feat: Normalize run options across copick-utils CLI

pyproject.toml

@@ -18,7 +18,7 @@ classifiers = [
 ]
 dynamic = ["version"]
 dependencies = [
-    "copick>=1.23.1",
+    "copick>=1.26.0",
     "click",
     "click-option-group",
     "numpy",

src/copick_utils/cli/clipmesh.py

@@ -1,7 +1,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -24,13 +24,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input meshes.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("mesh")
 @optgroup.group("\nReference Options", help="Options for reference surface (provide mesh, segmentation, or tomogram).")
 @add_reference_mesh_option(required=False)

src/copick_utils/cli/clippicks.py

@@ -3,7 +3,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -26,13 +26,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input picks.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("picks")
 @optgroup.group("\nReference Options", help="Options for reference surface (provide mesh, segmentation, or tomogram).")
 @add_reference_mesh_option(required=False)

src/copick_utils/cli/clipseg.py

@@ -1,7 +1,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -24,13 +24,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input segmentations.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("segmentation")
 @optgroup.group("\nReference Options", help="Options for reference surface (provide mesh, segmentation, or tomogram).")
 @add_reference_mesh_option(required=False)

src/copick_utils/cli/combine_labels.py

@@ -3,7 +3,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -17,13 +17,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input segmentations.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("segmentation")
 @add_workers_option
 @optgroup.group("\nOutput Options", help="Options related to the output segmentation.")

src/copick_utils/cli/enclosed.py

@@ -3,7 +3,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -17,13 +17,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input segmentations.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_dual_input_options("segmentation")
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @optgroup.option(

src/copick_utils/cli/expand_labels.py

@@ -3,7 +3,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -17,13 +17,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input segmentation.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("segmentation")
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @optgroup.option(

src/copick_utils/cli/filter_components.py

@@ -3,7 +3,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -17,13 +17,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input segmentation.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("segmentation")
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @optgroup.option(

src/copick_utils/cli/fit_spline.py

@@ -1,7 +1,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -15,12 +15,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input segmentation.")
-@optgroup.option(
-    "--run-names",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("segmentation")
 @optgroup.option(
     "--voxel-spacing",

src/copick_utils/cli/hull.py

@@ -2,7 +2,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -20,13 +20,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input meshes.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("mesh")
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @optgroup.option(

src/copick_utils/cli/mesh2caps.py

@@ -1,7 +1,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -20,13 +20,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input meshes.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("mesh")
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @add_cap_extraction_options

src/copick_utils/cli/mesh2picks.py

@@ -3,7 +3,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -17,13 +17,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input meshes.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("mesh")
 @add_tomogram_option(required=True)
 @optgroup.group("\nTool Options", help="Options related to this tool.")

src/copick_utils/cli/mesh2seg.py

@@ -1,7 +1,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -20,13 +20,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input meshes.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("mesh")
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @add_mesh_voxelization_options

src/copick_utils/cli/meshop.py

@@ -3,7 +3,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -25,13 +25,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to input meshes.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_multi_input_options("mesh")
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @add_boolean_operation_option

src/copick_utils/cli/picks2ellipsoid.py

@@ -1,7 +1,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -20,13 +20,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input picks.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("picks")
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @optgroup.option(

src/copick_utils/cli/picks2mesh.py

@@ -1,7 +1,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -20,13 +20,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input picks.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("picks")
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @optgroup.option(

src/copick_utils/cli/picks2plane.py

@@ -1,7 +1,7 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option
+from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -20,13 +20,8 @@
     no_args_is_help=True,
 )
 @add_config_option
+@add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input picks.")
-@optgroup.option(
-    "--run-names",
-    "-r",
-    multiple=True,
-    help="Specific run names to process (default: all runs).",
-)
 @add_input_option("picks")
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @optgroup.option(