FAIRmat-NFDI · lukaspie · Jun 18, 2025 · Jun 18, 2025 · Jun 18, 2025 · Jun 18, 2025
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.9.3
+    rev: v0.12.0
     hooks:
       # Run the linter.
       - id: ruff

diff --git a/pyproject.toml b/pyproject.toml
@@ -54,7 +54,7 @@ docs = [
 ]
 dev = [
     "mypy",
-    "ruff>=0.9.3",
+    "ruff>=0.12.0",
     "pytest",
     "pytest-timeout",
     "pytest-cov",
@@ -135,24 +135,31 @@ select = [
     "E", # pycodestyle
     "W", # pycodestyle
     "PL", # pylint
+    "UP", # pyupgrade
+    # "F401", # remove unused import
+    "I001", # sort imports   
     # "NPY201", # reactivate when np>2.0 is used
 ]
 ignore = [
+    "E402", # Module level import not at top of file
     "E501", # Line too long ({width} > {limit} characters)
     "E701", # Multiple statements on one line (colon)
     "E731", # Do not assign a lambda expression, use a def
-    "E402",  # Module level import not at top of file
+    "PLC0415", # `import` should be at the top-level of a file
+    "PLR0904", # too-many-public-methods
     "PLR0911", # Too many return statements
     "PLR0912", # Too many branches
     "PLR0913", # Too many arguments in function definition
     "PLR0915", # Too many statements
-    "PLR2004", # Magic value used instead of constant
-    "PLW0603", # Using the global statement
-    "PLW2901", # redefined-loop-name
+    "PLR0917", # too-many-positional-arguments
     "PLR1714", # consider-using-in
+    "PLR2004", # Magic value used instead of constant
     "PLR5501", # else-if-used
+    "PLW0603", # Using the global statement
+    "PLW2901", # redefined-loop-name,
 ]
 fixable = ["ALL"]
+isort.split-on-trailing-comma = false
 
 [tool.ruff.format]
 quote-style = "double"

diff --git a/src/pynxtools/__init__.py b/src/pynxtools/__init__.py
@@ -16,11 +16,11 @@
 # limitations under the License.
 #
 
-from typing import Dict
 import logging
 import os
 import re
 from datetime import datetime
+from typing import Dict
 
 from pynxtools._build_wrapper import get_vcs_version
 from pynxtools.definitions.dev_tools.globals.nxdl import get_nxdl_version

diff --git a/src/pynxtools/dataconverter/convert.py b/src/pynxtools/dataconverter/convert.py
@@ -373,12 +373,10 @@ def convert_cli(
         except TypeError as exc:
             sys.tracebacklimit = 0
             raise click.UsageError(
-                (
-                    "Please make sure you have the following entries in your "
-                    "parameter file:\n\n# NeXusParser Parameter File - v0.0.1"
-                    "\n\ndataconverter:\n\treader: value\n\tnxdl: value\n\tin"
-                    "put-file: value"
-                )
+                "Please make sure you have the following entries in your "
+                "parameter file:\n\n# NeXusParser Parameter File - v0.0.1"
+                "\n\ndataconverter:\n\treader: value\n\tnxdl: value\n\tin"
+                "put-file: value"
             ) from exc
     if nxdl is None:
         raise click.UsageError("Missing option '--nxdl'")

diff --git a/src/pynxtools/dataconverter/file_hashing.py b/src/pynxtools/dataconverter/file_hashing.py
@@ -28,7 +28,7 @@ def get_file_hashvalue(file_name: str) -> str:
             # Read and update hash string value in blocks of 4K
             for byte_block in iter(lambda: file_handle.read(4096), b""):
                 sha256_hash.update(byte_block)
-    except IOError:
+    except OSError:
         print(f"File {file_name} is not accessible !")
 
     return sha256_hash.hexdigest()
diff --git a/src/pynxtools/dataconverter/hdfdict.py b/src/pynxtools/dataconverter/hdfdict.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Taken from: https://github.com/SiggiGue/hdfdict/blob/master/hdfdict/hdfdict.py"""
 
 from collections import UserDict
@@ -196,7 +195,7 @@ def dump(data, hdf, *args, packer=pack_dataset, **kwargs):
     def _recurse(datadict, hdfobject):
         for key, value in datadict.items():
             if isinstance(key, tuple):
-                key = "_".join((str(i) for i in key))
+                key = "_".join(str(i) for i in key)
             if isinstance(value, (dict, LazyHdfDict)):
                 hdfgroup = hdfobject.create_group(key)
                 _recurse(value, hdfgroup)

diff --git a/src/pynxtools/dataconverter/helpers.py b/src/pynxtools/dataconverter/helpers.py
@@ -24,7 +24,7 @@
 from datetime import datetime, timezone
 from enum import Enum, auto
 from functools import lru_cache
-from typing import Any, Callable, List, Optional, Tuple, Union, Sequence, cast
+from typing import Any, Callable, List, Optional, Sequence, Tuple, Union, cast
 
 import h5py
 import lxml.etree as ET

diff --git a/src/pynxtools/dataconverter/nexus_tree.py b/src/pynxtools/dataconverter/nexus_tree.py
@@ -29,25 +29,24 @@
 """
 
 from functools import lru_cache, reduce
-from typing import Any, List, Dict, Literal, Optional, Set, Tuple, Union
+from typing import Any, Dict, List, Literal, Optional, Set, Tuple, Union
 
 import lxml.etree as ET
 from anytree.node.nodemixin import NodeMixin
 
-from pynxtools import get_definitions_url
+from pynxtools import NX_DOC_BASES, get_definitions_url
 from pynxtools.dataconverter.helpers import (
+    NEXUS_TO_PYTHON_DATA_TYPES,
     get_all_parents_for,
     get_nxdl_root_and_path,
-    is_variadic,
     is_appdef,
+    is_variadic,
     remove_namespace_from_tag,
-    NEXUS_TO_PYTHON_DATA_TYPES,
 )
 from pynxtools.definitions.dev_tools.utils.nxdl_utils import (
     get_nx_namefit,
     is_name_type,
 )
-from pynxtools import NX_DOC_BASES
 
 NexusType = Literal[
     "NX_BINARY",

diff --git a/src/pynxtools/dataconverter/readers/example/reader.py b/src/pynxtools/dataconverter/readers/example/reader.py
@@ -45,11 +45,11 @@ def read(
         data: dict = {}
 
         if not file_paths:
-            raise IOError("No input files were given to Example Reader.")
+            raise OSError("No input files were given to Example Reader.")
 
         for file_path in file_paths:
             file_extension = file_path[file_path.rindex(".") :]
-            with open(file_path, "r", encoding="utf-8") as input_file:
+            with open(file_path, encoding="utf-8") as input_file:
                 if file_extension == ".json":
                     data = json.loads(input_file.read())
 

diff --git a/src/pynxtools/dataconverter/readers/json_map/reader.py b/src/pynxtools/dataconverter/readers/json_map/reader.py
@@ -22,8 +22,8 @@
 from typing import Any, Tuple
 
 import numpy as np
-import yaml
 import xarray
+import yaml
 from mergedeep import merge
 
 from pynxtools.dataconverter import hdfdict
@@ -186,7 +186,7 @@ def read(
         for file_path in file_paths:
             file_extension = file_path[file_path.rindex(".") :]
             if file_extension == ".json":
-                with open(file_path, "r", encoding="utf-8") as input_file:
+                with open(file_path, encoding="utf-8") as input_file:
                     if ".mapping" in file_path:
                         mapping = json.loads(input_file.read())
                     else:
@@ -195,7 +195,7 @@ def read(
                 with open(file_path, "rb") as input_file:  # type: ignore[assignment]
                     data = pickle.load(input_file)  # type: ignore[arg-type]
             elif file_extension == ".yaml":
-                with open(file_path, "r") as input_file:
+                with open(file_path) as input_file:
                     merge(data, yaml.safe_load(input_file))
             else:
                 is_hdf5 = False
@@ -216,7 +216,7 @@ def read(
                 template = Template(
                     {x: "/hierarchical/path/in/your/datafile" for x in template}
                 )
-                raise IOError(
+                raise OSError(
                     "Please supply a JSON mapping file: "
                     " my_nxdl_map.mapping.json\n\n You can use this "
                     "template for the required fields: \n" + str(template)

diff --git a/src/pynxtools/dataconverter/readers/json_yml/reader.py b/src/pynxtools/dataconverter/readers/json_yml/reader.py
@@ -17,8 +17,8 @@
 #
 """An example reader implementation for the DataConverter."""
 
-from typing import Tuple, Any, Callable, Dict, List
 import os
+from typing import Any, Callable, Dict, List, Tuple
 
 from pynxtools.dataconverter.readers.base.reader import BaseReader
 from pynxtools.dataconverter.template import Template

diff --git a/src/pynxtools/dataconverter/readers/utils.py b/src/pynxtools/dataconverter/readers/utils.py
@@ -297,7 +297,7 @@ def parse_json(file_path: Union[str, Path]) -> Dict[str, Any]:
     Returns:
         Dict[str, Any]: The dictionary containing the data readout from the json.
     """
-    with open(file_path, "r", encoding="utf-8") as file:
+    with open(file_path, encoding="utf-8") as file:
         return json.load(file)
 
 

diff --git a/src/pynxtools/dataconverter/validation.py b/src/pynxtools/dataconverter/validation.py
@@ -16,22 +16,22 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-import re
 import copy
+import re
 from collections import defaultdict
 from functools import reduce
 from operator import getitem
 from typing import (
     Any,
+    Dict,
     Iterable,
     List,
+    Literal,
     Mapping,
     MutableMapping,
     Optional,
     Tuple,
     Union,
-    Dict,
-    Literal,
 )
 
 import h5py

diff --git a/src/pynxtools/dataconverter/writer.py b/src/pynxtools/dataconverter/writer.py
@@ -300,7 +300,7 @@ def add_units_key(dataset, path):
             except InvalidDictProvided as exc:
                 print(str(exc))
             except Exception as exc:
-                raise IOError(
+                raise OSError(
                     f"Unknown error occured writing the path: {path} "
                     f"with the following message: {str(exc)}"
                 ) from exc
@@ -335,7 +335,7 @@ def add_units_key(dataset, path):
                     )
                     dataset.attrs[entry_name[1:]] = data
             except Exception as exc:
-                raise IOError(
+                raise OSError(
                     f"Unknown error occured writing the path: {path}"
                     f", while writing the value: {value} "
                     f"with the following message: {str(exc)}"

diff --git a/src/pynxtools/eln_mapper/eln.py b/src/pynxtools/eln_mapper/eln.py
@@ -17,10 +17,10 @@
 # limitations under the License.
 #
 
-import re
 import logging
+import re
 from abc import ABC, abstractmethod
-from typing import Any, List, Dict, Optional
+from typing import Any, Dict, List, Optional
 
 import yaml
 

diff --git a/src/pynxtools/eln_mapper/eln_mapper.py b/src/pynxtools/eln_mapper/eln_mapper.py
@@ -16,8 +16,8 @@
 # limitations under the License.
 #
 
-from typing import Union, Optional
 from pathlib import Path
+from typing import Optional, Union
 
 import click
 

diff --git a/src/pynxtools/eln_mapper/reader_eln.py b/src/pynxtools/eln_mapper/reader_eln.py
@@ -19,13 +19,9 @@
 #
 
 import re
-from typing import List, Dict
+from typing import Dict, List
 
-from pynxtools.dataconverter.nexus_tree import (
-    NexusEntity,
-    NexusGroup,
-    NexusNode,
-)
+from pynxtools.dataconverter.nexus_tree import NexusEntity, NexusGroup, NexusNode
 from pynxtools.eln_mapper.eln import ElnGenerator
 
 

diff --git a/src/pynxtools/eln_mapper/schema_eln.py b/src/pynxtools/eln_mapper/schema_eln.py
@@ -18,13 +18,9 @@
 #
 
 import re
-from typing import List, Dict, Union, Tuple
+from typing import Dict, List, Tuple, Union
 
-from pynxtools.dataconverter.nexus_tree import (
-    NexusEntity,
-    NexusGroup,
-    NexusNode,
-)
+from pynxtools.dataconverter.nexus_tree import NexusEntity, NexusGroup, NexusNode
 from pynxtools.eln_mapper.eln import ElnGenerator
 
 NEXUS_TO_NOMAD_QUANTITY: Dict[str, Tuple[str, str]] = {

diff --git a/src/pynxtools/nomad/dataconverter.py b/src/pynxtools/nomad/dataconverter.py
@@ -18,7 +18,9 @@
 from pynxtools.dataconverter import convert as pynxtools_converter
 from pynxtools.dataconverter import writer as pynxtools_writer
 from pynxtools.dataconverter.template import Template
-from pynxtools.definitions.dev_tools.utils.nxdl_utils import get_app_defs_names  # pylint: disable=import-error
+from pynxtools.definitions.dev_tools.utils.nxdl_utils import (
+    get_app_defs_names,  # pylint: disable=import-error
+)
 
 m_package = Package(name="nexus_data_converter")
 
@@ -176,7 +178,7 @@ class ElnYamlConverter(EntryData):
     )
 
     def normalize(self, archive, logger):
-        super(ElnYamlConverter, self).normalize(archive, logger)
+        super().normalize(archive, logger)
 
         eln_dict = create_eln_dict(archive)
         write_yaml(archive, archive.data.output, eln_dict)
@@ -231,7 +233,7 @@ class NexusDataConverter(EntryData):
     )
 
     def normalize(self, archive, logger):
-        super(NexusDataConverter, self).normalize(archive, logger)
+        super().normalize(archive, logger)
 
         raw_path = archive.m_context.raw_path()
         eln_dict = create_eln_dict(archive)

diff --git a/src/pynxtools/nomad/parser.py b/src/pynxtools/nomad/parser.py
@@ -43,8 +43,11 @@
 
 import pynxtools.nomad.schema as nexus_schema
 from pynxtools.nexus.nexus import HandleNexus
-from pynxtools.nomad.utils import FIELD_STATISTICS
-from pynxtools.nomad.utils import REPLACEMENT_FOR_NX, get_quantity_base_name
+from pynxtools.nomad.utils import (
+    FIELD_STATISTICS,
+    REPLACEMENT_FOR_NX,
+    get_quantity_base_name,
+)
 from pynxtools.nomad.utils import _rename_nx_for_nomad as rename_nx_for_nomad
 
 

diff --git a/src/pynxtools/nomad/schema.py b/src/pynxtools/nomad/schema.py
@@ -75,14 +75,14 @@
     from nomad.normalizing.common import nomad_atoms_from_ase_atoms
     from nomad.normalizing.topology import add_system, add_system_info
     from nomad.units import ureg
-    from nomad.utils import get_logger, strip, hash
+    from nomad.utils import get_logger, hash, strip
 
 except ImportError as exc:
     raise ImportError(
         "Could not import nomad package. Please install the package 'nomad-lab'."
     ) from exc
 
-from pynxtools import get_definitions_url, NX_DOC_BASES
+from pynxtools import NX_DOC_BASES, get_definitions_url
 from pynxtools.definitions.dev_tools.utils.nxdl_utils import get_nexus_definitions_path
 from pynxtools.nomad.utils import (
     FIELD_STATISTICS,