Add default arguments for Typer Option

src/membrain_seg/annotations/extract_patch_cli.py

@@ -11,14 +11,15 @@
 @cli.command(name="extract_patches", no_args_is_help=True)
 def extract_patches(
     tomogram_path: str = Option(  # noqa: B008
-        help="Path to the tomogram to extract patches from.", **PKWARGS
+        ..., help="Path to the tomogram to extract patches from.", **PKWARGS
     ),
     segmentation_path: str = Option(  # noqa: B008
-        help="Path to the corresponding segmentation file.", **PKWARGS
+        ..., help="Path to the corresponding segmentation file.", **PKWARGS
     ),
     out_folder: str = Option(  # noqa: B008
+        ...,
         help="Path to the folder where extracted patches should be stored. \
-            (subdirectories will be created)"
+            (subdirectories will be created)",
     ),
     coords_file: str = Option(  # noqa: B008
         None,

src/membrain_seg/annotations/merge_corrections_cli.py

@@ -8,15 +8,17 @@
 @cli.command(name="merge_corrections", no_args_is_help=True)
 def merge_corrections(
     labels_dir: str = Option(  # noqa: B008
-        help="Path to the directory containing label files.", **PKWARGS
+        ..., help="Path to the directory containing label files.", **PKWARGS
     ),
     corrections_dir: str = Option(  # noqa: B008
+        ...,
         help="Path to the directory containing correction folders. Each correction \
         folder should have the \
         same name as the corresponding label file (without the file extension).",
         **PKWARGS,
     ),
     out_dir: str = Option(  # noqa: B008
+        ...,
         help="Path to the directory where corrected label files will be saved.",
         **PKWARGS,
     ),

src/membrain_seg/segmentation/cli/segment_cli.py

@@ -8,10 +8,12 @@
 @cli.command(name="segment", no_args_is_help=True)
 def segment(
     tomogram_path: str = Option(  # noqa: B008
-        help="Path to the tomogram to be segmented", **PKWARGS
+        ..., help="Path to the tomogram to be segmented", **PKWARGS
     ),
     ckpt_path: str = Option(  # noqa: B008
-        help="Path to the pre-trained model checkpoint that should be used.", **PKWARGS
+        ...,
+        help="Path to the pre-trained model checkpoint that should be used.",
+        **PKWARGS,
     ),
     out_folder: str = Option(  # noqa: B008
         "./predictions", help="Path to the folder where segmentations should be stored."

src/membrain_seg/segmentation/cli/train_cli.py

@@ -8,6 +8,7 @@
 @cli.command(name="train", no_args_is_help=True)
 def train(
     data_dir: str = Option(  # noqa: B008
+        ...,
         help='Data directory path, following the required structure. To learn more \
             about the required data structure, type "membrain data_structure_help"',
         **PKWARGS,
@@ -54,6 +55,7 @@ def train(
 @cli.command(name="train_advanced", no_args_is_help=True)
 def train_advanced(
     data_dir: str = Option(  # noqa: B008
+        ...,
         help='Data directory path, following the required structure. \
             To learn more about the required\
             data structure, type "membrain data_structure_help"',