diff --git a/pyproject.toml b/pyproject.toml index e613ebb..1683ae9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ classifiers = [ ] dynamic = ["version"] dependencies = [ - "copick>=1.23.1", + "copick>=1.26.0", "click", "click-option-group", "numpy", diff --git a/src/copick_utils/cli/clipmesh.py b/src/copick_utils/cli/clipmesh.py index 2cc74ed..c9e8f4f 100644 --- a/src/copick_utils/cli/clipmesh.py +++ b/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) diff --git a/src/copick_utils/cli/clippicks.py b/src/copick_utils/cli/clippicks.py index 69e712d..f05defd 100644 --- a/src/copick_utils/cli/clippicks.py +++ b/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) diff --git a/src/copick_utils/cli/clipseg.py b/src/copick_utils/cli/clipseg.py index c5db7e5..604eb1e 100644 --- a/src/copick_utils/cli/clipseg.py +++ b/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) diff --git a/src/copick_utils/cli/combine_labels.py b/src/copick_utils/cli/combine_labels.py index 590e32f..baac9f7 100644 --- a/src/copick_utils/cli/combine_labels.py +++ b/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.") diff --git a/src/copick_utils/cli/enclosed.py b/src/copick_utils/cli/enclosed.py index 8a8b1ca..9e54b67 100644 --- a/src/copick_utils/cli/enclosed.py +++ b/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( diff --git a/src/copick_utils/cli/expand_labels.py b/src/copick_utils/cli/expand_labels.py index 17d458e..4869955 100644 --- a/src/copick_utils/cli/expand_labels.py +++ b/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( diff --git a/src/copick_utils/cli/filter_components.py b/src/copick_utils/cli/filter_components.py index aae3b44..9e74a05 100644 --- a/src/copick_utils/cli/filter_components.py +++ b/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( diff --git a/src/copick_utils/cli/fit_spline.py b/src/copick_utils/cli/fit_spline.py index 5025b6d..2cd4647 100644 --- a/src/copick_utils/cli/fit_spline.py +++ b/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", diff --git a/src/copick_utils/cli/hull.py b/src/copick_utils/cli/hull.py index 12dc0ba..b40a752 100644 --- a/src/copick_utils/cli/hull.py +++ b/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( diff --git a/src/copick_utils/cli/mesh2caps.py b/src/copick_utils/cli/mesh2caps.py index f2e819e..e1eeb87 100644 --- a/src/copick_utils/cli/mesh2caps.py +++ b/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 diff --git a/src/copick_utils/cli/mesh2picks.py b/src/copick_utils/cli/mesh2picks.py index 84b4ec9..3fe1471 100644 --- a/src/copick_utils/cli/mesh2picks.py +++ b/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.") diff --git a/src/copick_utils/cli/mesh2seg.py b/src/copick_utils/cli/mesh2seg.py index c66aafd..21d098c 100644 --- a/src/copick_utils/cli/mesh2seg.py +++ b/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 diff --git a/src/copick_utils/cli/meshop.py b/src/copick_utils/cli/meshop.py index f427234..0c973a9 100644 --- a/src/copick_utils/cli/meshop.py +++ b/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 diff --git a/src/copick_utils/cli/picks2ellipsoid.py b/src/copick_utils/cli/picks2ellipsoid.py index 85a6ae7..70d0858 100644 --- a/src/copick_utils/cli/picks2ellipsoid.py +++ b/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( diff --git a/src/copick_utils/cli/picks2mesh.py b/src/copick_utils/cli/picks2mesh.py index 2052bd8..e1e656f 100644 --- a/src/copick_utils/cli/picks2mesh.py +++ b/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( diff --git a/src/copick_utils/cli/picks2plane.py b/src/copick_utils/cli/picks2plane.py index 2671563..2d77fa9 100644 --- a/src/copick_utils/cli/picks2plane.py +++ b/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( diff --git a/src/copick_utils/cli/picks2seg.py b/src/copick_utils/cli/picks2seg.py index 7706fda..abc98b5 100644 --- a/src/copick_utils/cli/picks2seg.py +++ b/src/copick_utils/cli/picks2seg.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.") @add_picks_painting_options diff --git a/src/copick_utils/cli/picks2sphere.py b/src/copick_utils/cli/picks2sphere.py index 6633b02..325f59a 100644 --- a/src/copick_utils/cli/picks2sphere.py +++ b/src/copick_utils/cli/picks2sphere.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( diff --git a/src/copick_utils/cli/picks2surface.py b/src/copick_utils/cli/picks2surface.py index ca682fe..2c6b2fc 100644 --- a/src/copick_utils/cli/picks2surface.py +++ b/src/copick_utils/cli/picks2surface.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( diff --git a/src/copick_utils/cli/picksin.py b/src/copick_utils/cli/picksin.py index 709f035..4287a41 100644 --- a/src/copick_utils/cli/picksin.py +++ b/src/copick_utils/cli/picksin.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 @@ -21,13 +21,8 @@ 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 volume (provide either mesh or segmentation).") @add_reference_mesh_option(required=False) diff --git a/src/copick_utils/cli/picksout.py b/src/copick_utils/cli/picksout.py index 66c0a92..ae720d5 100644 --- a/src/copick_utils/cli/picksout.py +++ b/src/copick_utils/cli/picksout.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 @@ -23,13 +23,8 @@ 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 volume (provide either mesh or segmentation).") @add_reference_mesh_option(required=False) diff --git a/src/copick_utils/cli/rescale.py b/src/copick_utils/cli/rescale.py index c4cacbf..67a8cf3 100644 --- a/src/copick_utils/cli/rescale.py +++ b/src/copick_utils/cli/rescale.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 rescaling.") @optgroup.option( diff --git a/src/copick_utils/cli/seg2mesh.py b/src/copick_utils/cli/seg2mesh.py index 69b48c8..3c2aa7c 100644 --- a/src/copick_utils/cli/seg2mesh.py +++ b/src/copick_utils/cli/seg2mesh.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 segmentations.") -@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.") @add_marching_cubes_options diff --git a/src/copick_utils/cli/seg2picks.py b/src/copick_utils/cli/seg2picks.py index 5fb8f18..7e0dcb7 100644 --- a/src/copick_utils/cli/seg2picks.py +++ b/src/copick_utils/cli/seg2picks.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 segmentations.") -@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.") @add_segmentation_processing_options diff --git a/src/copick_utils/cli/seg_stats.py b/src/copick_utils/cli/seg_stats.py index 0d23c23..7bc0860 100644 --- a/src/copick_utils/cli/seg_stats.py +++ b/src/copick_utils/cli/seg_stats.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_utils.cli.util import add_input_option, add_workers_option @@ -15,13 +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", - "-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( diff --git a/src/copick_utils/cli/segop.py b/src/copick_utils/cli/segop.py index 92214b0..2f91a34 100644 --- a/src/copick_utils/cli/segop.py +++ b/src/copick_utils/cli/segop.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 segmentations.") -@optgroup.option( - "--run-names", - "-r", - multiple=True, - help="Specific run names to process (default: all runs).", -) @add_multi_input_options("segmentation") @optgroup.group("\nTool Options", help="Options related to this tool.") @add_boolean_operation_option diff --git a/src/copick_utils/cli/separate_components.py b/src/copick_utils/cli/separate_components.py index aa7c98d..3c9da7a 100644 --- a/src/copick_utils/cli/separate_components.py +++ b/src/copick_utils/cli/separate_components.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.group("\nTool Options", help="Options related to this tool.") @optgroup.option( diff --git a/src/copick_utils/cli/skeletonize.py b/src/copick_utils/cli/skeletonize.py index d236445..ec068a8 100644 --- a/src/copick_utils/cli/skeletonize.py +++ b/src/copick_utils/cli/skeletonize.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 @@ -15,13 +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", - "-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( diff --git a/src/copick_utils/cli/split_labels.py b/src/copick_utils/cli/split_labels.py index b9191d1..f770c31 100644 --- a/src/copick_utils/cli/split_labels.py +++ b/src/copick_utils/cli/split_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 @@ -16,13 +16,8 @@ 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( diff --git a/src/copick_utils/cli/thickness_filter.py b/src/copick_utils/cli/thickness_filter.py index 462910c..5338ac7 100644 --- a/src/copick_utils/cli/thickness_filter.py +++ b/src/copick_utils/cli/thickness_filter.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( diff --git a/src/copick_utils/cli/validbox.py b/src/copick_utils/cli/validbox.py index 45b410f..ad9dd7e 100644 --- a/src/copick_utils/cli/validbox.py +++ b/src/copick_utils/cli/validbox.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 expand_output_uri, parse_copick_uri @@ -16,13 +16,8 @@ no_args_is_help=True, ) @add_config_option +@add_run_names_option @optgroup.group("\nInput Options", help="Options related to the input runs.") -@optgroup.option( - "--run-names", - "-r", - multiple=True, - help="Specific run names to process (default: all runs).", -) @add_tomogram_option(required=True) @optgroup.group("\nTool Options", help="Options related to this tool.") @optgroup.option( diff --git a/tests/test_run_names_option.py b/tests/test_run_names_option.py new file mode 100644 index 0000000..4e2d2a8 --- /dev/null +++ b/tests/test_run_names_option.py @@ -0,0 +1,37 @@ +"""Tests that copick-utils CLI commands use the shared run-selection option. + +All commands were de-duplicated onto ``add_run_names_option`` from +``copick.cli.util``; ``separate_components`` and ``fit_spline`` additionally +gained the ``-r`` short flag they previously lacked. +""" + +import pytest +from click.testing import CliRunner + + +@pytest.fixture +def runner(): + return CliRunner() + + +# A representative slice across the conversion / processing / logical groups, +# including the two commands that previously lacked the -r short flag. +COMMANDS = [ + ("copick_utils.cli.separate_components", "separate_components"), + ("copick_utils.cli.fit_spline", "fit_spline"), + ("copick_utils.cli.picks2seg", "picks2seg"), + ("copick_utils.cli.seg2picks", "seg2picks"), + ("copick_utils.cli.segop", "segop"), + ("copick_utils.cli.rescale", "rescale"), + ("copick_utils.cli.combine_labels", "combine"), +] + + +@pytest.mark.parametrize(("dotted", "attr"), COMMANDS) +def test_command_exposes_standard_run_option(runner, dotted, attr): + import importlib + + cmd = getattr(importlib.import_module(dotted), attr) + out = runner.invoke(cmd, ["--help"]).output + assert "--run-names" in out + assert "-r" in out