update ruff (#657)

Author: lukaspie

.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

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"

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

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'")

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()

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)

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

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",

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())
 

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)