lxml 4.8 includes a patch (by me :)) that allows pathlib Paths

for all of the API
lxml/lxml#337
This allows to eliminate some corner cases in the fleur parser

masci_tools/cmdline/commands/fleur_schema.py

@@ -98,7 +98,7 @@ def add_fleur_schema(schema_file, test_xml_file, overwrite, branch, api_key, fro
             project.files.raw(file_path=f'io/xml/{file_name}', ref=branch, streamed=True, action=f.write)
         echo.echo_success('Download successful')
 
-    xmlschema = etree.parse(os.fspath(schema_file))
+    xmlschema = etree.parse(schema_file)
     xmlschema, _ = clear_xml(xmlschema)
 
     namespaces = {'xsd': 'http://www.w3.org/2001/XMLSchema'}

masci_tools/io/io_fleurxml.py

@@ -50,13 +50,8 @@ def load_inpxml(inpxmlfile: XMLFileLike,
                           'Setting it to the current working directory.'
                           'If the tree contains xinclude tags these could fail')
             base_url = os.getcwd()
-        elif isinstance(base_url, Path):
-            base_url = os.fspath(base_url.resolve())
         xml_parse_func = partial(xml_parse_func, base_url=base_url)
 
-    if isinstance(inpxmlfile, Path):
-        inpxmlfile = os.fspath(inpxmlfile)
-
     if isinstance(inpxmlfile, etree._ElementTree):
         xmltree = inpxmlfile
     else:
@@ -116,13 +111,8 @@ def load_outxml(outxmlfile: XMLFileLike,
                           'Setting it to the current working directory.'
                           'If the tree contains xinclude tags these could fail')
             base_url = os.getcwd()
-        elif isinstance(base_url, Path):
-            base_url = os.fspath(base_url.resolve())
         xml_parse_func = partial(xml_parse_func, base_url=base_url)
 
-    if isinstance(outxmlfile, Path):
-        outxmlfile = os.fspath(outxmlfile)
-
     outfile_broken = False
 
     if isinstance(outxmlfile, etree._ElementTree):

masci_tools/io/parsers/fleur_schema/inpschema_todict.py

@@ -15,11 +15,12 @@
 """
 from __future__ import annotations
 
+import os
 from .fleur_schema_parser_functions import *  #pylint: disable=unused-wildcard-import
 from masci_tools.util.xml.common_functions import clear_xml
 from masci_tools.util.case_insensitive_dict import CaseInsensitiveDict, CaseInsensitiveFrozenSet
 from masci_tools.util.lockable_containers import LockableDict, LockableList
-from typing import AnyStr, Callable
+from typing import Callable
 try:
     from typing import TypedDict, Literal
 except ImportError:
@@ -49,7 +50,7 @@ class InputSchemaData(TypedDict, total=False):
                'unique_path_attribs', 'other_attribs', 'omitt_contained_tags', 'tag_info']
 
 
-def create_inpschema_dict(path: AnyStr, apply_patches: bool = True) -> InputSchemaData:
+def create_inpschema_dict(path: os.PathLike, apply_patches: bool = True) -> InputSchemaData:
     """
     Creates dictionary with information about the FleurInputSchema.xsd.
     The functions, whose results are added to the schema_dict and the corresponding keys
@@ -76,7 +77,7 @@ def create_inpschema_dict(path: AnyStr, apply_patches: bool = True) -> InputSche
     }
     schema_patches = [convert_string_to_float_expr, patch_forcetheorem_attributes, patch_text_types]
 
-    xmlschema = etree.parse(path)
+    xmlschema = etree.parse(path)  #type:ignore
     xmlschema, _ = clear_xml(xmlschema)
 
     xmlschema_evaluator = etree.XPathEvaluator(xmlschema, namespaces=NAMESPACES)

masci_tools/io/parsers/fleur_schema/outschema_todict.py

@@ -21,8 +21,9 @@
 from masci_tools.util.lockable_containers import LockableDict, LockableList
 from lxml import etree
 import copy
+import os
 from collections import UserList
-from typing import AnyStr, Callable
+from typing import Callable
 try:
     from typing import TypedDict, Literal
 except ImportError:
@@ -63,7 +64,7 @@ class OutputSchemaData(TypedDict, total=False):
                'omitt_contained_tags', 'tag_info', 'iteration_tag_info']
 
 
-def create_outschema_dict(path: AnyStr,
+def create_outschema_dict(path: os.PathLike,
                           inpschema_dict: inpschema_todict.InputSchemaData,
                           apply_patches: bool = True) -> OutputSchemaData:
     """
@@ -99,7 +100,7 @@ def create_outschema_dict(path: AnyStr,
     schema_patches = [fix_qpoints_typo, patch_text_types]
 
     #print(f'processing: {path}/FleurOutputSchema.xsd')
-    xmlschema = etree.parse(path)
+    xmlschema = etree.parse(path)  #type: ignore
     xmlschema, _ = clear_xml(xmlschema)
 
     xmlschema_evaluator = etree.XPathEvaluator(xmlschema, namespaces=NAMESPACES)

masci_tools/io/parsers/fleur_schema/schema_dict.py

@@ -681,11 +681,8 @@ def fromPath(cls, path: os.PathLike) -> InputSchemaDict:
 
         :return: InputSchemaDict object with the information for the provided file
         """
-        fspath = os.fspath(path)
-        schema_dict = create_inpschema_dict(fspath)
-
-        xmlschema_doc = etree.parse(fspath)
-        xmlschema = etree.XMLSchema(xmlschema_doc)
+        schema_dict = create_inpschema_dict(path)
+        xmlschema = etree.XMLSchema(file=path)  #type:ignore
 
         return cls(schema_dict, xmlschema=xmlschema)
 
@@ -845,25 +842,22 @@ def fromPath(cls,
         if inp_path is None:
             inp_path = Path(path).parent / 'FleurInputSchema.xsd'
 
-        fspath = os.fspath(path)
-        fsinp_path = os.fspath(inp_path)
-
         if inpschema_dict is None:
-            inpschema_dict = create_inpschema_dict(fsinp_path)  #type:ignore
+            inpschema_dict = create_inpschema_dict(inp_path)  #type:ignore
         inpschema_data = cast(InputSchemaData, inpschema_dict)
 
-        schema_dict = create_outschema_dict(fspath, inpschema_dict=inpschema_data)
+        schema_dict = create_outschema_dict(path, inpschema_dict=inpschema_data)
         schema_dict = merge_schema_dicts(inpschema_data, schema_dict)
 
         with tempfile.TemporaryDirectory() as td:
             td_path = Path(td)
             temp_input_schema_path = td_path / 'FleurInputSchema.xsd'
-            shutil.copy(fsinp_path, temp_input_schema_path)
+            shutil.copy(inp_path, temp_input_schema_path)
 
             temp_output_schema_path = td_path / 'FleurOutputSchema.xsd'
-            shutil.copy(fspath, temp_output_schema_path)
-            xmlschema_doc = etree.parse(os.fspath(temp_output_schema_path))
-            xmlschema = etree.XMLSchema(xmlschema_doc)
+            shutil.copy(path, temp_output_schema_path)
+
+            xmlschema = etree.XMLSchema(file=temp_output_schema_path)  #type:ignore
 
         return cls(schema_dict, xmlschema=xmlschema)
 

pyproject.toml

@@ -27,7 +27,7 @@ dependencies = [
             'matplotlib',
             'h5py',
             'pandas',
-            'lxml>=4.5',
+            'lxml~=4.8',
             'more_itertools',
             'seaborn',
             'deepdiff',

tests/cmdline/conftest.py

@@ -9,7 +9,7 @@
 
 
 @pytest.fixture
-def fake_schemas_and_test_files(tmp_path):
+def fake_schemas_and_test_files(tmp_path, test_file):
     """
     Helper fixture for add fleur schema tests
 
@@ -33,43 +33,41 @@ def dummy_migration(definitions):
 
     schema_file = schema_folder / 'FleurInputSchema.xsd'
 
-    inputschema = etree.parse(os.fspath(schema_file))
+    inputschema = etree.parse(schema_file)
     namespaces = {'xsd': 'http://www.w3.org/2001/XMLSchema'}
     root = inputschema.xpath('/xsd:schema', namespaces=namespaces)[0]
     root.attrib['version'] = '0.01'
     root = inputschema.xpath("//xsd:simpleType[@name='FleurVersionType']/xsd:restriction/xsd:enumeration",
                              namespaces=namespaces)[0]
     root.attrib['value'] = '0.01'
 
-    inputschema.write(os.fspath(tmp_path / 'FleurInputSchema.xsd'), encoding='utf-8', pretty_print=True)
+    inputschema.write(tmp_path / 'FleurInputSchema.xsd', encoding='utf-8', pretty_print=True)
 
     schema_file = schema_folder / 'FleurOutputSchema.xsd'
 
-    outputschema = etree.parse(os.fspath(schema_file))
+    outputschema = etree.parse(schema_file)
     namespaces = {'xsd': 'http://www.w3.org/2001/XMLSchema'}
     root = outputschema.xpath('/xsd:schema', namespaces=namespaces)[0]
     root.attrib['version'] = '0.01'
     root = outputschema.xpath("//xsd:simpleType[@name='FleurOutputVersionType']/xsd:restriction/xsd:enumeration",
                               namespaces=namespaces)[0]
     root.attrib['value'] = '0.01'
 
-    outputschema.write(os.fspath(tmp_path / 'FleurOutputSchema.xsd'), encoding='utf-8', pretty_print=True)
+    outputschema.write(tmp_path / 'FleurOutputSchema.xsd', encoding='utf-8', pretty_print=True)
 
-    xml_file = Path(__file__).parent.resolve() / Path('../files/fleur/Max-R5/SiLOXML/files/inp.xml')
-
-    xmltree = etree.parse(os.fspath(xml_file))
+    xml_file = test_file('fleur/Max-R5/SiLOXML/files/inp.xml')
+    xmltree = etree.parse(xml_file)
     root = xmltree.xpath('/fleurInput')[0]
     root.attrib['fleurInputVersion'] = '0.01'
-    xmltree.write(os.fspath(tmp_path / 'inp.xml'), encoding='utf-8', pretty_print=True)
-
-    xml_file = Path(__file__).parent.resolve() / Path('../files/fleur/Max-R5/SiLOXML/files/out.xml')
+    xmltree.write(tmp_path / 'inp.xml', encoding='utf-8', pretty_print=True)
 
-    xmltree = etree.parse(os.fspath(xml_file))
+    xml_file = test_file('fleur/Max-R5/SiLOXML/files/out.xml')
+    xmltree = etree.parse(xml_file)
     root = xmltree.xpath('/fleurOutput')[0]
     root.attrib['fleurOutputVersion'] = '0.01'
     root = xmltree.xpath('//fleurInput')[0]
     root.attrib['fleurInputVersion'] = '0.01'
-    xmltree.write(os.fspath(tmp_path / 'out.xml'), encoding='utf-8', pretty_print=True)
+    xmltree.write(tmp_path / 'out.xml', encoding='utf-8', pretty_print=True)
 
     try:
         yield tmp_path