Make CKA coherence test opt-in (--run-cka replaces --skip-cka)

CKA requires multiple models with shared subjects and is not always
applicable. Change from opt-out (--skip-cka) to opt-in (--run-cka)
so it only runs when explicitly requested.

Author: Barthelemy-Drabczuk

external/champollion_V1

@@ -426,7 +426,7 @@ def __init__(self):
          .add_flag("--verbose", "Enable verbose output.")
          .add_flag("--cpu", "Force CPU usage (disable CUDA).")
          .add_flag("--profiling", "Enable Python profiling (cProfile).")
-         .add_flag("--skip-cka", "Skip CKA coherence test after embeddings.")
+         .add_flag("--run-cka", "Run CKA coherence test after embeddings.")
          .add_flag("--no-cache", "Force re-extraction of archive (ignore cache).")
          .add_optional_argument(
             "--nb_jobs",
@@ -597,8 +597,8 @@ def _run_pipeline(self, local_dir):
 
         result = self.execute_command(cmd, shell=False)
 
-        # Run CKA coherence test by default (skip if --skip-cka)
-        if not self.args.skip_cka:
+        # Run CKA coherence test only if explicitly requested
+        if self.args.run_cka:
             self._run_cka_test()
 
         os.chdir(local_dir)

src/generate_embeddings.py

@@ -71,7 +71,7 @@ def test_flags_default_to_false(self):
         assert args.verbose is False
         assert args.cpu is False
         assert args.profiling is False
-        assert args.skip_cka is False
+        assert args.run_cka is False
         assert args.no_cache is False
 
     def test_flags_can_be_set(self):
@@ -85,7 +85,7 @@ def test_flags_can_be_set(self):
             "--verbose",
             "--cpu",
             "--profiling",
-            "--skip-cka",
+            "--run-cka",
             "--no-cache"
         ])
         assert args.overwrite is True
@@ -94,7 +94,7 @@ def test_flags_can_be_set(self):
         assert args.verbose is True
         assert args.cpu is True
         assert args.profiling is True
-        assert args.skip_cka is True
+        assert args.run_cka is True
         assert args.no_cache is True
 
     def test_nb_jobs_default_none(self):