make manifest internal_location relative for MultiIndex

src/sourmash/index.py

@@ -882,37 +882,59 @@ def sigloc_iter():
         return cls(manifest)
 
     @classmethod
-    def load_from_path(cls, pathname, force=False):
-        """
-        Create a MultiIndex from a path (filename or directory).
-
-        Note: this only uses LinearIndex.load(...), so will only load
-        signature JSON files.
-        """
+    def load_from_directory(cls, pathname, force=False):
         from .sourmash_args import traverse_find_sigs
-        if not os.path.exists(pathname): # CTB consider changing to isdir...
-            raise ValueError(f"'{pathname}' must exist.")
 
         index_list = []
         source_list = []
-        for thisfile in traverse_find_sigs([pathname], yield_all_files=force):
+
+        traversal = traverse_find_sigs([pathname], yield_all_files=force)
+        for thisfile in traversal:
             try:
                 idx = LinearIndex.load(thisfile)
+                index_list.append(idx)
 
-                if idx:
-                    index_list.append(idx)
-                    source_list.append(thisfile)
+                relpath = os.path.relpath(thisfile, pathname)
+                source_list.append(relpath)
             except (IOError, sourmash.exceptions.SourmashError):
                 if force:
                     continue    # ignore error
                 else:
                     raise       # stop loading!
 
+        # did we load anything? if not, error
         if not index_list:
             raise ValueError(f"no signatures to load under directory '{pathname}'")
 
         return cls.load(index_list, source_list)
 
+    @classmethod
+    def load_from_path(cls, pathname, force=False):
+        """
+        Create a MultiIndex from a path (filename or directory).
+
+        Note: this only uses LinearIndex.load(...), so will only load
+        signature JSON files.
+        """
+        if not os.path.exists(pathname):
+            raise ValueError(f"'{pathname}' must exist.")
+
+        if os.path.isdir(pathname): # traverse
+            return cls.load_from_directory(pathname, force=force)
+        else:                   # load as a .sig/JSON file
+            index_list = []
+            source_list = []
+            try:
+                idx = LinearIndex.load(pathname)
+                index_list = [idx]
+                source_list = [pathname]
+            except (IOError, sourmash.exceptions.SourmashError):
+                if not force:
+                    raise ValueError(f"no signatures to load from '{pathname}'")
+                return None
+
+            return cls.load(index_list, source_list)
+
     @classmethod
     def load_from_pathlist(cls, filename):
         """Create a MultiIndex from all files listed in a text file.