Update pre commit

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: check-json
@@ -19,16 +19,19 @@ repos:
       - id: check-merge-conflict
       - id: end-of-file-fixer
       - id: sort-simple-yaml
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.275
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.4
     hooks:
       - id: ruff
         args: [--no-cache, --fix, --exit-non-zero-on-fix]
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
+        exclude: |
+          notebooks/
+          tests/examples/
+      - id: ruff-format
+        exclude: |
+            notebooks/
+            tests/examples/
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.8.1
     hooks:
     - id: nbstripout

docs/conf.py

@@ -215,6 +215,7 @@ class ExecDirective(Directive):
     Credit goes to:
     https://stackoverflow.com/questions/27875455/displaying-dictionary-data-in-sphinx-documentation/29789910#29789910
     """
+
     has_content = True
 
     def run(self):

docs/drtsans/example_1d.py

@@ -8,9 +8,9 @@
 # files
 config["mask"] = "/SNS/EQSANS/shared/NeXusFiles/EQSANS/2017B_mp/beamstop60_mask_4m.nxs"
 config["flux"] = "/SNS/EQSANS/shared/instrument_configuration/bl6_flux_at_sample"
-config[
-    "sensitivity_file_path"
-] = "/SNS/EQSANS/shared/NeXusFiles/EQSANS/2017A_mp/Sensitivity_patched_thinPMMA_4m_79165_event.nxs"
+config["sensitivity_file_path"] = (
+    "/SNS/EQSANS/shared/NeXusFiles/EQSANS/2017A_mp/Sensitivity_patched_thinPMMA_4m_79165_event.nxs"
+)
 config["dark_current"] = "/SNS/EQSANS/shared/NeXusFiles/EQSANS/2017B_mp/EQSANS_86275.nxs.h5"
 
 # numeric values

pyproject.toml

@@ -86,6 +86,9 @@ line-length = 119
 [tool.ruff]
 cache-dir = "/tmp/ruff_cache"
 line-length = 119
+extend-exclude = ["notebooks", "tests/examples"]
+
+[tool.ruff.lint]
 # https://beta.ruff.rs/docs/rules/
 # suggestions: BLE blind exceptions, I sorts imports
 # Full pylint PL = PLC, PLE, PLR (~500 issues), PLW. Enable most

scripts/common_utils.py

@@ -1,4 +1,5 @@
-""" Common utility functions for all SANS """
+"""Common utility functions for all SANS"""
+
 import os
 import numpy as np
 import matplotlib.pyplot as plt

scripts/examples/plot_wavelength.py

@@ -1,6 +1,7 @@
 """
 Example script to plot the before and after k-correction data for a given slice and frame.
 """
+
 import glob
 import os
 from pathlib import Path

scripts/generate_report

@@ -3,6 +3,7 @@
 """
 Script to generate a report from an hdf5 log file
 """
+
 import sys
 import os
 import numpy as np

scripts/jupyter_notebooks/gpsans_spice_pixel_map_template.py

@@ -98,7 +98,7 @@ def show_calibration_stage1(raw_flood_ws_name, database_file):
     # Plot flood workspace raw and calibrated
     print("#####\n\nCompare applying the calibration to flood (stage 1)")
 
-    calibrated_flood_ws_name = f'demo_calibrated1_flood_{raw_flood_ws_name.split("flood_")[1]}'
+    calibrated_flood_ws_name = f"demo_calibrated1_flood_{raw_flood_ws_name.split('flood_')[1]}"
     apply_calibrations(
         raw_flood_ws_name,
         output_workspace=calibrated_flood_ws_name,

scripts/jupyter_notebooks/gpsans_spice_prepare_sensitivities_template.py

@@ -1,13 +1,14 @@
 """
-    SANS sensitivities preparation script
+SANS sensitivities preparation script
 
-    # goal
-    1. implement a universal mask_beam_center(flood_ws, beam_center_mask=None, beam_center_ws=None)
-       for 3 types of mask
-    2. add option for wing/main detector for BIOSANS:w
+# goal
+1. implement a universal mask_beam_center(flood_ws, beam_center_mask=None, beam_center_ws=None)
+   for 3 types of mask
+2. add option for wing/main detector for BIOSANS:w
 
 
 """
+
 import os
 import warnings
 from drtsans.mono.gpsans.prepare_sensitivities_correction import SpiceRun

scripts/prepare_sensitivities_biosans.py

@@ -1,6 +1,7 @@
 """
-    Sensitivities preparation script for Bio-SANS (CG3)
+Sensitivities preparation script for Bio-SANS (CG3)
 """
+
 from drtsans.mono.biosans.prepare_sensitivities_correction import PrepareSensitivityCorrection
 
 import os

scripts/prepare_sensitivities_gpsans.py

@@ -1,6 +1,7 @@
 """
-    Sensitivities preparation script for GP-SANS (CG2)
+Sensitivities preparation script for GP-SANS (CG2)
 """
+
 from drtsans.prepare_sensivities_correction import PrepareSensitivityCorrection
 
 

scripts/test_help/biosans_synthetic_sensitivity_dataset.py

@@ -9,6 +9,7 @@
 the Midrange Detector. See Fixture ``biosans_synthetic_sensitivity_dataset`` for detailed use
 
 """
+
 # local imports
 from drtsans.load import __monitor_counts
 from drtsans.mono.biosans.simulated_intensities import clone_component_intensities, insert_midrange_detector

src/drtsans/absolute_units.py

@@ -1,8 +1,9 @@
-r""" Links to Mantid algorithms
+r"""Links to Mantid algorithms
 DeleteWorkspace <https://docs.mantidproject.org/nightly/algorithms/DeleteWorkspace-v1.html>
 Divide          <https://docs.mantidproject.org/nightly/algorithms/Divide-v1.html>
 Multiply        <https://docs.mantidproject.org/nightly/algorithms/Multiply-v1.html>
 """
+
 from mantid.simpleapi import DeleteWorkspace, Divide, Multiply, mtd
 from mantid.dataobjects import WorkspaceSingleValue
 

src/drtsans/auto_wedge.py

@@ -244,9 +244,9 @@ def _export_to_h5(iq2d, rings, azimuthal_delta, peak_fit_dict, output_dir):
             function_data_set[0] = peak_fit_dict[index]["fit_function"]
 
     # add peak fitting result
-    for param_name in func_param_dict:
+    for param_name, param_value in func_param_dict.items():
         # form data set
-        data_set = np.array(func_param_dict[param_name])
+        data_set = np.array(param_value)
         fit_group.create_dataset(param_name, data=data_set)
 
     # close
@@ -501,8 +501,7 @@ def _estimatePeakParameters(intensity, azimuthal, azimuthal_start, window_half_w
             break
     # output
     print(
-        f"[WEDGE FIT] azimuthal: {azimuthal_new}, {azimuthal_last} with "
-        f"left and right as {left_index}, {right_index}"
+        f"[WEDGE FIT] azimuthal: {azimuthal_new}, {azimuthal_last} with left and right as {left_index}, {right_index}"
     )
 
     # now use the first two moments of the data within the window to give an improved center position (first moment)
@@ -837,7 +836,7 @@ def _fitQAndAzimuthal(
                 fit_result_dict[index]["error"] = error_reason
                 continue
             else:
-                fitted_peaks_message += f"spectrum {index-1}: Fitted peaks: {newlyFittedPeaks}\n"
+                fitted_peaks_message += f"spectrum {index - 1}: Fitted peaks: {newlyFittedPeaks}\n"
             for i in range(len(peakResults)):
                 peakResults[i].append(newlyFittedPeaks[i])
             q_centers_used.append(q_center)

src/drtsans/dataobjects.py

@@ -619,10 +619,10 @@ def __new__(cls, intensity, error, qx, qy, delta_qx=None, delta_qy=None, wavelen
 
             # Sanity check
             assert qx.shape == intensity.shape, (
-                f"qx and intensity must have same shapes.  " f"It is not now: {qx.shape} vs {intensity.shape}"
+                f"qx and intensity must have same shapes.  It is not now: {qx.shape} vs {intensity.shape}"
             )
             assert qy.shape == intensity.shape, (
-                f"qy and intensity must have same shapes.  " f"It is not now: {qy.shape} vs {intensity.shape}"
+                f"qy and intensity must have same shapes.  It is not now: {qy.shape} vs {intensity.shape}"
             )
 
         # pass everything to namedtuple

src/drtsans/detector.py

@@ -228,7 +228,7 @@ def _detector_first_ws_index(self, first_det_id):
                 self.first_index = ws_index
                 break
         else:
-            raise ValueError("Iterared WS and did not find first det id = " "{}".format(first_det_id))
+            raise ValueError("Iterared WS and did not find first det id = {}".format(first_det_id))
 
     def masked_ws_indices(self):
         """
@@ -256,7 +256,7 @@ def monitor_indices(self):
         return np.array([])
 
     def __str__(self):
-        return "Component: {} with {} pixels (dim x={}, dim y={})." " First index = {}.".format(
+        return "Component: {} with {} pixels (dim x={}, dim y={}). First index = {}.".format(
             self._component_name,
             self.dims,
             self.dim_x,

src/drtsans/determine_bins.py

@@ -31,7 +31,7 @@ def determine_1d_linear_bins(x_min, x_max, bins):
     # Check input x min and x max
     if x_min is None or x_max is None or x_min >= x_max:
         raise RuntimeError(
-            "x min {} and x max {} must not be None and x min shall be less than x max" "".format(x_min, x_max)
+            "x min {} and x max {} must not be None and x min shall be less than x max".format(x_min, x_max)
         )
     # force the number of bins to be an integer and error check it
     bins = int(bins)
@@ -104,9 +104,7 @@ def determine_1d_log_bins(x_min, x_max, decade_on_center, n_bins_per_decade=None
 
         # case that is not supported
         if decade_on_center:
-            assert n_bins_per_decade is not None, (
-                "For option decade_on_center, number of bins per decade " "is required"
-            )
+            assert n_bins_per_decade is not None, "For option decade_on_center, number of bins per decade is required"
         x_ref = x_min
 
         # calculate bin step size

src/drtsans/files/hdf5_rw.py

@@ -79,7 +79,7 @@ def match(self, other_node):
         # compare class type
         if not isinstance(other_node, type(self)):
             raise TypeError(
-                "Try to match instance of class {} (other) to {} (self)" "".format(type(other_node), type(self))
+                "Try to match instance of class {} (other) to {} (self)".format(type(other_node), type(self))
             )
 
         # compare name
@@ -89,16 +89,14 @@ def match(self, other_node):
         # compare attributes
         if set(self._attributes.keys()) != set(other_node.attributes.keys()):
             print(
-                "Data node {} Attributes are not same:\nself - other = {}]\nother - self = {}"
-                "".format(
+                "Data node {} Attributes are not same:\nself - other = {}]\nother - self = {}".format(
                     self.name,
                     set(self._attributes.keys()) - set(other_node.attributes.keys()),
                     set(other_node.attributes.keys()) - set(self._attributes.keys()),
                 )
             )
             raise KeyError(
-                "Data node {} Attributes are not same:\nself - other = {}]\nother - self = {}"
-                "".format(
+                "Data node {} Attributes are not same:\nself - other = {}]\nother - self = {}".format(
                     self.name,
                     set(self._attributes.keys()) - set(other_node.attributes.keys()),
                     set(other_node.attributes.keys()) - set(self._attributes.keys()),
@@ -109,7 +107,7 @@ def match(self, other_node):
         error_msg = ""
         for attr_name in self._attributes.keys():
             if self._attributes[attr_name] != other_node.attributes[attr_name]:
-                error_msg += "Mismatch attribute {} value: self = {}, other = {}" "".format(
+                error_msg += "Mismatch attribute {} value: self = {}, other = {}".format(
                     attr_name,
                     self._attributes[attr_name],
                     other_node.attributes[attr_name],
@@ -188,7 +186,7 @@ def write_attributes(self, curr_entry):
             except TypeError as type_error:
                 print(f"[ERROR] {self._name}-node attribute {attr_name} is of type {type(attr_name)}")
                 raise TypeError(
-                    f"[ERROR] {self._name}-node attribute {attr_name} is of type " f"{type(attr_name)}: {type_error}"
+                    f"[ERROR] {self._name}-node attribute {attr_name} is of type {type(attr_name)}: {type_error}"
                 )
 
 

src/drtsans/files/log_h5_reader.py

@@ -76,7 +76,7 @@ def compare_reduced_iq(test_log_file, gold_log_file, title: str, prefix: str):
 
     # Output error message
     if test_exception:
-        base_name = f'{prefix}{os.path.basename(test_log_file).split(".")[0]}'
+        base_name = f"{prefix}{os.path.basename(test_log_file).split('.')[0]}"
         report_difference(
             (test_q_vec, test_intensity_vec),
             (gold_q_vec, gold_intensity_vec),
@@ -211,7 +211,7 @@ def verify_cg2_reduction_results(sample_names, output_dir, gold_path, title, pre
         try:
             compare_reduced_iq(output_log_file, gold_log_file, title_i, prefix)
         except AssertionError as unmatched_error:
-            unmatched_errors = "Testing output {} is different from gold result {}:\n{}" "".format(
+            unmatched_errors = "Testing output {} is different from gold result {}:\n{}".format(
                 output_log_file, gold_log_file, unmatched_error
             )
     # END-FOR

src/drtsans/frame_mode.py

@@ -5,5 +5,6 @@ class FrameMode(Enum):
     r"""
     Selects if instrument operating in frame-skipping mode
     """
+
     not_skip = 0
     skip = 1

src/drtsans/geometry.py

@@ -131,7 +131,7 @@ def bank_workspace_index_range(input_workspace, component=""):
     for i in range(input_workspace.getNumberHistograms()):
         ids = input_workspace.getSpectrum(i).getDetectorIDs()
         if len(ids) > 1:
-            raise RuntimeError("do not know how to work with more than one " "detector per spectrum ({})".format(ids))
+            raise RuntimeError("do not know how to work with more than one detector per spectrum ({})".format(ids))
         if ids[0] == detector_id_first:
             first = i
             break
@@ -786,7 +786,7 @@ def translate_sample_by_z(workspace, z):
         )
         workspace = mtd[ws_name]
         logger.debug(
-            "Instrument sample position is moved to {}" "".format(workspace.getInstrument().getSample().getPos())
+            "Instrument sample position is moved to {}".format(workspace.getInstrument().getSample().getPos())
         )
 
     # update the appropriate log
@@ -836,8 +836,9 @@ def translate_detector_by_z(input_workspace, z=None, relative=True):
         update_log = True
         if (not relative) or (z != 0.0):
             logger.debug(
-                "Moving detector along Z = {}  is relative = {} to component {}"
-                "".format(z, relative, main_detector_name(input_workspace))
+                "Moving detector along Z = {}  is relative = {} to component {}".format(
+                    z, relative, main_detector_name(input_workspace)
+                )
             )
 
             MoveInstrumentComponent(

src/drtsans/instruments.py

@@ -224,7 +224,7 @@ def _empty_download(filepath):
 
     idf = os.path.join(str(output_directory), idf_xml)
     url = f"https://raw.githubusercontent.com/mantidproject/mantid/main/instrument/{idf_xml}"
-    result = subprocess.run(f"curl -o {idf} {url}", shell=True, capture_output=True, text=True)
+    result = subprocess.run(f"curl -o {idf} {url}", shell=True, capture_output=True, text=True, check=False)
     if result.returncode == 0 and not _empty_download(idf):
         return idf
     else:
@@ -328,7 +328,8 @@ def copy_to_newest_instrument(
     target.getAxis(0).setUnit(origin_unit)
     target.setYUnit(origin.YUnit())
     MergeRuns(
-        InputWorkspaces=[target_workspace, input_workspace], OutputWorkspace=target_workspace  # order is necessary
+        InputWorkspaces=[target_workspace, input_workspace],
+        OutputWorkspace=target_workspace,  # order is necessary
     )
     # Move components to the positions they have in input_workspace by reading their positions
     # in the logs. This is implicitly done when invoking algorithm LoadInstrument.

src/drtsans/iq.py

@@ -117,14 +117,16 @@ def valid_wedge(min_angle, max_angle) -> List[Tuple[float, float]]:
         if diff < 180.0:
             return [(min_angle, max_angle)]
         raise ValueError(
-            "wedge angle is greater than 180 degrees: {:.1f} - {:.1f} = {:.1f} < 180"
-            "".format(max_angle, min_angle, diff)
+            "wedge angle is greater than 180 degrees: {:.1f} - {:.1f} = {:.1f} < 180".format(
+                max_angle, min_angle, diff
+            )
         )
     diff = min_angle - max_angle
     if diff <= 180:
         raise ValueError(
-            "wedge angle is greater than 180 degrees: {:.1f} - {:.1f} = {:.1f} <= 180"
-            "".format(min_angle, max_angle, diff)
+            "wedge angle is greater than 180 degrees: {:.1f} - {:.1f} = {:.1f} <= 180".format(
+                min_angle, max_angle, diff
+            )
         )
     return [(min_angle, 270.1), (-90.1, max_angle)]
 

src/drtsans/mask_utils.py

@@ -258,9 +258,7 @@ def circular_mask_from_beam_center(input_workspace, radius, unit="mm"):
         <radius val="{}" />
     </infinite-cylinder>
     <algebra val="shape" />
-    """.format(
-        r
-    )
+    """.format(r)
     det_ids = FindDetectorsInShape(Workspace=input_workspace, ShapeXML=cylinder)
     return det_ids