swap ValueError for SourmashCommandFailed (#1709)

tests/test_cmd_signature.py

@@ -2391,7 +2391,7 @@ def test_sig_downsample_check_num_bounds_negative(runtmp):
     c=runtmp
     sig47 = utils.get_test_data('47.fa.sig')
 
-    with pytest.raises(ValueError):
+    with pytest.raises(SourmashCommandFailed):
         c.run_sourmash('sig', 'downsample', '--num', '-5', sig47)
 
     assert "ERROR: --num-hashes value must be positive" in c.last_result.err
@@ -2410,7 +2410,7 @@ def test_sig_downsample_check_num_bounds_more_than_maximum(runtmp):
     c=runtmp
     sig47 = utils.get_test_data('47.fa.sig')
 
-    with pytest.raises(ValueError):
+    with pytest.raises(SourmashCommandFailed):
         c.run_sourmash('sig', 'downsample', '--num', '100000', sig47)
 
     assert "WARNING: --num-hashes value should be <= 50000. Continuing anyway." in c.last_result.err

tests/test_sourmash.py

@@ -3552,7 +3552,7 @@ def test_multigather_check_scaled_bounds_less_than_minimum(c):
 
     cmd = 'multigather --query {} --db gcf_all -k 21 --scaled 50 --threshold-bp=0'.format(query_sig)
     cmd = cmd.split(' ')
-    # Note: this is the value error that is emited, but we want the Warning from below to be generated instead. (ValueError: new scaled 50.0 is lower than current sample scaled 10000)
+    # Note: this is the value error that is emitted, but we want the Warning from below to be generated instead. (ValueError: new scaled 50.0 is lower than current sample scaled 10000)
     with pytest.raises(SourmashCommandFailed) as exc:
         c.run_sourmash(*cmd)
 
@@ -4846,7 +4846,7 @@ def test_watch_check_num_bounds_negative(runtmp):
 
     c.run_sourmash('index', '--dna', '-k', '21', 'zzz', '1.sig')
 
-    with pytest.raises(ValueError) as exc:
+    with pytest.raises(SourmashCommandFailed) as exc:
         c.run_sourmash('watch', '--ksize', '21', '-n', '-5', '--dna', 'zzz', testdata0)
 
     assert "ERROR: --num-hashes value must be positive" in c.last_result.err

tests/test_sourmash_compute.py

@@ -46,7 +46,7 @@ def test_do_sourmash_compute_check_num_bounds_negative(runtmp):
     testdata3 = utils.get_test_data('short3.fa')
     sigfile = c.output('short.fa.sig')
 
-    with pytest.raises(ValueError):
+    with pytest.raises(SourmashCommandFailed):
         c.run_sourmash('compute', '-k', '31', '--num-hashes', '-5', '-o', sigfile, '--merge', '"name"', testdata1, testdata2, testdata3)
 
     assert "ERROR: --num-hashes value must be positive" in c.last_result.err