Disallow --rank with --subset

Imageomics · Nov 20, 2024 · a466465 · a466465
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Showing 3 changed files with 18 additions and 15 deletions.
diff --git a/README.md b/README.md
@@ -129,8 +129,8 @@ When a list of PIL images is passed the index of the image will be filled in for
 ## Command Line Usage
 ```
 bioclip predict [-h] [--format {table,csv}] [--output OUTPUT]
-                [--rank {kingdom,phylum,class,order,family,genus,species} | --cls CLS | --bins BINS]
-                [--subset SUBSET] [--k K] [--device DEVICE] image_file [image_file ...]
+                [--rank {kingdom,phylum,class,order,family,genus,species} | --cls CLS | --bins BINS | --subset SUBSET]
+                [--k K] [--device DEVICE] image_file [image_file ...]
 bioclip embed [-h] [--device=DEVICE] [--output=OUTPUT] [IMAGE_FILE...]
 
 Commands:
@@ -145,13 +145,13 @@ Options:
   --format=FORMAT      format of the output (table or csv) for predict mode [default: csv]
   --rank {kingdom,phylum,class,order,family,genus,species}
                         rank of the classification, default: species (when)
-  --cls CLS             classes to predict: either a comma separated list or a path to a text file of classes (one per line), when specified the
-                        --rank and --bins arguments are not allowed.
-  --bins BINS           path to CSV file with two columns with the first being classes and second being bin names, when specified the --cls
-                        argument is not allowed.
+  --cls CLS             classes to predict: either a comma separated list or a path to a text file of classes (one per line),
+                        when specified the --rank, --bins, and --subset arguments are not allowed.
+  --bins BINS           path to CSV file with two columns with the first being classes and second being bin names,
+                        when specified the --rank, --cls, and --subset arguments are not allowed.
   --subset SUBSET       CSV used to subset the tree of life embeddings. CSV first column
                         must be named one of kingdom,phylum,class,order,family,genus,species.
-                        When specified the --rank and --bins arguments are not allowed.
+                        When specified the --rank, --bins, and --cls arguments are not allowed.
   --k K                 number of top predictions to show, default: 5
   --device=DEVICE       device to use matrix math (cpu or cuda or mps) [default: cpu]
   --output=OUTFILE      print output to file OUTFILE [default: stdout]

diff --git a/src/bioclip/__main__.py b/src/bioclip/__main__.py
@@ -103,12 +103,12 @@ def create_parser():
     cls_group = predict_parser.add_mutually_exclusive_group(required=False)
     cls_group.add_argument('--rank', choices=['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'],
                                 help='rank of the classification, default: species (when)')
-    cls_help = "classes to predict: either a comma separated list or a path to a text file of classes (one per line), when specified the --rank and --bins arguments are not allowed."
+    cls_help = "classes to predict: either a comma separated list or a path to a text file of classes (one per line), when specified the --rank, --bins, and --subset arguments are not allowed."
     cls_group.add_argument('--cls', help=cls_help)
-    cls_group.add_argument('--bins', help='path to CSV file with two columns with the first being classes and second being bin names, when specified the --cls argument is not allowed.')
+    cls_group.add_argument('--bins', help='path to CSV file with two columns with the first being classes and second being bin names, when specified the --rank, --cls, and --subset arguments are not allowed.')
     subset_labels = ','.join(get_rank_labels())
-    SUBSET_HELP = f"path to CSV file used to subset the tree of life embeddings. CSV first column must be named one of {subset_labels}. When specified the --rank and --bins arguments are not allowed."
-    predict_parser.add_argument('--subset', help=SUBSET_HELP)
+    SUBSET_HELP = f"path to CSV file used to subset the tree of life embeddings. CSV first column must be named one of {subset_labels}. When specified the --rank, --bins, and --cls arguments are not allowed."
+    cls_group.add_argument('--subset', help=SUBSET_HELP)
     predict_parser.add_argument('--k', type=int, help='number of top predictions to show, default: 5')
 
     predict_parser.add_argument('--device', **device_arg)
@@ -148,8 +148,6 @@ def parse_args(input_args=None):
             args.rank = Rank[args.rank.upper()]
             if not args.k:
                 args.k = 5
-        elif args.subset:
-            raise ValueError("The --subset argument cannot be used with --cls or --bins.")
     return args
 
 

diff --git a/tests/test_main.py b/tests/test_main.py
@@ -76,13 +76,18 @@ def test_parse_args(self):
         self.assertEqual(args.k, 10)
 
         # test error when using --cls with --subset
-        with self.assertRaises(ValueError):
+        with self.assertRaises(SystemExit):
             parse_args(['predict', 'image.jpg', '--cls', 'class1,class2', '--subset', 'somefile.cvs'])
 
         # test error when using --bins with --subset
-        with self.assertRaises(ValueError):
+        with self.assertRaises(SystemExit):
             parse_args(['predict', 'image.jpg', '--bins', 'somefile.csv', '--subset', 'somefile.cvs'])
 
+        # test error when using --rank with --subset
+        with self.assertRaises(SystemExit):
+            parse_args(['predict', 'image.jpg', '--rank', 'class', '--subset', 'somefile.cvs'])
+
+
         # example showing filename
         args = parse_args(['predict', 'image.jpg', '--cls', 'classes.txt', '--k', '10'])
         self.assertEqual(args.cls, 'classes.txt')