Run ruff

docs/conf.py

@@ -20,8 +20,6 @@
 import os
 import sys
 
-import sphinx_rtd_theme  # noqa; F401 - install theme
-
 import nexgen
 
 sys.path.insert(0, os.path.abspath(".."))

src/nexgen/beamlines/ED_singla_nxs.py

@@ -13,11 +13,13 @@
 from ..nxs_utils.ScanUtils import calculate_scan_points
 from ..nxs_write.NXmxWriter import EDNXmxFileWriter
 from ..nxs_write.write_utils import find_number_of_images
-from ..tools.ED_tools import (extract_detector_info_from_master,
-                              extract_exposure_time_from_master,
-                              extract_start_time_from_master, find_beam_centre)
-from ..utils import (coerce_to_path, find_in_dict, get_iso_timestamp,
-                     get_nexus_filename)
+from ..tools.ED_tools import (
+    extract_detector_info_from_master,
+    extract_exposure_time_from_master,
+    extract_start_time_from_master,
+    find_beam_centre,
+)
+from ..utils import coerce_to_path, find_in_dict, get_iso_timestamp, get_nexus_filename
 from .ED_params import ED_coord_system, EDSingla, EDSource
 
 logger = logging.getLogger("nexgen.EDNeXusWriter")

src/nexgen/beamlines/GDAtools/GDAjson2params.py

@@ -38,7 +38,7 @@ def get_goniometer_axes_from_file(self) -> List[Axis]:
         """Read the axes information from the GDA-supplied json file."""
         axes_list = []
         for v in self.params.values():
-            if type(v) is dict and v["location"] == "sample":
+            if isinstance(v, dict) and v["location"] == "sample":
                 ax_depends = self._find_axis_depends_on(v["depends_on"])
                 ax_type = (
                     TransformationType.ROTATION
@@ -54,7 +54,7 @@ def get_detector_axes_from_file(self) -> List[Axis]:
         """Read the detector axes information from the GDA-supplied json file."""
         axes_list = []
         for v in self.params.values():
-            if type(v) is dict and v["location"] == "detector":
+            if isinstance(v, dict) and v["location"] == "detector":
                 ax_type = (
                     TransformationType.ROTATION
                     if v["type"] == "rotation"

src/nexgen/beamlines/I19_2_gda_nxs.py

@@ -12,16 +12,25 @@
 from numpy.typing import DTypeLike
 
 from .. import log
-from ..nxs_utils import (Attenuator, Beam, Detector, EigerDetector, Goniometer,
-                         Source, TristanDetector)
+from ..nxs_utils import (
+    Attenuator,
+    Beam,
+    Detector,
+    EigerDetector,
+    Goniometer,
+    Source,
+    TristanDetector,
+)
 from ..nxs_utils.Detector import DetectorType, UnknownDetectorTypeError
 from ..nxs_utils.ScanUtils import calculate_scan_points
 from ..nxs_write.NXmxWriter import EventNXmxFileWriter, NXmxFileWriter
 from ..utils import get_iso_timestamp, get_nexus_filename
 from .beamline_utils import BeamlineAxes, collection_summary_log
-from .GDAtools.ExtendedRequest import (ExtendedRequestIO,
-                                       read_det_position_from_xml,
-                                       read_scan_from_xml)
+from .GDAtools.ExtendedRequest import (
+    ExtendedRequestIO,
+    read_det_position_from_xml,
+    read_scan_from_xml,
+)
 from .GDAtools.GDAjson2params import JSONParamsIO
 
 # Define a logger object and a formatter

src/nexgen/beamlines/I19_2_nxs.py

@@ -13,8 +13,15 @@
 import numpy as np
 
 from .. import log
-from ..nxs_utils import (Attenuator, Beam, Detector, EigerDetector, Goniometer,
-                         Source, TristanDetector)
+from ..nxs_utils import (
+    Attenuator,
+    Beam,
+    Detector,
+    EigerDetector,
+    Goniometer,
+    Source,
+    TristanDetector,
+)
 from ..nxs_utils.ScanUtils import calculate_scan_points, identify_osc_axis
 from ..nxs_write.NXmxWriter import EventNXmxFileWriter, NXmxFileWriter
 from ..tools.Metafile import DectrisMetafile

src/nexgen/beamlines/SSX_Eiger_nxs.py

@@ -10,8 +10,7 @@
 import h5py
 
 from .. import log
-from ..nxs_utils import (Attenuator, Beam, Detector, EigerDetector, Goniometer,
-                         Source)
+from ..nxs_utils import Attenuator, Beam, Detector, EigerDetector, Goniometer, Source
 from ..nxs_write.NXmxWriter import NXmxFileWriter
 from ..tools.Metafile import DectrisMetafile
 from ..tools.MetaReader import define_vds_data_type, update_axes_from_meta

src/nexgen/beamlines/SSX_Tristan_nxs.py

@@ -8,8 +8,7 @@
 from pathlib import Path
 
 from .. import log
-from ..nxs_utils import (Attenuator, Beam, Detector, Goniometer, Source,
-                         TristanDetector)
+from ..nxs_utils import Attenuator, Beam, Detector, Goniometer, Source, TristanDetector
 from ..nxs_write.NXmxWriter import EventNXmxFileWriter
 from ..utils import Point3D, find_in_dict, get_iso_timestamp
 from .beamline_utils import collection_summary_log

src/nexgen/beamlines/SSX_chip.py

@@ -3,11 +3,10 @@
 """
 from __future__ import annotations
 
+from dataclasses import dataclass, field
 from pathlib import Path
 from typing import Any, Dict, List, Tuple
 
-from dataclasses import dataclass, field
-
 from ..nxs_utils.ScanUtils import ScanDirection
 
 # I24 chip tools

src/nexgen/beamlines/SSX_expt.py

@@ -15,8 +15,12 @@
 from ..nxs_utils import Axis, TransformationType
 from ..nxs_utils.ScanUtils import calculate_scan_points
 from .beamline_utils import PumpProbe
-from .SSX_chip import (Chip, compute_goniometer, fullchip_blocks_conversion,
-                       read_chip_map)
+from .SSX_chip import (
+    Chip,
+    compute_goniometer,
+    fullchip_blocks_conversion,
+    read_chip_map,
+)
 
 __all__ = ["run_extruder", "run_fixed_target", "run_3D_grid_scan"]
 

src/nexgen/beamlines/beamline_utils.py

@@ -4,12 +4,12 @@
 from __future__ import annotations
 
 import logging
+from dataclasses import dataclass
 from typing import List, Optional, Tuple
 
-from dataclasses import dataclass
 from dataclasses_json import DataClassJsonMixin
-from nexgen.nxs_utils import (Attenuator, Axis, Beam, Detector, Goniometer,
-                              Source)
+
+from nexgen.nxs_utils import Attenuator, Axis, Beam, Detector, Goniometer, Source
 from nexgen.utils import Point3D
 
 

src/nexgen/command_line/ED_nexus.py

@@ -11,11 +11,11 @@
 
 import freephil
 
-from . import config_parser, nexus_parser, version_parser
 from .. import log
 from ..beamlines.ED_params import ED_coord_system
 from ..beamlines.ED_singla_nxs import singla_nexus_writer
 from ..nxs_utils import Axis, TransformationType
+from . import config_parser, nexus_parser, version_parser
 
 logger = logging.getLogger("nexgen.EDNeXusGeneratorCLI")
 

src/nexgen/command_line/I19_2_cli.py

@@ -8,8 +8,8 @@
 from collections import namedtuple
 from datetime import datetime
 
-from . import version_parser
 from .. import log
+from . import version_parser
 
 logger = logging.getLogger("nexgen.I19-2_NeXus_cli")
 

src/nexgen/command_line/SSX_cli.py

@@ -7,10 +7,10 @@
 from pathlib import Path
 from typing import Tuple
 
-from . import version_parser
 from .. import log
 from ..beamlines.SSX_chip import CHIP_DICT_DEFAULT
 from ..utils import P
+from . import version_parser
 
 logger = logging.getLogger("nexgen.SSX_cli")
 

src/nexgen/command_line/cli_utils.py

@@ -14,17 +14,22 @@
 from scanspec.core import Path as ScanPath
 from scanspec.specs import Line
 
-from ..nxs_write.NXclassWriters import (write_NXdata, write_NXdatetime,
-                                        write_NXdetector,
-                                        write_NXdetector_module, write_NXentry,
-                                        write_NXinstrument, write_NXnote,
-                                        write_NXsample, write_NXsource)
+from ..nxs_write.NXclassWriters import (
+    write_NXdata,
+    write_NXdatetime,
+    write_NXdetector,
+    write_NXdetector_module,
+    write_NXentry,
+    write_NXinstrument,
+    write_NXnote,
+    write_NXsample,
+    write_NXsource,
+)
 from ..nxs_write.write_utils import find_number_of_images
 from ..tools.DataWriter import generate_event_files, generate_image_files
 from ..tools.MetaReader import overwrite_beam, overwrite_detector
 from ..tools.VDS_tools import image_vds_writer, vds_file_writer
-from ..utils import (coord2mcstas, get_filename_template, imgcif2mcstas,
-                     units_of_time)
+from ..utils import coord2mcstas, get_filename_template, imgcif2mcstas, units_of_time
 
 
 def split_arrays(axes_names: List, array: List) -> Dict[str, Tuple]:
@@ -280,9 +285,9 @@ def calculate_scan_range(
         Dict[str, ArrayLike]: A dictionary of ("axis_name": axis_range) key-value pairs.
     """
     if (
-        type(axes_names) is not list
-        or type(axes_starts) is not list
-        or type(axes_ends) is not list
+        not isinstance(axes_names, list)
+        or not isinstance(axes_starts, list)
+        or not isinstance(axes_ends, list)
     ):
         raise TypeError("Input values for axes must be passed as lists.")
 
@@ -411,7 +416,7 @@ def ScanReader(
         transl_start = [goniometer["starts"][i] for i in transl_idx]
         transl_end = [goniometer["ends"][i] for i in transl_idx]
         transl_increment = [goniometer["increments"][i] for i in transl_idx]
-        if n_images and type(n_images) is int:
+        if n_images and isinstance(n_images, int):
             TRANSL = calculate_scan_range(
                 transl_axes,
                 transl_start,
@@ -545,7 +550,7 @@ def call_writers(
         datafiles = [Path(f).expanduser().resolve() for f in datafiles]
 
     if metafile:
-        if type(metafile) is str:
+        if isinstance(metafile, str):
             metafile = Path(metafile).expanduser().resolve()
 
     # NXdata: entry/data

src/nexgen/command_line/copy_nexus.py

@@ -9,10 +9,9 @@
 
 import freephil
 
-from . import (config_parser, full_copy_parser, tristan_copy_parser,
-               version_parser)
 from .. import log
 from ..nxs_copy import CopyNexus, CopyTristanNexus
+from . import config_parser, full_copy_parser, tristan_copy_parser, version_parser
 
 # Define a logger object and a formatter
 logger = logging.getLogger("nexgen.CopyNeXus")

src/nexgen/command_line/nexus_generator.py

@@ -14,18 +14,30 @@
 import h5py
 import numpy as np
 
-from . import (add_tristan_spec, config_parser, demo_parser,
-               detectormode_parser, nexus_parser, phil2dict, version_parser)
 from .. import log
-from ..nxs_write.NXclassWriters import (write_NXdatetime, write_NXentry,
-                                        write_NXnote)
+from ..nxs_write.NXclassWriters import write_NXdatetime, write_NXentry, write_NXnote
 from ..tools.DataWriter import generate_event_files, generate_image_files
 from ..tools.MetaReader import overwrite_beam, overwrite_detector
 from ..tools.VDS_tools import image_vds_writer, vds_file_writer
-from ..utils import (get_filename_template, get_iso_timestamp,
-                     get_nexus_filename, units_of_time)
-from .cli_utils import ScanReader  # write_nexus_demo, write_nexus
-from .cli_utils import call_writers
+from ..utils import (
+    get_filename_template,
+    get_iso_timestamp,
+    get_nexus_filename,
+    units_of_time,
+)
+from . import (
+    add_tristan_spec,
+    config_parser,
+    demo_parser,
+    detectormode_parser,
+    nexus_parser,
+    phil2dict,
+    version_parser,
+)
+from .cli_utils import (
+    ScanReader,  # write_nexus_demo, write_nexus
+    call_writers,
+)
 
 # Define a logger object
 logger = logging.getLogger("nexgen.NeXusGenerator")

src/nexgen/command_line/phil_files_cli.py

@@ -11,8 +11,8 @@
 
 import freephil
 
-from . import config_parser, nexus_parser, version_parser
 from .. import log, templates
+from . import config_parser, nexus_parser, version_parser
 
 try:
     from importlib.resources import files

src/nexgen/nxs_copy/CopyTristanNexus.py

@@ -11,9 +11,13 @@
 
 from ..nxs_write.NXclassWriters import write_NXnote
 from ..nxs_write.write_utils import create_attributes
-from .copy_utils import (check_and_fix_det_axis, compute_ssx_axes,
-                         convert_scan_axis, get_nexus_tree,
-                         identify_tristan_scan_axis)
+from .copy_utils import (
+    check_and_fix_det_axis,
+    compute_ssx_axes,
+    convert_scan_axis,
+    get_nexus_tree,
+    identify_tristan_scan_axis,
+)
 
 tristan_logger = logging.getLogger("nexgen.CopyTristanNeXus")
 

src/nexgen/nxs_copy/copy_utils.py

@@ -141,7 +141,7 @@ def convert_scan_axis(nxsample: h5py.Group, nxdata: h5py.Group, ax: str):
 def check_and_fix_det_axis(nxs_in: h5py.File):
     det_z_grp = nxs_in["/entry/instrument/detector/transformations/detector_z"]
     det_z = det_z_grp["det_z"]
-    if type(det_z[()]) is bytes or type(det_z[()]) is str:
+    if isinstance(det_z[()], bytes) or isinstance(det_z[()], str):
         det_z_attrs = {}
         for k, v in det_z.attrs.items():
             det_z_attrs[k] = v

src/nexgen/nxs_utils/Axes.py

@@ -3,11 +3,10 @@
 """
 from __future__ import annotations
 
+from dataclasses import dataclass
 from enum import Enum
 from typing import Tuple
 
-from dataclasses import dataclass
-
 from ..utils import Point3D
 
 

src/nexgen/nxs_utils/Detector.py

@@ -3,9 +3,9 @@
 """
 from __future__ import annotations
 
+from dataclasses import dataclass, field
 from typing import Dict, List, Literal, Tuple, Union
 
-from dataclasses import dataclass, field
 from dataclasses_json import DataClassJsonMixin
 
 from ..utils import Point3D

src/nexgen/nxs_utils/Goniometer.py

@@ -10,8 +10,13 @@
 from numpy.typing import ArrayLike
 
 from .Axes import Axis
-from .ScanUtils import (GridScanOptions, ScanDirection, calculate_scan_points,
-                        identify_grid_scan_axes, identify_osc_axis)
+from .ScanUtils import (
+    GridScanOptions,
+    ScanDirection,
+    calculate_scan_points,
+    identify_grid_scan_axes,
+    identify_osc_axis,
+)
 
 
 class Goniometer:

src/nexgen/nxs_utils/Sample.py

@@ -4,6 +4,7 @@
 from __future__ import annotations
 
 from dataclasses import dataclass
+
 from dataclasses_json import DataClassJsonMixin
 
 

src/nexgen/nxs_utils/Source.py

@@ -4,8 +4,8 @@
 from __future__ import annotations
 
 from collections import namedtuple
-
 from dataclasses import dataclass
+
 from dataclasses_json import DataClassJsonMixin
 
 # Describe facility