
-class XmlDocument(object):
+class XmlDocument:
     """
     Base class for a generic XML document based on an XSD schema. The schema
     associated is used for checking types, validation of the XML data and for
@@ -118,11 +117,15 @@ def __init__(self, source=None, schema=None):
     def namespaces(self):
         """
         XML data namespaces map, a dictionary that maps prefixes to URI. An empty
-        dictionary if the XML data file is not loaded or it doesn't contain any
+        dictionary if the XML data file is not loaded or if it doesn't contain any
         namespace declaration.
         """
         return {k: v for k, v in self._namespaces.items()}
 
+    @property
+    def default_namespace(self):
+        return self._namespaces.get('', '')
+
     @classmethod
     def fetch_schema(cls, filename):
         filename = filename.strip()
@@ -442,20 +445,25 @@ def __init__(self, source=None, schema=None, input_builder=None):
             self.input_builder = self.DEFAULT_INPUT_BUILDER
         elif not isinstance(input_builder, type) or \
                 not issubclass(input_builder, RawInputConverter):
-            msg = "3rd argument must be a {!r} subclass"
-            raise XmlDocumentError(msg.format(RawInputConverter))
+            raise XmlDocumentError(f"3rd argument must be a {RawInputConverter!r} subclass")
         else:
             self.input_builder = input_builder
 
-        self.default_namespace = self.schema.target_namespace
-        qe_prefixes = ['qes', 'neb', 'qes_ph', 'qes_lr', 'qes_spectrum',
-                       'qes_xspectra', 'epw']
-        qe_nslist = list(map(self.schema.namespaces.get, qe_prefixes))
-        if self.default_namespace not in qe_nslist:
+        self._xpath_namespaces = {k: v for k, v in self.schema.namespaces.items() if k}
+
+        prefix = get_target_prefix(self.schema.namespaces, self.schema.target_namespace)
+        if prefix not in ('qes', 'neb', 'qes_ph', 'qes_lr',
+                          'qes_spectrum', 'qes_xspectra', 'epw'):
             raise NotImplementedError(
-                "Converter not implemented for this schema {}".format(self.default_namespace)
+                f"Converter not implemented for namespace {self.schema.target_namespace!r}"
             )
 
+    def _xsd_find(self, path, xsd_element=None):
+        if xsd_element is None:
+            return self.schema.find(path, self._xpath_namespaces)
+        else:
+            return xsd_element.find(path, self._xpath_namespaces)
+
     @property
     def input_path(self):
         """The path to XML input section."""
@@ -491,15 +499,15 @@ def get_fortran_input(self, use_defaults=True):
             raise XmlDocumentError("Missing input {!r} in XML data!".format(input_path))
 
         for schema_root in self.schema.elements.values():
-            if schema_root.find(input_path):
+            if self._xsd_find(input_path, schema_root):
                 break
         else:
             raise XmlDocumentError("Missing input element in XSD schema!")
 
         # Extract values from input's subtree of the XML document
         for elem, path in etree_iter_path(input_root, path=input_path):
             rel_path = path.replace(input_path, '.')
-            xsd_element = schema_root.find(path)
+            xsd_element = self._xsd_find(path, schema_root)
             if xsd_element is None:
                 logger.error("%r doesn't match any element!", path)
                 continue
@@ -546,7 +554,7 @@ def get_atomic_positions(self):
         path = './/output//atomic_positions'
         elem = self.find(path)
         if elem is not None:
-            atomic_positions = self.schema.find(path).decode(elem)
+            atomic_positions = self._xsd_find(path).decode(elem)
             atoms = atomic_positions.get('atom')
             if not isinstance(atoms, list):
                 atoms = [atoms]
@@ -564,7 +572,7 @@ def get_cell_parameters(self):
         path = './/output//cell'
         elem = self.find(path)
         if elem is not None:
-            cell = self.schema.find(path).decode(elem)
+            cell = self._xsd_find(path).decode(elem)
             return [cell['a1'], cell['a2'], cell['a3']]
 
     @requires_xml_data
@@ -577,7 +585,7 @@ def get_stress(self):
         path = './/output//stress'
         elem = self.find(path)
         if elem is not None:
-            stress = self.schema.find(path).decode(elem)
+            stress = self._xsd_find(path).decode(elem)
             try:
                 stress = stress['$']
             except TypeError:
@@ -595,10 +603,9 @@ def get_forces(self):
         path = './/output/forces'
         elem = self.find(path)
         if elem is not None:
-            forces = self.schema.find(path).decode(elem)
+            forces = self._xsd_find(path).decode(elem)
             path = './/output//atomic_positions'
-            breakpoint()
-            atomic_positions = self.schema.find(path).decode(self.find(path))
+            atomic_positions = self._xsd_find(path).decode(self.find(path))
             atoms = atomic_positions.get('atom', [])
             if not isinstance(atoms, list):
                 atoms = [atoms]
@@ -616,7 +623,7 @@ def get_k_points(self):
         :return: nested list with k_points
         """
         path = './/output//ks_energies/k_point'
-        return [self.schema.find(path).decode(e)['$'] for e in self.findall(path)]
+        return [self._xsd_find(path).decode(e)['$'] for e in self.findall(path)]
 
     @requires_xml_data
     def get_ks_eigenvalues(self):
@@ -628,7 +635,7 @@ def get_ks_eigenvalues(self):
         path = './/output//ks_energies/eigenvalues'
         eigenvalues = []
         for e in self.findall(path):
-            obj = self.schema.find(path).decode(e)
+            obj = self._xsd_find(path).decode(e)
             if isinstance(obj, dict):
                 eigenvalues.append(obj['$'])  # pragma: no cover
             else:
@@ -644,7 +651,7 @@ def get_total_energy(self):
         :return: total energy in Hartree Units
         """
         path = './/output//etot'
-        return self.schema.find(path).decode(self.find(path))
+        return self._xsd_find(path).decode(self.find(path))
 
 
 class PhononDocument(QeDocument):