Pre commits

Notion task: https://www.notion.so/qim-dtu/Pre-commit-pipeline-1728f41887814960b6f5870460995cf4

All developers need to hook the pre-commit into the git commit command. The required packages are pre-commit and ruff. After they have been installed, the pre-commits are hooked onto git by running pre-commit install.

The details on how it works and how to use it are all in described in Notion.

qim3d/cli/__init__.py

 import argparse
-import webbrowser
+import os
 import platform
+import webbrowser
+
 import outputformat as ouf
+
 import qim3d
-import os
 
 QIM_TITLE = ouf.rainbow(
     rf"""
@@ -16,126 +18,123 @@ QIM_TITLE = ouf.rainbow(
 
     """,
     return_str=True,
-    cmap="hot",
+    cmap='hot',
 )
 
 
 def parse_tuple(arg):
     # Remove parentheses if they are included and split by comma
-    return tuple(map(int, arg.strip("()").split(",")))
+    return tuple(map(int, arg.strip('()').split(',')))
 
 
 def main():
-    parser = argparse.ArgumentParser(description="qim3d command-line interface.")
-    subparsers = parser.add_subparsers(title="Subcommands", dest="subcommand")
+    parser = argparse.ArgumentParser(description='qim3d command-line interface.')
+    subparsers = parser.add_subparsers(title='Subcommands', dest='subcommand')
 
     # GUIs
-    gui_parser = subparsers.add_parser("gui", help="Graphical User Interfaces.")
+    gui_parser = subparsers.add_parser('gui', help='Graphical User Interfaces.')
 
     gui_parser.add_argument(
-        "--data-explorer", action="store_true", help="Run data explorer."
-    )
-    gui_parser.add_argument("--iso3d", action="store_true", help="Run iso3d.")
-    gui_parser.add_argument(
-        "--annotation-tool", action="store_true", help="Run annotation tool."
+        '--data-explorer', action='store_true', help='Run data explorer.'
     )
+    gui_parser.add_argument('--iso3d', action='store_true', help='Run iso3d.')
     gui_parser.add_argument(
-        "--local-thickness", action="store_true", help="Run local thickness tool."
+        '--annotation-tool', action='store_true', help='Run annotation tool.'
     )
     gui_parser.add_argument(
-        "--layers", action="store_true", help="Run Layers."
+        '--local-thickness', action='store_true', help='Run local thickness tool.'
     )
-    gui_parser.add_argument("--host", default="0.0.0.0", help="Desired host.")
+    gui_parser.add_argument('--layers', action='store_true', help='Run Layers.')
+    gui_parser.add_argument('--host', default='0.0.0.0', help='Desired host.')
     gui_parser.add_argument(
-        "--platform", action="store_true", help="Use QIM platform address"
+        '--platform', action='store_true', help='Use QIM platform address'
     )
     gui_parser.add_argument(
-        "--no-browser", action="store_true", help="Do not launch browser."
+        '--no-browser', action='store_true', help='Do not launch browser.'
     )
 
     # Viz
-    viz_parser = subparsers.add_parser("viz", help="Volumetric visualization.")
-    viz_parser.add_argument("source", help="Path to the image file")
+    viz_parser = subparsers.add_parser('viz', help='Volumetric visualization.')
+    viz_parser.add_argument('source', help='Path to the image file')
     viz_parser.add_argument(
-        "-m",
-        "--method",
+        '-m',
+        '--method',
         type=str,
-        metavar="METHOD",
-        default="itk-vtk",
-        help="Which method is used to display file.",
+        metavar='METHOD',
+        default='itk-vtk',
+        help='Which method is used to display file.',
     )
     viz_parser.add_argument(
-        "--destination", default="k3d.html", help="Path to save html file."
+        '--destination', default='k3d.html', help='Path to save html file.'
     )
     viz_parser.add_argument(
-        "--no-browser", action="store_true", help="Do not launch browser."
+        '--no-browser', action='store_true', help='Do not launch browser.'
     )
 
     # Preview
     preview_parser = subparsers.add_parser(
-        "preview", help="Preview of the image in CLI"
+        'preview', help='Preview of the image in CLI'
     )
     preview_parser.add_argument(
-        "filename",
+        'filename',
         type=str,
-        metavar="FILENAME",
-        help="Path to image that will be displayed",
+        metavar='FILENAME',
+        help='Path to image that will be displayed',
     )
     preview_parser.add_argument(
-        "--slice",
+        '--slice',
         type=int,
-        metavar="S",
+        metavar='S',
         default=None,
-        help="Specifies which slice of the image will be displayed.\nDefaults to middle slice. If number exceeds number of slices, last slice will be displayed.",
+        help='Specifies which slice of the image will be displayed.\nDefaults to middle slice. If number exceeds number of slices, last slice will be displayed.',
     )
     preview_parser.add_argument(
-        "--axis",
+        '--axis',
         type=int,
-        metavar="AX",
+        metavar='AX',
         default=0,
-        help="Specifies from which axis will be the slice taken. Defaults to 0.",
+        help='Specifies from which axis will be the slice taken. Defaults to 0.',
     )
     preview_parser.add_argument(
-        "--resolution",
+        '--resolution',
         type=int,
-        metavar="RES",
+        metavar='RES',
         default=80,
-        help="Resolution of displayed image. Defaults to 80.",
+        help='Resolution of displayed image. Defaults to 80.',
     )
     preview_parser.add_argument(
-        "--absolute_values",
-        action="store_false",
-        help="By default set the maximum value to be 255 so the contrast is strong. This turns it off.",
+        '--absolute_values',
+        action='store_false',
+        help='By default set the maximum value to be 255 so the contrast is strong. This turns it off.',
     )
 
     # File Convert
     convert_parser = subparsers.add_parser(
-        "convert",
-        help="Convert files to different formats without loading the entire file into memory",
+        'convert',
+        help='Convert files to different formats without loading the entire file into memory',
     )
     convert_parser.add_argument(
-        "input_path",
+        'input_path',
         type=str,
-        metavar="Input path",
-        help="Path to image that will be converted",
+        metavar='Input path',
+        help='Path to image that will be converted',
     )
     convert_parser.add_argument(
-        "output_path",
+        'output_path',
         type=str,
-        metavar="Output path",
-        help="Path to save converted image",
+        metavar='Output path',
+        help='Path to save converted image',
     )
     convert_parser.add_argument(
-        "--chunks",
+        '--chunks',
         type=parse_tuple,
-        metavar="Chunk shape",
+        metavar='Chunk shape',
         default=(64, 64, 64),
-        help="Chunk size for the zarr file. Defaults to (64, 64, 64).",
+        help='Chunk size for the zarr file. Defaults to (64, 64, 64).',
     )
     args = parser.parse_args()
 
-    if args.subcommand == "gui":
-
+    if args.subcommand == 'gui':
         arghost = args.host
         inbrowser = not args.no_browser  # Should automatically open in browser
 
@@ -152,7 +151,7 @@ def main():
             interface_class = qim3d.gui.layers2d.Interface
         else:
             print(
-                "Please select a tool by choosing one of the following flags:\n\t--data-explorer\n\t--iso3d\n\t--annotation-tool\n\t--local-thickness"
+                'Please select a tool by choosing one of the following flags:\n\t--data-explorer\n\t--iso3d\n\t--annotation-tool\n\t--local-thickness'
             )
             return
         interface = (
@@ -164,31 +163,27 @@ def main():
         else:
             interface.launch(inbrowser=inbrowser, force_light_mode=False)
 
-    elif args.subcommand == "viz":
-
-        if args.method == "itk-vtk":
-
+    elif args.subcommand == 'viz':
+        if args.method == 'itk-vtk':
             # We need the full path to the file for the viewer
             current_dir = os.getcwd()
             full_path = os.path.normpath(os.path.join(current_dir, args.source))
-            qim3d.viz.itk_vtk(full_path, open_browser = not args.no_browser)
+            qim3d.viz.itk_vtk(full_path, open_browser=not args.no_browser)
 
-
-        elif args.method == "k3d":
+        elif args.method == 'k3d':
             volume = qim3d.io.load(str(args.source))
-            print("\nGenerating k3d plot...")
+            print('\nGenerating k3d plot...')
             qim3d.viz.volumetric(volume, show=False, save=str(args.destination))
-            print(f"Done, plot available at <{args.destination}>")
+            print(f'Done, plot available at <{args.destination}>')
             if not args.no_browser:
-                print("Opening in default browser...")
+                print('Opening in default browser...')
                 webbrowser.open_new_tab(args.destination)
         else:
             raise NotImplementedError(
                 f"Method '{args.method}' is not valid. Try 'k3d' or default 'itk-vtk-viewer'"
             )
 
-    elif args.subcommand == "preview":
-
+    elif args.subcommand == 'preview':
         image = qim3d.io.load(args.filename)
 
         qim3d.viz.image_preview(
@@ -199,22 +194,21 @@ def main():
             relative_intensity=args.absolute_values,
         )
 
-    elif args.subcommand == "convert":
-
+    elif args.subcommand == 'convert':
         qim3d.io.convert(args.input_path, args.output_path, chunk_shape=args.chunks)
 
     elif args.subcommand is None:
         print(QIM_TITLE)
         welcome_text = (
-            "\nqim3d is a Python package for 3D image processing and visualization.\n"
+            '\nqim3d is a Python package for 3D image processing and visualization.\n'
             f"For more information, please visit {ouf.c('https://platform.qim.dk/qim3d/', color='orange', return_str=True)}\n"
-            " \n"
+            ' \n'
             "For more information on each subcommand, type 'qim3d <subcommand> --help'.\n"
         )
         print(welcome_text)
         parser.print_help()
-        print("\n")
+        print('\n')
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     main()