patch command and main

negate/__main__.py

@@ -14,6 +14,8 @@
 from typing import Any
 
 from negate.io.console import CLI_LOGGER, set_root_folder
+from negate.io.blurb import BlurbText
+from negate.extract.unified_core import ExtractionModule
 
 ROOT_FOLDER = Path(__file__).resolve().parent.parent
 CONFIG_PATH = ROOT_FOLDER / "config"
@@ -106,7 +108,9 @@ def _load_model_choices() -> ModelChoices:
     return choices
 
 
-def _build_parser(blurb: BlurbText, choices: ModelChoices, list_results: list[str], list_model: list[str], inference_pair: list[str]) -> argparse.ArgumentParser:
+def _build_parser(
+    blurb: BlurbText, choices: ModelChoices, list_results: list[str], list_model: list[str], inference_pair: list[str]
+) -> argparse.ArgumentParser:
     parser = argparse.ArgumentParser(description="Negate CLI")
     subparsers = parser.add_subparsers(dest="cmd", required=True)
 
@@ -115,11 +119,13 @@ def _build_parser(blurb: BlurbText, choices: ModelChoices, list_results: list[st
     train_parser.add_argument("-l", "--loop", action="store_true", help=blurb.loop)
     train_parser.add_argument("-f", "--features", choices=list_results, default=None, help=blurb.features_load)
 
-    process_parser = subparsers.add_parser("process", help="Run all decompose/extract module combinations")
+    module_list = ", ".join(mod.name for mod in ExtractionModule)
+    process_help = f"Run all decompose/extract module combinations. Available modules: {module_list}"
+    process_parser = subparsers.add_parser("process", help=process_help)
     process_parser.add_argument("path", help=blurb.unidentified_path)
     process_parser.add_argument("-v", "--verbose", action="store_true", help=blurb.verbose)
     process_parser.add_argument("--transposed", default=None, help="Comma-separated transposed indices")
-    process_parser.add_argument("--combination", default=None, help="Comma-separated module names")
+    process_parser.add_argument("--combination", default=None, help=f"Comma-separated module names from: {module_list}")
     process_parser.add_argument("--train", choices=["convnext", "xgboost"], default=None, help="Train model after processing")
 
     vit_help = f"Vison {blurb.model_desc} {choices.default_vit}".strip()

negate/command.py

@@ -8,6 +8,7 @@
 from pathlib import Path
 from typing import Any
 import time as timer_module
+from negate.io.console import configure_runtime_logging, CLI_LOGGER
 
 start_ns = timer_module.perf_counter()
 

results/20260412_080531/results_real_20260412_080531.json

@@ -0,0 +1,3 @@
+{
+    "x_p": "{'image_mean_ff': 0.5551752934617227, 'image_std': 0.0977445244532872, 'image_mean': (28894107043657, 57788214087314), 'diff_mean': (25353770906193, 50707541812387), 'laplace_mean': (24083985868529, 48167971737058), 'sobel_mean': (26436775610593, 52873551221187), 'image_tc': (16, 16), 'diff_tc': (29, 29), 'laplace_tc': (25, 25), 'sobel_tc': (25, 25), 'spectral_tc': (16, 16)}"
+}

tests/test_main_help.py

@@ -0,0 +1,77 @@
+# SPDX-License-Identifier: MPL-2.0 AND LicenseRef-Commons-Clause-License-Condition-1.0
+# <!-- // /*  d a r k s h a p e s */ -->
+
+"""Test suite for CLI help text."""
+
+import argparse
+import sys
+from io import StringIO
+from negate.extract.unified_core import ExtractionModule
+
+
+def test_process_help_includes_all_modules():
+    """Verify process command help lists all ExtractionModule options."""
+    from negate.__main__ import _load_blurb_text, _load_model_choices, _build_parser
+
+    blurb = _load_blurb_text()
+    choices = _load_model_choices()
+
+    parser = _build_parser(
+        blurb=blurb,
+        choices=choices,
+        list_results=[],
+        list_model=[],
+        inference_pair=[],
+    )
+
+    help_output = StringIO()
+    try:
+        parser.parse_args(["process", "-h"])
+    except SystemExit:
+        pass
+
+    help_text = parser.format_help()
+    process_subparser = None
+
+    for action in parser._subparsers._actions:
+        if isinstance(action, argparse._SubParsersAction):
+            if "process" in action.choices:
+                process_subparser = action.choices["process"]
+                break
+
+    assert process_subparser is not None, "process subparser not found"
+
+    process_help = process_subparser.format_help()
+
+    for module in ExtractionModule:
+        assert module.name in process_help, f"Module {module.name} not found in process help text"
+
+
+def test_process_help_module_list_matches_enum():
+    """Verify the module list in help matches ExtractionModule enum."""
+    from negate.__main__ import _load_blurb_text, _load_model_choices, _build_parser
+
+    blurb = _load_blurb_text()
+    choices = _load_model_choices()
+
+    parser = _build_parser(
+        blurb=blurb,
+        choices=choices,
+        list_results=[],
+        list_model=[],
+        inference_pair=[],
+    )
+
+    for action in parser._subparsers._actions:
+        if isinstance(action, argparse._SubParsersAction):
+            if "process" in action.choices:
+                process_subparser = action.choices["process"]
+                break
+
+    process_help = process_subparser.format_help()
+
+    module_names = [mod.name for mod in ExtractionModule]
+    for module_name in module_names:
+        assert module_name in process_help, f"Module {module_name} missing from help"
+
+    assert len(module_names) == len(ExtractionModule), "Module list count mismatch"