[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/scan.py

@@ -74,7 +74,6 @@ class Scan(object):
     """
 
     def __init__(self, name: str, nexus_dict: NexusEntry) -> None:
-
         self.name: str = name
         self._nexus_dict: NexusEntry = nexus_dict
         self.data: dict = self.get_data_columns()

src/tavi/data/scan_data.py

@@ -9,7 +9,6 @@ class ScanData1D(object):
     ZERO = 1e-6
 
     def __init__(self, x: np.ndarray, y: np.ndarray) -> None:
-
         # ind = np.argsort(x)
         # self.x = x[ind]
         # self.y = y[ind]
@@ -188,7 +187,6 @@ def rebin_grid_renorm(self, rebin_params: tuple, norm_col: np.ndarray, norm_val:
 
 
 class ScanData2D(object):
-
     ZEROS = 1e-6
 
     def __init__(self, x: np.ndarray, y: np.ndarray, z: np.ndarray) -> None:

src/tavi/data/scan_group.py

@@ -65,7 +65,6 @@ def _get_data_1d(
         norm_to: Optional[tuple[float, str]],
         **rebin_params_dict: Optional[tuple],
     ) -> ScanData1D:
-
         x_axis, y_axis = axes
         x_array = np.array([])
         y_array = np.array([])
@@ -130,7 +129,6 @@ def _get_data_2d(
         norm_to: Optional[tuple[float, str]],
         **rebin_params_dict: Optional[tuple],
     ) -> ScanData2D:
-
         if not isinstance(rebin_params, tuple):
             raise ValueError(f"rebin parameters ={rebin_params} needs to be a tuple.")
         if not len(rebin_params) == 2:

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/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

@@ -90,7 +90,7 @@ 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

@@ -144,7 +144,6 @@ 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)
@@ -157,7 +156,6 @@ def test_spice_to_nexus_one():
 
 
 def test_spice_to_nexus_empty():
-
     path_to_spice_folder = "./test_data/exp815"
     path_to_nexus = "./test_data/spice_to_nxdict_test_empty.h5"
     scan0002 = NexusEntry.from_spice(path_to_spice_folder, 2)
@@ -191,7 +189,6 @@ def test_get_dataset_names():
 
 @pytest.fixture
 def nexus_entries():
-
     analyser = {
         "attrs": {"EX_required": "true", "NX_class": "NXcrystal", "type": "NX_CHAR"},
         "a1": {

tests/test_tavi_data.py

@@ -79,7 +79,6 @@ def tavi_exp0424():
 
 
 def test_get_scan(tavi_exp0424):
-
     scan0034 = tavi_exp0424.get_scan(scan_num=("IPTS32124_CG4C_exp0424", 34))
     assert scan0034.name == "scan0034"
     assert scan0034.scan_info.scan_num == 34