[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.pre-commit-config.yaml

@@ -19,4 +19,3 @@ repos:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]
     - id: ruff-format
-

.vscode/settings.json

@@ -4,4 +4,4 @@
     ],
     "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
-}
+}

docs/conf.py

@@ -4,6 +4,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 import os
 import sys
+
 import versioningit
 
 sys.path.insert(0, os.path.abspath("../src"))
@@ -59,7 +60,9 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "alabaster"  # "sphinx_rtd_theme", please add corresponding package to environment.yml if you want to use it
+html_theme = (
+    "alabaster"  # "sphinx_rtd_theme", please add corresponding package to environment.yml if you want to use it
+)
 autosummary_generate = True
 
 # Napoleon settings

src/tavi/configuration.py

@@ -4,9 +4,9 @@
 
 import os
 import shutil
-
 from configparser import ConfigParser
 from pathlib import Path
+
 from mantid.kernel import Logger
 
 logger = Logger("PACKAGENAME")

src/tavi/data/plotter.py

@@ -5,7 +5,6 @@
 
 
 class Plot1D(object):
-
     def __init__(
         self,
         x: np.ndarray,

src/tavi/data/spice_reader.py

@@ -71,7 +71,7 @@ def read_spice_ubconf(ub_file_name: str) -> dict:
     Returns:
     """
     ubconf: dict[str, Any] = {}
-    with open(ub_file_name, 'r', encoding="utf-8") as f:
+    with open(ub_file_name, "r", encoding="utf-8") as f:
         all_content = f.readlines()
 
     for idx, line in enumerate(all_content):
@@ -129,8 +129,8 @@ def _create_spicelogs(path_to_scan_file: str) -> dict:
 
     scan_path = os.path.abspath(path_to_scan_file)
     (*folder_path, _, _) = scan_path.split("/")
-    ub_file_path = os.path.join('/',*folder_path,"UBConf", metadata["ubconf"])
-    ub_temp_file_path = os.path.join('/',*folder_path,"UBConf", "temp", metadata["ubconf"])
+    ub_file_path = os.path.join("/", *folder_path, "UBConf", metadata["ubconf"])
+    ub_temp_file_path = os.path.join("/", *folder_path, "UBConf", "temp", metadata["ubconf"])
 
     if os.path.isfile(ub_file_path):
         ub_conf_dict = {"file_path": ub_file_path}

src/tavi/data/ubconf.py

@@ -25,9 +25,7 @@ def convert_spice_ub_to_nexus(
     """Convert all UBConf files into one NeXus entry named UBConf.h5"""
 
     if verbose:
-        disp_str = (
-            f"Converting SPICE UBConf files at {path_to_spice_folder} to an NeXus entry at {path_to_hdf5_folder}"
-        )
+        disp_str = f"Converting SPICE UBConf files at {path_to_spice_folder} to an NeXus entry at {path_to_hdf5_folder}"
         print(disp_str)
 
     p = Path(path_to_spice_folder)
@@ -37,7 +35,6 @@ def convert_spice_ub_to_nexus(
     ub_conf_dicts = {ub_file.parts[-1].split(".")[0]: _read_spice_ub(ub_file) for ub_file in ub_files_all}
 
     with h5py.File(path_to_hdf5_folder + "UBConf.h5", "w") as root:
-
         for ub_name, ub_data in ub_conf_dicts.items():
             ub_entry = root.create_group(ub_name)
             ub_entry.attrs["NX_class"] = "NXcollection"

src/tavi/instrument/instrument_params/cg4c.json

@@ -70,4 +70,4 @@
         "v_post_sample": 600,
         "v_post_ana": 600
     }
-}
+}

src/tavi/instrument/instrument_params/hb1a.json

@@ -69,4 +69,4 @@
         "v_post_sample": 600,
         "v_post_ana": 600
     }
-}
+}

src/tavi/instrument/instrument_params/hb3.json

@@ -73,4 +73,4 @@
         "v_post_sample": 300,
         "v_post_ana": 600
     }
-}
+}

src/tavi/instrument/instrument_params/hb3_mnte.json

@@ -73,4 +73,4 @@
         "v_post_sample": 120,
         "v_post_ana": 120
     }
-}
+}

src/tavi/instrument/instrument_params/takin_test.json

@@ -72,4 +72,4 @@
         "v_post_sample": 30,
         "v_post_ana": 30
     }
-}
+}

src/tavi/instrument/resolution/ellipse_curve.py

@@ -143,7 +143,6 @@ def generate_plot(self, ax, c="black", linestyle="solid"):
         pts = self.generate_ellipse()
 
         if self.grid_helper is None:
-
             s = ax.plot(
                 pts[0],
                 pts[1],

src/tavi/instrument/resolution/ellipsoid.py

@@ -43,7 +43,6 @@ def __init__(
         sample: Xtal,
         projection: Optional[tuple] = ((1, 0, 0), (0, 1, 0), (0, 0, 1)),
     ) -> None:
-
         self.STATUS: Optional[bool] = None
         self.q: Optional[tuple[float, float, float]] = None
         self.hkl: tuple[float, float, float] = hkl

src/tavi/instrument/tas.py

@@ -100,7 +100,7 @@ def calculate_ub_matrix(self, peaks: tuple[Peak, ...]):
         if not isinstance(self.sample, Xtal):
             raise ValueError("sample needs to be Xtal class for UB calculation.")
 
-        match (num_of_peaks := len(peaks)):
+        match num_of_peaks := len(peaks):
             case 2:
                 ubconf = self._find_u_from_two_peaks(peaks)
                 self.sample.set_orientation(ubconf)

tests/test_fit.py

@@ -7,7 +7,6 @@
 
 
 def test_fit_single_peak():
-
     nexus_file_name = "./test_data/IPTS32124_CG4C_exp0424/scan0042.h5"
     _, s1 = Scan.from_nexus_file(nexus_file_name)
 
@@ -26,7 +25,6 @@ def test_fit_single_peak():
 
 
 def test_fit_two_peak():
-
     nexus_file_name = "./test_data/IPTS32124_CG4C_exp0424/scan0042.h5"
     _, s1 = Scan.from_nexus_file(nexus_file_name)
 

tests/test_nxentry.py

@@ -142,7 +142,6 @@ def test_get_from_daslogs():
 
 
 def test_spice_to_nexus_one():
-
     path_to_spice_folder = "./test_data/exp424"
     path_to_nexus = "./test_data/spice_to_nxdict_test_scan0034.h5"
     scan0034 = NexusEntry.from_spice(path_to_spice_folder, 34)
@@ -168,7 +167,6 @@ def test_spice_to_nexus_all():
 
 @pytest.fixture
 def nexus_entries():
-
     analyser = {
         "attrs": {"EX_required": "true", "NX_class": "NXcrystal", "type": "NX_CHAR"},
         "a1": {