update ruff version and format files.

Author: RubelMozumder

dev-requirements.txt

@@ -181,7 +181,7 @@ regex==2024.11.6
     # via mkdocs-material
 requests==2.32.3
     # via mkdocs-material
-ruff==0.8.2
+ruff==0.9.2
     # via pynxtools (pyproject.toml)
 scipy==1.14.1
     # via ase

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

@@ -106,22 +106,16 @@ def read(
 
         # virtual datasets slicing
         my_path = str(f"{os.path.dirname(__file__)}/../../../data/")
-        template[("/ENTRY[entry]" "/test_virtual" "_dataset/sliced" "_dataset")] = {
-            "link": (
-                f"{my_path}/xarray_saved_small_" "calibration.h5:/binned/BinnedData"
-            ),
+        template[("/ENTRY[entry]/test_virtual_dataset/sliced_dataset")] = {
+            "link": (f"{my_path}/xarray_saved_small_calibration.h5:/binned/BinnedData"),
             "shape": np.index_exp[:, 1, :, :],
         }
-        template[("/ENTRY[entry]" "/test_virtual" "_dataset/slic" "ed_dataset2")] = {
-            "link": (
-                f"{my_path}/xarray_saved_small" "_calibration.h5:/binned/BinnedData"
-            ),
+        template[("/ENTRY[entry]/test_virtual_dataset/sliced_dataset2")] = {
+            "link": (f"{my_path}/xarray_saved_small_calibration.h5:/binned/BinnedData"),
             "shape": np.index_exp[:, :, :, 1],
         }
-        template[("/ENTRY[entry]" "/test_virtual" "_dataset/slic" "ed_dataset3")] = {
-            "link": (
-                f"{my_path}/xarray_saved_small" "_calibration.h5:/binned/BinnedData"
-            ),
+        template[("/ENTRY[entry]/test_virtual_dataset/sliced_dataset3")] = {
+            "link": (f"{my_path}/xarray_saved_small_calibration.h5:/binned/BinnedData"),
             "shape": np.index_exp[:, :, :, 2:4],
         }
 

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

@@ -56,7 +56,7 @@ def get_val_nested_keystring_from_dict(keystring, data):
         return data[current_key].values
     if isinstance(data[current_key], xarray.core.dataset.Dataset):
         raise NotImplementedError(
-            "Xarray datasets are not supported. " "You can only use xarray dataarrays."
+            "Xarray datasets are not supported. You can only use xarray dataarrays."
         )
 
     return data[current_key]

src/pynxtools/dataconverter/writer.py

@@ -21,11 +21,11 @@
 
 import copy
 import logging
-import sys
 import xml.etree.ElementTree as ET
 
 import h5py
 import numpy as np
+import pint
 
 from pynxtools.dataconverter import helpers
 from pynxtools.dataconverter.exceptions import InvalidDictProvided
@@ -183,6 +183,9 @@ def handle_dicts_entries(data, grp, entry_name, output_path, path):
         return None
 
 
+xx = []
+
+
 class Writer:
     """The writer class for writing a NeXus file in accordance with a given NXDL.
 
@@ -259,8 +262,11 @@ def _put_data_into_hdf5(self):
 
         def add_units_key(dataset, path):
             units_key = f"{path}/@units"
-            if units_key in self.data.keys() and self.data[units_key] is not None:
-                dataset.attrs["units"] = self.data[units_key]
+            units = self.data.get(units_key, None)
+            units = str(units) if isinstance(units, pint.Unit) else units
+            if units:
+                dataset.attrs["units"] = units
+                xx.append(units)
 
         for path, value in self.data.items():
             try:

src/pynxtools/nexus/nexus.py

@@ -439,7 +439,7 @@ def process_node(hdf_node, hdf_path, parser, logger, doc=True):
             if len(hdf_node.shape) <= 1
             else str(decode_if_string(hdf_node[0])).split("\n")
         )
-        logger.debug(f'value: {val[0]} {"..." if len(val) > 1 else ""}')
+        logger.debug(f"value: {val[0]} {'...' if len(val) > 1 else ''}")
     else:
         logger.debug(
             f"===== GROUP (/{hdf_path} "
@@ -460,7 +460,7 @@ def process_node(hdf_node, hdf_path, parser, logger, doc=True):
     for key, value in hdf_node.attrs.items():
         logger.debug(f"===== ATTRS (/{hdf_path}@{key})")
         val = str(decode_if_string(value)).split("\n")
-        logger.debug(f'value: {val[0]} {"..." if len(val) > 1 else ""}')
+        logger.debug(f"value: {val[0]} {'...' if len(val) > 1 else ''}")
         (req_str, nxdef, nxdl_path) = get_nxdl_doc(hdf_info, logger, doc, attr=key)
         if (
             parser is not None

src/pynxtools/testing/nexus_conversion.py

@@ -103,9 +103,9 @@ def convert_to_nexus(
         """
         Test the example data for the reader plugin.
         """
-        assert hasattr(
-            self.reader, "supported_nxdls"
-        ), f"Reader{self.reader} must have supported_nxdls attribute"
+        assert hasattr(self.reader, "supported_nxdls"), (
+            f"Reader{self.reader} must have supported_nxdls attribute"
+        )
         assert callable(self.reader.read), f"Reader{self.reader} must have read method"
 
         if isinstance(self.files_or_dir, (list, tuple)):

src/pynxtools/testing/nomad_example.py

@@ -124,6 +124,6 @@ def example_upload_entry_point_valid(
                     os.path.abspath(os.path.join(dirpath, filename))
                 )
 
-        assert (
-            sorted(real_upload_files) == sorted(expected_upload_files)
-        ), f"Uploaded files {real_upload_files} do not match the expected files: {expected_upload_files}"
+        assert sorted(real_upload_files) == sorted(expected_upload_files), (
+            f"Uploaded files {real_upload_files} do not match the expected files: {expected_upload_files}"
+        )

tests/dataconverter/test_helpers.py

@@ -172,13 +172,13 @@ def fixture_filled_test_data(template, tmp_path):
     template["/ENTRY[my_entry]/program_name"] = "Testing program"
     template["/ENTRY[my_entry]/NXODD_name[nxodd_name]/type"] = "2nd type"
     template["/ENTRY[my_entry]/NXODD_name[nxodd_name]/date_value"] = (
-        "2022-01-22T12" ":14:12.05018+00:00"
+        "2022-01-22T12:14:12.05018+00:00"
     )
     template["/ENTRY[my_entry]/required_group/description"] = "An example description"
     template["/ENTRY[my_entry]/required_group2/description"] = "An example description"
     template["/ENTRY[my_entry]/does/not/exist"] = "random"
     template["/ENTRY[my_entry]/links/ext_link"] = {
-        "link": f"{tmp_path}/" f"xarray_saved_small_cali" f"bration.h5:/axes/ax3"
+        "link": f"{tmp_path}/xarray_saved_small_calibration.h5:/axes/ax3"
     }
     return template
 

tests/nexus/test_nexus.py

@@ -124,12 +124,12 @@ def test_decode_if_string(string_obj, decode, expected):
 
     # Handle np.ndarray outputs
     if isinstance(expected, np.ndarray):
-        assert isinstance(
-            result, np.ndarray
-        ), f"Expected ndarray, but got {type(result)}"
-        assert (
-            result == expected
-        ).all(), f"Failed for {string_obj} with decode={decode}"
+        assert isinstance(result, np.ndarray), (
+            f"Expected ndarray, but got {type(result)}"
+        )
+        assert (result == expected).all(), (
+            f"Failed for {string_obj} with decode={decode}"
+        )
     # Handle list outputs
     elif isinstance(expected, list):
         assert isinstance(result, list), f"Expected list, but got {type(result)}"