[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

scripts/test_plotter.py

@@ -1,5 +1,4 @@
 import matplotlib.pylab as plt
-
 from tavi.data.tavi import TAVI
 from tavi.instrument.resolution.cooper_nathans import CN
 from tavi.plotter import Plot1DManager, Plot2DManager

scripts/test_rez.py

@@ -1,7 +1,6 @@
 # from tavi.instrument.instrument_params.python_dicts.takin_test import instrument_params
 # from tests.test_data_folder.test_samples.python_samples.sample_test import test_xtal
 import matplotlib.pylab as plt
-
 from tavi.instrument.resolution.cooper_nathans import CN
 from tavi.plotter import Plot1DManager, Plot2DManager
 

scripts/test_scan.py

@@ -1,5 +1,4 @@
 import matplotlib.pyplot as plt
-
 from tavi.data.tavi import TAVI
 
 

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_group.py

@@ -31,7 +31,6 @@ def __init__(
         signal_axes=(None, None, None),
         background_axes=(None, None, None),
     ):
-
         self.signals = signals
         self.backgrounds = backgrounds
         self.signal_axes = list(signal_axes)
@@ -165,7 +164,6 @@ def plot_waterfall(self, contour_plot, shifts=None, ylim=None, xlim=None, fmt="o
         fig, ax = plt.subplots()
         shift = 0
         for i in range(num):
-
             if np.isnan(z[:, i]).all():  # all nan
                 continue
             else:

src/tavi/data/spice_to_nexus.py

@@ -1,8 +1,9 @@
-import numpy as np
-import h5py
 import os
-from pathlib import Path
 from datetime import datetime
+from pathlib import Path
+
+import h5py
+import numpy as np
 
 # from tavi.instrument.instrument_params.takin_test import instrument_params
 
@@ -421,7 +422,6 @@ def spicelogs_to_nexus(nxentry):
     #    mcu
 
     if spice_logs.attrs["preset_type"] == "normal":
-
         preset_channel = spice_logs.attrs["preset_channel"]
 
         nxentry["monitor"].create_dataset(name="mode", data=preset_channel, maxshape=None)
@@ -458,7 +458,6 @@ def spicelogs_to_nexus(nxentry):
     # --------------------------- data links ---------------------------
 
     def find_val(val, grp, prefix=""):
-
         for obj_name, obj in grp.items():
             if obj_name in ("SPICElogs", "data"):
                 continue
@@ -749,7 +748,6 @@ def convert_spice_to_nexus(path_to_spice_folder, path_to_hdf5):
     p = Path(path_to_spice_folder)
 
     with h5py.File(path_to_hdf5, "w") as root:
-
         # ----------------------------- ub info ------------------------------------
         ub_files = sorted((p / "UBConf").glob("*.ini"))
         tmp_ub_files = sorted((p / "UBConf/tmp").glob("*.ini"))
@@ -797,7 +795,6 @@ def convert_spice_to_nexus(path_to_spice_folder, path_to_hdf5):
             # metadata to attibutes
             exp_str = ["scan_title", "users", "local_contact", "experiment"]
             for k, v in headers.items():
-
                 if "," in v and k not in exp_str:  # vectors
                     spice_logs.attrs[k] = np.array([float(v0) for v0 in v.split(",")])
                 elif v.replace(".", "").isnumeric():  # numebrs only

src/tavi/instrument/instrument_params/cg4c.json

@@ -70,4 +70,4 @@
         "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/python_dicts/hb3.py

@@ -1,5 +1,4 @@
 import numpy as np
-
 from tavi.utilities import *
 
 source = {

src/tavi/instrument/instrument_params/takin_test.json

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

src/tavi/instrument/resolution/backups/cooper_nathans_bak.py

@@ -1,8 +1,8 @@
 import numpy as np
 import numpy.linalg as la
-from tavi.utilities import *
-from tavi.instrument.tas import TAS
 from tavi.instrument.resolution.reso_ellipses import ResoEllipsoid
+from tavi.instrument.tas import TAS
+from tavi.utilities import *
 
 
 class CN(TAS):

src/tavi/instrument/resolution/backups/reso_ellipses_bak.py

@@ -1,11 +1,9 @@
-import numpy as np
-import numpy.linalg as la
-import mpl_toolkits.mplot3d as mplot3d
 import matplotlib
 import matplotlib.pyplot as plt
+import numpy as np
+import numpy.linalg as la
 from tavi.utilities import *
 
-
 np.set_printoptions(floatmode="fixed", precision=4)
 
 
@@ -25,7 +23,6 @@ class ResoEllipsoid(object):
     g_eps = 1e-8
 
     def __init__(self):
-
         self.q = None
         self.en = None
         self.frame = None
@@ -279,9 +276,9 @@ def ellfkt(rad, vecs, phi):
         labelQup = "Qup (1/A)"
 
         if use_tex:
-            labelQpara = "$Q_{\parallel}$ (\AA$^{-1}$)"
-            labelQperp = "$Q_{\perp}$ (\AA$^{-1}$)"
-            labelQup = "$Q_{up}$ (\AA$^{-1}$)"
+            labelQpara = r"$Q_{\parallel}$ (\AA$^{-1}$)"
+            labelQperp = r"$Q_{\perp}$ (\AA$^{-1}$)"
+            labelQup = r"$Q_{up}$ (\AA$^{-1}$)"
 
         # Qpara, E axis
 

src/tavi/instrument/resolution/cooper_nathans.py

@@ -1,6 +1,5 @@
 import numpy as np
 import numpy.linalg as la
-
 from tavi.instrument.resolution.reso_ellipses import ResoEllipsoid
 from tavi.instrument.tas import TAS
 from tavi.utilities import *

src/tavi/instrument/resolution/reso_ellipses.py

@@ -1,7 +1,7 @@
+import matplotlib.pyplot as plt
 import numpy as np
 import numpy.linalg as la
-import matplotlib.pyplot as plt
-from mpl_toolkits.axisartist import Subplot, Axes
+from mpl_toolkits.axisartist import Axes, Subplot
 from mpl_toolkits.axisartist.grid_finder import MaxNLocator
 from mpl_toolkits.axisartist.grid_helper_curvelinear import GridHelperCurveLinear
 from tavi.utilities import *
@@ -141,7 +141,6 @@ 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],
@@ -196,7 +195,6 @@ class ResoEllipsoid(object):
     g_eps = 1e-8
 
     def __init__(self):
-
         self.STATUS = None
         self.q = None
         self.hkl = None

src/tavi/instrument/tas_cmponents.py

@@ -1,5 +1,4 @@
 import numpy as np
-
 from tavi.utilities import *
 
 

src/tavi/plotter.py

@@ -1,13 +1,12 @@
 import matplotlib.pylab as plt
-from mpl_toolkits.axisartist import Axes
 import numpy as np
+from mpl_toolkits.axisartist import Axes
 
 
 class Plot1DManager(object):
     """Manage a plot"""
 
     def __init__(self) -> None:
-
         _, self.ax = plt.subplots()
         self.title = None
         self.xlim = None
@@ -16,7 +15,6 @@ def __init__(self) -> None:
         self.ylabel = None
 
     def set_labels(self):
-
         if self.xlim is not None:
             self.ax.set_xlim(left=self.xlim[0], right=self.xlim[1])
         if self.ylim is not None:
@@ -29,7 +27,6 @@ def set_labels(self):
         self.ax.legend()
 
     def rez_plot_1D(self, tas, projection, hkl, en, ef, R0, axis):
-
         rez = tas.cooper_nathans(
             ei=ef + en,
             ef=ef,
@@ -61,7 +58,6 @@ class Plot2DManager(object):
     """Manage a plot"""
 
     def __init__(self, grid_helper=None) -> None:
-
         self.fig = plt.figure(figsize=(10, 6))
         self.ax = self.fig.add_subplot(111, axes_class=Axes, grid_helper=grid_helper)
 
@@ -76,7 +72,6 @@ def __init__(self, grid_helper=None) -> None:
         self.cmap = "turbo"
 
     def set_labels(self):
-
         if self.xlim is not None:
             self.ax.set_xlim(left=self.xlim[0], right=self.xlim[1])
         if self.ylim is not None:
@@ -122,7 +117,6 @@ def plot_contour(
         self.set_labels()
 
     def rez_plot(self, tas, projection, q1, q2, q3, en, ef, R0):
-
         qe_list = np.empty((4,), dtype=object)
         plot_axes = []
         perp_axes = []
@@ -142,7 +136,6 @@ def rez_plot(self, tas, projection, q1, q2, q3, en, ef, R0):
             for q2 in qe_list[1]:
                 for q3 in qe_list[2]:
                     for ei0 in qe_list[3]:
-
                         h, k, l = tuple(np.array(p1) * q1 + np.array(p2) * q2 + np.array(p3) * q3)
 
                         rez = tas.cooper_nathans(

src/tavi/sample/sample.py

@@ -1,5 +1,4 @@
 import numpy as np
-
 from tavi.utilities import *
 
 np.set_printoptions(floatmode="fixed", precision=4)

src/tavi/sample/xtal.py

@@ -1,5 +1,4 @@
 import numpy as np
-
 from tavi.sample.sample import Sample
 from tavi.utilities import *
 

tests/test_sample.py

@@ -1,6 +1,5 @@
 import numpy as np
 import pytest
-
 from tavi.sample.xtal import Xtal