[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -11,20 +11,20 @@ repos:
           - id: check-yaml
           - id: check-added-large-files
     - repo: https://github.com/pycqa/isort
-      rev: 7.0.0
+      rev: 8.0.1
       hooks:
           - id: isort
             args: [--profile, black, --filter-files]
     - repo: https://github.com/PyCQA/autoflake
-      rev: v2.3.1
+      rev: v2.3.3
       hooks:
           - id: autoflake
     - repo: https://github.com/asottile/pyupgrade
       rev: v3.21.2
       hooks:
           - id: pyupgrade
     - repo: https://github.com/psf/black-pre-commit-mirror
-      rev: 25.12.0
+      rev: 26.3.1
       hooks:
           - id: black
             language_version: python3

ppafm/cli/fitting/fitting.py

@@ -188,7 +188,7 @@ def comp_msd(x=[]):
     parser.add_option( "--nobounds",     action="store_true",               help="Skipf the first optimization step with bounds",     default=False)
     # fmt: on
 
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     opt_dict = vars(options)
     parameters.apply_options(opt_dict)  # setting up all the options according to their
     x_new, bounds = set_fit_dict(opt=opt_dict)

ppafm/cli/fitting/plotLine.py

@@ -54,7 +54,7 @@ def selectLine(BIGarray, MIN, MAX, startingPoint, endPoint, nsteps):
 parser.add_option( "--nodisp",                           action="store_true", default=False, help="Do NOT show the " "plots on the screen",  )
 # fmt: on
 
-(options, args) = parser.parse_args()
+options, args = parser.parse_args()
 opt_dict = vars(options)
 if options.points == []:
     sys.exit("Error!! The '-p' or '--points' argument is required\npython plotLine.py -p XMINxYMINxZMIN XMAXxYMAXxZMAX")

ppafm/cli/fitting/plotZ.py

@@ -21,12 +21,8 @@ def find_minimum(array, precision=0.0001):
         i += 1
 
 
-HELP_MSG = (
-    """Use this program in the following way:
-"""
-    + os.path.basename(main.__file__)
-    + """ -p "X1xY1" [-p "X2xY2" ...]  """
-)
+HELP_MSG = """Use this program in the following way:
+""" + os.path.basename(main.__file__) + """ -p "X1xY1" [-p "X2xY2" ...]  """
 
 # fmt: off
 parser = OptionParser()
@@ -42,7 +38,7 @@ def find_minimum(array, precision=0.0001):
 # parser.add_option( "--yrange", action="store", type="float", help="y positions of the tip range (min,max,n) [A]", nargs=3)
 # fmt: on
 
-(options, args) = parser.parse_args()
+options, args = parser.parse_args()
 opt_dict = vars(options)
 print(options)
 if options.npy:

ppafm/cli/plot_results.py

@@ -279,7 +279,7 @@ def main(argv=None):
                         os.makedirs(dir_name_amplitude)
 
                     if parameters.tiltedScan:
-                        (f_out, lvec, _, atomic_info_or_head) = io.load_vec_field(dirname + "/OutF", data_format=args.output_format)
+                        f_out, lvec, _, atomic_info_or_head = io.load_vec_field(dirname + "/OutF", data_format=args.output_format)
                         dfs = common.Fz2df_tilt(
                             f_out,
                             parameters.scanTilt,
@@ -292,7 +292,7 @@ def main(argv=None):
                         lvec_df[0] = lvec_df[0] + lvec_df[3] / lvec_3_norm * amplitude / 2
                         lvec_df[3] = lvec_df[3] / lvec_3_norm * (lvec_3_norm - amplitude)
                     else:
-                        (fzs, lvec, _, atomic_info_or_head) = io.load_scal_field(dirname + "/OutFz", data_format=args.output_format)
+                        fzs, lvec, _, atomic_info_or_head = io.load_scal_field(dirname + "/OutFz", data_format=args.output_format)
                         if applied_bias:
                             r_tip = parameters.Rtip
                             for iz, z in enumerate(tip_positions_z):

ppafm/cli/utilities/cube2xsf.py

@@ -19,7 +19,7 @@
     parser.add_option( "-i", "--input",  action="store", type="string", help="input file")
     parser.add_option( "-o", "--output", action="store", type="string", help="output file")
     # fmt: on
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
     if options.input == None:
         sys.exit("ERROR!!! Please, specify the input file with the '-i' option \n\n" + HELP_MSG)
 

ppafm/cli/utilities/extract_densities.py

@@ -20,7 +20,7 @@
 parser.add_option( "--dz",             action="store", type="float",   help="use dz with step",                           default=-0.1         )
 parser.add_option( "--plot",           action="store_false"        ,   help="plot extracted ?",                           default=True         )
 # fmt: on
-(options, args) = parser.parse_args()
+options, args = parser.parse_args()
 
 fname, fext = os.path.splitext(options.i)
 fext = fext[1:]

ppafm/cli/utilities/fitPauli.py

@@ -33,7 +33,7 @@
 parser.add_option( "--not_plot",   action="store_false"        ,  help="do not-plot the lines above atoms",       default= True            )
 parser.add_option( "--debug",      action="store_true"         ,  help="plot and pr. all lines and data from fit",default= False           )
 # fmt: on
-(options, args) = parser.parse_args()
+options, args = parser.parse_args()
 
 # ====== functions
 

ppafm/cli/utilities/plotQuad.py

@@ -16,7 +16,7 @@
 parser.add_option( "-i",                 action="store", type="string", help="input file",                   default='OutFz'        )
 parser.add_option("-f","--data_format" , action="store", type="string", help="Specify the output format of the vector and scalar field. Supported formats are: xsf,npy", default="xsf")
 # fmt: on
-(options, args) = parser.parse_args()
+options, args = parser.parse_args()
 
 try:
     points = np.genfromtxt(options.p)

ppafm/cli/utilities/plotZcurves.py

@@ -16,7 +16,7 @@
 parser.add_option( "--iz",               action="store", type="int",    help="z-slice index to plot legend", default=15                 )
 parser.add_option("-f","--data_format" , action="store", type="string", help="Specify the output format of the vector and scalar field. Supported formats are: xsf,npy", default="xsf")
 # fmt: on
-(options, args) = parser.parse_args()
+options, args = parser.parse_args()
 
 try:
     points = np.genfromtxt(options.p)

ppafm/cli/utilities/xsf2png.py

@@ -31,7 +31,7 @@
 parser.add_option( "--atoms",  action="store",      type="string", default='input_plot.xyz', help="xyz geometry file",                           )
 parser.add_option( "--bonds",  action="store_true",                default=False,            help="plot bonds to images" )
 # fmt: on
-(options, args) = parser.parse_args()
+options, args = parser.parse_args()
 
 
 atoms = None

ppafm/fieldFFT.py

@@ -31,7 +31,7 @@ def getSize(inp_axis, dims, sampleSize):
 
 def getMGrid(dims, dd):
     "returns coordinate arrays X, Y, Z"
-    (dx, dy, dz) = dd
+    dx, dy, dz = dd
     XYZ = np.mgrid[0 : dims[0], 0 : dims[1], 0 : dims[2]].astype(float)
     # fmt: off
     xshift = dims[0]//2;  xshift_ = xshift;

ppafm/io.py

@@ -560,9 +560,7 @@ def _orthoLvec(sh, dd):
     return [[0, 0, 0], [sh[2] * dd[0], 0, 0], [0, sh[1] * dd[1], 0], [0, 0, sh[0] * dd[2]]]
 
 
-XSF_HEAD_DEFAULT = (
-    headScan
-) = """
+XSF_HEAD_DEFAULT = headScan = """
 ATOMS
  1   0.0   0.0   0.0
 
@@ -934,8 +932,7 @@ def load_scal_field(fname, data_format="xsf"):
 #end
 """
 
-DEFAULT_POV_HEAD = (
-    """
+DEFAULT_POV_HEAD = """
 // ***********************************************
 // Camera & other global settings
 // ***********************************************
@@ -950,9 +947,7 @@ def load_scal_field(fname, data_format="xsf"):
   up       < 0, Zoom, 0 >
   look_at  < .0.0,  0.0,  0.0 >
 }
-"""
-    + DEFAULT_POV_HEAD_NO_CAM
-)
+""" + DEFAULT_POV_HEAD_NO_CAM
 
 
 def makePovCam(pos, up=[0.0, 1.0, 0.0], rg=[-1.0, 0.0, 0.0], fw=[0.0, 0.0, 100.0], lpos=[0.0, 0.0, -100.0], W=10.0, H=10.0):

ppafm/ml/CorrectionLoop.py

@@ -14,7 +14,6 @@
 
 """
 
-
 import numpy as np
 
 from .. import common as PPU
@@ -475,7 +474,7 @@ def Job_CorrectionLoop(simulator, atoms, bonds, geom_fname="input.xyz", nstep=10
 
     parser = OptionParser()
     parser.add_option("-j", "--job", action="store", type="string", help="[train/loop]")
-    (options, args) = parser.parse_args()
+    options, args = parser.parse_args()
 
     logger.info(" UNIT_TEST START : CorrectionLoop ... ")