fix cli testing issues

Author: katosh

kompot/anndata/differential_abundance.py

@@ -442,7 +442,7 @@ def compute_differential_abundance(
 
         # Create landmarks info
         landmarks_info = {
-            'shape': landmarks_shape,
+            'shape': list(landmarks_shape),  # Convert tuple to list for HDF5 serialization
             'dtype': landmarks_dtype,
             'source': 'computed',
             'n_landmarks': landmarks_shape[0],

kompot/cli/da.py

@@ -128,6 +128,12 @@ def add_da_parser(subparsers) -> argparse.ArgumentParser:
         help='Length scale multiplication factor (default: 10.0)'
     )
 
+    parser.add_argument(
+        '--random-state',
+        type=int,
+        help='Random seed for reproducible landmark selection (default: None)'
+    )
+
     # Boolean flags
     parser.add_argument(
         '--store-landmarks',
@@ -171,7 +177,7 @@ def run_da(args):
     # Convert args to dict, removing None values and CLI-specific args
     args_dict = {
         k: v for k, v in vars(args).items()
-        if v is not None and k not in ['input', 'output', 'config', 'func', 'verbose']
+        if v is not None and k not in ['input', 'output', 'config', 'func', 'verbose', 'command']
     }
 
     # Rename CLI args to match function parameters

kompot/cli/de.py

@@ -130,6 +130,13 @@ def add_de_parser(subparsers) -> argparse.ArgumentParser:
         help='Number of null genes for FDR estimation (default: 2000)'
     )
 
+    parser.add_argument(
+        '--null-seed',
+        type=int,
+        default=42,
+        help='Random seed for null gene selection and shuffling (default: 42)'
+    )
+
     # Boolean flags
     parser.add_argument(
         '--no-progress',
@@ -185,7 +192,7 @@ def run_de(args):
     # Convert args to dict, removing None values and CLI-specific args
     args_dict = {
         k: v for k, v in vars(args).items()
-        if v is not None and k not in ['input', 'output', 'config', 'func', 'verbose']
+        if v is not None and k not in ['input', 'output', 'config', 'func', 'verbose', 'command']
     }
 
     # Rename CLI args to match function parameters

kompot/cli/dm.py

@@ -84,9 +84,38 @@ def add_dm_parser(subparsers) -> argparse.ArgumentParser:
     )
 
     parser.add_argument(
-        '--use-adjacency-matrix',
-        action='store_true',
-        help='Use adjacency matrix if available'
+        '--seed',
+        type=int,
+        default=0,
+        help='Random seed for reproducibility (default: 0)'
+    )
+
+    parser.add_argument(
+        '--kernel-key',
+        type=str,
+        default='DM_Kernel',
+        help='Key to store kernel in adata.obsp (default: DM_Kernel)'
+    )
+
+    parser.add_argument(
+        '--sim-key',
+        type=str,
+        default='DM_Similarity',
+        help='Key to store similarity in adata.obsp (default: DM_Similarity)'
+    )
+
+    parser.add_argument(
+        '--eigval-key',
+        type=str,
+        default='DM_EigenValues',
+        help='Key to store eigenvalues in adata.uns (default: DM_EigenValues)'
+    )
+
+    parser.add_argument(
+        '--eigvec-key',
+        type=str,
+        default='DM_EigenVectors',
+        help='Key to store eigenvectors in adata.obsm (default: DM_EigenVectors)'
     )
 
     parser.set_defaults(func=run_dm)
@@ -127,16 +156,22 @@ def run_dm(args):
     # Convert args to dict, removing None values and CLI-specific args
     args_dict = {
         k: v for k, v in vars(args).items()
-        if v is not None and k not in ['input', 'output', 'config', 'func', 'verbose']
+        if v is not None and k not in ['input', 'output', 'config', 'func', 'verbose', 'command']
     }
 
-    # Rename CLI args to match function parameters
+    # Rename CLI args to match function parameters (convert hyphens to underscores)
     if 'pca_key' in args_dict:
         args_dict['pca_key'] = args_dict.pop('pca_key')
     if 'n_components' in args_dict:
         args_dict['n_components'] = args_dict.pop('n_components')
-    if 'use_adjacency_matrix' in args_dict:
-        args_dict['use_adjacency_matrix'] = args_dict.pop('use_adjacency_matrix')
+    if 'kernel_key' in args_dict:
+        args_dict['kernel_key'] = args_dict.pop('kernel_key')
+    if 'sim_key' in args_dict:
+        args_dict['sim_key'] = args_dict.pop('sim_key')
+    if 'eigval_key' in args_dict:
+        args_dict['eigval_key'] = args_dict.pop('eigval_key')
+    if 'eigvec_key' in args_dict:
+        args_dict['eigvec_key'] = args_dict.pop('eigvec_key')
 
     # Merge with config (CLI args take precedence)
     params = merge_args_with_config(args_dict, config)

kompot/cli/main.py

@@ -19,7 +19,7 @@ def main():
     parser.add_argument(
         '--version',
         action='version',
-        version='%(prog)s 0.5.2'
+        version='%(prog)s 0.6.0'
     )
 
     parser.add_argument(

tests/test_cli.py

@@ -437,6 +437,9 @@ def test_dm_missing_pca(self, sample_adata, temp_dir):
         """Test error when PCA is missing."""
         input_file = Path(temp_dir) / 'input.h5ad'
         output_file = Path(temp_dir) / 'output.h5ad'
+
+        # Remove PCA from sample data
+        del sample_adata.obsm['X_pca']
         sample_adata.write_h5ad(input_file)
 
         # Run CLI without PCA in data