[MRG] fix sig check manifest rebuilding

src/sourmash/cli/sig/check.py

@@ -26,6 +26,10 @@ 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(
         '-o', '--output-missing', metavar='FILE',
         help='output picklist with remaining unmatched entries to this file',

src/sourmash/sig/__main__.py

@@ -1296,7 +1296,7 @@ def check(args):
     check signature db(s) against a picklist.
     """
     from sourmash.picklist import PickStyle
-    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)
@@ -1335,7 +1335,7 @@ def check(args):
             sys.exit(-1)
 
         # has manifest, or ok to build (require_manifest=False) - continue!
-        manifest = sourmash_args.get_manifest(idx, rebuild=True)
+        manifest = sourmash_args.get_manifest(idx, require=True)
         manifest_rows = manifest._select(picklist=picklist)
         total_rows_examined += len(manifest)
         total_manifest_rows += manifest_rows

src/sourmash/sourmash_args.py

@@ -766,6 +766,7 @@ def get_manifest(idx, *, require=True, rebuild=False):
     Retrieve a manifest for this idx, loaded with `load_file_as_index`.
 
     If a manifest exists and `rebuild` is False, return the manifest.
+    Even if a manifest exists and `rebuild` is True, rebuild the manifest.
     If a manifest does not exist or `rebuild` is True, try to build one.
     If a manifest cannot be built and `require` is True, error exit.
 
@@ -785,6 +786,7 @@ def get_manifest(idx, *, require=True, rebuild=False):
 
     # need to build one...
     try:
+        debug_literal("get_manifest: rebuilding manifest")
         m = CollectionManifest.create_manifest(idx._signatures_with_internal(),
                                                include_signature=False)
         debug_literal("get_manifest: rebuilt manifest.")