Run isort

src/nexgen/beamlines/ED_singla_nxs.py

@@ -14,7 +14,8 @@
 from ..nxs_write.NXmxWriter import EDNXmxFileWriter
 from ..nxs_write.write_utils import find_number_of_images
 from ..tools.ED_tools import extract_from_SINGLA_master, find_beam_centre
-from ..utils import coerce_to_path, find_in_dict, get_iso_timestamp, get_nexus_filename
+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/I19_2_gda_nxs.py

@@ -12,25 +12,16 @@
 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

@@ -13,15 +13,8 @@
 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

@@ -10,7 +10,8 @@
 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

@@ -8,7 +8,8 @@
 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

@@ -3,10 +3,11 @@
 """
 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

@@ -15,12 +15,8 @@
 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 log
 from . import version_parser
+from .. import log
 
 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

@@ -14,22 +14,17 @@
 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]:

src/nexgen/command_line/copy_nexus.py

@@ -9,9 +9,10 @@
 
 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

@@ -14,27 +14,18 @@
 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 . import (
-    add_tristan_spec,
-    config_parser,
-    demo_parser,
-    detectormode_parser,
-    nexus_parser,
-    phil2dict,
-    version_parser,
-)
-from .cli_utils import ScanReader, call_writers  # write_nexus_demo, write_nexus
+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
+                        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 log, templates
 from . import config_parser, nexus_parser, version_parser
+from .. import log, templates
 
 try:
     from importlib.resources import files

src/nexgen/nxs_copy/CopyTristanNexus.py

@@ -11,13 +11,9 @@
 
 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_utils/Axes.py

@@ -3,10 +3,11 @@
 """
 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

@@ -10,13 +10,8 @@
 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

@@ -4,7 +4,6 @@
 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 import dataclass
 from dataclasses_json import DataClassJsonMixin
 
 # Describe facility

src/nexgen/nxs_write/NXclassWriters.py

@@ -8,29 +8,19 @@
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, get_args
 
+import h5py  # isort: skip
 import numpy as np
 from numpy.typing import ArrayLike
 
 from ..nxs_utils import Axis
-from ..utils import (
-    MAX_SUFFIX_DIGITS,
-    get_iso_timestamp,
-    units_of_length,
-    units_of_time,
-    ureg,
-)
-from .write_utils import (
-    TSdset,
-    calculate_origin,
-    create_attributes,
-    set_dependency,
-    write_compressed_copy,
-)
+from ..utils import (MAX_SUFFIX_DIGITS, get_iso_timestamp, units_of_length,
+                     units_of_time, ureg)
+from .write_utils import (TSdset, calculate_origin, create_attributes,
+                          set_dependency, write_compressed_copy)
 
 # from hdf5plugin import Bitshuffle   # noqa: F401
 
 
-import h5py  # isort: skip
 
 
 NXclass_logger = logging.getLogger("nexgen.NXclass_writers")

src/nexgen/nxs_write/NXmxWriter.py

@@ -16,30 +16,15 @@
 from ..nxs_utils.Detector import Detector
 from ..nxs_utils.Goniometer import Goniometer
 from ..nxs_utils.Source import Attenuator, Beam, Source
-from ..tools.VDS_tools import (
-    clean_unused_links,
-    image_vds_writer,
-    jungfrau_vds_writer,
-    vds_file_writer,
-)
-from ..utils import (
-    MAX_FRAMES_PER_DATASET,
-    MAX_SUFFIX_DIGITS,
-    coord2mcstas,
-    get_filename_template,
-)
-from .NXclassWriters import (
-    write_NXcoordinate_system_set,
-    write_NXdata,
-    write_NXdatetime,
-    write_NXdetector,
-    write_NXdetector_module,
-    write_NXentry,
-    write_NXinstrument,
-    write_NXnote,
-    write_NXsample,
-    write_NXsource,
-)
+from ..tools.VDS_tools import (clean_unused_links, image_vds_writer,
+                               jungfrau_vds_writer, vds_file_writer)
+from ..utils import (MAX_FRAMES_PER_DATASET, MAX_SUFFIX_DIGITS, coord2mcstas,
+                     get_filename_template)
+from .NXclassWriters import (write_NXcoordinate_system_set, write_NXdata,
+                             write_NXdatetime, write_NXdetector,
+                             write_NXdetector_module, write_NXentry,
+                             write_NXinstrument, write_NXnote, write_NXsample,
+                             write_NXsource)
 from .write_utils import TSdset, calculate_estimated_end_time
 
 # Logger