Update pre-commit hooks and run formatter on all files (#129)

Author: stefsmeets

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
     #   - id: check-json
     #   - id: check-added-large-files
   - repo: https://github.com/stefsmeets/nbcheckorder/
-    rev: v0.2.0
+    rev: v0.3.0
     hooks:
       - id: nbcheckorder
         # This notebook is not executed at all, which fails the check
@@ -26,11 +26,11 @@ repos:
             docs/examples/montage_processing.ipynb
           )$
   - repo: https://github.com/myint/docformatter
-    rev: master  # https://github.com/PyCQA/docformatter/issues/293
+    rev: 'v1.7.7'
     hooks:
       - id: docformatter
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: 'v0.7.0'
+    rev: 'v0.11.10'
     hooks:
       - id: ruff
         args: [--fix]

scripts/process_tvips.py

@@ -140,7 +140,7 @@ def img_convert(credlog, tiff_path=None, pets_path='PETS', mrc_path='RED', smv_p
     print('# TVIPS header')
     print(f'Camera:                   {camera}')
     print(f'Acquisition time:         {acquisition_time:.3f} s')
-    print(f'Exposure time:            {exposure_time/1000:.3f} s')
+    print(f'Exposure time:            {exposure_time / 1000:.3f} s')
     print(f'Overhead time:            {overhead:.3f} s')
     print(f'Binning (X/Y):            {binning_x} {binning_y} px/bin')
     print(f'Image resolution (X/Y):   {image_res_x_tvips} {image_res_y_tvips} pixels')
@@ -150,15 +150,15 @@ def img_convert(credlog, tiff_path=None, pets_path='PETS', mrc_path='RED', smv_p
     print(
         f'Physical pixelsize (X/Y): {physical_pixelsize_x_tvips} {physical_pixelsize_y_tvips} μm'
     )
-    print(f'High tension:             {high_tension/1000} kV')
+    print(f'High tension:             {high_tension / 1000} kV')
     print(f'Wavelength:               {wavelength_tvips} Ångstrom')
     print(f'Camera length:            {camera_length_tvips} mm')
 
     # implement this later if it turns out to be necessary
     assert pixelsize_x_tvips == pixelsize_y_tvips, 'Pixelsize is different in X / Y direction'
-    assert (
-        physical_pixelsize_x_tvips == physical_pixelsize_y_tvips
-    ), 'Physical pixelsize is different in X / Y direction'
+    assert physical_pixelsize_x_tvips == physical_pixelsize_y_tvips, (
+        'Physical pixelsize is different in X / Y direction'
+    )
 
     buffer = []
 
@@ -176,9 +176,9 @@ def img_convert(credlog, tiff_path=None, pets_path='PETS', mrc_path='RED', smv_p
             if img.min() >= 0 and img.max() < 2**16:
                 img = img.astype(np.uint16)
 
-        assert (
-            img.dtype.type is np.uint16
-        ), f'Image (#{i}:{fn.stem}) dtype is {img.dtype} (must be np.uint16)'
+        assert img.dtype.type is np.uint16, (
+            f'Image (#{i}:{fn.stem}) dtype is {img.dtype} (must be np.uint16)'
+        )
 
         h = {'ImageGetTime': timestamp, 'ImageExposureTime': exposure_time}
 

src/instamatic/acquire_at_items.py

@@ -184,5 +184,5 @@ def start(self, start_index: int = 0):
 
         dt = t1 - t0
         n_items = i + 1
-        print(f'Total time taken: {dt:.0f} s for {n_items} items ({dt/n_items:.2f} s/item)')
+        print(f'Total time taken: {dt:.0f} s for {n_items} items ({dt / n_items:.2f} s/item)')
         print('\nAll done!')

src/instamatic/calibrate/calibrate_brightness.py

@@ -174,7 +174,7 @@ def calibrate_brightness_from_image_fn(fns):
 
 def calibrate_brightness(fns=None, ctrl=None, confirm=True):
     if not fns:
-        if confirm and not input("\n >> Go too 2500x mag (type 'go' to start): " '') == 'go':
+        if confirm and not input("\n >> Go too 2500x mag (type 'go' to start): ") == 'go':
             return
         else:
             calib = calibrate_brightness_live(ctrl, save_images=True)

src/instamatic/calibrate/calibrate_movie_delays.py

@@ -372,15 +372,15 @@ def _get_movie_times(exposure_=1e-6) -> MovieTimes:
     ratio = mte.frame1_times.mean() / mte.exposure
     if ratio > 1.1:
         msg = (
-            f'Exposure times exceed expected by {(ratio-1)*100}%. '
+            f'Exposure times exceed expected by {(ratio - 1) * 100}%. '
             f'Consider using longer exposure or smaller header.'
         )
         warnings.warn(msg, CalibWarning)
 
     ratio = mtr.total_times.mean() / mte.total_times.mean()
     if ratio > 0.5:
         msg = (
-            f'Total time is dominated ({ratio*100}%) by header collection. '
+            f'Total time is dominated ({ratio * 100}%) by header collection. '
             f'Consider using longer exposure or smaller header.'
         )
         warnings.warn(msg, CalibWarning)

src/instamatic/calibrate/calibrate_stage_lowmag.py

@@ -278,7 +278,7 @@ def calibrate_stage_lowmag_live(ctrl, gridsize=5, stepsize=50000, save_images=Fa
     i = 0
     for dx, dy in np.stack([x_grid, y_grid]).reshape(2, -1).T:
         print()
-        print(f'Position {i+1}/{tot}: x: {x_cent+dx:.0f}, y: {y_cent+dy:.0f}')
+        print(f'Position {i + 1}/{tot}: x: {x_cent + dx:.0f}, y: {y_cent + dy:.0f}')
 
         ctrl.stage.set(x=x_cent + dx, y=y_cent + dy)
         print(ctrl.stage)

src/instamatic/calibrate/calibrate_stage_mag1.py

@@ -128,7 +128,7 @@ def calibrate_mag1_live(
             stage = ctrl.stage.get()
 
             print()
-            print(f'Position {I+1}/{tot}')
+            print(f'Position {I + 1}/{tot}')
             print(stage)
 
             outfile = work_drc / f'calib_{i:04d}' if save_images else None

src/instamatic/calibrate/calibrate_stagematrix.py

@@ -467,7 +467,7 @@ def main_entry():
         dest='overlap',
         type=float,
         metavar='X',
-        help=('Specify the approximate overlap between images for cross ' 'correlation.'),
+        help=('Specify the approximate overlap between images for cross correlation.'),
     )
 
     parser.add_argument(
@@ -476,7 +476,7 @@ def main_entry():
         dest='stage_length',
         type=int,
         help=(
-            'Specify the minimum length (in stage coordinates) the calibration ' 'should cover.'
+            'Specify the minimum length (in stage coordinates) the calibration should cover.'
         ),
     )
 
@@ -486,9 +486,7 @@ def main_entry():
         dest='min_n_step',
         type=int,
         metavar='N',
-        help=(
-            'Specify the minimum number of steps to take along X and Y for the ' 'calibration.'
-        ),
+        help=('Specify the minimum number of steps to take along X and Y for the calibration.'),
     )
 
     parser.add_argument(

src/instamatic/camera/camera_merlin.py

@@ -237,10 +237,7 @@ def get_image(self, exposure: float = None, **kwargs) -> np.ndarray:
             self.setup_soft_trigger(exposure=exposure)
         elif self._frame_number == self.MAX_NUMFRAMESTOACQUIRE:
             logger.debug(
-                (
-                    'Maximum frame number reached for this acquisition, '
-                    'resetting soft trigger.'
-                )
+                ('Maximum frame number reached for this acquisition, resetting soft trigger.')
                 % self.MAX_NUMFRAMESTOACQUIRE
             )
             self.setup_soft_trigger(exposure=exposure)

src/instamatic/camera/merlin_io.py

@@ -115,9 +115,9 @@ def load_mib(buffer: bytes, skip: int = 0):
         ]
     )
 
-    assert (
-        len(buffer) % merlin_frame_dtype.itemsize == 0
-    ), 'buffer size must be a multiple of item size'
+    assert len(buffer) % merlin_frame_dtype.itemsize == 0, (
+        'buffer size must be a multiple of item size'
+    )
 
     data = np.frombuffer(
         buffer,