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

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

fiducialreg/imref.py

@@ -18,7 +18,6 @@ class DimensionManager:
     def __init__(
         self, DimensionName="", NumberOfSamples=2, Delta=1, StartCoordinateInWorld=0.5
     ):
-
         if DimensionName not in ["X", "Y", "Z"]:
             raise ValueError("DimensionName must be X, Y, or Z")
         self.DimensionName = DimensionName

llspy/__main__.py

@@ -9,7 +9,6 @@
     from llspy.bin.llspy_gui import main
 
 if __name__ == "__main__":
-
     import logging
 
     logger = logging.getLogger(__name__)

llspy/camcalib.py

@@ -168,7 +168,6 @@ def process_dark_images(folder, callback=None, callback2=None):
 
 
 def process_bright_images(folder, darkavg, darkstd, callback=None, save=True):
-
     ch0list, ch1list = get_channel_list(folder)
     pre, post = combine_stacks(ch0list, ch1list, darkavg)
 
@@ -203,7 +202,6 @@ def process_bright_images(folder, darkavg, darkstd, callback=None, save=True):
 
 
 if __name__ == "__main__":
-
     # this script assumes you have aquired a series of 2-channel zstacks
     # (not actually a stack,  turn off Z galvo,  and Z and Sample Piezos
     # the first channel is "bright" and "even" (such as 488 laser sheet exciting FITC)

llspy/camera.py

@@ -364,7 +364,6 @@ def correct_stacks(
 
 
 if __name__ == "__main__":
-
     from llspy import llsdir, samples
 
     paramfile = samples.camparams  # path to the calibration file

llspy/gui/camcalibgui.py

@@ -126,7 +126,6 @@ def setFolder(self):
             self.darkSTDineEdit.setText(os.path.join(folder, "dark_STD.tif"))
 
     def processFolder(self):
-
         folder = self.camCalibFolderLineEdit.text()
 
         darkavg = None
@@ -214,7 +213,6 @@ def _abort(self):
 
 
 if __name__ == "__main__":
-
     app = QtW.QApplication(sys.argv)
     # dlg = LogWindow()
     # dlg.show()

llspy/gui/img_dialog.py

@@ -73,7 +73,6 @@ def __init__(self, name, wave=None, parent=None):
 
 
 class DataModel(QtCore.QObject):
-
     _idxChanged = QtCore.Signal()
     _dataChanged = QtCore.Signal()
 
@@ -294,7 +293,6 @@ def __getitem__(self, tczTuple):
 
 
 class MplCanvas(FigureCanvas):
-
     _contrastChanged = QtCore.Signal()
 
     def __init__(self):
@@ -582,7 +580,6 @@ def update_sliders(self):
             self.update_axis_slider(axis, n)
 
     def initialize(self):
-
         datamax = self.data.max()
         datamin = self.data.min()
         # dataRange = datamax - datamin

llspy/gui/mainwindow.py

@@ -1138,14 +1138,12 @@ def displayPreview(self, array, dx, dz, params=None):
             viewer.dims.ndisplay = 3
             self.spimwins.append(viewer)
         elif self.prevBackendSpimagineRadio.isChecked() and _SPIMAGINE_IMPORTED:
-
             if np.squeeze(array).ndim > 4:
                 arrays = [array[:, i] for i in range(array.shape[1])]
             else:
                 arrays = [np.squeeze(array)]
 
             for arr in arrays:
-
                 datamax = arr.max()
                 datamin = arr.min()
                 dataRange = datamax - datamin
@@ -1660,7 +1658,6 @@ def concatenateSelected(self):
             [self.listbox.addPath(p) for p in selectedPaths]
 
     def undoRenameSelected(self):
-
         box = QtW.QMessageBox()
         box.setWindowTitle("Undo Renaming")
         box.setText(
@@ -1712,7 +1709,6 @@ def renameSelected(self):
             [self.listbox.addPath(osp.join(item, p)) for p in os.listdir(item)]
 
     def mergeMIPtool(self):
-
         if len(self.listbox.selectedPaths()):
             for obj in self.listbox.selectedObjects():
                 obj.mergemips()

llspy/gui/qtlogger.py

@@ -27,7 +27,6 @@ def formatException(self, exc_info):
 
 
 class NotificationHandler(QObject, logging.Handler):
-
     emitSignal = Signal(str)
 
     def __init__(self):

llspy/gui/workers.py

@@ -154,7 +154,6 @@ def onFinished(self, exitCode, exitStatus):
 
 
 class CompressionWorker(SubprocessWorker):
-
     status_update = QtCore.Signal(str, int)
 
     def __init__(self, path, mode="compress", binary=None, wid=1, **kwargs):
@@ -235,7 +234,6 @@ def untar(self, tarball, delete=True):
             with tarfile.open(tarball) as tar:
 
                 def is_within_directory(directory, target):
-
                     abs_directory = os.path.abspath(directory)
                     abs_target = os.path.abspath(target)
 
@@ -244,7 +242,6 @@ def is_within_directory(directory, target):
                     return prefix == abs_directory
 
                 def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
-
                     for member in tar.getmembers():
                         member_path = os.path.join(path, member.name)
                         if not is_within_directory(path, member_path):
@@ -345,7 +342,6 @@ def split(a, n):
 
 
 class LLSitemWorker(QtCore.QObject):
-
     sig_starting_item = QtCore.Signal(str, int)  # item path, numfiles
 
     status_update = QtCore.Signal(str)  # update mainGUI status
@@ -438,7 +434,6 @@ def work(self):
 
         # only call cudaDeconv if we need to deskew or deconvolve
         if self.P.nIters > 0 or (self.P.deskew != 0 and self.P.saveDeskewedRaw):
-
             try:
                 # check the binary path and create object
                 binary = llspy.cudabinwrapper.CUDAbin(_CUDABIN)
@@ -547,7 +542,6 @@ def on_CUDAworker_done(self, worker_id):
                 self.post_process()
 
     def post_process(self):
-
         if self.P.doReg:
             self.status_update.emit(f"Doing Channel Registration: {self.E.basename}")
             try:

llspy/libcudawrapper.py

@@ -417,7 +417,6 @@ def RL_decon(
             plt.show()
             RL_cleanup()
         elif sys.argv[1] == "camcor":
-
             import time
 
             from llspy import llsdir, samples

llspy/llsdir.py

@@ -1226,7 +1226,6 @@ def median_and_trim(
         trimX=(0, 0),
         **kwargs,
     ):
-
         trim = (trimZ, trimY, trimX)
 
         outpath = self.path.joinpath("Corrected")

llspy/xzpsf.py

@@ -80,7 +80,6 @@ def find_settext(path, filepattern="*Settings.txt"):
 
 
 if __name__ == "__main__":
-
     import argparse
 
     parser = argparse.ArgumentParser()

setup.cfg

@@ -7,7 +7,7 @@ url = https://github.com/tlambert03/LLSpy
 author = Talley Lambert
 author_email = [email protected]
 license = BSD 3-clause
-license_file = LICENSE
+license_files = LICENSE
 classifiers =
     Development Status :: 3 - Alpha
     Intended Audience :: Science/Research
@@ -18,11 +18,6 @@ classifiers =
     Programming Language :: Python
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: 3.6
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
     Topic :: Scientific/Engineering
     Topic :: Scientific/Engineering :: Visualization
 
@@ -41,7 +36,7 @@ install_requires =
     voluptuous
     watchdog
     numba;python_version < '3.10'
-python_requires = >=3.6
+python_requires = >=3.8
 include_package_data = True
 zip_safe = False