fix: Normalize more CLI flags.

src/copick_utils/cli/fit_spline.py

@@ -1,7 +1,12 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
+from copick.cli.util import (
+    add_config_option,
+    add_debug_option,
+    add_run_names_option,
+    resolve_deprecated_option,
+)
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -18,12 +23,15 @@
 @add_run_names_option
 @optgroup.group("\nInput Options", help="Options related to the input segmentation.")
 @add_input_option("segmentation")
+# TODO:remove once deprecation takes effect -- legacy --voxel-spacing/-vs override (vs now comes from the input URI)
 @optgroup.option(
     "--voxel-spacing",
     "-vs",
     type=float,
-    required=True,
-    help="Voxel spacing for coordinate scaling.",
+    required=False,
+    default=None,
+    hidden=True,
+    help="Deprecated: the @voxel_spacing in -i/--input is used instead.",
 )
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @optgroup.option(
@@ -111,14 +119,14 @@ def fit_spline(
     Examples:
 
         \b
-        # Fit splines to skeletonized components
+        # Fit splines to skeletonized components (voxel spacing from the @10.0 in -i)
         copick process fit_spline -i "skeleton:skel/inst-.*@10.0" \\
-            -o "skeleton:spline/spline-{input_session_id}" --spacing-distance 4.4 --voxel-spacing 10.0
+            -o "skeleton:spline/spline-{input_session_id}" --spacing-distance 4.4
 
         \b
         # Process a single skeleton component
         copick process fit_spline -i "skeleton:skel/skel-0@10.0" \\
-            -o "skeleton:spline/spline-0" --spacing-distance 2.0 --voxel-spacing 10.0
+            -o "skeleton:spline/spline-0" --spacing-distance 2.0
 
     See Also:
 
@@ -147,6 +155,24 @@ def fit_spline(
 
     # Extract parameters for logging only
     input_params = parse_copick_uri(input_uri, "segmentation")
+
+    # Voxel spacing comes from the @voxel_spacing in the input URI; the legacy
+    # --voxel-spacing/-vs flag remains a deprecated override.
+    uri_vs_raw = input_params.get("voxel_spacing")
+    uri_vs = float(uri_vs_raw) if uri_vs_raw not in (None, "*") else None
+    # TODO:remove once deprecation takes effect -- legacy -vs override (drop the voxel_spacing param; use uri_vs directly)
+    voxel_spacing = resolve_deprecated_option(
+        uri_vs,
+        voxel_spacing,
+        old_flag="--voxel-spacing/-vs",
+        new_flag="the @voxel_spacing in -i/--input",
+        logger=logger,
+    )
+    if voxel_spacing is None:
+        raise click.BadParameter(
+            "Input URI must include a specific voxel spacing (e.g., @10.0), or pass --voxel-spacing/-vs.",
+        )
+
     logger.info(f"Fitting splines to segmentations '{input_params['name']}'")
     logger.info(
         f"Source segmentation pattern: {input_params['name']} ({input_params['user_id']}/{input_params['session_id']})",

src/copick_utils/cli/picks2mesh.py

@@ -1,7 +1,12 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
+from copick.cli.util import (
+    add_config_option,
+    add_debug_option,
+    add_run_names_option,
+    resolve_deprecated_option,
+)
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -26,11 +31,20 @@
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @optgroup.option(
     "--mesh-type",
-    "-t",
+    "-mt",
     type=click.Choice(["convex_hull", "alpha_shape"]),
     default="convex_hull",
     help="Type of mesh to create.",
 )
+# TODO:remove once deprecation takes effect -- legacy -t alias (reserve -t for --tomogram)
+@optgroup.option(
+    "-t",
+    "legacy_mesh_type",
+    type=click.Choice(["convex_hull", "alpha_shape"]),
+    default=None,
+    hidden=True,
+    help="Deprecated: use -mt/--mesh-type instead.",
+)
 @optgroup.option(
     "--alpha",
     "-a",
@@ -54,6 +68,7 @@ def picks2mesh(
     run_names,
     input_uri,
     mesh_type,
+    legacy_mesh_type,
     alpha,
     use_clustering,
     clustering_method,
@@ -114,6 +129,15 @@ def picks2mesh(
 
     logger = get_logger(__name__, debug=debug)
 
+    # TODO:remove once deprecation takes effect -- legacy -t alias resolution (also drop the legacy_mesh_type param)
+    mesh_type = resolve_deprecated_option(
+        mesh_type,
+        legacy_mesh_type,
+        old_flag="-t",
+        new_flag="-mt/--mesh-type",
+        logger=logger,
+    )
+
     root = copick.from_file(config)
     run_names_list = list(run_names) if run_names else None
 

src/copick_utils/cli/thickness_filter.py

@@ -3,7 +3,12 @@
 import click
 import copick
 from click_option_group import optgroup
-from copick.cli.util import add_config_option, add_debug_option, add_run_names_option
+from copick.cli.util import (
+    add_config_option,
+    add_debug_option,
+    add_run_names_option,
+    resolve_deprecated_option,
+)
 from copick.util.log import get_logger
 from copick.util.uri import parse_copick_uri
 
@@ -23,11 +28,21 @@
 @optgroup.group("\nTool Options", help="Options related to this tool.")
 @optgroup.option(
     "--min-thickness",
-    "-t",
+    "-mt",
     type=float,
-    required=True,
+    required=False,
+    default=None,
     help="Minimum thickness (diameter) of structures to keep. Unit set by --thickness-unit.",
 )
+# TODO:remove once deprecation takes effect -- legacy -t alias (reserve -t for --tomogram); also restore --min-thickness required=True
+@optgroup.option(
+    "-t",
+    "legacy_min_thickness",
+    type=float,
+    default=None,
+    hidden=True,
+    help="Deprecated: use -mt/--min-thickness instead.",
+)
 @optgroup.option(
     "--thickness-unit",
     type=click.Choice(["angstrom", "voxel"]),
@@ -43,6 +58,7 @@ def thickness_filter(
     run_names,
     input_uri,
     min_thickness,
+    legacy_min_thickness,
     thickness_unit,
     workers,
     output_uri,
@@ -88,6 +104,17 @@ def thickness_filter(
 
     logger = get_logger(__name__, debug=debug)
 
+    # TODO:remove once deprecation takes effect -- legacy -t alias resolution (drop legacy_min_thickness + None-check)
+    min_thickness = resolve_deprecated_option(
+        min_thickness,
+        legacy_min_thickness,
+        old_flag="-t",
+        new_flag="-mt/--min-thickness",
+        logger=logger,
+    )
+    if min_thickness is None:
+        raise click.BadParameter("Missing required option: -mt/--min-thickness.")
+
     root = copick.from_file(config)
     run_names_list = list(run_names) if run_names else None
 

src/copick_utils/cli/util.py

@@ -335,17 +335,20 @@ def add_distance_options(func: click.Command) -> click.Command:
 # ============================================================================
 
 
-def add_input_option(object_type: str, func: click.Command = None) -> Callable:
+def add_input_option(object_type: str, func: click.Command = None, required: bool = True) -> Callable:
     """
     Add --input/-i option for URI-based input selection.
 
     Supports copick URI format with pattern matching:
     - Picks/Meshes: object_name:user_id/session_id
     - Segmentations: name:user_id/session_id@voxel_spacing?multilabel=true
+    - Tomograms: tomo_type@voxel_spacing
 
     Args:
-        object_type (str): Type of object ('picks', 'mesh', 'segmentation').
+        object_type (str): Type of object ('picks', 'mesh', 'segmentation', 'tomogram').
         func (click.Command, optional): The Click command to which the option will be added.
+        required (bool): Whether the option is required. Default is True. Pass False for
+            commands that keep deprecated fallback flags (e.g. --tomo-alg/--voxel-size).
 
     Returns:
         Callable: The Click command with the input option added.
@@ -358,6 +361,7 @@ def add_input_option_decorator(_func: click.Command) -> click.Command:
             "picks": "object_name:user_id/session_id",
             "mesh": "object_name:user_id/session_id",
             "segmentation": "name:user_id/session_id@voxel_spacing",
+            "tomogram": "tomo_type@voxel_spacing",
         }
 
         help_text = (
@@ -369,7 +373,7 @@ def add_input_option_decorator(_func: click.Command) -> click.Command:
             "-i",
             "input_uri",
             type=CopickURI(object_type, "input"),
-            required=True,
+            required=required,
             help=help_text,
         )
         return opt(_func)
@@ -380,7 +384,12 @@ def add_input_option_decorator(_func: click.Command) -> click.Command:
         return add_input_option_decorator(func)
 
 
-def add_output_option(object_type: str, func: click.Command = None, default_tool: str = None) -> Callable:
+def add_output_option(
+    object_type: str,
+    func: click.Command = None,
+    default_tool: str = None,
+    required: bool = True,
+) -> Callable:
     """
     Add --output/-o option for URI-based output specification with smart defaults.
 
@@ -411,21 +420,25 @@ def add_output_option_decorator(_func: click.Command) -> click.Command:
             "picks": '"ribosome", "ribosome/my-session", or "/my-session"',
             "mesh": '"membrane", "membrane/my-session", or "/my-session"',
             "segmentation": '"membrane", "membrane/my-session", or "/my-session"',
+            "tomogram": '"wbp@20.0" or "denoised@10.0"',
         }
 
-        voxel_suffix = "@voxel_spacing" if object_type == "segmentation" else ""
-        help_text = (
-            f"Output {object_type} URI. "
-            f"Supports smart defaults (e.g., {shorthand_examples.get(object_type, 'shorthand')}). "
-            f"Full format: object_name:user_id/session_id{voxel_suffix}."
-        )
+        voxel_suffix = "@voxel_spacing" if object_type in ("segmentation", "tomogram") else ""
+        if object_type == "tomogram":
+            help_text = f"Output tomogram URI (format: tomo_type{voxel_suffix}). Example: 'wbp@20.0'."
+        else:
+            help_text = (
+                f"Output {object_type} URI. "
+                f"Supports smart defaults (e.g., {shorthand_examples.get(object_type, 'shorthand')}). "
+                f"Full format: object_name:user_id/session_id{voxel_suffix}."
+            )
 
         opt = optgroup.option(
             "--output",
             "-o",
             "output_uri",
             type=CopickURI(object_type, "output"),
-            required=True,
+            required=required,
             help=help_text,
         )
         return opt(_func)

tests/test_flag_normalization.py

@@ -0,0 +1,57 @@
+"""Tests for the Part 2 CLI flag normalization in copick-utils.
+
+- picks2mesh / thickness_filter: `-t` is reserved for tomogram refs; their old
+  `-t` short flag moved to `-mt` with a hidden `-t` deprecated alias.
+- fit_spline: voxel spacing now comes from the input URI's `@voxel_spacing`; the
+  `--voxel-spacing/-vs` flag is a hidden deprecated override.
+"""
+
+import pytest
+from click.testing import CliRunner
+
+
+@pytest.fixture
+def runner():
+    return CliRunner()
+
+
+def _hidden_alias(cmd, flag):
+    param = next((p for p in cmd.params if flag in getattr(p, "opts", [])), None)
+    return param, (param.hidden if param else None)
+
+
+def test_picks2mesh_reserves_t_for_tomogram(runner):
+    from copick_utils.cli.picks2mesh import picks2mesh
+
+    out = runner.invoke(picks2mesh, ["--help"]).output
+    assert "--mesh-type" in out and "-mt" in out
+    assert "-t " not in out  # -t no longer shown (reserved for --tomogram)
+
+    param, hidden = _hidden_alias(picks2mesh, "-t")
+    assert param is not None and hidden is True
+    assert param.name == "legacy_mesh_type"
+
+
+def test_thickness_filter_reserves_t_for_tomogram(runner):
+    from copick_utils.cli.thickness_filter import thickness_filter
+
+    out = runner.invoke(thickness_filter, ["--help"]).output
+    assert "--min-thickness" in out and "-mt" in out
+    assert "-t " not in out
+
+    param, hidden = _hidden_alias(thickness_filter, "-t")
+    assert param is not None and hidden is True
+    assert param.name == "legacy_min_thickness"
+
+
+def test_fit_spline_derives_vs_from_uri(runner):
+    from copick_utils.cli.fit_spline import fit_spline
+
+    out = runner.invoke(fit_spline, ["--help"]).output
+    assert "-i" in out and "--input" in out
+    # voxel spacing is derived from the input URI; the flag is hidden + deprecated
+    assert "--voxel-spacing" not in out
+    assert "-vs" not in out
+
+    param, hidden = _hidden_alias(fit_spline, "--voxel-spacing")
+    assert param is not None and hidden is True