drop support for python 3.9 (EOL), add python 3.13 (#707)

Author: lukaspie

.github/workflows/plugin_test.yaml

@@ -1,4 +1,4 @@
-# This workflow will install Python 3.9 and run the tests of all supported plugins.
+# This workflow will install Python 3.12 and run the tests of all supported plugins.
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: test plugins

.github/workflows/pytest.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4
@@ -30,7 +30,6 @@ jobs:
         run: |
           uv pip install coverage coveralls
       - name: Install nomad
-        if: "${{ matrix.python-version != '3.8' && matrix.python-version != '3.9'}}"
         run: |
           uv pip install nomad-lab[infrastructure]@git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git
       - name: Install pynx

pyproject.toml

@@ -12,12 +12,12 @@ authors = [
 description = "Extend NeXus for experiments and characterization in Materials Science and Materials Engineering and serve as a NOMAD parser implementation for NeXus."
 readme = "README.md"
 license = { file = "LICENSE" }
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "License :: OSI Approved :: Apache Software License",
     "Operating System :: OS Independent",
 ]

src/pynxtools/_build_wrapper.py

@@ -14,7 +14,7 @@
     pass
 
 
-def get_vcs_version(tag_match="*[0-9]*") -> Optional[str]:
+def get_vcs_version(tag_match="*[0-9]*") -> str | None:
     """
     The version of the Nexus standard and the NeXus Definition language
     based on git tags and commits

src/pynxtools/dataconverter/convert.py

@@ -43,18 +43,7 @@
 logger = logging.getLogger("pynxtools")
 
 
-if sys.version_info >= (3, 10):
-    from importlib.metadata import entry_points
-else:
-    try:
-        from importlib_metadata import entry_points
-    except ImportError:
-        # If importlib_metadata is not present
-        # we provide a dummy function just returning an empty list.
-        # pylint: disable=W0613
-        def entry_points(group):
-            """Dummy function for importlib_metadata"""
-            return []
+from importlib.metadata import entry_points
 
 
 class ValidationFailed(Exception):
@@ -106,7 +95,7 @@ def transfer_data_into_template(
     input_file,
     reader,
     nxdl_name,
-    nxdl_root: Optional[ET._Element] = None,
+    nxdl_root: ET._Element | None = None,
     skip_verify: bool = False,
     **kwargs,
 ):

src/pynxtools/dataconverter/hdfdict.py

@@ -15,7 +15,7 @@
 def hdf_file(hdf, lazy=True, *args, **kwargs):
     """Context manager that yields an h5 file if `hdf` is a string,
     otherwise it yields hdf as is."""
-    if isinstance(hdf, (str, Path)):
+    if isinstance(hdf, str | Path):
         if not lazy:
             # The file can be closed after reading
             # therefore the context manager is used.
@@ -221,7 +221,7 @@ def dump(data, hdf, packer=pack_dataset, mode="w", *args, **kwargs):
 
     def _recurse(datadict, hdfobject):
         for key, value in datadict.items():
-            if isinstance(value, (dict, LazyHdfDict)):
+            if isinstance(value, dict | LazyHdfDict):
                 hdfgroup = hdfobject.create_group(key)
                 _recurse(value, hdfgroup)
             else:

src/pynxtools/dataconverter/helpers.py

@@ -25,7 +25,7 @@
 from datetime import datetime, timezone
 from enum import Enum, auto
 from functools import cache, lru_cache
-from typing import Any, Callable, Literal, Optional, Union, cast
+from typing import Any, Literal, Optional, Union, cast
 
 import h5py
 import lxml.etree as ET
@@ -132,7 +132,7 @@ def __init__(self):
 
         self.logging = True
 
-    def _log(self, path: str, log_type: ValidationProblem, value: Optional[Any], *args):
+    def _log(self, path: str, log_type: ValidationProblem, value: Any | None, *args):
         if value is None:
             value = "<unknown>"
 
@@ -287,7 +287,7 @@ def collect_and_log(
         self,
         path: str,
         log_type: ValidationProblem,
-        value: Optional[Any],
+        value: Any | None,
         *args,
         **kwargs,
     ):
@@ -359,7 +359,7 @@ def get_nxdl_name_from_elem(xml_element) -> str:
     return name_to_add
 
 
-def get_nxdl_name_for(xml_elem: ET._Element) -> Optional[str]:
+def get_nxdl_name_for(xml_elem: ET._Element) -> str | None:
     """
     Get the name of the element from the NXDL element.
     For an entity having a name this is just the name.
@@ -625,7 +625,7 @@ def convert_nexus_to_caps(nexus_name):
     return nexus_name[2:].upper()
 
 
-def contains_uppercase(field_name: Optional[str]) -> bool:
+def contains_uppercase(field_name: str | None) -> bool:
     """Helper function to check if a field name contains uppercase characters."""
     if field_name is None:
         return False
@@ -648,7 +648,7 @@ def convert_nexus_to_suggested_name(nexus_name):
     return nexus_name[2:]
 
 
-def convert_data_converter_entry_to_nxdl_path_entry(entry) -> Union[str, None]:
+def convert_data_converter_entry_to_nxdl_path_entry(entry) -> str | None:
     """
     Helper function to convert data converter style entry to NXDL style entry:
     ENTRY[entry] -> ENTRY
@@ -784,7 +784,7 @@ def is_positive_int(value: Any) -> bool:
     return bool(np.all(value > 0))
 
 
-def convert_str_to_bool_safe(value: str) -> Optional[bool]:
+def convert_str_to_bool_safe(value: str) -> bool | None:
     """Only returns True or False if someone mistakenly adds quotation marks but mean a bool.
 
     For everything else it raises a ValueError.
@@ -988,7 +988,7 @@ def is_valid_enum(
                 )
 
 
-def split_class_and_name_of(name: str) -> tuple[Optional[str], str]:
+def split_class_and_name_of(name: str) -> tuple[str | None, str]:
     """
     Return the class and the name of a data dict entry of the form
     `split_class_and_name_of("ENTRY[entry]")`, which will return `("ENTRY", "entry")`.
@@ -1225,7 +1225,7 @@ def get_first_group(root):
     return root
 
 
-def check_for_valid_atom_types(atoms: Union[str, list]):
+def check_for_valid_atom_types(atoms: str | list):
     """Check for whether atom exists in periodic table."""
 
     if isinstance(atoms, list):
@@ -1357,7 +1357,7 @@ def extract_atom_types(formula, mode="hill"):
 
 
 # pylint: disable=too-many-branches
-def transform_to_intended_dt(str_value: Any) -> Optional[Any]:
+def transform_to_intended_dt(str_value: Any) -> Any | None:
     """Transform string to the intended data type, if not then return str_value.
 
     E.g '2.5E-2' will be transfor into 2.5E-2
@@ -1407,7 +1407,7 @@ def transform_to_intended_dt(str_value: Any) -> Optional[Any]:
                 modified_parts: list = []
                 for part in parts:
                     part = transform_to_intended_dt(part)
-                    if isinstance(part, (int, float)):
+                    if isinstance(part, int | float):
                         modified_parts.append(part)
                     else:
                         return str_value
@@ -1430,9 +1430,7 @@ def nested_dict_to_slash_separated_path(
             flattened_dict[path] = val
 
 
-def clean_str_attr(
-    attr: Optional[Union[str, bytes]], encoding: str = "utf-8"
-) -> Optional[str]:
+def clean_str_attr(attr: str | bytes | None, encoding: str = "utf-8") -> str | None:
     """
     Return the attribute as a string.
 

src/pynxtools/dataconverter/nexus_tree.py

@@ -156,7 +156,7 @@ class NexusNode(NodeMixin):
 
     name: str
     nx_type: Literal["group", "field", "attribute", "choice"]
-    name_type: Optional[Literal["specified", "any", "partial"]] = "specified"
+    name_type: Literal["specified", "any", "partial"] | None = "specified"
     optionality: Literal["required", "recommended", "optional"] = "required"
     variadic: bool = False
     inheritance: list[ET._Element]
@@ -165,8 +165,8 @@ class NexusNode(NodeMixin):
     nxdl_base: str
     occurrence_limits: tuple[
         # TODO: Use Annotated[int, Field(strict=True, ge=0)] for py>3.8
-        Optional[int],
-        Optional[int],
+        int | None,
+        int | None,
     ] = (None, None)
     lvl_map = {
         "required": ("required",),
@@ -202,12 +202,12 @@ def __init__(
         self,
         name: str,
         nx_type: Literal["group", "field", "attribute", "choice"],
-        name_type: Optional[Literal["specified", "any", "partial"]] = "specified",
+        name_type: Literal["specified", "any", "partial"] | None = "specified",
         optionality: Literal["required", "recommended", "optional"] = "required",
-        variadic: Optional[bool] = None,
+        variadic: bool | None = None,
         parent: Optional["NexusNode"] = None,
-        inheritance: Optional[list[Any]] = None,
-        nxdl_base: Optional[str] = None,
+        inheritance: list[Any] | None = None,
+        nxdl_base: str | None = None,
     ) -> None:
         super().__init__()
         self.name = name
@@ -322,9 +322,9 @@ def get_child_for(self, xml_elem: ET._Element) -> Optional["NexusNode"]:
 
     def get_all_direct_children_names(
         self,
-        node_type: Optional[str] = None,
-        nx_class: Optional[str] = None,
-        depth: Optional[int] = None,
+        node_type: str | None = None,
+        nx_class: str | None = None,
+        depth: int | None = None,
         only_appdef: bool = False,
     ) -> set[str]:
         """
@@ -485,7 +485,7 @@ def required_fields_and_attrs_names(
 
         return req_children
 
-    def get_docstring(self, depth: Optional[int] = None) -> dict[str, str]:
+    def get_docstring(self, depth: int | None = None) -> dict[str, str]:
         """
         Gets the docstrings of the current node and its parents up to a certain depth.
 
@@ -765,8 +765,8 @@ class NexusGroup(NexusNode):
     nx_class: str
     occurrence_limits: tuple[
         # TODO: Use Annotated[int, Field(strict=True, ge=0)] for py>3.8
-        Optional[int],
-        Optional[int],
+        int | None,
+        int | None,
     ] = (None, None)
 
     def _check_sibling_namefit(self):
@@ -920,11 +920,11 @@ class NexusEntity(NexusNode):
     """
 
     nx_type: Literal["field", "attribute"]
-    unit: Optional[NexusUnitCategory] = None
+    unit: NexusUnitCategory | None = None
     dtype: NexusType = "NX_CHAR"
-    items: Optional[list[str]] = None
+    items: list[str] | None = None
     open_enum: bool = False
-    shape: Optional[tuple[Optional[int], ...]] = None
+    shape: tuple[int | None, ...] | None = None
 
     def _check_compatibility_with(self, xml_elem: ET._Element) -> bool:
         """Check compatibility of this node with an XML element from the (possible) inheritance"""
@@ -1018,7 +1018,7 @@ def _check_dimensions_fit(xml_elem: ET._Element) -> bool:
                         return True
                 elem_dim = elem_dimensions.findall("nx:dim", namespaces=namespaces)
                 elem_dimension_rank = rank if rank is not None else len(rank)
-                dims: list[Optional[int]] = [None] * int(rank)
+                dims: list[int | None] = [None] * int(rank)
 
                 for dim in elem_dim:
                     idx = int(dim.attrib["index"])
@@ -1134,7 +1134,7 @@ def _set_shape(self):
                 return
         xml_dim = dimension.findall("nx:dim", namespaces=namespaces)
         rank = rank if rank is not None else len(xml_dim)
-        dims: list[Optional[int]] = [None] * int(rank)
+        dims: list[int | None] = [None] * int(rank)
         for dim in xml_dim:
             idx = int(dim.attrib["index"])
             if "value" not in dim.attrib:

src/pynxtools/dataconverter/readers/json_map/reader.py

@@ -45,11 +45,11 @@ def get_val_nested_keystring_from_dict(keystring, data):
     Fetches data from the actual data dict using path strings without a leading '/':
         'path/to/data/in/dict'
     """
-    if isinstance(keystring, (list, dict)):
+    if isinstance(keystring, list | dict):
         return keystring
 
     current_key = keystring.split("/")[0]
-    if isinstance(data[current_key], (dict, hdfdict.LazyHdfDict)):
+    if isinstance(data[current_key], dict | hdfdict.LazyHdfDict):
         return get_val_nested_keystring_from_dict(
             keystring[keystring.find("/") + 1 :], data[current_key]
         )
@@ -68,7 +68,7 @@ def get_attrib_nested_keystring_from_dict(keystring, data):
     Fetches all attributes from the data dict using path strings without a leading '/':
         'path/to/data/in/dict'
     """
-    if isinstance(keystring, (list, dict)):
+    if isinstance(keystring, list | dict):
         return keystring
 
     key_splits = keystring.split("/")

src/pynxtools/dataconverter/readers/json_yml/reader.py

@@ -18,7 +18,8 @@
 """An example reader implementation for the DataConverter."""
 
 import os
-from typing import Any, Callable
+from collections.abc import Callable
+from typing import Any
 
 from pynxtools.dataconverter.readers.base.reader import BaseReader
 from pynxtools.dataconverter.template import Template