Apply formatting

pyzebra/anatric.py

@@ -2,11 +2,7 @@ import subprocess
 import xml.etree.ElementTree as ET
 
 
-DATA_FACTORY_IMPLEMENTATION = [
+DATA_FACTORY_IMPLEMENTATION = ["trics", "morph", "d10"]
-    "trics",
-    "morph",
-    "d10",
-]
 
 REFLECTION_PRINTER_FORMATS = [
     "rafin",

pyzebra/app/app.py

@@ -31,13 +31,16 @@ bokeh_logger.setLevel(logging.WARNING)
 bokeh_logger.addHandler(bokeh_handler)
 bokeh_log_textareainput = TextAreaInput(title="server output:", height=150)
 
+
 def proposal_textinput_callback(_attr, _old, _new):
     apply_button.disabled = False
 
+
 proposal_textinput = TextInput(title="Proposal number:", name="")
 proposal_textinput.on_change("value_input", proposal_textinput_callback)
 doc.proposal_textinput = proposal_textinput
 
+
 def apply_button_callback():
     proposal = proposal_textinput.value.strip()
     if proposal:
@@ -52,6 +55,7 @@ def apply_button_callback():
 
     proposal_textinput.name = proposal_path
 
+
 apply_button = Button(label="Apply", button_type="primary")
 apply_button.on_click(apply_button_callback)
 

pyzebra/app/cli.py

@@ -39,7 +39,7 @@ def main():
     )
 
     parser.add_argument(
-        "--anatric-path", type=str, default=ANATRIC_PATH, help="path to anatric executable",
+        "--anatric-path", type=str, default=ANATRIC_PATH, help="path to anatric executable"
     )
 
     parser.add_argument(
@@ -49,9 +49,7 @@ def main():
         help="path to Sxtal_Refgen executable",
     )
 
-    parser.add_argument(
+    parser.add_argument("--spind-path", type=str, default=None, help="path to spind scripts folder")
-        "--spind-path", type=str, default=None, help="path to spind scripts folder",
-    )
 
     parser.add_argument(
         "--args",

pyzebra/app/handler.py

@@ -2,8 +2,7 @@ from bokeh.application.handlers import Handler
 
 
 class PyzebraHandler(Handler):
-    """Provides a mechanism for generic bokeh applications to build up new streamvis documents.
+    """Provides a mechanism for generic bokeh applications to build up new streamvis documents."""
-    """
 
     def __init__(self, anatric_path, spind_path):
         """Initialize a pyzebra handler for bokeh applications.

pyzebra/app/panel_ccl_compare.py

@@ -537,7 +537,7 @@ def create():
 
         n = len(params)
         fitparams = dict(
-            param=params, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n,
+            param=params, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n
         )
 
         if function == "linear":

pyzebra/app/panel_ccl_integrate.py

@@ -517,7 +517,7 @@ def create():
 
         n = len(params)
         fitparams = dict(
-            param=params, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n,
+            param=params, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n
         )
 
         if function == "linear":

pyzebra/app/panel_ccl_prepare.py

@@ -348,7 +348,7 @@ def create():
     # Define resolution function
     def _res_fun(stt, wave, res_mult):
         expr = np.tan(stt / 2 * np.pi / 180)
-        fwhm = np.sqrt(0.4639 * expr ** 2 - 0.4452 * expr + 0.1506) * res_mult  # res in deg
+        fwhm = np.sqrt(0.4639 * expr**2 - 0.4452 * expr + 0.1506) * res_mult  # res in deg
         return fwhm
 
     def plot_file_callback():
@@ -598,7 +598,7 @@ def create():
 
         ellipse_source.data.update(x=el_x, y=el_y, w=el_w, h=el_h, c=el_c)
         scan_source.data.update(
-            xs=scan_xs, ys=scan_ys, x=scan_x, y=scan_y, m=scan_m, s=scan_s, c=scan_c, l=scan_l,
+            xs=scan_xs, ys=scan_ys, x=scan_x, y=scan_y, m=scan_m, s=scan_s, c=scan_c, l=scan_l
         )
 
         arrow1.visible = True
@@ -691,7 +691,7 @@ def create():
     )
 
     k_vectors = TextAreaInput(
-        title="k vectors:", value="0.0 0.0 0.0\n0.5 0.0 0.0\n0.5 0.5 0.0", width=150,
+        title="k vectors:", value="0.0 0.0 0.0\n0.5 0.0 0.0\n0.5 0.5 0.0", width=150
     )
     res_mult_ni = NumericInput(title="Resolution mult:", value=10, mode="int", width=100)
 

pyzebra/app/panel_hdf_anatric.py

@@ -169,7 +169,7 @@ def create():
         config.dataFactory_implementation = new
 
     dataFactory_implementation_select = Select(
-        title="DataFactory implement.:", options=DATA_FACTORY_IMPLEMENTATION, width=145,
+        title="DataFactory implement.:", options=DATA_FACTORY_IMPLEMENTATION, width=145
     )
     dataFactory_implementation_select.on_change("value", dataFactory_implementation_select_callback)
 
@@ -200,7 +200,7 @@ def create():
         config.reflectionPrinter_format = new
 
     reflectionPrinter_format_select = Select(
-        title="ReflectionPrinter format:", options=REFLECTION_PRINTER_FORMATS, width=145,
+        title="ReflectionPrinter format:", options=REFLECTION_PRINTER_FORMATS, width=145
     )
     reflectionPrinter_format_select.on_change("value", reflectionPrinter_format_select_callback)
 

pyzebra/app/panel_hdf_param_study.py

@@ -322,9 +322,7 @@ def create():
     # ---- tools
     wheelzoomtool = WheelZoomTool(maintain_focus=False)
     overview_plot_x.toolbar.logo = None
-    overview_plot_x.add_tools(
+    overview_plot_x.add_tools(PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool())
-        PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool(),
-    )
     overview_plot_x.toolbar.active_scroll = wheelzoomtool
 
     # ---- axes
@@ -360,9 +358,7 @@ def create():
     # ---- tools
     wheelzoomtool = WheelZoomTool(maintain_focus=False)
     overview_plot_y.toolbar.logo = None
-    overview_plot_y.add_tools(
+    overview_plot_y.add_tools(PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool())
-        PanTool(), BoxZoomTool(), wheelzoomtool, ResetTool(),
-    )
     overview_plot_y.toolbar.active_scroll = wheelzoomtool
 
     # ---- axes

pyzebra/app/panel_spind.py

@@ -128,7 +128,7 @@ def create():
 
             spind_out_file = os.path.join(temp_dir, "spind.txt")
             spind_res = dict(
-                label=[], crystal_id=[], match_rate=[], matched_peaks=[], column_5=[], ub_matrix=[],
+                label=[], crystal_id=[], match_rate=[], matched_peaks=[], column_5=[], ub_matrix=[]
             )
             try:
                 with open(spind_out_file) as f_out:

pyzebra/ccl_io.py

@@ -175,7 +175,7 @@ def parse_1D(fileobj, data_type):
 
             # "om" -> "omega"
             scan["scan_motor"] = "omega"
-            scan["scan_motors"] = ["omega", ]
+            scan["scan_motors"] = ["omega"]
             # overwrite metadata, because it only refers to the scan center
             half_dist = (scan["n_points"] - 1) / 2 * scan["angle_step"]
             scan["omega"] = np.linspace(
@@ -354,7 +354,7 @@ def export_ccl_compare(dataset1, dataset2, path, export_target, hkl_precision=2)
         area_n1, area_s1 = scan1["area"]
         area_n2, area_s2 = scan2["area"]
         area_n = area_n1 - area_n2
-        area_s = np.sqrt(area_s1 ** 2 + area_s2 ** 2)
+        area_s = np.sqrt(area_s1**2 + area_s2**2)
         area_str = f"{area_n:10.2f}{area_s:10.2f}"
 
         ang_str = ""

pyzebra/ccl_process.py

@@ -18,9 +18,7 @@ PARAM_PRECISIONS = {
     "ub": 0.01,
 }
 
-MAX_RANGE_GAP = {
+MAX_RANGE_GAP = {"omega": 0.5}
-    "omega": 0.5,
-}
 
 MOTOR_POS_PRECISION = 0.01
 

pyzebra/h5.py

@@ -2,9 +2,10 @@ import h5py
 import numpy as np
 from lmfit.models import Gaussian2dModel, GaussianModel
 
-META_MATRIX = ("UB", )
+META_MATRIX = ("UB",)
-META_CELL = ("cell", )
+META_CELL = ("cell",)
-META_STR = ("name", )
+META_STR = ("name",)
+
 
 def read_h5meta(filepath):
     """Open and parse content of a h5meta file.
@@ -137,7 +138,7 @@ def read_detector_data(filepath, cami_meta=None):
             else:
                 raise ValueError("No angles that vary")
 
-        scan["scan_motors"] = [scan["scan_motor"], ]
+        scan["scan_motors"] = [scan["scan_motor"]]
 
         # optional parameters
         if "/entry1/sample/magnetic_field" in h5f:

pyzebra/xtal.py

@@ -362,8 +362,7 @@ def angtohkl(wave, ddist, gammad, om, ch, ph, nud, x, y):
 
 
 def ang2hkl(wave, ddist, gammad, om, ch, ph, nud, ub, x, y):
-    """Calculate hkl-indices of a reflection from its position (x,y,angles) at the 2d-detector
+    """Calculate hkl-indices of a reflection from its position (x,y,angles) at the 2d-detector"""
-    """
     ga, nu = det2pol(ddist, gammad, nud, x, y)
     z1 = z1frmd(wave, ga, om, ch, ph, nu)
     ubinv = np.linalg.inv(ub)
@@ -373,8 +372,7 @@ def ang2hkl(wave, ddist, gammad, om, ch, ph, nud, ub, x, y):
 
 
 def ang2hkl_1d(wave, ddist, ga, om, ch, ph, nu, ub):
-    """Calculate hkl-indices of a reflection from its position (angles) at the 1d-detector
+    """Calculate hkl-indices of a reflection from its position (angles) at the 1d-detector"""
-    """
     z1 = z1frmd(wave, ga, om, ch, ph, nu)
     ubinv = np.linalg.inv(ub)
     hkl = ubinv @ z1
@@ -383,8 +381,7 @@ def ang2hkl_1d(wave, ddist, ga, om, ch, ph, nu, ub):
 
 
 def ang_proc(wave, ddist, gammad, om, ch, ph, nud, x, y):
-    """Utility function to calculate ch, ph, ga, om
+    """Utility function to calculate ch, ph, ga, om"""
-    """
     ga, nu = det2pol(ddist, gammad, nud, x, y)
     z1 = z1frmd(wave, ga, om, ch, ph, nu)
     ch2, ph2 = eqchph(z1)
@@ -403,4 +400,4 @@ def gauss(x, *p):
         Gaussian function
     """
     A, mu, sigma = p
-    return A * np.exp(-((x - mu) ** 2) / (2.0 * sigma ** 2))
+    return A * np.exp(-((x - mu) ** 2) / (2.0 * sigma**2))