[MRG] add -d/--debug to sourmash sig describe; upgrade output err…

…ors. (#1782)

* add -d/--debug to various commands

* upgrade output error messages

* add message about using --debug

src/sourmash/cli/sig/describe.py

@@ -11,6 +11,10 @@ def subparser(subparsers):
         '-q', '--quiet', action='store_true',
         help='suppress non-error output'
     )
+    subparser.add_argument(
+        '-d', '--debug', action='store_true',
+        help='provide debugging output'
+    )
     subparser.add_argument(
         '--csv', metavar='FILE',
         help='output information to a CSV file'

src/sourmash/sig/__main__.py

@@ -202,7 +202,7 @@ def describe(args):
     """
     provide basic info on signatures
     """
-    set_quiet(args.quiet)
+    set_quiet(args.quiet, args.debug)
     moltype = sourmash_args.calculate_moltype(args)
     picklist = sourmash_args.load_picklist(args)
     pattern_search = sourmash_args.load_include_exclude_db_patterns(args)
@@ -287,7 +287,8 @@ def manifest(args):
         loader = sourmash_args.load_file_as_index(args.location,
                                                   yield_all_files=args.force)
     except ValueError as exc:
-        error(f"Cannot open '{args.location}'.")
+        error(f"Cannot open '{args.location}' as a sourmash signature collection.")
+        error("Use -d/--debug for details.")
         sys.exit(-1)
 
     rebuild = True
@@ -1193,6 +1194,7 @@ def kmers(args):
 _SketchInfo = namedtuple('_SketchInfo', 'ksize, moltype, scaled, num, abund')
 
 
+# NOTE: also aliased as 'summarize'
 def fileinfo(args):
     """
     provide summary information on the given path (collection, index, etc.)
@@ -1209,7 +1211,8 @@ def fileinfo(args):
         idx = sourmash_args.load_file_as_index(args.path,
                                                yield_all_files=args.force)
     except ValueError:
-        error(f"Cannot open '{args.path}'.")
+        error(f"Cannot open '{args.path}' as a sourmash signature collection.")
+        error("Use -d/--debug for details.")
         sys.exit(-1)
 
     print_bool = lambda x: "yes" if x else "no"

tests/test_cmd_signature.py

@@ -3572,7 +3572,7 @@ def test_sig_manifest_does_not_exist(runtmp):
         runtmp.run_sourmash('sig', 'manifest', 'does-not-exist',
                             '-o', 'out.csv')
 
-    assert "Cannot open 'does-not-exist'." in runtmp.last_result.err
+    assert "Cannot open 'does-not-exist' as a sourmash signature collection." in runtmp.last_result.err
 
 
 def test_sig_manifest_7_allzip_1(runtmp):

tests/test_cmd_signature_fileinfo.py

@@ -329,4 +329,4 @@ def test_sig_fileinfo_does_not_exist(runtmp):
     with pytest.raises(SourmashCommandFailed):
         runtmp.run_sourmash('sig', 'fileinfo', 'does-not-exist')
 
-    assert "Cannot open 'does-not-exist'." in runtmp.last_result.err
+    assert "Cannot open 'does-not-exist' as a sourmash signature collection" in runtmp.last_result.err