diff --git a/src/sourmash/__init__.py b/src/sourmash/__init__.py
index 53ee6e4803..b6107d08c0 100644
--- a/src/sourmash/__init__.py
+++ b/src/sourmash/__init__.py
@@ -44,10 +44,10 @@ class MinHash - hash sketch class
 MAX_HASH = get_minhash_max_hash()
 
 from .signature import (
-    load_signatures as load_signatures_private,
-    load_one_signature,
+    load_signatures_from_json,
+    load_one_signature_from_json,
     SourmashSignature,
-    save_signatures,
+    save_signatures_to_json,
 )
 
 
@@ -69,7 +69,33 @@ def load_signatures(*args, **kwargs):
     has been removed and the function no longer outputs to stderr.
     Moreover, do_raise is now True by default.
     """
-    return load_signatures_private(*args, **kwargs)
+    return load_signatures_from_json(*args, **kwargs)
+
+
+@deprecated(
+    deprecated_in="4.8.9",
+    removed_in="5.0",
+    current_version=VERSION,
+    details="Use load_file_as_signatures instead.",
+)
+def load_one_signature(*args, **kwargs):
+    """Load a JSON string with signatures into classes.
+
+    Returns list of SourmashSignature objects.
+
+    Note, the order is not necessarily the same as what is in the source file.
+    """
+    return load_one_signature_from_json(*args, **kwargs)
+
+
+@deprecated(
+    deprecated_in="4.8.9",
+    removed_in="5.0",
+    current_version=VERSION,
+    details="use sourmash_args.SaveSignaturesToLocation instead.",
+)
+def save_signatures(*args, **kwargs):
+    return save_signatures_to_json(*args, **kwargs)
 
 
 from .sbtmh import load_sbt_index as load_sbt_index_private
diff --git a/src/sourmash/index/__init__.py b/src/sourmash/index/__init__.py
index ffd698b423..c0577220db 100644
--- a/src/sourmash/index/__init__.py
+++ b/src/sourmash/index/__init__.py
@@ -46,7 +46,8 @@
 )
 from sourmash.manifest import CollectionManifest
 from sourmash.logging import debug_literal
-from sourmash.signature import load_signatures, save_signatures
+from sourmash.signature import load_signatures_from_json, save_signatures_to_json
+
 from sourmash.minhash import (
     flatten_and_downsample_scaled,
     flatten_and_downsample_num,
@@ -425,12 +426,12 @@ def insert(self, node):
 
     def save(self, path):
         with open(path, "w") as fp:
-            save_signatures(self.signatures(), fp)
+            save_signatures_to_json(self.signatures(), fp)
 
     @classmethod
     def load(cls, location, filename=None):
         "Load signatures from a JSON signature file."
-        si = load_signatures(location, do_raise=True)
+        si = load_signatures_from_json(location, do_raise=True)
 
         if filename is None:
             filename = location
@@ -639,7 +640,7 @@ def _signatures_with_internal(self):
                 or self.traverse_yield_all
             ):
                 sig_data = self.storage.load(filename)
-                for ss in load_signatures(sig_data):
+                for ss in load_signatures_from_json(sig_data):
                     yield ss, filename
 
     def signatures(self):
@@ -653,7 +654,7 @@ def signatures(self):
             # yield all signatures found in manifest
             for filename in manifest.locations():
                 data = self.storage.load(filename)
-                for ss in load_signatures(data):
+                for ss in load_signatures_from_json(data):
                     # in case multiple signatures are in the file, check
                     # to make sure we want to return each one.
                     if ss in manifest:
@@ -682,7 +683,7 @@ def select(x):
                             return True
 
                     data = self.storage.load(filename)
-                    for ss in load_signatures(data):
+                    for ss in load_signatures_from_json(data):
                         if select(ss):
                             yield ss
 
diff --git a/src/sourmash/save_load.py b/src/sourmash/save_load.py
index 1f73c116c7..850d7f2b10 100644
--- a/src/sourmash/save_load.py
+++ b/src/sourmash/save_load.py
@@ -299,8 +299,8 @@ def _get_signatures_from_rust(siglist):
     # minhash (and hence one md5sum) per signature, while
     # Rust supports multiple. For now, go through serializing
     # and deserializing the signature! See issue #1167 for more.
-    json_str = sourmash.save_signatures(siglist)
-    yield from sourmash.signature.load_signatures(json_str)
+    json_str = sigmod.save_signatures_to_json(siglist)
+    yield from sigmod.load_signatures_from_json(json_str)
 
 
 class SaveSignatures_NoOutput(Base_SaveSignaturesToLocation):
@@ -362,7 +362,7 @@ def add(self, ss):
                 i += 1
 
         with open(outname, "wb") as fp:
-            sigmod.save_signatures([ss], fp, compression=1)
+            sigmod.save_signatures_to_json([ss], fp, compression=1)
 
 
 class SaveSignatures_SqliteIndex(Base_SaveSignaturesToLocation):
@@ -425,7 +425,7 @@ def open(self):
 
     def close(self):
         if self.location == "-":
-            sourmash.save_signatures(self.keep, sys.stdout)
+            sigmod.save_signatures_to_json(self.keep, sys.stdout)
         else:
             # text mode? encode in utf-8
             mode = "w"
@@ -437,7 +437,7 @@ def close(self):
                 mode = "wb"
 
             with open(self.location, mode, encoding=encoding) as fp:
-                sourmash.save_signatures(self.keep, fp, compression=self.compress)
+                sigmod.save_signatures_to_json(self.keep, fp, compression=self.compress)
 
     def add(self, ss):
         super().add(ss)
@@ -470,6 +470,7 @@ def close(self):
         manifest_data = manifest_fp.getvalue().encode("utf-8")
 
         self.storage.save(manifest_name, manifest_data, overwrite=True, compress=True)
+
         self.storage.flush()
         self.storage.close()
 
@@ -523,7 +524,7 @@ def add(self, add_sig):
             raise ValueError("this output is not open")
 
         for ss in _get_signatures_from_rust([add_sig]):
-            buf = sigmod.save_signatures([ss], compression=1)
+            buf = sigmod.save_signatures_to_json([ss], compression=1)
             md5 = ss.md5sum()
 
             storage = self.storage
diff --git a/src/sourmash/sbt.py b/src/sourmash/sbt.py
index 452ca29375..ccb7fc3d78 100644
--- a/src/sourmash/sbt.py
+++ b/src/sourmash/sbt.py
@@ -162,7 +162,7 @@ def signatures(self):
         if self.manifest:
             # if manifest, use it & load using direct path to storage.
             # this will be faster when using picklists.
-            from .signature import load_one_signature
+            from .signature import load_one_signature_from_json
 
             manifest = self.manifest
 
@@ -175,7 +175,7 @@ def signatures(self):
                 buf = self.storage.load(loc)
                 # if more than one signature can be in a file, we need
                 # to recheck picklists here.
-                ss = load_one_signature(buf)
+                ss = load_one_signature_from_json(buf)
                 yield ss
         else:
             # no manifest? iterate over all leaves.
diff --git a/src/sourmash/sbt_storage.py b/src/sourmash/sbt_storage.py
index 1b7a9e7d78..1bb7e4b7c3 100644
--- a/src/sourmash/sbt_storage.py
+++ b/src/sourmash/sbt_storage.py
@@ -8,6 +8,7 @@
 import zipfile
 from abc import ABC
 from pathlib import Path
+import warnings
 
 from ._lowlevel import ffi, lib
 from .utils import RustObject, rustcall, decode_str
@@ -279,27 +280,31 @@ def _write_to_zf(self, zf, path, content, *, compress=False):
         zi.external_attr = perms
 
     def save(self, path, content, *, overwrite=False, compress=False):
-        # First try to save to self.zipfile, if it is not writable
-        # or would introduce duplicates then try to save it in the buffer
-        if overwrite:
-            newpath = path
-            do_write = True
-        else:
-            newpath, do_write = self._generate_filename(self.zipfile, path, content)
-        if do_write:
-            try:
-                self._write_to_zf(self.zipfile, newpath, content, compress=compress)
-            except (ValueError, RuntimeError):
-                # Can't write in the zipfile, write in buffer instead
-                # CTB: do we need to generate a new filename wrt to the
-                # bufferzip, too? Not sure this code is working as intended...
-                if self.bufferzip:
-                    self._write_to_zf(
-                        self.bufferzip, newpath, content, compress=compress
-                    )
-                else:
-                    # Throw error, can't write the data
-                    raise ValueError("can't write data")
+        # ignore UserWarnings for duplicate filenames.
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+
+            # First try to save to self.zipfile, if it is not writable
+            # or would introduce duplicates then try to save it in the buffer
+            if overwrite:
+                newpath = path
+                do_write = True
+            else:
+                newpath, do_write = self._generate_filename(self.zipfile, path, content)
+            if do_write:
+                try:
+                    self._write_to_zf(self.zipfile, newpath, content, compress=compress)
+                except (ValueError, RuntimeError):
+                    # Can't write in the zipfile, write in buffer instead
+                    # CTB: do we need to generate a new filename wrt to the
+                    # bufferzip, too? Not sure this code is working as intended...
+                    if self.bufferzip:
+                        self._write_to_zf(
+                            self.bufferzip, newpath, content, compress=compress
+                        )
+                    else:
+                        # Throw error, can't write the data
+                        raise ValueError("can't write data")
 
         return newpath
 
diff --git a/src/sourmash/sbtmh.py b/src/sourmash/sbtmh.py
index 3fa7aa23f2..9bc1586dd4 100644
--- a/src/sourmash/sbtmh.py
+++ b/src/sourmash/sbtmh.py
@@ -52,7 +52,7 @@ def save(self, path):
         # content...)
         self.data
 
-        buf = signature.save_signatures([self.data], compression=1)
+        buf = signature.save_signatures_to_json([self.data], compression=1)
         return self.storage.save(path, buf)
 
     def update(self, parent):
@@ -70,7 +70,7 @@ def update(self, parent):
     def data(self):
         if self._data is None:
             buf = BytesIO(self.storage.load(self._path))
-            self._data = signature.load_one_signature(buf)
+            self._data = signature.load_one_signature_from_json(buf)
         return self._data
 
     @data.setter
diff --git a/src/sourmash/signature.py b/src/sourmash/signature.py
index 3faa5e856b..6f0a9d7b83 100644
--- a/src/sourmash/signature.py
+++ b/src/sourmash/signature.py
@@ -379,7 +379,7 @@ def _detect_input_type(data):
     return SigInput.UNKNOWN
 
 
-def load_signatures(
+def load_signatures_from_json(
     data,
     ksize=None,
     select_moltype=None,
@@ -469,8 +469,10 @@ def load_signatures(
             raise
 
 
-def load_one_signature(data, ksize=None, select_moltype=None, ignore_md5sum=False):
-    sigiter = load_signatures(
+def load_one_signature_from_json(
+    data, ksize=None, select_moltype=None, ignore_md5sum=False
+):
+    sigiter = load_signatures_from_json(
         data, ksize=ksize, select_moltype=select_moltype, ignore_md5sum=ignore_md5sum
     )
 
@@ -487,7 +489,7 @@ def load_one_signature(data, ksize=None, select_moltype=None, ignore_md5sum=Fals
     raise ValueError("expected to load exactly one signature")
 
 
-def save_signatures(siglist, fp=None, compression=0):
+def save_signatures_to_json(siglist, fp=None, compression=0):
     "Save multiple signatures into a JSON string (or into file handle 'fp')"
     attached_refs = weakref.WeakKeyDictionary()
 
diff --git a/tests/test_cmd_signature.py b/tests/test_cmd_signature.py
index 04133a6796..432881b3b9 100644
--- a/tests/test_cmd_signature.py
+++ b/tests/test_cmd_signature.py
@@ -12,7 +12,11 @@
 
 import sourmash_tst_utils as utils
 import sourmash
-from sourmash.signature import load_signatures
+from sourmash.signature import (
+    load_signatures_from_json,
+    save_signatures_to_json,
+    load_one_signature_from_json,
+)
 from sourmash.manifest import CollectionManifest
 from sourmash_tst_utils import SourmashCommandFailed
 
@@ -68,8 +72,8 @@ def test_sig_merge_1_use_full_signature_in_cmd(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_merge_sig = sourmash.load_one_signature(sig47and63)
-    actual_merge_sig = sourmash.load_one_signature(out)
+    test_merge_sig = load_one_signature_from_json(sig47and63)
+    actual_merge_sig = load_one_signature_from_json(out)
 
     print(test_merge_sig.minhash)
     print(actual_merge_sig.minhash)
@@ -101,8 +105,8 @@ def test_sig_merge_1_fromfile_picklist(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_merge_sig = sourmash.load_one_signature(sig47and63)
-    actual_merge_sig = sourmash.load_one_signature(out)
+    test_merge_sig = load_one_signature_from_json(sig47and63)
+    actual_merge_sig = load_one_signature_from_json(out)
 
     print(test_merge_sig.minhash)
     print(actual_merge_sig.minhash)
@@ -137,8 +141,8 @@ def test_sig_merge_1_fromfile_picklist_gz(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_merge_sig = sourmash.load_one_signature(sig47and63)
-    actual_merge_sig = sourmash.load_one_signature(out)
+    test_merge_sig = load_one_signature_from_json(sig47and63)
+    actual_merge_sig = load_one_signature_from_json(out)
 
     print(test_merge_sig.minhash)
     print(actual_merge_sig.minhash)
@@ -158,8 +162,8 @@ def test_sig_merge_1(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_merge_sig = sourmash.load_one_signature(sig47and63)
-    actual_merge_sig = sourmash.load_one_signature(out)
+    test_merge_sig = load_one_signature_from_json(sig47and63)
+    actual_merge_sig = load_one_signature_from_json(out)
 
     print(test_merge_sig.minhash)
     print(actual_merge_sig.minhash)
@@ -178,8 +182,8 @@ def test_sig_merge_1_multisig(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_merge_sig = sourmash.load_one_signature(sig47and63)
-    actual_merge_sig = sourmash.load_one_signature(out)
+    test_merge_sig = load_one_signature_from_json(sig47and63)
+    actual_merge_sig = load_one_signature_from_json(out)
 
     print(test_merge_sig.minhash)
     print(actual_merge_sig.minhash)
@@ -211,7 +215,7 @@ def test_sig_merge_1_name(c):
         assignedSigName,
     )
 
-    test_merge_sig = sourmash.load_one_signature(outsig)
+    test_merge_sig = load_one_signature_from_json(outsig)
 
     print("outsig", outsig)
     print("xx_test_merge_sig.name", test_merge_sig.name)
@@ -230,8 +234,8 @@ def test_sig_merge_1_ksize_moltype(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_merge_sig = sourmash.load_one_signature(sig2and63)
-    actual_merge_sig = sourmash.load_one_signature(out)
+    test_merge_sig = load_one_signature_from_json(sig2and63)
+    actual_merge_sig = load_one_signature_from_json(out)
 
     print(test_merge_sig.minhash)
     print(actual_merge_sig.minhash)
@@ -262,8 +266,8 @@ def test_sig_merge_2(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_merge_sig = sourmash.load_one_signature(sig47)
-    actual_merge_sig = sourmash.load_one_signature(out)
+    test_merge_sig = load_one_signature_from_json(sig47)
+    actual_merge_sig = load_one_signature_from_json(out)
 
     print(out)
 
@@ -277,7 +281,7 @@ def test_sig_merge_3_abund_ab_ok(c):
     sig63abund = utils.get_test_data("track_abund/63.fa.sig")
 
     c.run_sourmash("sig", "merge", sig47abund, sig63abund)
-    sourmash.load_one_signature(c.last_result.out)
+    load_one_signature_from_json(c.last_result.out)
     # CTB: should check that this merge did what we think it should do!
 
 
@@ -323,13 +327,13 @@ def test_sig_filter_1(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    filtered_sigs = list(load_signatures(out))
+    filtered_sigs = list(load_signatures_from_json(out))
     filtered_sigs.sort(key=lambda x: str(x))
 
     assert len(filtered_sigs) == 2
 
-    mh47 = sourmash.load_one_signature(sig47).minhash
-    mh63 = sourmash.load_one_signature(sig63).minhash
+    mh47 = load_one_signature_from_json(sig47).minhash
+    mh63 = load_one_signature_from_json(sig63).minhash
 
     assert filtered_sigs[0].minhash == mh47
     assert filtered_sigs[1].minhash == mh63
@@ -344,8 +348,8 @@ def test_sig_filter_2(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    filtered_sig = sourmash.load_one_signature(out)
-    test_sig = sourmash.load_one_signature(sig47)
+    filtered_sig = load_one_signature_from_json(out)
+    test_sig = load_one_signature_from_json(sig47)
 
     abunds = test_sig.minhash.hashes
     abunds = {k: v for (k, v) in abunds.items() if v >= 2 and v <= 5}
@@ -363,8 +367,8 @@ def test_sig_filter_3(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    filtered_sig = sourmash.load_one_signature(out)
-    test_sig = sourmash.load_one_signature(sig47)
+    filtered_sig = load_one_signature_from_json(out)
+    test_sig = load_one_signature_from_json(sig47)
 
     abunds = test_sig.minhash.hashes
     abunds = {k: v for (k, v) in abunds.items() if v >= 2}
@@ -382,8 +386,8 @@ def test_sig_filter_3_ksize_select(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    filtered_sig = sourmash.load_one_signature(out)
-    test_sig = sourmash.load_one_signature(psw_mag, ksize=31)
+    filtered_sig = load_one_signature_from_json(out)
+    test_sig = load_one_signature_from_json(psw_mag, ksize=31)
 
     abunds = test_sig.minhash.hashes
     abunds = {k: v for (k, v) in abunds.items() if v >= 2}
@@ -404,8 +408,8 @@ def test_sig_merge_flatten(c):
     print(c.last_result)
     out = c.last_result.out
 
-    test_merge_sig = sourmash.load_one_signature(sig47and63)
-    actual_merge_sig = sourmash.load_one_signature(out)
+    test_merge_sig = load_one_signature_from_json(sig47and63)
+    actual_merge_sig = load_one_signature_from_json(out)
 
     print(test_merge_sig.minhash)
     print(actual_merge_sig.minhash)
@@ -426,8 +430,8 @@ def test_sig_merge_flatten_2(c):
     print(c.last_result)
     out = c.last_result.out
 
-    test_merge_sig = sourmash.load_one_signature(sig47and63)
-    actual_merge_sig = sourmash.load_one_signature(out)
+    test_merge_sig = load_one_signature_from_json(sig47and63)
+    actual_merge_sig = load_one_signature_from_json(out)
 
     print(test_merge_sig.minhash)
     print(actual_merge_sig.minhash)
@@ -459,8 +463,8 @@ def test_sig_intersect_1(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_intersect_sig = sourmash.load_one_signature(sig47and63)
-    actual_intersect_sig = sourmash.load_one_signature(out)
+    test_intersect_sig = load_one_signature_from_json(sig47and63)
+    actual_intersect_sig = load_one_signature_from_json(out)
 
     print(test_intersect_sig.minhash)
     print(actual_intersect_sig.minhash)
@@ -492,8 +496,8 @@ def test_sig_intersect_1_fromfile_picklist(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_intersect_sig = sourmash.load_one_signature(sig47and63)
-    actual_intersect_sig = sourmash.load_one_signature(out)
+    test_intersect_sig = load_one_signature_from_json(sig47and63)
+    actual_intersect_sig = load_one_signature_from_json(out)
 
     print(test_intersect_sig.minhash)
     print(actual_intersect_sig.minhash)
@@ -514,8 +518,8 @@ def test_sig_intersect_2(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_intersect_sig = sourmash.load_one_signature(sig47and63)
-    actual_intersect_sig = sourmash.load_one_signature(out)
+    test_intersect_sig = load_one_signature_from_json(sig47and63)
+    actual_intersect_sig = load_one_signature_from_json(out)
 
     print(test_intersect_sig.minhash)
     print(actual_intersect_sig.minhash)
@@ -534,11 +538,11 @@ def test_sig_intersect_3(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    actual_intersect_sig = sourmash.load_one_signature(out)
+    actual_intersect_sig = load_one_signature_from_json(out)
 
     # actually do an intersection ourselves for the test
-    mh47 = sourmash.load_one_signature(sig47).minhash
-    mh63 = sourmash.load_one_signature(sig63).minhash
+    mh47 = load_one_signature_from_json(sig47).minhash
+    mh63 = load_one_signature_from_json(sig63).minhash
     mh47_abunds = mh47.hashes
     mh63_mins = set(mh63.hashes.keys())
 
@@ -566,11 +570,11 @@ def test_sig_intersect_4(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    actual_intersect_sig = sourmash.load_one_signature(out)
+    actual_intersect_sig = load_one_signature_from_json(out)
 
     # actually do an intersection ourselves for the test
-    mh47 = sourmash.load_one_signature(sig47).minhash
-    mh63 = sourmash.load_one_signature(sig63).minhash
+    mh47 = load_one_signature_from_json(sig47).minhash
+    mh63 = load_one_signature_from_json(sig63).minhash
     mh47_abunds = mh47.hashes
     mh63_mins = set(mh63.hashes.keys())
 
@@ -631,8 +635,8 @@ def test_sig_intersect_7(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_intersect_sig = sourmash.load_one_signature(sig47)
-    actual_intersect_sig = sourmash.load_one_signature(out)
+    test_intersect_sig = load_one_signature_from_json(sig47)
+    actual_intersect_sig = load_one_signature_from_json(out)
 
     print(test_intersect_sig.minhash)
     print(actual_intersect_sig.minhash)
@@ -650,7 +654,7 @@ def test_sig_intersect_8_multisig(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    actual_intersect_sig = sourmash.load_one_signature(out)
+    actual_intersect_sig = load_one_signature_from_json(out)
 
     assert not len(actual_intersect_sig.minhash)
 
@@ -664,11 +668,11 @@ def test_sig_inflate_1(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    actual_inflate_sig = sourmash.load_one_signature(out)
+    actual_inflate_sig = load_one_signature_from_json(out)
     actual_inflate_mh = actual_inflate_sig.minhash
 
     # should be identical to track_abund sig
-    sig47 = sourmash.load_one_signature(sig47_abund)
+    sig47 = load_one_signature_from_json(sig47_abund)
     mh47 = sig47.minhash
 
     assert actual_inflate_sig.name == sig47.name
@@ -684,11 +688,11 @@ def test_sig_inflate_2(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    actual_inflate_sig = sourmash.load_one_signature(out)
+    actual_inflate_sig = load_one_signature_from_json(out)
 
     # actually do an inflation ourselves for the test
-    mh47 = sourmash.load_one_signature(sig47).minhash
-    mh63 = sourmash.load_one_signature(sig63).minhash
+    mh47 = load_one_signature_from_json(sig47).minhash
+    mh63 = load_one_signature_from_json(sig63).minhash
     mh47_abunds = mh47.hashes
     mh63_mins = set(mh63.hashes.keys())
 
@@ -723,7 +727,7 @@ def test_sig_inflate_4_picklist(runtmp):
     sig63 = utils.get_test_data("63.fa.sig")
     sig47_flat = utils.get_test_data("47.fa.sig")
 
-    ss63 = sourmash.load_one_signature(sig63, ksize=31)
+    ss63 = load_one_signature_from_json(sig63, ksize=31)
 
     _write_file(runtmp, "pl.csv", ["md5", ss63.md5sum()])
 
@@ -736,11 +740,11 @@ def test_sig_inflate_4_picklist(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    actual_inflate_sig = sourmash.load_one_signature(out)
+    actual_inflate_sig = load_one_signature_from_json(out)
 
     # actually do an inflation ourselves for the test
-    mh47 = sourmash.load_one_signature(sig47).minhash
-    mh63 = sourmash.load_one_signature(sig63).minhash
+    mh47 = load_one_signature_from_json(sig47).minhash
+    mh63 = load_one_signature_from_json(sig63).minhash
     mh47_abunds = mh47.hashes
     mh63_mins = set(mh63.hashes.keys())
 
@@ -779,9 +783,31 @@ def test_sig_subtract_1(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test1_sig = sourmash.load_one_signature(sig47)
-    test2_sig = sourmash.load_one_signature(sig63)
-    actual_subtract_sig = sourmash.load_one_signature(out)
+    test1_sig = load_one_signature_from_json(sig47)
+    test2_sig = load_one_signature_from_json(sig63)
+    actual_subtract_sig = load_one_signature_from_json(out)
+
+    mins = set(test1_sig.minhash.hashes.keys())
+    mins -= set(test2_sig.minhash.hashes.keys())
+
+    assert set(actual_subtract_sig.minhash.hashes.keys()) == set(mins)
+
+
+def test_sig_subtract_1_sigzip(runtmp):
+    c = runtmp
+    # subtract of 63 from 47
+    sig47 = utils.get_test_data("47.fa.sig.zip")
+    sig63 = utils.get_test_data("63.fa.sig.zip")
+    c.run_sourmash("sig", "subtract", sig47, sig63)
+
+    # stdout should be new signature
+    out = c.last_result.out
+
+    from sourmash import sourmash_args
+
+    test1_sig = sourmash_args.load_one_signature(sig47)
+    test2_sig = sourmash_args.load_one_signature(sig63)
+    actual_subtract_sig = load_one_signature_from_json(out)
 
     mins = set(test1_sig.minhash.hashes.keys())
     mins -= set(test2_sig.minhash.hashes.keys())
@@ -822,9 +848,9 @@ def test_sig_subtract_1_abund(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test1_sig = sourmash.load_one_signature(sig47)
-    test2_sig = sourmash.load_one_signature(sig63)
-    actual_subtract_sig = sourmash.load_one_signature(out)
+    test1_sig = load_one_signature_from_json(sig47)
+    test2_sig = load_one_signature_from_json(sig63)
+    actual_subtract_sig = load_one_signature_from_json(out)
     assert actual_subtract_sig.minhash.track_abundance
 
     mins = set(test1_sig.minhash.hashes.keys())
@@ -867,9 +893,9 @@ def test_sig_subtract_1_flatten(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test1_sig = sourmash.load_one_signature(sig47)
-    test2_sig = sourmash.load_one_signature(sig63)
-    actual_subtract_sig = sourmash.load_one_signature(out)
+    test1_sig = load_one_signature_from_json(sig47)
+    test2_sig = load_one_signature_from_json(sig63)
+    actual_subtract_sig = load_one_signature_from_json(out)
     assert not actual_subtract_sig.minhash.track_abundance
 
     mins = set(test1_sig.minhash.hashes.keys())
@@ -888,7 +914,7 @@ def test_sig_subtract_1_multisig(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    actual_subtract_sig = sourmash.load_one_signature(out)
+    actual_subtract_sig = load_one_signature_from_json(out)
 
     assert not set(actual_subtract_sig.minhash.hashes.keys())
 
@@ -954,8 +980,8 @@ def test_sig_rename_1(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_rename_sig = sourmash.load_one_signature(sig47)
-    actual_rename_sig = sourmash.load_one_signature(out)
+    test_rename_sig = load_one_signature_from_json(sig47)
+    actual_rename_sig = load_one_signature_from_json(out)
 
     print(test_rename_sig.minhash)
     print(actual_rename_sig.minhash)
@@ -987,8 +1013,8 @@ def test_sig_rename_1_fromfile_picklist(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_rename_sig = sourmash.load_one_signature(sig47)
-    actual_rename_sig = sourmash.load_one_signature(out)
+    test_rename_sig = load_one_signature_from_json(sig47)
+    actual_rename_sig = load_one_signature_from_json(out)
 
     print(test_rename_sig.minhash)
     print(actual_rename_sig.minhash)
@@ -1009,7 +1035,7 @@ def test_sig_rename_1_multisig(c):
     out = c.last_result.out
 
     n = 0
-    for sig in load_signatures(out):
+    for sig in load_signatures_from_json(out):
         assert sig.name == "fiz bar"
         n += 1
 
@@ -1027,7 +1053,7 @@ def test_sig_rename_1_multisig_ksize(c):
     out = c.last_result.out
 
     n = 0
-    for sig in load_signatures(out):
+    for sig in load_signatures_from_json(out):
         assert sig.name == "fiz bar"
         n += 1
 
@@ -1045,7 +1071,7 @@ def test_sig_rename_2_output_to_same(c):
 
     c.run_sourmash("sig", "rename", "-d", inplace, "fiz bar", "-o", inplace)
 
-    actual_rename_sig = sourmash.load_one_signature(inplace)
+    actual_rename_sig = load_one_signature_from_json(inplace)
     assert actual_rename_sig.name == "fiz bar"
 
 
@@ -1104,8 +1130,8 @@ def test_sig_cat_1(c):
     # stdout should be same signature
     out = c.last_result.out
 
-    test_cat_sig = sourmash.load_one_signature(sig47)
-    actual_cat_sig = sourmash.load_one_signature(out)
+    test_cat_sig = load_one_signature_from_json(sig47)
+    actual_cat_sig = load_one_signature_from_json(out)
 
     assert actual_cat_sig == test_cat_sig
 
@@ -1119,8 +1145,8 @@ def test_sig_cat_1_no_unique(c):
     # stdout should be same signature
     out = c.last_result.out
 
-    test_cat_sig = sourmash.load_one_signature(sig47)
-    actual_cat_sigs = load_signatures(out)
+    test_cat_sig = load_one_signature_from_json(sig47)
+    actual_cat_sigs = load_signatures_from_json(out)
 
     for n, sig in enumerate(actual_cat_sigs):
         assert sig == test_cat_sig
@@ -1139,8 +1165,8 @@ def test_sig_cat_1_unique(c):
     out = c.last_result.out
     err = c.last_result.err
 
-    test_cat_sig = sourmash.load_one_signature(sig47)
-    actual_cat_sigs = load_signatures(out)
+    test_cat_sig = load_one_signature_from_json(sig47)
+    actual_cat_sigs = load_signatures_from_json(out)
 
     for n, sig in enumerate(actual_cat_sigs):
         assert sig == test_cat_sig
@@ -1161,7 +1187,7 @@ def test_sig_cat_2(c):
     # stdout should be same signatures
     out = c.last_result.out
 
-    siglist = list(load_signatures(out))
+    siglist = list(load_signatures_from_json(out))
     print(len(siglist))
 
     assert (
@@ -1181,7 +1207,7 @@ def test_sig_cat_2_out(c):
     # stdout should be same signatures
     out = c.output("out.sig")
 
-    siglist = list(load_signatures(out))
+    siglist = list(load_signatures_from_json(out))
     print(len(siglist))
 
     assert (
@@ -1206,7 +1232,7 @@ def test_sig_cat_2_out_inplace(c):
     # stdout should be same signatures
     out = input_sig
 
-    siglist = list(load_signatures(out))
+    siglist = list(load_signatures_from_json(out))
     print(len(siglist))
 
     assert (
@@ -1234,14 +1260,14 @@ def test_sig_cat_3_filelist(c):
     # make this a list, not a set, because a set will collapse identical
     # signatures. `sig cat` does not collapse identical signatures, although
     # the pathlist function will ignore duplicate files.
-    siglist = list(load_signatures(out))
+    siglist = list(load_signatures_from_json(out))
 
     # verify the number of signatures matches what we expect to see based
     # on the input files
     all_sigs = []
-    all_sigs += list(load_signatures(sig47))
-    all_sigs += list(load_signatures(sig47abund))
-    all_sigs += list(load_signatures(multisig))
+    all_sigs += list(load_signatures_from_json(sig47))
+    all_sigs += list(load_signatures_from_json(sig47abund))
+    all_sigs += list(load_signatures_from_json(multisig))
 
     assert len(all_sigs) == len(siglist)
 
@@ -1270,7 +1296,7 @@ def test_sig_cat_4_filelist_with_dbs(c):
     # stdout should be same signatures
     out = c.output("out.sig")
 
-    siglist = list(load_signatures(out))
+    siglist = list(load_signatures_from_json(out))
     print(len(siglist))
     # print("siglist: ",siglist)
     # print("\n")
@@ -1278,8 +1304,8 @@ def test_sig_cat_4_filelist_with_dbs(c):
     # verify the number of signatures matches what we expect to see based
     # on the input files
     all_sigs = []
-    all_sigs += list(load_signatures(sig47))
-    all_sigs += list(load_signatures(sig47abund))
+    all_sigs += list(load_signatures_from_json(sig47))
+    all_sigs += list(load_signatures_from_json(sig47abund))
     all_sigs += list(sourmash.load_file_as_signatures(sbt))
 
     assert len(all_sigs) == len(siglist)
@@ -1309,7 +1335,7 @@ def test_sig_cat_5_from_file(c):
     # stdout should be same signatures
     out = c.output("out.sig")
 
-    siglist = list(load_signatures(out))
+    siglist = list(load_signatures_from_json(out))
     print(len(siglist))
     # print("siglist: ",siglist)
     # print("\n")
@@ -1317,8 +1343,8 @@ def test_sig_cat_5_from_file(c):
     # verify the number of signatures matches what we expect to see based
     # on the input files
     all_sigs = []
-    all_sigs += list(load_signatures(sig47))
-    all_sigs += list(load_signatures(sig47abund))
+    all_sigs += list(load_signatures_from_json(sig47))
+    all_sigs += list(load_signatures_from_json(sig47abund))
     all_sigs += list(sourmash.load_file_as_signatures(sbt))
 
     assert len(all_sigs) == len(siglist)
@@ -1359,7 +1385,7 @@ def test_sig_cat_5_from_file_picklist(runtmp):
     # stdout should be same signatures
     out = c.output("out.sig")
 
-    siglist = list(load_signatures(out))
+    siglist = list(load_signatures_from_json(out))
     print(len(siglist))
     # print("siglist: ",siglist)
     # print("\n")
@@ -1367,7 +1393,7 @@ def test_sig_cat_5_from_file_picklist(runtmp):
     # verify the number of signatures matches what we expect to see based
     # on the input files
     all_sigs = []
-    all_sigs += list(load_signatures(sig47, ksize=31))
+    all_sigs += list(load_signatures_from_json(sig47, ksize=31))
 
     assert len(all_sigs) == len(siglist)
 
@@ -1426,8 +1452,8 @@ def test_sig_split_1(runtmp):
 
     assert os.path.exists(c.output(outname))
 
-    test_split_sig = sourmash.load_one_signature(sig47)
-    actual_split_sig = sourmash.load_one_signature(c.output(outname))
+    test_split_sig = load_one_signature_from_json(sig47)
+    actual_split_sig = load_one_signature_from_json(c.output(outname))
 
     assert actual_split_sig == test_split_sig
 
@@ -1453,8 +1479,8 @@ def test_sig_split_1_fromfile_picklist(runtmp):
 
     assert os.path.exists(c.output(outname))
 
-    test_split_sig = sourmash.load_one_signature(sig47)
-    actual_split_sig = sourmash.load_one_signature(c.output(outname))
+    test_split_sig = load_one_signature_from_json(sig47)
+    actual_split_sig = load_one_signature_from_json(c.output(outname))
 
     assert actual_split_sig == test_split_sig
 
@@ -1487,12 +1513,12 @@ def test_sig_split_2(c):
     assert os.path.exists(c.output(outname1))
     assert os.path.exists(c.output(outname2))
 
-    test_split_sig = sourmash.load_one_signature(sig47)
+    test_split_sig = load_one_signature_from_json(sig47)
 
-    actual_split_sig = sourmash.load_one_signature(c.output(outname1))
+    actual_split_sig = load_one_signature_from_json(c.output(outname1))
     assert actual_split_sig == test_split_sig
 
-    actual_split_sig = sourmash.load_one_signature(c.output(outname2))
+    actual_split_sig = load_one_signature_from_json(c.output(outname2))
     assert actual_split_sig == test_split_sig
 
 
@@ -1509,12 +1535,12 @@ def test_sig_split_2_outdir(c):
     assert os.path.exists(c.output(outname1))
     assert os.path.exists(c.output(outname2))
 
-    test_split_sig = sourmash.load_one_signature(sig47)
+    test_split_sig = load_one_signature_from_json(sig47)
 
-    actual_split_sig = sourmash.load_one_signature(c.output(outname1))
+    actual_split_sig = load_one_signature_from_json(c.output(outname1))
     assert actual_split_sig == test_split_sig
 
-    actual_split_sig = sourmash.load_one_signature(c.output(outname2))
+    actual_split_sig = load_one_signature_from_json(c.output(outname2))
     assert actual_split_sig == test_split_sig
 
 
@@ -1531,12 +1557,12 @@ def test_sig_split_2_output_dir(c):
     assert os.path.exists(c.output(outname1))
     assert os.path.exists(c.output(outname2))
 
-    test_split_sig = sourmash.load_one_signature(sig47)
+    test_split_sig = load_one_signature_from_json(sig47)
 
-    actual_split_sig = sourmash.load_one_signature(c.output(outname1))
+    actual_split_sig = load_one_signature_from_json(c.output(outname1))
     assert actual_split_sig == test_split_sig
 
-    actual_split_sig = sourmash.load_one_signature(c.output(outname2))
+    actual_split_sig = load_one_signature_from_json(c.output(outname2))
     assert actual_split_sig == test_split_sig
 
 
@@ -1679,8 +1705,8 @@ def test_sig_extract_1(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -1697,8 +1723,8 @@ def test_sig_extract_1_from_file(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -1713,8 +1739,8 @@ def test_sig_extract_2(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     print(test_extract_sig.minhash)
     print(actual_extract_sig.minhash)
@@ -1733,8 +1759,8 @@ def test_sig_extract_2_zipfile(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     print(test_extract_sig.minhash)
     print(actual_extract_sig.minhash)
@@ -1760,8 +1786,8 @@ def test_sig_extract_4(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     print(test_extract_sig.minhash)
     print(actual_extract_sig.minhash)
@@ -1787,7 +1813,7 @@ def test_sig_extract_6(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    siglist = load_signatures(out)
+    siglist = load_signatures_from_json(out)
     siglist = list(siglist)
 
     assert len(siglist) == 2
@@ -1802,7 +1828,7 @@ def test_sig_extract_7(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    siglist = load_signatures(out)
+    siglist = load_signatures_from_json(out)
     siglist = list(siglist)
 
     assert len(siglist) == 1
@@ -1817,7 +1843,7 @@ def test_sig_extract_7_no_ksize(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    siglist = load_signatures(out)
+    siglist = load_signatures_from_json(out)
     siglist = list(siglist)
 
     assert len(siglist) == 3
@@ -1889,8 +1915,8 @@ def test_sig_extract_8_picklist_md5(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -1931,8 +1957,8 @@ def test_sig_extract_8_picklist_md5_zipfile(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2014,8 +2040,8 @@ def test_sig_extract_8_picklist_md5_include(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2055,8 +2081,8 @@ def test_sig_extract_8_picklist_md5_exclude(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig63)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig63)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2115,8 +2141,8 @@ def test_sig_extract_8_picklist_md5_require_all(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2158,8 +2184,8 @@ def test_sig_extract_8_picklist_name(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2191,8 +2217,8 @@ def test_sig_extract_8_picklist_name_exclude(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig63)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig63)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2224,8 +2250,8 @@ def test_sig_extract_8_picklist_ident(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2257,8 +2283,8 @@ def test_sig_extract_8_picklist_ident_exclude(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig63)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig63)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2290,8 +2316,8 @@ def test_sig_extract_8_picklist_ident_dot(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2323,8 +2349,8 @@ def test_sig_extract_8_picklist_ident_dot_exclude(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig63)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig63)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2356,8 +2382,8 @@ def test_sig_extract_8_picklist_md5_short(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2389,8 +2415,8 @@ def test_sig_extract_8_picklist_md5_short_exclude(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig63)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig63)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2422,8 +2448,8 @@ def test_sig_extract_8_picklist_md5_short_alias(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2455,8 +2481,8 @@ def test_sig_extract_8_picklist_md5_short_alias_exclude(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig63)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig63)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2561,8 +2587,8 @@ def test_sig_extract_8_picklist_md5_short_alias_with_md5_selector(runtmp):
     # stdout should be new signature
     out = runtmp.last_result.out
 
-    test_extract_sig = sourmash.load_one_signature(sig47)
-    actual_extract_sig = sourmash.load_one_signature(out)
+    test_extract_sig = load_one_signature_from_json(sig47)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig == test_extract_sig
 
@@ -2651,7 +2677,7 @@ def test_sig_extract_8_picklist_md5_nomatch_exclude(runtmp):
 
     # stdout should be both signatures
     out = runtmp.last_result.out
-    extract_siglist = list(load_signatures(out))
+    extract_siglist = list(load_signatures_from_json(out))
     print(len(extract_siglist))
     s47 = sourmash.load_file_as_signatures(sig47)
     s63 = sourmash.load_file_as_signatures(sig63)
@@ -2687,7 +2713,7 @@ def test_sig_extract_9_picklist_md5_ksize_hp_select(runtmp):
 
     # stdout should be new signature
     out = runtmp.last_result.out
-    actual_extract_sig = sourmash.load_one_signature(out)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     print(actual_extract_sig.md5sum)
     assert str(actual_extract_sig) == "GCA_001593925"
@@ -2715,7 +2741,7 @@ def test_sig_extract_9_picklist_md5_ksize_hp_select_exclude(runtmp):
 
     # stdout should be new signature
     out = runtmp.last_result.out
-    actual_extract_sig = sourmash.load_one_signature(out)
+    actual_extract_sig = load_one_signature_from_json(out)
     print(actual_extract_sig.md5sum)
 
     assert str(actual_extract_sig) == "GCA_001593935"
@@ -2745,7 +2771,7 @@ def test_sig_extract_10_picklist_md5_dups_and_empty(runtmp):
 
     # stdout should be new signature
     out = runtmp.last_result.out
-    actual_extract_sig = sourmash.load_one_signature(out)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig.minhash.ksize == 19
     assert actual_extract_sig.minhash.moltype == "hp"
@@ -2779,7 +2805,7 @@ def test_sig_extract_10_picklist_md5_dups_and_empty_exclude(runtmp):
 
     # stdout should be new signature
     out = runtmp.last_result.out
-    actual_extract_sig = sourmash.load_one_signature(out)
+    actual_extract_sig = load_one_signature_from_json(out)
 
     assert actual_extract_sig.minhash.ksize == 19
     assert actual_extract_sig.minhash.moltype == "hp"
@@ -2966,20 +2992,20 @@ def test_sig_extract_11_pattern_exclude(runtmp):
 def test_sig_extract_identical_md5s(runtmp):
     # test that we properly handle different signatures with identical md5s
     sig47 = utils.get_test_data("47.fa.sig")
-    ss = load_signatures(sig47)
+    ss = load_signatures_from_json(sig47)
     sig = list(ss)[0]
     new_sig = sig.to_mutable()
     new_sig.name = "foo"
     sig47foo = runtmp.output("foo.sig")
     # this was only a problem when the signatures are stored in the same file
     with open(sig47foo, "w") as fp:
-        sourmash.save_signatures([new_sig, sig], fp)
+        save_signatures_to_json([new_sig, sig], fp)
 
     runtmp.run_sourmash("sig", "extract", "--name", "foo", sig47foo)
 
     out = runtmp.last_result.out
     print(out)
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -2999,12 +3025,12 @@ def test_sig_flatten_1(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    siglist = load_signatures(out)
+    siglist = load_signatures_from_json(out)
     siglist = list(siglist)
 
     assert len(siglist) == 1
 
-    test_flattened = sourmash.load_one_signature(sig47)
+    test_flattened = load_one_signature_from_json(sig47)
     assert test_flattened.minhash == siglist[0].minhash
 
 
@@ -3030,12 +3056,12 @@ def test_sig_flatten_1_from_file(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    siglist = load_signatures(out)
+    siglist = load_signatures_from_json(out)
     siglist = list(siglist)
 
     assert len(siglist) == 1
 
-    test_flattened = sourmash.load_one_signature(sig47)
+    test_flattened = load_one_signature_from_json(sig47)
     assert test_flattened.minhash == siglist[0].minhash
 
 
@@ -3050,12 +3076,12 @@ def test_sig_flatten_1_select_name(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    siglist = load_signatures(out)
+    siglist = load_signatures_from_json(out)
     siglist = list(siglist)
 
     assert len(siglist) == 1
 
-    test_flattened = sourmash.load_one_signature(sig47)
+    test_flattened = load_one_signature_from_json(sig47)
     assert test_flattened.minhash == siglist[0].minhash
 
 
@@ -3071,12 +3097,12 @@ def test_sig_flatten_1_select_md5(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    siglist = load_signatures(out)
+    siglist = load_signatures_from_json(out)
     siglist = list(siglist)
 
     assert len(siglist) == 1
 
-    test_flattened = sourmash.load_one_signature(sig47)
+    test_flattened = load_one_signature_from_json(sig47)
     assert test_flattened.minhash == siglist[0].minhash
 
 
@@ -3089,7 +3115,7 @@ def test_sig_flatten_2_ksize(runtmp):
     # stdout should be new signature
     out = c.last_result.out
 
-    siglist = load_signatures(out)
+    siglist = load_signatures_from_json(out)
     siglist = list(siglist)
 
     assert len(siglist) == 1
@@ -3104,8 +3130,8 @@ def test_sig_downsample_1_scaled(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_downsample_sig = sourmash.load_one_signature(sig47)
-    actual_downsample_sig = sourmash.load_one_signature(out)
+    test_downsample_sig = load_one_signature_from_json(sig47)
+    actual_downsample_sig = load_one_signature_from_json(out)
 
     test_mh = test_downsample_sig.minhash.downsample(scaled=10000)
 
@@ -3121,7 +3147,7 @@ def test_sig_downsample_1_scaled_downsample_multisig(c):
     # stdout should be new signatures
     out = c.last_result.out
 
-    for sig in load_signatures(out):
+    for sig in load_signatures_from_json(out):
         assert sig.minhash.scaled == 10000
 
 
@@ -3134,12 +3160,12 @@ def test_sig_downsample_1_scaled_to_num(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    actual_downsample_sig = sourmash.load_one_signature(out)
+    actual_downsample_sig = load_one_signature_from_json(out)
     actual_mins = actual_downsample_sig.minhash.hashes.keys()
     actual_mins = list(actual_mins)
     actual_mins.sort()
 
-    test_downsample_sig = sourmash.load_one_signature(sig47)
+    test_downsample_sig = load_one_signature_from_json(sig47)
     test_mins = test_downsample_sig.minhash.hashes.keys()
     test_mins = list(test_mins)
     test_mins.sort()
@@ -3206,10 +3232,10 @@ def test_sig_downsample_2_num(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_downsample_sig = sourmash.load_one_signature(
+    test_downsample_sig = load_one_signature_from_json(
         sigs11, ksize=21, select_moltype="DNA"
     )
-    actual_downsample_sig = sourmash.load_one_signature(out)
+    actual_downsample_sig = load_one_signature_from_json(out)
     test_mh = test_downsample_sig.minhash.downsample(num=500)
 
     assert actual_downsample_sig.minhash == test_mh
@@ -3226,10 +3252,10 @@ def test_sig_downsample_2_num_to_scaled(c):
     # stdout should be new signature
     out = c.last_result.out
 
-    test_downsample_sig = sourmash.load_one_signature(
+    test_downsample_sig = load_one_signature_from_json(
         sigs11, ksize=21, select_moltype="DNA"
     )
-    actual_downsample_sig = sourmash.load_one_signature(out)
+    actual_downsample_sig = load_one_signature_from_json(out)
 
     test_mins = test_downsample_sig.minhash.hashes.keys()
     actual_mins = actual_downsample_sig.minhash.hashes.keys()
@@ -3648,7 +3674,7 @@ def test_sig_describe_empty(c):
 
     outsig = c.output("xxx.sig")
     with open(outsig, "w") as fp:
-        sourmash.save_signatures([ss], fp)
+        save_signatures_to_json([ss], fp)
 
     ss = sourmash.load_file_as_signatures(outsig)
     ss = list(ss)
@@ -3906,8 +3932,8 @@ def test_import_export_1(c):
     c.run_sourmash("sig", "export", inp, "-o", outp, "-k", "21", "--dna")
     c.run_sourmash("sig", "import", outp)
 
-    original = sourmash.load_one_signature(inp, ksize=21, select_moltype="DNA")
-    roundtrip = sourmash.load_one_signature(c.last_result.out)
+    original = load_one_signature_from_json(inp, ksize=21, select_moltype="DNA")
+    roundtrip = load_one_signature_from_json(c.last_result.out)
 
     assert original.minhash == roundtrip.minhash
 
@@ -3921,8 +3947,8 @@ def test_import_export_1_by_md5(c):
     c.run_sourmash("sig", "export", inp, "-o", outp, "--md5", "1437d8eae6")
     c.run_sourmash("sig", "import", outp)
 
-    original = sourmash.load_one_signature(inp, ksize=21, select_moltype="DNA")
-    roundtrip = sourmash.load_one_signature(c.last_result.out)
+    original = load_one_signature_from_json(inp, ksize=21, select_moltype="DNA")
+    roundtrip = load_one_signature_from_json(c.last_result.out)
 
     assert original.minhash == roundtrip.minhash
 
@@ -3938,8 +3964,8 @@ def test_import_export_2(c):
     msh_sig = utils.get_test_data("genome-s11.fa.gz.msh.json_dump")
 
     c.run_sourmash("sig", "import", msh_sig)
-    imported = sourmash.load_one_signature(c.last_result.out)
-    compare = sourmash.load_one_signature(sig1, ksize=21, select_moltype="DNA")
+    imported = load_one_signature_from_json(c.last_result.out)
+    compare = load_one_signature_from_json(sig1, ksize=21, select_moltype="DNA")
 
     assert imported.minhash == compare.minhash
 
@@ -4240,7 +4266,7 @@ def test_sig_kmers_1_dna(runtmp):
     seqfile = utils.get_test_data("short.fa")
 
     runtmp.sourmash("sketch", "dna", seqfile, "-p", "scaled=1")
-    ss = sourmash.load_one_signature(runtmp.output("short.fa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("short.fa.sig"))
     mh = ss.minhash
     assert mh.moltype == "DNA"
 
@@ -4298,7 +4324,7 @@ def test_sig_kmers_1_dna_more_in_query(runtmp):
     seqfile = utils.get_test_data("short.fa")
 
     runtmp.sourmash("sketch", "dna", seqfile, "-p", "scaled=1")
-    ss = sourmash.load_one_signature(runtmp.output("short.fa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("short.fa.sig"))
     mh = ss.minhash
     assert mh.moltype == "DNA"
 
@@ -4326,7 +4352,7 @@ def test_sig_kmers_1_dna_empty_seq(runtmp):
     seqfile = utils.get_test_data("short.fa")
 
     runtmp.sourmash("sketch", "dna", seqfile, "-p", "scaled=1")
-    ss = sourmash.load_one_signature(runtmp.output("short.fa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("short.fa.sig"))
     mh = ss.minhash
     assert mh.moltype == "DNA"
 
@@ -4353,7 +4379,7 @@ def test_sig_kmers_1_dna_empty_sig(runtmp):
     mh = sourmash.MinHash(ksize=31, n=0, scaled=1)
     ss = sourmash.SourmashSignature(mh, name="empty")
     with open(runtmp.output("empty.sig"), "w") as fp:
-        sourmash.save_signatures([ss], fp)
+        save_signatures_to_json([ss], fp)
 
     with pytest.raises(SourmashCommandFailed):
         runtmp.sourmash("sig", "kmers", "--sig", "empty.sig", "--seq", seqfile)
@@ -4374,7 +4400,7 @@ def test_sig_kmers_1_dna_single_sig(runtmp):
     mh.add_hash(1070961951490202715)
     ss = sourmash.SourmashSignature(mh, name="small")
     with open(runtmp.output("small.sig"), "w") as fp:
-        sourmash.save_signatures([ss], fp)
+        save_signatures_to_json([ss], fp)
 
     runtmp.sourmash("sig", "kmers", "--sig", "small.sig", "--seq", seqfile)
 
@@ -4392,7 +4418,7 @@ def test_sig_kmers_1_dna_lowscaled(runtmp):
     seqfile = utils.get_test_data("short.fa")
 
     runtmp.sourmash("sketch", "dna", seqfile, "-p", "scaled=100")
-    ss = sourmash.load_one_signature(runtmp.output("short.fa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("short.fa.sig"))
     mh = ss.minhash
     assert mh.moltype == "DNA"
 
@@ -4450,7 +4476,7 @@ def test_sig_kmers_1_dna_num(runtmp):
     seqfile = utils.get_test_data("short.fa")
 
     runtmp.sourmash("sketch", "dna", seqfile, "-p", "num=50")
-    ss = sourmash.load_one_signature(runtmp.output("short.fa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("short.fa.sig"))
     mh = ss.minhash
     assert mh.moltype == "DNA"
 
@@ -4508,7 +4534,7 @@ def test_sig_kmers_1_dna_translate_protein(runtmp):
     seqfile = utils.get_test_data("short.fa")
 
     runtmp.sourmash("sketch", "translate", seqfile, "-p", "scaled=1")
-    ss = sourmash.load_one_signature(runtmp.output("short.fa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("short.fa.sig"))
     mh = ss.minhash
     assert mh.moltype == "protein"
 
@@ -4567,7 +4593,7 @@ def test_sig_kmers_1_dna_translate_dayhoff(runtmp):
     seqfile = utils.get_test_data("short.fa")
 
     runtmp.sourmash("sketch", "translate", seqfile, "-p", "scaled=1,dayhoff")
-    ss = sourmash.load_one_signature(runtmp.output("short.fa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("short.fa.sig"))
     mh = ss.minhash
     assert mh.moltype == "dayhoff"
 
@@ -4626,7 +4652,7 @@ def test_sig_kmers_1_dna_translate_hp(runtmp):
     seqfile = utils.get_test_data("short.fa")
 
     runtmp.sourmash("sketch", "translate", seqfile, "-p", "scaled=1,hp")
-    ss = sourmash.load_one_signature(runtmp.output("short.fa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("short.fa.sig"))
     mh = ss.minhash
     assert mh.moltype == "hp"
 
@@ -4685,7 +4711,7 @@ def test_sig_kmers_2_protein(runtmp):
     seqfile = utils.get_test_data("ecoli.faa")
 
     runtmp.sourmash("sketch", "protein", seqfile, "-p", "scaled=1")
-    ss = sourmash.load_one_signature(runtmp.output("ecoli.faa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("ecoli.faa.sig"))
     mh = ss.minhash
     assert mh.moltype == "protein"
 
@@ -4744,7 +4770,7 @@ def test_sig_kmers_2_dayhoff(runtmp):
     seqfile = utils.get_test_data("ecoli.faa")
 
     runtmp.sourmash("sketch", "protein", seqfile, "-p", "scaled=1,dayhoff")
-    ss = sourmash.load_one_signature(runtmp.output("ecoli.faa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("ecoli.faa.sig"))
     mh = ss.minhash
     assert mh.moltype == "dayhoff"
 
@@ -4803,7 +4829,7 @@ def test_sig_kmers_2_hp(runtmp):
     seqfile = utils.get_test_data("ecoli.faa")
 
     runtmp.sourmash("sketch", "protein", seqfile, "-p", "scaled=1,hp")
-    ss = sourmash.load_one_signature(runtmp.output("ecoli.faa.sig"))
+    ss = load_one_signature_from_json(runtmp.output("ecoli.faa.sig"))
     mh = ss.minhash
     assert mh.moltype == "hp"
 
diff --git a/tests/test_cmd_signature_grep.py b/tests/test_cmd_signature_grep.py
index fa1a5b7dfb..4e5a26f289 100644
--- a/tests/test_cmd_signature_grep.py
+++ b/tests/test_cmd_signature_grep.py
@@ -11,7 +11,7 @@
 import sourmash_tst_utils as utils
 import sourmash
 from sourmash_tst_utils import SourmashCommandFailed
-from sourmash.signature import load_signatures
+from sourmash.signature import load_signatures_from_json, save_signatures_to_json
 
 ## command line tests
 
@@ -23,7 +23,7 @@ def test_grep_1_sig_name(runtmp):
     runtmp.run_sourmash("sig", "grep", "Shewanella", sig47)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -46,7 +46,7 @@ def test_grep_1_sig_name_case_insensitive(runtmp):
     runtmp.run_sourmash("sig", "grep", "-i", "shewanella", sig47)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -70,7 +70,7 @@ def test_grep_2_sig_md5(runtmp):
     runtmp.run_sourmash("sig", "grep", "ce52952152f0", sig47)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -92,7 +92,7 @@ def test_grep_2_sig_md5_case_insensitive(runtmp):
     runtmp.run_sourmash("sig", "grep", "-i", "CE52952152f0", sig47)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -106,7 +106,7 @@ def test_grep_3_filename(runtmp):
     runtmp.run_sourmash("sig", "grep", "47.fa", sig47)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -121,7 +121,7 @@ def test_grep_3_filename_regexp(runtmp):
     runtmp.run_sourmash("sig", "grep", "^47.fa", sig47)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -150,7 +150,7 @@ def test_grep_4_no_manifest_ok(runtmp):
 
     runtmp.run_sourmash("sig", "grep", "e60265", sbt, "--no-require-manifest")
 
-    ss = load_signatures(runtmp.last_result.out)
+    ss = load_signatures_from_json(runtmp.last_result.out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -164,7 +164,7 @@ def test_grep_5_zip_include(runtmp):
     runtmp.run_sourmash("sig", "grep", "--dna", "OS223", allzip)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -193,7 +193,7 @@ def test_grep_5_zip_include_picklist(runtmp):
     print(err)
     assert "for given picklist, found 2 matches to 2 distinct values" in err
 
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -208,7 +208,7 @@ def test_grep_5_zip_include_case_insensitive(runtmp):
     runtmp.run_sourmash("sig", "grep", "--dna", "-i", "os223", allzip)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -223,7 +223,7 @@ def test_grep_5_zip_exclude(runtmp):
     runtmp.run_sourmash("sig", "grep", "--dna", "-v", "OS185", allzip)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -238,7 +238,7 @@ def test_grep_5_zip_exclude_case_insensitive(runtmp):
     runtmp.run_sourmash("sig", "grep", "--dna", "-vi", "os185", allzip)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -253,7 +253,7 @@ def test_grep_6_zip_manifest_csv(runtmp):
     runtmp.run_sourmash("sig", "grep", "--dna", "OS223", allzip, "--csv", "match.csv")
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -264,7 +264,7 @@ def test_grep_6_zip_manifest_csv(runtmp):
     runtmp.run_sourmash("sig", "cat", allzip, "--picklist", "match.csv::manifest")
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -281,7 +281,7 @@ def test_grep_6_zip_manifest_csv_gz(runtmp):
     )
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -296,7 +296,7 @@ def test_grep_6_zip_manifest_csv_gz(runtmp):
     runtmp.run_sourmash("sig", "cat", allzip, "--picklist", "match.csv.gz::manifest")
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
@@ -414,19 +414,19 @@ def test_sig_grep_8_count(runtmp):
 def test_sig_grep_identical_md5s(runtmp):
     # test that we properly handle different signatures with identical md5s
     sig47 = utils.get_test_data("47.fa.sig")
-    ss = load_signatures(sig47)
+    ss = load_signatures_from_json(sig47)
     sig = list(ss)[0]
     new_sig = sig.to_mutable()
     new_sig.name = "foo"
     sig47foo = runtmp.output("foo.sig")
     # this was only a problem when the signatures are stored in the same file
     with open(sig47foo, "w") as fp:
-        sourmash.save_signatures([new_sig, sig], fp)
+        save_signatures_to_json([new_sig, sig], fp)
 
     runtmp.run_sourmash("sig", "grep", "-i", "foo", sig47foo)
 
     out = runtmp.last_result.out
-    ss = load_signatures(out)
+    ss = load_signatures_from_json(out)
     ss = list(ss)
     assert len(ss) == 1
     ss = ss[0]
diff --git a/tests/test_deprecated.py b/tests/test_deprecated.py
index 34097dd695..a28e9c0bcf 100644
--- a/tests/test_deprecated.py
+++ b/tests/test_deprecated.py
@@ -9,6 +9,6 @@ def test_load_textmode(track_abundance):
     # to make sure we still support it =/
     sigfile = utils.get_test_data("genome-s10+s11.sig")
     with open(sigfile) as sigfp:
-        siglist = list(signature.load_signatures(sigfp))
+        siglist = list(signature.load_signatures_from_json(sigfp))
     loaded_sig = siglist[0]
     assert loaded_sig.name == "genome-s10+s11"
diff --git a/tests/test_index.py b/tests/test_index.py
index b207376443..2c1799d113 100644
--- a/tests/test_index.py
+++ b/tests/test_index.py
@@ -18,6 +18,7 @@
     MultiIndex,
     StandaloneManifestIndex,
 )
+from sourmash.signature import load_one_signature_from_json, save_signatures_to_json
 from sourmash.index.revindex import RevIndex
 from sourmash.sbt import SBT, GraphFactory
 from sourmash import sourmash_args
@@ -96,7 +97,7 @@ def test_simple_index(n_children):
 def test_linear_index_prefetch_empty():
     # check that an exception is raised upon for an empty LinearIndex
     sig2 = utils.get_test_data("2.fa.sig")
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
 
     lidx = LinearIndex()
 
@@ -119,8 +120,8 @@ def minhash(self):
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
     fake = FakeSignature()
 
     lidx = LinearIndex()
@@ -150,8 +151,8 @@ def test_linear_index_search_subj_has_abundance():
     queryfile = utils.get_test_data("47.fa.sig")
     subjfile = utils.get_test_data("track_abund/47.fa.sig")
 
-    qs = sourmash.load_one_signature(queryfile)
-    ss = sourmash.load_one_signature(subjfile)
+    qs = load_one_signature_from_json(queryfile)
+    ss = load_one_signature_from_json(subjfile)
 
     linear = LinearIndex()
     linear.insert(ss)
@@ -167,8 +168,8 @@ def test_linear_index_gather_subj_has_abundance():
     queryfile = utils.get_test_data("47.fa.sig")
     subjfile = utils.get_test_data("track_abund/47.fa.sig")
 
-    qs = sourmash.load_one_signature(queryfile)
-    ss = sourmash.load_one_signature(subjfile)
+    qs = load_one_signature_from_json(queryfile)
+    ss = load_one_signature_from_json(subjfile)
 
     linear = LinearIndex()
     linear.insert(ss)
@@ -186,7 +187,7 @@ def test_index_search_subj_scaled_is_lower():
     sigfile = utils.get_test_data(
         "scaled100/GCF_000005845.2_ASM584v2_genomic.fna.gz.sig.gz"
     )
-    ss = sourmash.load_one_signature(sigfile)
+    ss = load_one_signature_from_json(sigfile)
 
     # double check :)
     assert ss.minhash.scaled == 100
@@ -209,7 +210,7 @@ def test_index_search_subj_num_is_lower():
     # check that subject sketches are appropriately downsampled for num
     # sketches
     sigfile = utils.get_test_data("num/47.fa.sig")
-    ss = sourmash.load_one_signature(sigfile, ksize=31)
+    ss = load_one_signature_from_json(sigfile, ksize=31)
 
     # double check :)
     assert ss.minhash.num == 500
@@ -231,7 +232,7 @@ def test_index_search_subj_num_is_lower():
 def test_index_search_query_num_is_lower():
     # check that query sketches are appropriately downsampled for num.
     sigfile = utils.get_test_data("num/47.fa.sig")
-    qs = sourmash.load_one_signature(sigfile, ksize=31)
+    qs = load_one_signature_from_json(sigfile, ksize=31)
 
     # double check :)
     assert qs.minhash.num == 500
@@ -254,8 +255,8 @@ def test_linear_index_search_abund():
     sig47 = utils.get_test_data("track_abund/47.fa.sig")
     sig63 = utils.get_test_data("track_abund/63.fa.sig")
 
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     lidx = LinearIndex()
     lidx.insert(ss47)
@@ -272,8 +273,8 @@ def test_linear_index_search_abund_downsample_query():
     sig47 = utils.get_test_data("track_abund/47.fa.sig")
     sig63 = utils.get_test_data("track_abund/63.fa.sig")
 
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     # forcibly downsample ss47 for the purpose of this test :)
     ss47 = ss47.to_mutable()
@@ -295,8 +296,8 @@ def test_linear_index_search_abund_downsample_subj():
     sig47 = utils.get_test_data("track_abund/47.fa.sig")
     sig63 = utils.get_test_data("track_abund/63.fa.sig")
 
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     # forcibly downsample ss63 for the purpose of this test :)
     ss63 = ss63.to_mutable()
@@ -318,8 +319,8 @@ def test_linear_index_search_abund_requires_threshold():
     sig47 = utils.get_test_data("track_abund/47.fa.sig")
     sig63 = utils.get_test_data("track_abund/63.fa.sig")
 
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     lidx = LinearIndex()
     lidx.insert(ss47)
@@ -336,8 +337,8 @@ def test_linear_index_search_abund_query_flat():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("track_abund/63.fa.sig")
 
-    ss47 = sourmash.load_one_signature(sig47, ksize=31)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss47 = load_one_signature_from_json(sig47, ksize=31)
+    ss63 = load_one_signature_from_json(sig63)
 
     lidx = LinearIndex()
     lidx.insert(ss47)
@@ -356,8 +357,8 @@ def test_linear_index_search_abund_subj_flat():
     sig47 = utils.get_test_data("track_abund/47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     lidx = LinearIndex()
     lidx.insert(ss47)
@@ -378,9 +379,9 @@ def test_linear_index_save(runtmp):
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     linear = LinearIndex()
     linear.insert(ss2)
@@ -409,13 +410,13 @@ def test_linear_index_load(runtmp):
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     filename = runtmp.output("foo")
     with open(filename, "w") as fp:
-        sourmash.save_signatures([ss2, ss47, ss63], fp)
+        save_signatures_to_json([ss2, ss47, ss63], fp)
 
     linear = LinearIndex.load(filename)
 
@@ -430,9 +431,9 @@ def test_linear_index_save_load(runtmp):
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     linear = LinearIndex()
     linear.insert(ss2)
@@ -1081,9 +1082,9 @@ def test_multi_index_search():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     lidx1 = LinearIndex.load(sig2)
     lidx2 = LinearIndex.load(sig47)
@@ -1135,9 +1136,9 @@ def test_multi_index_gather():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47)
-    sourmash.load_one_signature(sig63)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47)
+    load_one_signature_from_json(sig63)
 
     lidx1 = LinearIndex.load(sig2)
     lidx2 = LinearIndex.load(sig47)
@@ -1165,9 +1166,9 @@ def test_multi_index_signatures():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     lidx1 = LinearIndex.load(sig2)
     lidx2 = LinearIndex.load(sig47)
@@ -1478,9 +1479,9 @@ def test_linear_index_gather_ignore():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47, ksize=31)
-    ss63 = sourmash.load_one_signature(sig63, ksize=31)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47, ksize=31)
+    ss63 = load_one_signature_from_json(sig63, ksize=31)
 
     # construct an index...
     lidx = LinearIndex([ss2, ss47, ss63])
@@ -1511,9 +1512,9 @@ def test_lca_index_gather_ignore():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47, ksize=31)
-    ss63 = sourmash.load_one_signature(sig63, ksize=31)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47, ksize=31)
+    ss63 = load_one_signature_from_json(sig63, ksize=31)
 
     # construct an index...
     db = LCA_Database(ksize=31, scaled=1000)
@@ -1545,9 +1546,9 @@ def test_sbt_index_gather_ignore():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47, ksize=31)
-    ss63 = sourmash.load_one_signature(sig63, ksize=31)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47, ksize=31)
+    ss63 = load_one_signature_from_json(sig63, ksize=31)
 
     # construct an index...
     factory = GraphFactory(5, 100, 3)
@@ -1715,9 +1716,9 @@ def test_lazy_index_1():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     lidx = LinearIndex()
     lidx.insert(ss2)
@@ -1776,7 +1777,7 @@ def minhash(self):
 def test_lazy_index_4_bool():
     # test some basic features of LazyLinearIndex
     sig2 = utils.get_test_data("2.fa.sig")
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
 
     # test bool false/true
     lidx = LinearIndex()
@@ -1816,9 +1817,9 @@ def test_revindex_index_search():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     lidx = RevIndex(template=ss2.minhash)
     lidx.insert(ss2)
@@ -1861,9 +1862,9 @@ def test_revindex_gather():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     lidx = RevIndex(template=ss2.minhash)
     lidx.insert(ss2)
@@ -1887,9 +1888,9 @@ def test_revindex_gather_ignore():
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss2 = sourmash.load_one_signature(sig2, ksize=31)
-    ss47 = sourmash.load_one_signature(sig47, ksize=31)
-    ss63 = sourmash.load_one_signature(sig63, ksize=31)
+    ss2 = load_one_signature_from_json(sig2, ksize=31)
+    ss47 = load_one_signature_from_json(sig47, ksize=31)
+    ss63 = load_one_signature_from_json(sig63, ksize=31)
 
     # construct an index...
     lidx = RevIndex(template=ss2.minhash, signatures=[ss2, ss47, ss63])
@@ -1919,8 +1920,8 @@ def test_standalone_manifest_signatures(runtmp):
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    ss47 = sourmash.load_one_signature(sig47)
-    ss63 = sourmash.load_one_signature(sig63)
+    ss47 = load_one_signature_from_json(sig47)
+    ss63 = load_one_signature_from_json(sig63)
 
     lidx1 = LinearIndex.load(sig47)
     lidx2 = LinearIndex.load(sig63)
@@ -1943,8 +1944,8 @@ def test_standalone_manifest_signatures_prefix(runtmp):
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    sourmash.load_one_signature(sig47)
-    sourmash.load_one_signature(sig63)
+    load_one_signature_from_json(sig47)
+    load_one_signature_from_json(sig63)
 
     lidx1 = LinearIndex.load(sig47)
     lidx2 = LinearIndex.load(sig63)
@@ -1967,8 +1968,8 @@ def test_standalone_manifest_signatures_prefix_fail(runtmp):
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
 
-    sourmash.load_one_signature(sig47)
-    sourmash.load_one_signature(sig63)
+    load_one_signature_from_json(sig47)
+    load_one_signature_from_json(sig63)
 
     lidx1 = LinearIndex.load(sig47)
     lidx2 = LinearIndex.load(sig63)
@@ -2147,7 +2148,7 @@ def test_standalone_manifest_prefetch_lazy(runtmp):
     # ok! now test prefetch... should get one match legit, to 47,
     # and then no matches to 2, and then error.
 
-    ss47 = sourmash.load_one_signature(sig47)
+    ss47 = load_one_signature_from_json(sig47)
     idx = idx.select(ksize=31)
     g = idx.prefetch(ss47, threshold_bp=0)
 
diff --git a/tests/test_jaccard.py b/tests/test_jaccard.py
index 87093ee194..6fd9b7a1b1 100644
--- a/tests/test_jaccard.py
+++ b/tests/test_jaccard.py
@@ -5,6 +5,7 @@
 
 import pytest
 from sourmash import MinHash
+from sourmash.signature import load_signatures_from_json
 
 import sourmash_tst_utils as utils
 
@@ -172,16 +173,14 @@ def test_abund_similarity_zero():
 
 
 def test_jaccard_on_real_data():
-    from sourmash.signature import load_signatures
-
     afile = "n10000/GCF_000005845.2_ASM584v2_genomic.fna.gz.sig.gz"
     a = utils.get_test_data(afile)
-    sig1 = list(load_signatures(a))[0]
+    sig1 = list(load_signatures_from_json(a))[0]
     mh1 = sig1.minhash
 
     bfile = "n10000/GCF_000006945.1_ASM694v1_genomic.fna.gz.sig.gz"
     b = utils.get_test_data(bfile)
-    sig2 = list(load_signatures(b))[0]
+    sig2 = list(load_signatures_from_json(b))[0]
     mh2 = sig2.minhash
 
     assert mh1.similarity(mh2) == 0.0183
@@ -204,16 +203,14 @@ def test_jaccard_on_real_data():
 
 
 def test_scaled_on_real_data():
-    from sourmash.signature import load_signatures
-
     afile = "scaled100/GCF_000005845.2_ASM584v2_genomic.fna.gz.sig.gz"
     a = utils.get_test_data(afile)
-    sig1 = list(load_signatures(a))[0]
+    sig1 = list(load_signatures_from_json(a))[0]
     mh1 = sig1.minhash
 
     bfile = "scaled100/GCF_000006945.1_ASM694v1_genomic.fna.gz.sig.gz"
     b = utils.get_test_data(bfile)
-    sig2 = list(load_signatures(b))[0]
+    sig2 = list(load_signatures_from_json(b))[0]
     mh2 = sig2.minhash
 
     assert round(mh1.similarity(mh2), 5) == 0.01644
@@ -237,16 +234,14 @@ def test_scaled_on_real_data():
 
 
 def test_scaled_on_real_data_2():
-    from sourmash.signature import load_signatures
-
     afile = "scaled100/GCF_000005845.2_ASM584v2_genomic.fna.gz.sig.gz"
     a = utils.get_test_data(afile)
-    sig1 = list(load_signatures(a))[0]
+    sig1 = list(load_signatures_from_json(a))[0]
     mh1 = sig1.minhash
 
     bfile = "scaled100/GCF_000006945.1_ASM694v1_genomic.fna.gz.sig.gz"
     b = utils.get_test_data(bfile)
-    sig2 = list(load_signatures(b))[0]
+    sig2 = list(load_signatures_from_json(b))[0]
     mh2 = sig2.minhash
 
     assert round(mh1.similarity(mh2), 5) == 0.01644
@@ -270,11 +265,9 @@ def test_scaled_on_real_data_2():
 
 
 def test_downsample_scaled_with_num():
-    from sourmash.signature import load_signatures
-
     afile = "scaled100/GCF_000005845.2_ASM584v2_genomic.fna.gz.sig.gz"
     a = utils.get_test_data(afile)
-    sig1 = list(load_signatures(a))[0]
+    sig1 = list(load_signatures_from_json(a))[0]
     mh1 = sig1.minhash
 
     with pytest.raises(ValueError) as exc:
diff --git a/tests/test_lca.py b/tests/test_lca.py
index 7db105628e..f844422ef3 100644
--- a/tests/test_lca.py
+++ b/tests/test_lca.py
@@ -10,7 +10,8 @@
 
 import sourmash_tst_utils as utils
 import sourmash
-from sourmash import load_one_signature, SourmashSignature, sourmash_args
+from sourmash import SourmashSignature, sourmash_args
+from sourmash.signature import save_signatures_to_json, load_one_signature_from_json
 
 from sourmash.search import make_jaccard_search_query
 from sourmash.lca import lca_utils
@@ -21,7 +22,7 @@
 
 def test_api_create_search():
     # create a database and then search for result.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     assert len(lca_db) == 0
@@ -43,8 +44,8 @@ def test_api_create_search():
 def test_api_find_picklist_select():
     # does 'find' respect picklists?
 
-    sig47 = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
-    sig63 = sourmash.load_one_signature(utils.get_test_data("63.fa.sig"), ksize=31)
+    sig47 = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
+    sig63 = load_one_signature_from_json(utils.get_test_data("63.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lca_db.insert(sig47)
@@ -75,8 +76,8 @@ def test_api_find_picklist_select():
 def test_api_find_picklist_select_exclude():
     # does 'find' respect picklists?
 
-    sig47 = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
-    sig63 = sourmash.load_one_signature(utils.get_test_data("63.fa.sig"), ksize=31)
+    sig47 = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
+    sig63 = load_one_signature_from_json(utils.get_test_data("63.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lca_db.insert(sig47)
@@ -106,7 +107,7 @@ def test_api_find_picklist_select_exclude():
 
 def test_api_create_insert():
     # test some internal implementation stuff: create & then insert a sig.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lca_db.insert(ss)
@@ -133,7 +134,7 @@ def test_api_create_insert():
 
 def test_api_create_insert_bad_ksize():
     # can we insert a ksize=21 signature into a ksize=31 DB? hopefully not.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=21, scaled=1000)
     with pytest.raises(ValueError):
@@ -142,8 +143,8 @@ def test_api_create_insert_bad_ksize():
 
 def test_api_create_insert_bad_ident():
     # can we insert a signature with no/empty ident?
-    ss1 = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
-    ss2 = sourmash.load_one_signature(utils.get_test_data("63.fa.sig"), ksize=31)
+    ss1 = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss2 = load_one_signature_from_json(utils.get_test_data("63.fa.sig"), ksize=31)
     ss1 = ss1.to_mutable()
     ss2 = ss2.to_mutable()
 
@@ -162,7 +163,7 @@ def test_api_create_insert_bad_ident():
 def test_api_create_insert_bad_scaled():
     # can we insert a scaled=1000 signature into a scaled=500 DB?
     # hopefully not.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
     assert ss.minhash.scaled == 1000
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=500)
@@ -173,7 +174,7 @@ def test_api_create_insert_bad_scaled():
 def test_api_create_insert_bad_moltype():
     # can we insert a DNAsignature into a protein DB?
     # hopefully not.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
     assert ss.minhash.moltype == "DNA"
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=500, moltype="protein")
@@ -184,7 +185,7 @@ def test_api_create_insert_bad_moltype():
 def test_api_create_insert_ident():
     # test some internal implementation stuff: signature inserted with
     # different ident than name.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lca_db.insert(ss, ident="foo")
@@ -213,8 +214,8 @@ def test_api_create_insert_ident():
 
 def test_api_create_insert_two():
     # check internal details if multiple signatures are inserted.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
-    ss2 = sourmash.load_one_signature(utils.get_test_data("63.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss2 = load_one_signature_from_json(utils.get_test_data("63.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lca_db.insert(ss, ident="foo")
@@ -254,7 +255,7 @@ def test_api_create_insert_two():
 
 def test_api_create_insert_w_lineage():
     # test some internal implementation stuff - insert signature w/lineage
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lineage = (LineagePair("rank1", "name1"), LineagePair("rank2", "name2"))
@@ -292,7 +293,7 @@ def test_api_create_insert_w_lineage():
 
 def test_api_create_insert_w_bad_lineage():
     # test some internal implementation stuff - insert signature w/bad lineage
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lineage = ([LineagePair("rank1", "name1"), LineagePair("rank2", "name2")],)
@@ -303,7 +304,7 @@ def test_api_create_insert_w_bad_lineage():
 
 def test_api_create_insert_w_bad_lineage_2():
     # test some internal implementation stuff - insert signature w/bad lineage
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lineage = 1  # something non-iterable...
@@ -314,7 +315,7 @@ def test_api_create_insert_w_bad_lineage_2():
 
 def test_api_create_gather():
     # create a database, and then run gather on it.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lca_db.insert(ss)
@@ -328,7 +329,7 @@ def test_api_create_gather():
 
 def test_api_add_genome_lineage():
     # LCA_Databases can store/retrieve arbitrary lineages/taxonomies.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
     lineage = (LineagePair("rank1", "name1"), (LineagePair("rank2", "name2")))
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
@@ -344,8 +345,8 @@ def test_api_add_genome_lineage():
 def test_api_insert_update():
     # check that cached parts of LCA_Database are updated when a new
     # signature is inserted.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
-    ss2 = sourmash.load_one_signature(utils.get_test_data("63.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss2 = load_one_signature_from_json(utils.get_test_data("63.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lca_db.insert(ss)
@@ -369,7 +370,7 @@ def test_api_insert_update():
 def test_api_insert_retrieve_check_name():
     # check that signatures retrieved from LCA_Database objects have the
     # right name.
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lca_db.insert(ss)
@@ -383,8 +384,8 @@ def test_api_insert_retrieve_check_name():
 
 def test_api_create_insert_two_then_scale():
     # construct database, THEN downsample
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
-    ss2 = sourmash.load_one_signature(utils.get_test_data("63.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss2 = load_one_signature_from_json(utils.get_test_data("63.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lca_db.insert(ss)
@@ -404,8 +405,8 @@ def test_api_create_insert_two_then_scale():
 
 def test_api_create_insert_two_then_scale_then_add():
     # construct database, THEN downsample, then add another
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
-    ss2 = sourmash.load_one_signature(utils.get_test_data("63.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss2 = load_one_signature_from_json(utils.get_test_data("63.fa.sig"), ksize=31)
 
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
     lca_db.insert(ss)
@@ -431,8 +432,8 @@ def test_api_create_insert_two_then_scale_then_add():
 
 def test_api_create_insert_scale_two():
     # downsample while constructing database
-    ss = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"), ksize=31)
-    ss2 = sourmash.load_one_signature(utils.get_test_data("63.fa.sig"), ksize=31)
+    ss = load_one_signature_from_json(utils.get_test_data("47.fa.sig"), ksize=31)
+    ss2 = load_one_signature_from_json(utils.get_test_data("63.fa.sig"), ksize=31)
 
     # downsample to 5000 while inserting:
     lca_db = sourmash.lca.LCA_Database(ksize=31, scaled=5000)
@@ -584,7 +585,7 @@ def test_lca_index_find_picklist_check_overlap():
     # (bug #1638)
 
     query_fn = utils.get_test_data("47.fa.sig")
-    query_sig = sourmash.load_one_signature(query_fn, ksize=31)
+    query_sig = load_one_signature_from_json(query_fn, ksize=31)
     db_fn = utils.get_test_data("lca/47+63.lca.json")
     db, ksize, scaled = lca_utils.load_single_database(db_fn)
 
@@ -641,7 +642,7 @@ def test_lca_index_select_picklist_twice():
 def test_search_db_scaled_gt_sig_scaled():
     dbfile = utils.get_test_data("lca/47+63.lca.json")
     db, ksize, scaled = lca_utils.load_single_database(dbfile)
-    sig = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"))
+    sig = load_one_signature_from_json(utils.get_test_data("47.fa.sig"))
 
     results = db.search(sig, threshold=0.01, ignore_abundance=True)
     match_sig = results[0][1]
@@ -653,7 +654,7 @@ def test_search_db_scaled_gt_sig_scaled():
 def test_search_db_scaled_lt_sig_scaled():
     dbfile = utils.get_test_data("lca/47+63.lca.json")
     db, ksize, scaled = lca_utils.load_single_database(dbfile)
-    sig = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"))
+    sig = load_one_signature_from_json(utils.get_test_data("47.fa.sig"))
 
     sig = sig.to_mutable()
     sig.minhash = sig.minhash.downsample(scaled=100000)
@@ -663,14 +664,14 @@ def test_search_db_scaled_lt_sig_scaled():
     assert results[0].score == 1.0
     match = results[0].signature
 
-    orig_sig = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"))
+    orig_sig = load_one_signature_from_json(utils.get_test_data("47.fa.sig"))
     assert orig_sig.minhash.jaccard(match.minhash, downsample=True) == 1.0
 
 
 def test_gather_db_scaled_gt_sig_scaled():
     dbfile = utils.get_test_data("lca/47+63.lca.json")
     db, ksize, scaled = lca_utils.load_single_database(dbfile)
-    sig = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"))
+    sig = load_one_signature_from_json(utils.get_test_data("47.fa.sig"))
 
     result = db.best_containment(sig, threshold=0.01, ignore_abundance=True)
     match_sig = result[1]
@@ -682,7 +683,7 @@ def test_gather_db_scaled_gt_sig_scaled():
 def test_gather_db_scaled_lt_sig_scaled():
     dbfile = utils.get_test_data("lca/47+63.lca.json")
     db, ksize, scaled = lca_utils.load_single_database(dbfile)
-    sig = sourmash.load_one_signature(utils.get_test_data("47.fa.sig"))
+    sig = load_one_signature_from_json(utils.get_test_data("47.fa.sig"))
     sig_minhash = sig.minhash.downsample(scaled=100000)
 
     result = db.best_containment(sig, threshold=0.01, ignore_abundance=True)
@@ -1383,7 +1384,7 @@ def test_single_classify_zip_query(runtmp):
     db1 = utils.get_test_data("lca/delmont-1.lca.json")
     input_sig = utils.get_test_data("lca/TARA_ASE_MAG_00031.sig")
 
-    query_ss = sourmash.load_one_signature(input_sig, ksize=31)
+    query_ss = load_one_signature_from_json(input_sig, ksize=31)
     query_zipfile = runtmp.output("query.zip")
     with sourmash_args.SaveSignaturesToLocation(query_zipfile) as save_sig:
         save_sig.add(query_ss)
@@ -1436,13 +1437,13 @@ def test_single_classify_to_output(runtmp):
 def test_single_classify_to_output_no_name(runtmp):
     db1 = utils.get_test_data("lca/delmont-1.lca.json")
     input_sig = utils.get_test_data("lca/TARA_ASE_MAG_00031.sig")
-    ss = sourmash.load_one_signature(input_sig, ksize=31)
+    ss = load_one_signature_from_json(input_sig, ksize=31)
 
     outsig_filename = runtmp.output("q.sig")
     with open(outsig_filename, "w") as fp:
         # remove name from signature here --
         new_sig = sourmash.SourmashSignature(ss.minhash, filename="xyz")
-        sourmash.save_signatures([new_sig], fp)
+        save_signatures_to_json([new_sig], fp)
 
     cmd = [
         "lca",
@@ -2255,7 +2256,7 @@ def test_single_summarize_scaled_zip_query(runtmp):
     db1 = utils.get_test_data("lca/delmont-1.lca.json")
     input_sig = utils.get_test_data("lca/TARA_ASE_MAG_00031.sig")
 
-    query_ss = sourmash.load_one_signature(input_sig, ksize=31)
+    query_ss = load_one_signature_from_json(input_sig, ksize=31)
     query_zipfile = runtmp.output("query.zip")
     with sourmash_args.SaveSignaturesToLocation(query_zipfile) as save_sig:
         save_sig.add(query_ss)
@@ -2399,9 +2400,9 @@ def test_multi_summarize_with_zip_unassigned_singleton(runtmp, lca_db_format):
     query_zipfile = runtmp.output("query.zip")
     with sourmash_args.SaveSignaturesToLocation(query_zipfile) as save_sig:
         input_sig1 = utils.get_test_data("lca/TARA_ASE_MAG_00031.sig")
-        sig1 = sourmash.load_one_signature(input_sig1, ksize=31)
+        sig1 = load_one_signature_from_json(input_sig1, ksize=31)
         input_sig2 = utils.get_test_data("lca/TARA_PSW_MAG_00136.sig")
-        sig2 = sourmash.load_one_signature(input_sig2, ksize=31)
+        sig2 = load_one_signature_from_json(input_sig2, ksize=31)
 
         save_sig.add(sig1)
         save_sig.add(sig2)
@@ -2914,7 +2915,7 @@ def test_lca_index_empty(runtmp, lca_db_format):
     sig47file = utils.get_test_data("47.fa.sig")
     sig63file = utils.get_test_data("63.fa.sig")
 
-    sig63 = load_one_signature(sig63file, ksize=31)
+    sig63 = load_one_signature_from_json(sig63file, ksize=31)
 
     # create an empty spreadsheet
     with open(c.output("empty.csv"), "w") as fp:
@@ -2955,9 +2956,9 @@ def test_lca_gather_threshold_1():
     sig47file = utils.get_test_data("47.fa.sig")
     sig63file = utils.get_test_data("63.fa.sig")
 
-    sig2 = load_one_signature(sig2file, ksize=31)
-    sig47 = load_one_signature(sig47file, ksize=31)
-    sig63 = load_one_signature(sig63file, ksize=31)
+    sig2 = load_one_signature_from_json(sig2file, ksize=31)
+    sig47 = load_one_signature_from_json(sig47file, ksize=31)
+    sig63 = load_one_signature_from_json(sig63file, ksize=31)
 
     # construct LCA Database
     db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
@@ -3015,9 +3016,9 @@ def test_lca_gather_threshold_5():
     sig47file = utils.get_test_data("47.fa.sig")
     sig63file = utils.get_test_data("63.fa.sig")
 
-    sig2 = load_one_signature(sig2file, ksize=31)
-    sig47 = load_one_signature(sig47file, ksize=31)
-    sig63 = load_one_signature(sig63file, ksize=31)
+    sig2 = load_one_signature_from_json(sig2file, ksize=31)
+    sig47 = load_one_signature_from_json(sig47file, ksize=31)
+    sig63 = load_one_signature_from_json(sig63file, ksize=31)
 
     # construct LCA Database
     db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
@@ -3061,9 +3062,9 @@ def test_gather_multiple_return():
     sig47file = utils.get_test_data("47.fa.sig")
     sig63file = utils.get_test_data("63.fa.sig")
 
-    sig2 = load_one_signature(sig2file, ksize=31)
-    sig47 = load_one_signature(sig47file, ksize=31)
-    sig63 = load_one_signature(sig63file, ksize=31)
+    sig2 = load_one_signature_from_json(sig2file, ksize=31)
+    sig47 = load_one_signature_from_json(sig47file, ksize=31)
+    sig63 = load_one_signature_from_json(sig63file, ksize=31)
 
     # construct LCA Database
     db = sourmash.lca.LCA_Database(ksize=31, scaled=1000)
@@ -3088,8 +3089,8 @@ def test_lca_db_protein_build():
         "prot/protein/GCA_001593935.1_ASM159393v1_protein.faa.gz.sig"
     )
 
-    sig1 = sourmash.load_one_signature(sigfile1)
-    sig2 = sourmash.load_one_signature(sigfile2)
+    sig1 = load_one_signature_from_json(sigfile1)
+    sig2 = load_one_signature_from_json(sigfile2)
 
     db = sourmash.lca.LCA_Database(ksize=19, scaled=100, moltype="protein")
     assert db.insert(sig1)
@@ -3119,8 +3120,8 @@ def test_lca_db_protein_save_load(c):
         "prot/protein/GCA_001593935.1_ASM159393v1_protein.faa.gz.sig"
     )
 
-    sig1 = sourmash.load_one_signature(sigfile1)
-    sig2 = sourmash.load_one_signature(sigfile2)
+    sig1 = load_one_signature_from_json(sigfile1)
+    sig2 = load_one_signature_from_json(sigfile2)
 
     db = sourmash.lca.LCA_Database(ksize=19, scaled=100, moltype="protein")
     assert db.insert(sig1)
@@ -3187,8 +3188,8 @@ def test_lca_db_protein_command_index(runtmp, lca_db_format):
     db2 = x[0]
     assert db2.moltype == "protein"
 
-    sig1 = sourmash.load_one_signature(sigfile1)
-    sig2 = sourmash.load_one_signature(sigfile2)
+    sig1 = load_one_signature_from_json(sigfile1)
+    sig2 = load_one_signature_from_json(sigfile2)
 
     # check reconstruction --
     mh_list = [x.minhash for x in db2.signatures()]
@@ -3230,8 +3231,8 @@ def test_lca_db_hp_build():
         "prot/hp/GCA_001593935.1_ASM159393v1_protein.faa.gz.sig"
     )
 
-    sig1 = sourmash.load_one_signature(sigfile1)
-    sig2 = sourmash.load_one_signature(sigfile2)
+    sig1 = load_one_signature_from_json(sigfile1)
+    sig2 = load_one_signature_from_json(sigfile2)
 
     db = sourmash.lca.LCA_Database(ksize=19, scaled=100, moltype="hp")
     assert db.insert(sig1)
@@ -3261,8 +3262,8 @@ def test_lca_db_hp_save_load(c):
         "prot/hp/GCA_001593935.1_ASM159393v1_protein.faa.gz.sig"
     )
 
-    sig1 = sourmash.load_one_signature(sigfile1)
-    sig2 = sourmash.load_one_signature(sigfile2)
+    sig1 = load_one_signature_from_json(sigfile1)
+    sig2 = load_one_signature_from_json(sigfile2)
 
     db = sourmash.lca.LCA_Database(ksize=19, scaled=100, moltype="hp")
     assert db.insert(sig1)
@@ -3327,8 +3328,8 @@ def test_lca_db_hp_command_index(runtmp, lca_db_format):
     db2 = x[0]
     assert db2.moltype == "hp"
 
-    sig1 = sourmash.load_one_signature(sigfile1)
-    sig2 = sourmash.load_one_signature(sigfile2)
+    sig1 = load_one_signature_from_json(sigfile1)
+    sig2 = load_one_signature_from_json(sigfile2)
 
     # check reconstruction --
     mh_list = [x.minhash for x in db2.signatures()]
@@ -3370,8 +3371,8 @@ def test_lca_db_dayhoff_build():
         "prot/dayhoff/GCA_001593935.1_ASM159393v1_protein.faa.gz.sig"
     )
 
-    sig1 = sourmash.load_one_signature(sigfile1)
-    sig2 = sourmash.load_one_signature(sigfile2)
+    sig1 = load_one_signature_from_json(sigfile1)
+    sig2 = load_one_signature_from_json(sigfile2)
 
     db = sourmash.lca.LCA_Database(ksize=19, scaled=100, moltype="dayhoff")
     assert db.insert(sig1)
@@ -3401,8 +3402,8 @@ def test_lca_db_dayhoff_save_load(c):
         "prot/dayhoff/GCA_001593935.1_ASM159393v1_protein.faa.gz.sig"
     )
 
-    sig1 = sourmash.load_one_signature(sigfile1)
-    sig2 = sourmash.load_one_signature(sigfile2)
+    sig1 = load_one_signature_from_json(sigfile1)
+    sig2 = load_one_signature_from_json(sigfile2)
 
     db = sourmash.lca.LCA_Database(ksize=19, scaled=100, moltype="dayhoff")
     assert db.insert(sig1)
@@ -3467,8 +3468,8 @@ def test_lca_db_dayhoff_command_index(runtmp, lca_db_format):
     db2 = x[0]
     assert db2.moltype == "dayhoff"
 
-    sig1 = sourmash.load_one_signature(sigfile1)
-    sig2 = sourmash.load_one_signature(sigfile2)
+    sig1 = load_one_signature_from_json(sigfile1)
+    sig2 = load_one_signature_from_json(sigfile2)
 
     # check reconstruction --
     mh_list = [x.minhash for x in db2.signatures()]
@@ -3701,8 +3702,8 @@ def test_lca_db_protein_save_twice(runtmp, lca_db_format):
         "prot/protein/GCA_001593935.1_ASM159393v1_protein.faa.gz.sig"
     )
 
-    sig1 = sourmash.load_one_signature(sigfile1)
-    sig2 = sourmash.load_one_signature(sigfile2)
+    sig1 = load_one_signature_from_json(sigfile1)
+    sig2 = load_one_signature_from_json(sigfile2)
 
     db = sourmash.lca.LCA_Database(ksize=19, scaled=100, moltype="protein")
     assert db.insert(sig1)
diff --git a/tests/test_minhash.py b/tests/test_minhash.py
index 474f1e231a..f181381485 100644
--- a/tests/test_minhash.py
+++ b/tests/test_minhash.py
@@ -1723,7 +1723,8 @@ def test_distance_matrix(track_abundance):
     import numpy
 
     siglist = [
-        next(signature.load_signatures(utils.get_test_data(f))) for f in utils.SIG_FILES
+        next(signature.load_signatures_from_json(utils.get_test_data(f)))
+        for f in utils.SIG_FILES
     ]
 
     D1 = numpy.zeros([len(siglist), len(siglist)])
diff --git a/tests/test_np_utils.py b/tests/test_np_utils.py
index e23ca361a0..d9edcb171f 100644
--- a/tests/test_np_utils.py
+++ b/tests/test_np_utils.py
@@ -1,5 +1,5 @@
 import numpy as np
-from sourmash.signature import SourmashSignature
+from sourmash import SourmashSignature
 import sourmash
 from sourmash.np_utils import to_memmap
 
diff --git a/tests/test_prefetch.py b/tests/test_prefetch.py
index 44c6b4aac5..fc73a2d724 100644
--- a/tests/test_prefetch.py
+++ b/tests/test_prefetch.py
@@ -12,7 +12,12 @@
 import sourmash_tst_utils as utils
 import sourmash
 from sourmash_tst_utils import SourmashCommandFailed
-from sourmash import signature, sourmash_args
+from sourmash import SourmashSignature, sourmash_args
+from sourmash.signature import (
+    save_signatures_to_json,
+    load_signatures_from_json,
+    load_one_signature_from_json,
+)
 
 
 def approx_eq(val1, val2):
@@ -332,7 +337,7 @@ def test_prefetch_matches(runtmp, linear_gather):
 
     expected_matches = [sig63, sig47]
     for match, expected in zip(sigs.signatures(), expected_matches):
-        ss = sourmash.load_one_signature(expected, ksize=31)
+        ss = load_one_signature_from_json(expected, ksize=31)
         assert match == ss
 
 
@@ -343,8 +348,8 @@ def test_prefetch_matches_to_dir(runtmp, linear_gather):
     sig2 = utils.get_test_data("2.fa.sig")
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
-    ss63 = sourmash.load_one_signature(sig63)
-    ss47 = sourmash.load_one_signature(sig47)
+    ss63 = load_one_signature_from_json(sig63)
+    ss47 = load_one_signature_from_json(sig47)
 
     matches_out = c.output("matches_dir/")
 
@@ -385,8 +390,8 @@ def test_prefetch_matches_to_sig_gz(runtmp, linear_gather):
     sig2 = utils.get_test_data("2.fa.sig")
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
-    ss63 = sourmash.load_one_signature(sig63)
-    ss47 = sourmash.load_one_signature(sig47)
+    ss63 = load_one_signature_from_json(sig63)
+    ss47 = load_one_signature_from_json(sig47)
 
     matches_out = c.output("matches.sig.gz")
 
@@ -431,8 +436,8 @@ def test_prefetch_matches_to_zip(runtmp, linear_gather):
     sig2 = utils.get_test_data("2.fa.sig")
     sig47 = utils.get_test_data("47.fa.sig")
     sig63 = utils.get_test_data("63.fa.sig")
-    ss63 = sourmash.load_one_signature(sig63)
-    ss47 = sourmash.load_one_signature(sig47)
+    ss63 = load_one_signature_from_json(sig63)
+    ss47 = load_one_signature_from_json(sig47)
 
     matches_out = c.output("matches.zip")
 
@@ -496,14 +501,14 @@ def test_prefetch_matching_hashes(runtmp, linear_gather):
     assert c.last_result.status == 0
     assert os.path.exists(matches_out)
 
-    ss47 = sourmash.load_one_signature(sig47, ksize=31)
-    ss63 = sourmash.load_one_signature(sig63, ksize=31)
+    ss47 = load_one_signature_from_json(sig47, ksize=31)
+    ss63 = load_one_signature_from_json(sig63, ksize=31)
     matches = set(ss47.minhash.hashes) & set(ss63.minhash.hashes)
 
     intersect = ss47.minhash.copy_and_clear()
     intersect.add_many(matches)
 
-    ss = sourmash.load_one_signature(matches_out)
+    ss = load_one_signature_from_json(matches_out)
     assert ss.name.endswith("-known")
     assert ss.minhash == intersect
 
@@ -536,13 +541,13 @@ def test_prefetch_nomatch_hashes(runtmp, linear_gather):
     assert c.last_result.status == 0
     assert os.path.exists(nomatch_out)
 
-    ss47 = sourmash.load_one_signature(sig47, ksize=31)
-    ss63 = sourmash.load_one_signature(sig63, ksize=31)
+    ss47 = load_one_signature_from_json(sig47, ksize=31)
+    ss63 = load_one_signature_from_json(sig63, ksize=31)
 
     remain = ss47.minhash.to_mutable()
     remain.remove_many(ss63.minhash.hashes)
 
-    ss = sourmash.load_one_signature(nomatch_out)
+    ss = load_one_signature_from_json(nomatch_out)
     assert ss.name.endswith("-unknown")
     assert ss.minhash == remain
 
@@ -756,7 +761,7 @@ def test_prefetch_downsample_multiple(runtmp, linear_gather):
     query_sig = utils.get_test_data("GCF_000006945.2-s500.sig")
 
     # load in the hashes and do split them into four bins, randomly.
-    ss = sourmash.load_one_signature(query_sig)
+    ss = load_one_signature_from_json(query_sig)
     hashes = list(ss.minhash.hashes)
 
     random.seed(a=1)  # fix seed so test is reproducible
@@ -775,10 +780,10 @@ def test_prefetch_downsample_multiple(runtmp, linear_gather):
 
     gathersigs = []
     for i in range(4):
-        binsig = signature.SourmashSignature(mh_bins[i], name=f"bin{i}")
+        binsig = SourmashSignature(mh_bins[i], name=f"bin{i}")
 
         with open(runtmp.output(f"bin{i}.sig"), "wb") as fp:
-            sourmash.save_signatures([binsig], fp)
+            save_signatures_to_json([binsig], fp)
 
         gathersigs.append(f"bin{i}.sig")
 
diff --git a/tests/test_signature.py b/tests/test_signature.py
index b82a02364e..6365b58856 100644
--- a/tests/test_signature.py
+++ b/tests/test_signature.py
@@ -5,11 +5,13 @@
 import sourmash
 from sourmash.signature import (
     SourmashSignature,
-    save_signatures,
-    load_signatures,
-    load_one_signature,
     FrozenSourmashSignature,
 )
+from sourmash.signature import (
+    save_signatures_to_json,
+    load_signatures_from_json,
+    load_one_signature_from_json,
+)
 import sourmash_tst_utils as utils
 from sourmash.minhash import MinHash, FrozenMinHash
 from sourmash_tst_utils import SourmashCommandFailed
@@ -137,8 +139,8 @@ def test_roundtrip(track_abundance):
     e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
     e.add_kmer("AT" * 10)
     sig = SourmashSignature(e)
-    s = save_signatures([sig])
-    siglist = list(load_signatures(s))
+    s = save_signatures_to_json([sig])
+    siglist = list(load_signatures_from_json(s))
     sig2 = siglist[0]
 
     assert sig.similarity(sig2) == 1.0
@@ -167,8 +169,8 @@ def test_load_signature_ksize_nonint(track_abundance):
     e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
     e.add_kmer("AT" * 10)
     sig = SourmashSignature(e)
-    s = save_signatures([sig])
-    siglist = list(load_signatures(s, ksize="20"))
+    s = save_signatures_to_json([sig])
+    siglist = list(load_signatures_from_json(s, ksize="20"))
     sig2 = siglist[0]
 
     assert sig.similarity(sig2) == 1.0
@@ -180,8 +182,8 @@ def test_roundtrip_empty(track_abundance):
     e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
 
     sig = SourmashSignature(e)
-    s = save_signatures([sig])
-    siglist = list(load_signatures(s))
+    s = save_signatures_to_json([sig])
+    siglist = list(load_signatures_from_json(s))
     sig2 = siglist[0]
 
     assert sig.similarity(sig2) == 0
@@ -192,8 +194,8 @@ def test_roundtrip_scaled(track_abundance):
     e = MinHash(n=0, ksize=20, track_abundance=track_abundance, max_hash=10)
     e.add_hash(5)
     sig = SourmashSignature(e)
-    s = save_signatures([sig])
-    siglist = list(load_signatures(s))
+    s = save_signatures_to_json([sig])
+    siglist = list(load_signatures_from_json(s))
     sig2 = siglist[0]
     e2 = sig2.minhash
 
@@ -207,8 +209,8 @@ def test_roundtrip_seed(track_abundance):
     e = MinHash(n=1, ksize=20, track_abundance=track_abundance, seed=10)
     e.add_hash(5)
     sig = SourmashSignature(e)
-    s = save_signatures([sig])
-    siglist = list(load_signatures(s))
+    s = save_signatures_to_json([sig])
+    siglist = list(load_signatures_from_json(s))
     sig2 = siglist[0]
     e2 = sig2.minhash
 
@@ -291,8 +293,8 @@ def test_save_load_multisig(track_abundance):
     e2 = MinHash(n=1, ksize=25, track_abundance=track_abundance)
     sig2 = SourmashSignature(e2)
 
-    x = save_signatures([sig1, sig2])
-    y = list(load_signatures(x))
+    x = save_signatures_to_json([sig1, sig2])
+    y = list(load_signatures_from_json(x))
 
     print(x)
 
@@ -303,19 +305,19 @@ def test_save_load_multisig(track_abundance):
 
 
 def test_load_one_fail_nosig(track_abundance):
-    x = save_signatures([])
+    x = save_signatures_to_json([])
     print((x,))
     with pytest.raises(ValueError):
-        load_one_signature(x)
+        load_one_signature_from_json(x)
 
 
 def test_load_one_succeed(track_abundance):
     e1 = MinHash(n=1, ksize=20, track_abundance=track_abundance)
     sig1 = SourmashSignature(e1)
 
-    x = save_signatures([sig1])
+    x = save_signatures_to_json([sig1])
 
-    y = load_one_signature(x)
+    y = load_one_signature_from_json(x)
     assert sig1 == y
 
 
@@ -326,10 +328,10 @@ def test_load_one_fail_multisig(track_abundance):
     e2 = MinHash(n=1, ksize=20, track_abundance=track_abundance)
     sig2 = SourmashSignature(e2)
 
-    x = save_signatures([sig1, sig2])
+    x = save_signatures_to_json([sig1, sig2])
 
     with pytest.raises(ValueError):
-        load_one_signature(x)
+        load_one_signature_from_json(x)
 
 
 def test_save_minified(track_abundance):
@@ -339,11 +341,11 @@ def test_save_minified(track_abundance):
     e2 = MinHash(n=1, ksize=25, track_abundance=track_abundance)
     sig2 = SourmashSignature(e2, name="bar baz")
 
-    x = save_signatures([sig1, sig2])
+    x = save_signatures_to_json([sig1, sig2])
     assert b"\n" not in x
     assert len(x.split(b"\n")) == 1
 
-    y = list(load_signatures(x))
+    y = list(load_signatures_from_json(x))
     assert len(y) == 2
     assert any(sig.name == "foo" for sig in y)
     assert any(sig.name == "bar baz" for sig in y)
@@ -351,9 +353,9 @@ def test_save_minified(track_abundance):
 
 def test_load_minified(track_abundance):
     sigfile = utils.get_test_data("genome-s10+s11.sig")
-    sigs = load_signatures(sigfile)
+    sigs = load_signatures_from_json(sigfile)
 
-    minified = save_signatures(sigs)
+    minified = save_signatures_to_json(sigs)
     with open(sigfile) as f:
         orig_file = f.read()
     assert len(minified) < len(orig_file)
@@ -364,13 +366,13 @@ def test_load_compressed(track_abundance):
     e1 = MinHash(n=1, ksize=20, track_abundance=track_abundance)
     sig1 = SourmashSignature(e1)
 
-    x = save_signatures([sig1], compression=5)
+    x = save_signatures_to_json([sig1], compression=5)
 
-    y = load_one_signature(x)
+    y = load_one_signature_from_json(x)
     assert sig1 == y
 
     sigfile = utils.get_test_data("genome-s10+s11.sig.gz")
-    load_signatures(sigfile)
+    load_signatures_from_json(sigfile)
 
 
 def test_binary_fp(tmpdir, track_abundance):
@@ -380,19 +382,19 @@ def test_binary_fp(tmpdir, track_abundance):
     path = tmpdir.join("1.sig")
     with open(str(path), "wb") as fp:
         sig = SourmashSignature(e)
-        save_signatures([sig], fp)
+        save_signatures_to_json([sig], fp)
 
 
-def test_load_signatures_no_file_do_raise(tmpdir):
+def test_load_signatures_from_json_no_file_do_raise(tmpdir):
     path = tmpdir.join("dne.sig")
-    siglist = load_signatures(path, do_raise=True)
+    siglist = load_signatures_from_json(path, do_raise=True)
     with pytest.raises(Exception):
         list(siglist)
 
 
-def test_load_signatures_no_file_do_not_raise(tmpdir):
+def test_load_signatures_from_json_no_file_do_not_raise(tmpdir):
     path = tmpdir.join("dne.sig")
-    siglist = load_signatures(path)
+    siglist = load_signatures_from_json(path)
     siglist = list(siglist)
     assert not siglist
 
@@ -446,8 +448,8 @@ def test_max_containment_equal():
 def test_containment_ANI():
     f1 = utils.get_test_data("2.fa.sig")
     f2 = utils.get_test_data("2+63.fa.sig")
-    ss1 = sourmash.load_one_signature(f1, ksize=31)
-    ss2 = sourmash.load_one_signature(f2, ksize=31)
+    ss1 = sourmash.load_one_signature_from_json(f1, ksize=31)
+    ss2 = sourmash.load_one_signature_from_json(f2, ksize=31)
 
     s1_cont_s2 = ss1.containment_ani(ss2, estimate_ci=True)
     s2_cont_s1 = ss2.containment_ani(ss1, estimate_ci=True)
@@ -482,8 +484,8 @@ def test_containment_ANI():
 def test_containment_ANI_precalc_containment():
     f1 = utils.get_test_data("47+63.fa.sig")
     f2 = utils.get_test_data("2+63.fa.sig")
-    ss1 = sourmash.load_one_signature(f1, ksize=31)
-    ss2 = sourmash.load_one_signature(f2, ksize=31)
+    ss1 = sourmash.load_one_signature_from_json(f1, ksize=31)
+    ss2 = sourmash.load_one_signature_from_json(f2, ksize=31)
     # precalc containments and assert same results
     s1c = ss1.contained_by(ss2)
     s2c = ss2.contained_by(ss1)
@@ -505,8 +507,8 @@ def test_containment_ANI_precalc_containment():
 def test_avg_containment():
     f1 = utils.get_test_data("47+63.fa.sig")
     f2 = utils.get_test_data("2+63.fa.sig")
-    ss1 = sourmash.load_one_signature(f1, ksize=31)
-    ss2 = sourmash.load_one_signature(f2, ksize=31)
+    ss1 = sourmash.load_one_signature_from_json(f1, ksize=31)
+    ss2 = sourmash.load_one_signature_from_json(f2, ksize=31)
     # check average_containment_ani
     ac_s1 = ss1.avg_containment(ss2)
     ac_s2 = ss2.avg_containment(ss1)
@@ -521,8 +523,8 @@ def test_avg_containment():
 def test_avg_containment_ani():
     f1 = utils.get_test_data("47+63.fa.sig")
     f2 = utils.get_test_data("2+63.fa.sig")
-    ss1 = sourmash.load_one_signature(f1, ksize=31)
-    ss2 = sourmash.load_one_signature(f2, ksize=31)
+    ss1 = sourmash.load_one_signature_from_json(f1, ksize=31)
+    ss2 = sourmash.load_one_signature_from_json(f2, ksize=31)
     # check average_containment_ani
     ac_s1 = ss1.avg_containment_ani(ss2)
     ac_s2 = ss2.avg_containment_ani(ss1)
@@ -536,8 +538,8 @@ def test_avg_containment_ani():
 def test_containment_ANI_downsample():
     f2 = utils.get_test_data("2+63.fa.sig")
     f3 = utils.get_test_data("47+63.fa.sig")
-    ss2 = sourmash.load_one_signature(f2, ksize=31)
-    ss3 = sourmash.load_one_signature(f3, ksize=31)
+    ss2 = sourmash.load_one_signature_from_json(f2, ksize=31)
+    ss3 = sourmash.load_one_signature_from_json(f3, ksize=31)
     # check that downsampling works properly
     print(ss2.minhash.scaled)
 
@@ -571,8 +573,8 @@ def test_containment_ANI_downsample():
 def test_jaccard_ANI():
     f1 = utils.get_test_data("2.fa.sig")
     f2 = utils.get_test_data("2+63.fa.sig")
-    ss1 = sourmash.load_one_signature(f1, ksize=31)
-    ss2 = sourmash.load_one_signature(f2)
+    ss1 = sourmash.load_one_signature_from_json(f1, ksize=31)
+    ss2 = sourmash.load_one_signature_from_json(f2)
 
     print("\nJACCARD_ANI", ss1.jaccard_ani(ss2))
 
@@ -590,8 +592,8 @@ def test_jaccard_ANI():
 def test_jaccard_ANI_untrustworthy():
     f1 = utils.get_test_data("2.fa.sig")
     f2 = utils.get_test_data("2+63.fa.sig")
-    ss1 = sourmash.load_one_signature(f1, ksize=31)
-    ss2 = sourmash.load_one_signature(f2)
+    ss1 = sourmash.load_one_signature_from_json(f1, ksize=31)
+    ss2 = sourmash.load_one_signature_from_json(f2)
 
     print("\nJACCARD_ANI", ss1.jaccard_ani(ss2))
 
@@ -608,8 +610,8 @@ def test_jaccard_ANI_untrustworthy():
 def test_jaccard_ANI_precalc_jaccard():
     f1 = utils.get_test_data("47+63.fa.sig")
     f2 = utils.get_test_data("2+63.fa.sig")
-    ss1 = sourmash.load_one_signature(f1, ksize=31)
-    ss2 = sourmash.load_one_signature(f2)
+    ss1 = sourmash.load_one_signature_from_json(f1, ksize=31)
+    ss2 = sourmash.load_one_signature_from_json(f2)
     # precalc jaccard and assert same result
     jaccard = ss1.jaccard(ss2)
     print("\nJACCARD_ANI", ss1.jaccard_ani(ss2, jaccard=jaccard))
@@ -626,8 +628,8 @@ def test_jaccard_ANI_precalc_jaccard():
 def test_jaccard_ANI_downsample():
     f1 = utils.get_test_data("47+63.fa.sig")
     f2 = utils.get_test_data("2+63.fa.sig")
-    ss1 = sourmash.load_one_signature(f1, ksize=31)
-    ss2 = sourmash.load_one_signature(f2)
+    ss1 = sourmash.load_one_signature_from_json(f1, ksize=31)
+    ss2 = sourmash.load_one_signature_from_json(f2)
 
     print(ss1.minhash.scaled)
     ss1 = ss1.to_mutable()
diff --git a/tests/test_sourmash.py b/tests/test_sourmash.py
index 23647e517b..c3f0858395 100644
--- a/tests/test_sourmash.py
+++ b/tests/test_sourmash.py
@@ -23,6 +23,8 @@
 from sourmash.sbt import SBT, Node
 from sourmash.sbtmh import SigLeaf, load_sbt_index
 from sourmash.search import SearchResult, GatherResult
+from sourmash.signature import load_one_signature_from_json as load_one_signature
+from sourmash.signature import load_signatures_from_json
 
 try:
     import matplotlib
@@ -161,7 +163,7 @@ def test_compare_serial(runtmp):
 
     sigs = []
     for fn in testsigs:
-        sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype="dna"))
+        sigs.append(load_one_signature(fn, ksize=21, select_moltype="dna"))
 
     cmp_calc = numpy.zeros([len(sigs), len(sigs)])
     for i, si in enumerate(sigs):
@@ -170,7 +172,7 @@ def test_compare_serial(runtmp):
 
         sigs = []
         for fn in testsigs:
-            sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype="dna"))
+            sigs.append(load_one_signature(fn, ksize=21, select_moltype="dna"))
     assert (cmp_out == cmp_calc).all()
 
 
@@ -189,7 +191,7 @@ def test_compare_serial_distance(runtmp):
 
     sigs = []
     for fn in testsigs:
-        sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype="dna"))
+        sigs.append(load_one_signature(fn, ksize=21, select_moltype="dna"))
 
     cmp_calc = numpy.zeros([len(sigs), len(sigs)])
     for i, si in enumerate(sigs):
@@ -198,7 +200,7 @@ def test_compare_serial_distance(runtmp):
 
         sigs = []
         for fn in testsigs:
-            sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype="dna"))
+            sigs.append(load_one_signature(fn, ksize=21, select_moltype="dna"))
     assert (cmp_out == cmp_calc).all()
 
 
@@ -219,7 +221,7 @@ def test_compare_parallel(runtmp):
 
     sigs = []
     for fn in testsigs:
-        sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype="dna"))
+        sigs.append(load_one_signature(fn, ksize=21, select_moltype="dna"))
 
     cmp_calc = numpy.zeros([len(sigs), len(sigs)])
     for i, si in enumerate(sigs):
@@ -228,7 +230,7 @@ def test_compare_parallel(runtmp):
 
         sigs = []
         for fn in testsigs:
-            sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype="dna"))
+            sigs.append(load_one_signature(fn, ksize=21, select_moltype="dna"))
     assert (cmp_out == cmp_calc).all()
 
 
@@ -252,7 +254,7 @@ def test_compare_do_serial_compare_with_from_file(runtmp):
 
     sigs = []
     for fn in testsigs:
-        sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype="dna"))
+        sigs.append(load_one_signature(fn, ksize=21, select_moltype="dna"))
 
     cmp_calc = numpy.zeros([len(sigs), len(sigs)])
     for i, si in enumerate(sigs):
@@ -261,7 +263,7 @@ def test_compare_do_serial_compare_with_from_file(runtmp):
 
         sigs = []
         for fn in testsigs:
-            sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype="dna"))
+            sigs.append(load_one_signature(fn, ksize=21, select_moltype="dna"))
 
     assert numpy.array_equal(numpy.sort(cmp_out.flat), numpy.sort(cmp_calc.flat))
 
@@ -281,7 +283,7 @@ def test_compare_do_basic_compare_using_rna_arg(runtmp):
 
     sigs = []
     for fn in testsigs:
-        sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype="dna"))
+        sigs.append(load_one_signature(fn, ksize=21, select_moltype="dna"))
 
     cmp_calc = numpy.zeros([len(sigs), len(sigs)])
     for i, si in enumerate(sigs):
@@ -305,7 +307,7 @@ def test_compare_do_basic_using_nucleotide_arg(runtmp):
 
     sigs = []
     for fn in testsigs:
-        sigs.append(sourmash.load_one_signature(fn, ksize=21, select_moltype="dna"))
+        sigs.append(load_one_signature(fn, ksize=21, select_moltype="dna"))
 
     cmp_calc = numpy.zeros([len(sigs), len(sigs)])
     for i, si in enumerate(sigs):
@@ -638,7 +640,7 @@ def _load_compare_matrix_and_sigs(compare_csv, sigfiles, *, ksize=31):
     # load in all the input signatures
     idx_to_sig = {}
     for idx, filename in enumerate(sigfiles):
-        ss = sourmash.load_one_signature(filename, ksize=ksize)
+        ss = load_one_signature(filename, ksize=ksize)
         idx_to_sig[idx] = ss
 
     return mat, idx_to_sig
@@ -2198,9 +2200,9 @@ def test_search_containment_abund(runtmp):
 
     # save!
     with open(runtmp.output("a.sig"), "w") as fp:
-        sourmash.save_signatures([x], fp)
+        signature.save_signatures_to_json([x], fp)
     with open(runtmp.output("b.sig"), "w") as fp:
-        sourmash.save_signatures([y], fp)
+        signature.save_signatures_to_json([y], fp)
 
     # run sourmash search --containment
     with pytest.raises(SourmashCommandFailed) as exc:
@@ -2242,9 +2244,9 @@ def test_search_containment_abund_ignore(runtmp):
 
     # save!
     with open(runtmp.output("a.sig"), "w") as fp:
-        sourmash.save_signatures([x], fp)
+        signature.save_signatures_to_json([x], fp)
     with open(runtmp.output("b.sig"), "w") as fp:
-        sourmash.save_signatures([y], fp)
+        signature.save_signatures_to_json([y], fp)
 
     # run sourmash search
     runtmp.sourmash(
@@ -3313,7 +3315,7 @@ def test_do_sourmash_index_abund(c):
     testdata2 = utils.get_test_data("lca-root/TOBG_MED-875.fna.gz.sig")
 
     with open(testdata2):
-        ss = sourmash.load_one_signature(testdata2, ksize=31)
+        ss = load_one_signature(testdata2, ksize=31)
         assert ss.minhash.track_abundance == True
 
     sbtname = "foo"
@@ -3688,7 +3690,7 @@ def test_do_sourmash_check_sbt_filenames(runtmp):
     sig_names = set()
     sig_md5s = set()
     for f in files:
-        sig = signature.load_one_signature(f)
+        sig = load_one_signature(f)
         sig_names.add(sig.name)
         sig_md5s.add(sig.md5sum())
 
@@ -3839,10 +3841,10 @@ def test_compare_with_abundance_1(runtmp):
     s2 = signature.SourmashSignature(E2, filename="e2", name="e2")
 
     with open(runtmp.output("e1.sig"), "w") as f:
-        signature.save_signatures([s1], f)
+        signature.save_signatures_to_json([s1], f)
 
     with open(runtmp.output("e2.sig"), "w") as f:
-        signature.save_signatures([s2], f)
+        signature.save_signatures_to_json([s2], f)
 
     runtmp.sourmash("search", "e1.sig", "e2.sig", "-k", "5")
 
@@ -3863,10 +3865,10 @@ def test_compare_with_abundance_2(runtmp):
     s2 = signature.SourmashSignature(E2, filename="e2", name="e2")
 
     with open(runtmp.output("e1.sig"), "w") as f:
-        signature.save_signatures([s1], f)
+        signature.save_signatures_to_json([s1], f)
 
     with open(runtmp.output("e2.sig"), "w") as f:
-        signature.save_signatures([s2], f)
+        signature.save_signatures_to_json([s2], f)
 
     runtmp.sourmash("search", "e1.sig", "e2.sig", "-k", "5")
 
@@ -3888,10 +3890,10 @@ def test_compare_with_abundance_3(runtmp):
     s2 = signature.SourmashSignature(E2, filename="e2", name="e2")
 
     with open(runtmp.output("e1.sig"), "w") as f:
-        signature.save_signatures([s1], f)
+        signature.save_signatures_to_json([s1], f)
 
     with open(runtmp.output("e2.sig"), "w") as f:
-        signature.save_signatures([s2], f)
+        signature.save_signatures_to_json([s2], f)
 
     runtmp.sourmash("search", "e1.sig", "e2.sig", "-k", "5")
 
@@ -4417,7 +4419,7 @@ def test_gather_f_match_orig(runtmp, linear_gather, prefetch_gather):
     print(runtmp.last_result.out)
     print(runtmp.last_result.err)
 
-    combined_sig = sourmash.load_one_signature(testdata_combined, ksize=21)
+    combined_sig = load_one_signature(testdata_combined, ksize=21)
     remaining_mh = combined_sig.minhash.to_mutable()
 
     def approx_equal(a, b, n=5):
@@ -4434,7 +4436,7 @@ def approx_equal(a, b, n=5):
             # double check -- should match 'search --containment'.
             # (this is kind of useless for a 1.0 contained_by, I guess)
             filename = row["filename"]
-            match = sourmash.load_one_signature(filename, ksize=21)
+            match = load_one_signature(filename, ksize=21)
             assert match.contained_by(combined_sig) == 1.0
 
             # check other fields, too.
@@ -5439,12 +5441,12 @@ def test_multigather_metagenome_output_unique(runtmp):
 
     # change 'filename' on 'combined.sig' to something else
     orig_query_sig = utils.get_test_data("gather/combined.sig")
-    sketch = sourmash.load_one_signature(orig_query_sig)
+    sketch = load_one_signature(orig_query_sig)
     ss = signature.SourmashSignature(sketch.minhash, filename="named_query")
 
     query_sig = runtmp.output("the_query.sig")
     with open(query_sig, "w") as f:
-        signature.save_signatures([ss], f)
+        signature.save_signatures_to_json([ss], f)
 
     cmd = f"multigather --query {query_sig} --db {testdata_sigs_arg} -k 21 --threshold-bp=0 -U"
     cmd = cmd.split(" ")
@@ -5736,8 +5738,8 @@ def test_gather_metagenome_output_unassigned_nomatches(
     print(c.last_result.out)
     assert "No matches found for --threshold-bp at 50.0 kbp." in c.last_result.err
 
-    x = sourmash.load_one_signature(query_sig, ksize=31)
-    y = sourmash.load_one_signature(c.output("foo.sig"))
+    x = load_one_signature(query_sig, ksize=31)
+    y = load_one_signature(c.output("foo.sig"))
 
     assert x.minhash == y.minhash
 
@@ -5771,8 +5773,8 @@ def test_gather_metagenome_output_unassigned_nomatches_protein(
     c.run_sourmash("sig", "describe", c.output("foo.sig"))
     print(c.last_result.out)
 
-    x = sourmash.load_one_signature(query_sig, ksize=57)
-    y = sourmash.load_one_signature(c.output("foo.sig"))
+    x = load_one_signature(query_sig, ksize=57)
+    y = load_one_signature(c.output("foo.sig"))
 
     assert x.minhash == y.minhash
     assert y.minhash.moltype == "protein"
@@ -5979,7 +5981,7 @@ def test_gather_downsample_multiple(runtmp, linear_gather, prefetch_gather):
     query_sig = utils.get_test_data("GCF_000006945.2-s500.sig")
 
     # load in the hashes and do split them into four bins, randomly.
-    ss = sourmash.load_one_signature(query_sig)
+    ss = load_one_signature(query_sig)
     hashes = list(ss.minhash.hashes)
 
     random.seed(a=1)  # fix seed so test is reproducible
@@ -6001,7 +6003,7 @@ def test_gather_downsample_multiple(runtmp, linear_gather, prefetch_gather):
         binsig = signature.SourmashSignature(mh_bins[i], name=f"bin{i}")
 
         with open(runtmp.output(f"bin{i}.sig"), "wb") as fp:
-            sourmash.save_signatures([binsig], fp)
+            sourmash.save_signatures_to_json([binsig], fp)
 
         gathersigs.append(f"bin{i}.sig")
 
@@ -6461,7 +6463,7 @@ def test_gather_abund_10_1(runtmp, prefetch_gather, linear_gather):
     for prod, f_weighted in zip(weighted_calc, f_weighted_list):
         assert prod / total_weighted == f_weighted, (prod, f_weighted)
 
-    query_sig = sourmash.load_one_signature(query)
+    query_sig = load_one_signature(query)
     query_mh = query_sig.minhash
 
     total_bp_analyzed = sum(unique_overlaps) + remaining_bps[-1]
@@ -6569,11 +6571,11 @@ def test_gather_output_unassigned_with_abundance(
 
     assert os.path.exists(c.output("unassigned.sig"))
 
-    nomatch = sourmash.load_one_signature(c.output("unassigned.sig"))
+    nomatch = load_one_signature(c.output("unassigned.sig"))
     assert nomatch.minhash.track_abundance
 
-    query_ss = sourmash.load_one_signature(query)
-    against_ss = sourmash.load_one_signature(against)
+    query_ss = load_one_signature(query)
+    against_ss = load_one_signature(against)
 
     # unassigned should have nothing that is in the database
     nomatch_mh = nomatch.minhash
@@ -6663,8 +6665,8 @@ def test_multigather_output_unassigned_with_abundance(runtmp, sig_save_extension
     nomatch = list(nomatch)[0]
     assert nomatch.minhash.track_abundance
 
-    query_ss = sourmash.load_one_signature(query)
-    against_ss = sourmash.load_one_signature(against)
+    query_ss = load_one_signature(query)
+    against_ss = load_one_signature(against)
 
     # unassigned should have nothing that is in the database
     nomatch_mh = nomatch.minhash
@@ -7208,7 +7210,7 @@ def test_license_cc0(runtmp):
     sigfile = runtmp.output("short.fa.sig")
     assert os.path.exists(sigfile)
 
-    sig = next(signature.load_signatures(sigfile))
+    sig = next(load_signatures_from_json(sigfile))
     assert str(sig).endswith("short.fa")
 
     assert sig.license == "CC0"
@@ -7231,7 +7233,7 @@ def test_license_load_non_cc0():
     sigfile = utils.get_test_data("bad-license.sig")
 
     try:
-        next(signature.load_signatures(sigfile, do_raise=True))
+        next(load_signatures_from_json(sigfile, do_raise=True))
     except Exception as e:
         assert "sourmash only supports CC0-licensed signatures" in str(e)
 
@@ -8146,8 +8148,8 @@ def test_search_jaccard_ani_downsample(runtmp):
 
     sig47 = utils.get_test_data("47.fa.sig")
     sig4763 = utils.get_test_data("47+63.fa.sig")
-    ss47 = sourmash.load_one_signature(sig47)
-    ss4763 = sourmash.load_one_signature(sig4763)
+    ss47 = load_one_signature(sig47)
+    ss4763 = load_one_signature(sig4763)
     print(f"SCALED: sig1: {ss47.minhash.scaled}, sig2: {ss4763.minhash.scaled}")
 
     c.run_sourmash("search", sig47, sig4763, "-o", "xxx.csv")
@@ -8188,7 +8190,7 @@ def test_search_jaccard_ani_downsample(runtmp):
         assert round(float(row["ani"]), 3) == 0.993
 
     # downsample manually and assert same ANI
-    ss47_ds = signature.load_one_signature(ds_sig47)
+    ss47_ds = load_one_signature(ds_sig47)
     print("SCALED:", ss47_ds.minhash.scaled, ss4763.minhash.scaled)
     ani_info = ss47_ds.jaccard_ani(ss4763, downsample=True)
     print(ani_info)
@@ -8403,7 +8405,7 @@ def test_compare_containment_ani_asymmetry(runtmp):
     # load in all the input signatures
     idx_to_sig = {}
     for idx, filename in enumerate(testdata_sigs):
-        ss = sourmash.load_one_signature(filename, ksize=31)
+        ss = load_one_signature(filename, ksize=31)
         idx_to_sig[idx] = ss
 
     # check explicit containment against output of compare
diff --git a/tests/test_sourmash_args.py b/tests/test_sourmash_args.py
index 8f58a0a25f..916cabb1e3 100644
--- a/tests/test_sourmash_args.py
+++ b/tests/test_sourmash_args.py
@@ -19,6 +19,8 @@
 from sourmash.index import LinearIndex
 from sourmash.cli.utils import add_ksize_arg
 
+from sourmash.signature import load_signatures_from_json, save_signatures_to_json
+
 
 def test_save_signatures_api_none():
     # save to sigfile
@@ -69,7 +71,7 @@ def test_save_signatures_to_location_1_stdout():
 
     output = output_capture.getvalue()
 
-    saved = list(sourmash.signature.load_signatures(output))
+    saved = list(load_signatures_from_json(output))
     assert ss2 in saved
     assert ss47 in saved
     assert len(saved) == 2
@@ -88,7 +90,7 @@ def test_save_signatures_to_location_1_sig_is_default(runtmp):
         save_sig.add(ss2)
         save_sig.add(ss47)
 
-    saved = list(sourmash.signature.load_signatures(outloc))
+    saved = list(load_signatures_from_json(outloc))
     assert ss2 in saved
     assert ss47 in saved
     assert len(saved) == 2
@@ -281,7 +283,7 @@ def test_save_signatures_to_location_3_zip_add_fail(runtmp):
     outloc = runtmp.output("foo.zip")
     with zipfile.ZipFile(outloc, "x") as zf:
         with zf.open("xyz.sig", "w") as fp:
-            sourmash.save_signatures([ss2], fp=fp, compression=1)
+            save_signatures_to_json([ss2], fp=fp, compression=1)
 
     # verify it can be loaded, yada yada
     saved = list(sourmash.load_file_as_signatures(outloc))
@@ -307,7 +309,7 @@ def test_save_signatures_to_location_3_zip_add_with_manifest(runtmp):
     outloc = runtmp.output("foo.zip")
     with zipfile.ZipFile(outloc, "x") as zf:
         with zf.open("xyz.sig", "w") as fp:
-            sourmash.save_signatures([ss2], fp=fp, compression=1)
+            save_signatures_to_json([ss2], fp=fp, compression=1)
 
         # make a manifest row...
         row = manifest.CollectionManifest.make_manifest_row(
diff --git a/tests/test_sourmash_compute.py b/tests/test_sourmash_compute.py
index f6f6370785..ddab496cbb 100644
--- a/tests/test_sourmash_compute.py
+++ b/tests/test_sourmash_compute.py
@@ -24,6 +24,8 @@
 from sourmash import VERSION
 from sourmash_tst_utils import SourmashCommandFailed
 
+from sourmash.signature import load_signatures_from_json
+
 
 def test_do_sourmash_compute():
     with utils.TempDirectory() as location:
@@ -35,7 +37,7 @@ def test_do_sourmash_compute():
         sigfile = os.path.join(location, "short.fa.sig")
         assert os.path.exists(sigfile)
 
-        sig = next(signature.load_signatures(sigfile))
+        sig = next(load_signatures_from_json(sigfile))
         assert str(sig).endswith("short.fa")
 
 
@@ -127,7 +129,7 @@ def test_do_sourmash_compute_outdir(c):
     sigfile = os.path.join(c.location, "short.fa.sig")
     assert os.path.exists(sigfile)
 
-    sig = next(signature.load_signatures(sigfile))
+    sig = next(load_signatures_from_json(sigfile))
     assert str(sig).endswith("short.fa")
 
 
@@ -269,7 +271,7 @@ def test_do_sourmash_compute_singleton():
         sigfile = os.path.join(location, "short.fa.sig")
         assert os.path.exists(sigfile)
 
-        sig = next(signature.load_signatures(sigfile))
+        sig = next(load_signatures_from_json(sigfile))
         assert sig.name.endswith("shortName")
 
 
@@ -285,7 +287,7 @@ def test_do_sourmash_compute_name():
         sigfile = os.path.join(location, "foo.sig")
         assert os.path.exists(sigfile)
 
-        sig = next(signature.load_signatures(sigfile))
+        sig = next(load_signatures_from_json(sigfile))
         assert sig.name == "foo"
 
         status, out, err = utils.runscript(
@@ -297,7 +299,7 @@ def test_do_sourmash_compute_name():
         sigfile2 = os.path.join(location, "foo2.sig")
         assert os.path.exists(sigfile2)
 
-        sig2 = next(signature.load_signatures(sigfile))
+        sig2 = next(load_signatures_from_json(sigfile))
         assert sig2.name == "foo"
         assert sig.name == sig2.name
 
@@ -346,7 +348,7 @@ def test_do_sourmash_compute_name_from_first():
         sigfile = os.path.join(location, "short3.fa.sig")
         assert os.path.exists(sigfile)
 
-        sig = next(signature.load_signatures(sigfile))
+        sig = next(load_signatures_from_json(sigfile))
         assert sig.name == "firstname"
 
 
@@ -359,7 +361,7 @@ def test_do_sourmash_compute_multik():
         outfile = os.path.join(location, "short.fa.sig")
         assert os.path.exists(outfile)
 
-        siglist = list(signature.load_signatures(outfile))
+        siglist = list(load_signatures_from_json(outfile))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 21 in ksizes
@@ -380,7 +382,7 @@ def test_do_sourmash_compute_multik_with_protein():
 
         with open(outfile) as fp:
             sigdata = fp.read()
-            siglist = list(signature.load_signatures(sigdata))
+            siglist = list(load_signatures_from_json(sigdata))
             assert len(siglist) == 4
             ksizes = set([x.minhash.ksize for x in siglist])
             assert 21 in ksizes
@@ -407,7 +409,7 @@ def test_do_sourmash_compute_multik_with_dayhoff():
 
         with open(outfile) as fp:
             sigdata = fp.read()
-            siglist = list(signature.load_signatures(sigdata))
+            siglist = list(load_signatures_from_json(sigdata))
             assert len(siglist) == 2
             ksizes = set([x.minhash.ksize for x in siglist])
             assert 7 in ksizes
@@ -429,7 +431,7 @@ def test_do_sourmash_compute_multik_with_dayhoff_and_dna():
 
         with open(outfile) as fp:
             sigdata = fp.read()
-            siglist = list(signature.load_signatures(sigdata))
+            siglist = list(load_signatures_from_json(sigdata))
             assert len(siglist) == 4
             ksizes = set([x.minhash.ksize for x in siglist])
             assert 21 in ksizes
@@ -458,7 +460,7 @@ def test_do_sourmash_compute_multik_with_hp():
 
         with open(outfile) as fp:
             sigdata = fp.read()
-            siglist = list(signature.load_signatures(sigdata))
+            siglist = list(load_signatures_from_json(sigdata))
             assert len(siglist) == 2
             ksizes = set([x.minhash.ksize for x in siglist])
             assert 7 in ksizes
@@ -480,7 +482,7 @@ def test_do_sourmash_compute_multik_with_hp_and_dna():
 
         with open(outfile) as fp:
             sigdata = fp.read()
-            siglist = list(signature.load_signatures(sigdata))
+            siglist = list(load_signatures_from_json(sigdata))
             assert len(siglist) == 4
             ksizes = set([x.minhash.ksize for x in siglist])
             assert 7 in ksizes
@@ -503,7 +505,7 @@ def test_do_sourmash_compute_multik_with_dayhoff_dna_protein():
 
         with open(outfile) as fp:
             sigdata = fp.read()
-            siglist = list(signature.load_signatures(sigdata))
+            siglist = list(load_signatures_from_json(sigdata))
             assert len(siglist) == 6
             ksizes = set([x.minhash.ksize for x in siglist])
             assert 21 in ksizes
@@ -529,7 +531,7 @@ def test_do_sourmash_compute_multik_with_dayhoff_hp_dna_protein():
 
         with open(outfile) as fp:
             sigdata = fp.read()
-            siglist = list(signature.load_signatures(sigdata))
+            siglist = list(load_signatures_from_json(sigdata))
             assert len(siglist) == 8
             ksizes = set([x.minhash.ksize for x in siglist])
             assert 7 in ksizes
@@ -581,7 +583,7 @@ def test_do_sourmash_compute_multik_only_protein(c):
 
     with open(outfile) as fp:
         sigdata = fp.read()
-        siglist = list(signature.load_signatures(sigdata))
+        siglist = list(load_signatures_from_json(sigdata))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 7 in ksizes
@@ -622,7 +624,7 @@ def test_do_sourmash_compute_multik_only_protein_no_rna(c):
 
     with open(outfile) as fp:
         sigdata = fp.read()
-        siglist = list(signature.load_signatures(sigdata))
+        siglist = list(load_signatures_from_json(sigdata))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 7 in ksizes
@@ -644,7 +646,7 @@ def test_do_sourmash_compute_protein_bad_sequences():
 
         with open(outfile) as fp:
             sigdata = fp.read()
-            siglist = list(signature.load_signatures(sigdata))
+            siglist = list(load_signatures_from_json(sigdata))
             assert len(siglist) == 2
             ksizes = set([x.minhash.ksize for x in siglist])
             assert 7 in ksizes
@@ -665,7 +667,7 @@ def test_do_sourmash_compute_multik_input_is_protein():
 
         with open(outfile) as fp:
             sigdata = fp.read()
-            siglist = list(signature.load_signatures(sigdata))
+            siglist = list(load_signatures_from_json(sigdata))
             assert len(siglist) == 2
             ksizes = set([x.minhash.ksize for x in siglist])
             assert 7 in ksizes
@@ -688,7 +690,7 @@ def test_do_sourmash_compute_multik_outfile():
         )
         assert os.path.exists(outfile)
 
-        siglist = list(signature.load_signatures(outfile))
+        siglist = list(load_signatures_from_json(outfile))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 21 in ksizes
@@ -706,7 +708,7 @@ def test_do_sourmash_compute_with_scaled_1():
         )
         assert os.path.exists(outfile)
 
-        siglist = list(signature.load_signatures(outfile))
+        siglist = list(load_signatures_from_json(outfile))
         assert len(siglist) == 2
 
         scaled_vals = [x.minhash.scaled for x in siglist]
@@ -725,7 +727,7 @@ def test_do_sourmash_compute_with_scaled_2():
         )
         assert os.path.exists(outfile)
 
-        siglist = list(signature.load_signatures(outfile))
+        siglist = list(load_signatures_from_json(outfile))
         assert len(siglist) == 2
 
         max_hashes = [x.minhash._max_hash for x in siglist]
@@ -744,7 +746,7 @@ def test_do_sourmash_compute_with_scaled():
         )
         assert os.path.exists(outfile)
 
-        siglist = list(signature.load_signatures(outfile))
+        siglist = list(load_signatures_from_json(outfile))
         assert len(siglist) == 2
 
         max_hashes = [x.minhash._max_hash for x in siglist]
@@ -797,7 +799,7 @@ def test_do_sourmash_compute_with_seed():
         )
         assert os.path.exists(outfile)
 
-        siglist = list(signature.load_signatures(outfile))
+        siglist = list(load_signatures_from_json(outfile))
         assert len(siglist) == 2
 
         seeds = [x.minhash.seed for x in siglist]
@@ -826,11 +828,11 @@ def test_do_sourmash_check_protein_comparisons():
         sig2 = os.path.join(location, "ecoli.genes.fna.sig")
         assert os.path.exists(sig2)
 
-        # I'm not sure why load_signatures is randomizing order, but ok.
-        x = list(signature.load_signatures(sig1))
+        # I'm not sure why load_signatures_from_json is randomizing order, but ok.
+        x = list(load_signatures_from_json(sig1))
         sig1_aa, sig2_aa = sorted(x, key=lambda x: x.name)
 
-        x = list(signature.load_signatures(sig2))
+        x = list(load_signatures_from_json(sig2))
         sig1_trans, sig2_trans = sorted(x, key=lambda x: x.name)
 
         name1 = sig1_aa.name.split()[0]
@@ -862,13 +864,13 @@ def test_do_sourmash_check_knowngood_dna_comparisons(c):
     sig1 = c.output("ecoli.genes.fna.sig")
     assert os.path.exists(sig1)
 
-    x = list(signature.load_signatures(sig1))
+    x = list(load_signatures_from_json(sig1))
     sig1, sig2 = sorted(x, key=lambda x: x.name)
     print(sig1.name)
     print(sig2.name)
 
     knowngood = utils.get_test_data("benchmark.dna.sig")
-    good = list(signature.load_signatures(knowngood))[0]
+    good = list(load_signatures_from_json(knowngood))[0]
 
     assert sig2.similarity(good) == 1.0
 
@@ -881,11 +883,11 @@ def test_do_sourmash_check_knowngood_dna_comparisons_use_rna(c):
     sig1 = c.output("ecoli.genes.fna.sig")
     assert os.path.exists(sig1)
 
-    x = list(signature.load_signatures(sig1))
+    x = list(load_signatures_from_json(sig1))
     sig1, sig2 = sorted(x, key=lambda x: x.name)
 
     knowngood = utils.get_test_data("benchmark.dna.sig")
-    good = list(signature.load_signatures(knowngood))[0]
+    good = list(load_signatures_from_json(knowngood))[0]
 
     assert sig2.similarity(good) == 1.0
 
@@ -903,11 +905,11 @@ def test_do_sourmash_check_knowngood_input_protein_comparisons():
         sig1 = os.path.join(location, "ecoli.faa.sig")
         assert os.path.exists(sig1)
 
-        x = list(signature.load_signatures(sig1))
+        x = list(load_signatures_from_json(sig1))
         sig1_aa, sig2_aa = sorted(x, key=lambda x: x.name)
 
         knowngood = utils.get_test_data("benchmark.input_prot.sig")
-        good_aa = list(signature.load_signatures(knowngood))[0]
+        good_aa = list(load_signatures_from_json(knowngood))[0]
 
         assert sig1_aa.similarity(good_aa) == 1.0
 
@@ -925,11 +927,11 @@ def test_do_sourmash_check_knowngood_protein_comparisons():
         sig1 = os.path.join(location, "ecoli.genes.fna.sig")
         assert os.path.exists(sig1)
 
-        x = list(signature.load_signatures(sig1))
+        x = list(load_signatures_from_json(sig1))
         sig1_trans, sig2_trans = sorted(x, key=lambda x: x.name)
 
         knowngood = utils.get_test_data("benchmark.prot.sig")
-        good_trans = list(signature.load_signatures(knowngood))[0]
+        good_trans = list(load_signatures_from_json(knowngood))[0]
 
         assert sig2_trans.similarity(good_trans) == 1.0
 
diff --git a/tests/test_sourmash_sketch.py b/tests/test_sourmash_sketch.py
index 98448e4d6b..550b24a948 100644
--- a/tests/test_sourmash_sketch.py
+++ b/tests/test_sourmash_sketch.py
@@ -26,6 +26,8 @@
 
 from sourmash.command_sketch import _signatures_for_sketch_factory
 from sourmash_tst_utils import SourmashCommandFailed
+from sourmash.signature import load_one_signature_from_json as load_one_signature
+from sourmash.signature import load_signatures_from_json
 
 
 def test_do_sourmash_sketch_check_scaled_bounds_negative(runtmp):
@@ -601,7 +603,7 @@ def test_do_sourmash_sketchdna(runtmp):
     sigfile = runtmp.output("short.fa.sig")
     assert os.path.exists(sigfile)
 
-    sig = next(signature.load_signatures(sigfile))
+    sig = next(load_signatures_from_json(sigfile))
     assert str(sig).endswith("short.fa")
 
 
@@ -612,7 +614,7 @@ def test_do_sourmash_sketchdna_check_sequence_succeed(runtmp):
     sigfile = runtmp.output("short.fa.sig")
     assert os.path.exists(sigfile)
 
-    sig = next(signature.load_signatures(sigfile))
+    sig = next(load_signatures_from_json(sigfile))
     assert str(sig).endswith("short.fa")
 
 
@@ -656,7 +658,7 @@ def test_do_sourmash_sketchdna_from_file(runtmp):
     sigfile = runtmp.output("short.fa.sig")
     assert os.path.exists(sigfile)
 
-    sig = next(signature.load_signatures(sigfile))
+    sig = next(load_signatures_from_json(sigfile))
     assert str(sig).endswith("short.fa")
 
 
@@ -709,7 +711,7 @@ def test_do_sourmash_sketchdna_outdir(c):
     sigfile = os.path.join(c.location, "short.fa.sig")
     assert os.path.exists(sigfile)
 
-    sig = next(signature.load_signatures(sigfile))
+    sig = next(load_signatures_from_json(sigfile))
     assert str(sig).endswith("short.fa")
 
 
@@ -724,7 +726,7 @@ def test_do_sourmash_sketchdna_output_dir(c):
     sigfile = os.path.join(c.location, "short.fa.sig")
     assert os.path.exists(sigfile)
 
-    sig = next(signature.load_signatures(sigfile))
+    sig = next(load_signatures_from_json(sigfile))
     assert str(sig).endswith("short.fa")
 
 
@@ -865,7 +867,7 @@ def test_do_sourmash_sketchdna_singleton(runtmp):
     sigfile = runtmp.output("short.fa.sig")
     assert os.path.exists(sigfile)
 
-    sig = next(signature.load_signatures(sigfile))
+    sig = next(load_signatures_from_json(sigfile))
     assert str(sig).endswith("shortName")
 
 
@@ -876,7 +878,7 @@ def test_do_sourmash_sketchdna_name(runtmp):
     sigfile = runtmp.output("foo.sig")
     assert os.path.exists(sigfile)
 
-    sig = next(signature.load_signatures(sigfile))
+    sig = next(load_signatures_from_json(sigfile))
     assert sig.name == "foo"
 
     runtmp.sourmash("sketch", "dna", "--name", "foo", testdata1, "-o", "foo2.sig")
@@ -884,7 +886,7 @@ def test_do_sourmash_sketchdna_name(runtmp):
     sigfile2 = runtmp.output("foo2.sig")
     assert os.path.exists(sigfile2)
 
-    sig2 = next(signature.load_signatures(sigfile))
+    sig2 = next(load_signatures_from_json(sigfile))
     assert sig2.name == "foo"
     assert sig.name == sig2.name
 
@@ -918,7 +920,7 @@ def test_do_sourmash_sketchdna_name_from_first(runtmp):
     sigfile = runtmp.output("short3.fa.sig")
     assert os.path.exists(sigfile)
 
-    sig = next(signature.load_signatures(sigfile))
+    sig = next(load_signatures_from_json(sigfile))
     assert sig.name == "firstname"
 
 
@@ -929,7 +931,7 @@ def test_do_sourmash_sketchdna_multik(runtmp):
     outfile = runtmp.output("short.fa.sig")
     assert os.path.exists(outfile)
 
-    siglist = list(signature.load_signatures(outfile))
+    siglist = list(load_signatures_from_json(outfile))
     assert len(siglist) == 2
     ksizes = set([x.minhash.ksize for x in siglist])
     assert 21 in ksizes
@@ -984,7 +986,7 @@ def test_do_sketch_translate_multik_with_protein(runtmp):
 
     with open(outfile) as fp:
         sigdata = fp.read()
-        siglist = list(signature.load_signatures(sigdata))
+        siglist = list(load_signatures_from_json(sigdata))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 7 in ksizes
@@ -1007,7 +1009,7 @@ def test_do_sketch_translate_multik_with_protein_from_file(runtmp):
 
     with open(outfile) as fp:
         sigdata = fp.read()
-        siglist = list(signature.load_signatures(sigdata))
+        siglist = list(load_signatures_from_json(sigdata))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 7 in ksizes
@@ -1025,7 +1027,7 @@ def test_do_sketch_translate_multik_with_dayhoff(runtmp):
 
     with open(outfile) as fp:
         sigdata = fp.read()
-        siglist = list(signature.load_signatures(sigdata))
+        siglist = list(load_signatures_from_json(sigdata))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 7 in ksizes
@@ -1042,7 +1044,7 @@ def test_do_sketch_translate_multik_with_hp(runtmp):
 
     with open(outfile) as fp:
         sigdata = fp.read()
-        siglist = list(signature.load_signatures(sigdata))
+        siglist = list(load_signatures_from_json(sigdata))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 7 in ksizes
@@ -1060,7 +1062,7 @@ def test_do_sourmash_sketch_translate_multik_only_protein(c):
 
     with open(outfile) as fp:
         sigdata = fp.read()
-        siglist = list(signature.load_signatures(sigdata))
+        siglist = list(load_signatures_from_json(sigdata))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 7 in ksizes
@@ -1077,7 +1079,7 @@ def test_do_sourmash_sketch_translate_bad_sequences(runtmp):
 
     with open(outfile) as fp:
         sigdata = fp.read()
-        siglist = list(signature.load_signatures(sigdata))
+        siglist = list(load_signatures_from_json(sigdata))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 7 in ksizes
@@ -1093,7 +1095,7 @@ def test_do_sketch_protein_multik_input(runtmp):
 
     with open(outfile) as fp:
         sigdata = fp.read()
-        siglist = list(signature.load_signatures(sigdata))
+        siglist = list(load_signatures_from_json(sigdata))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 7 in ksizes
@@ -1120,7 +1122,7 @@ def test_do_sketch_protein_multik_input_from_file(runtmp):
 
     with open(outfile) as fp:
         sigdata = fp.read()
-        siglist = list(signature.load_signatures(sigdata))
+        siglist = list(load_signatures_from_json(sigdata))
         assert len(siglist) == 2
         ksizes = set([x.minhash.ksize for x in siglist])
         assert 7 in ksizes
@@ -1139,7 +1141,7 @@ def test_do_sourmash_sketchdna_multik_outfile(runtmp):
 
     assert os.path.exists(outfile)
 
-    siglist = list(signature.load_signatures(outfile))
+    siglist = list(load_signatures_from_json(outfile))
     assert len(siglist) == 2
     ksizes = set([x.minhash.ksize for x in siglist])
     assert 21 in ksizes
@@ -1156,7 +1158,7 @@ def test_do_sourmash_sketchdna_with_scaled_1(runtmp):
 
     assert os.path.exists(outfile)
 
-    siglist = list(signature.load_signatures(outfile))
+    siglist = list(load_signatures_from_json(outfile))
     assert len(siglist) == 2
 
     scaled_vals = [x.minhash.scaled for x in siglist]
@@ -1174,7 +1176,7 @@ def test_do_sourmash_sketchdna_with_scaled_2(runtmp):
 
     assert os.path.exists(outfile)
 
-    siglist = list(signature.load_signatures(outfile))
+    siglist = list(load_signatures_from_json(outfile))
     assert len(siglist) == 2
 
     max_hashes = [x.minhash._max_hash for x in siglist]
@@ -1192,7 +1194,7 @@ def test_do_sourmash_sketchdna_with_scaled(runtmp):
 
     assert os.path.exists(outfile)
 
-    siglist = list(signature.load_signatures(outfile))
+    siglist = list(load_signatures_from_json(outfile))
     assert len(siglist) == 2
 
     max_hashes = [x.minhash._max_hash for x in siglist]
@@ -1244,7 +1246,7 @@ def test_do_sketch_with_seed(runtmp):
 
     assert os.path.exists(outfile)
 
-    siglist = list(signature.load_signatures(outfile))
+    siglist = list(load_signatures_from_json(outfile))
     assert len(siglist) == 2
 
     seeds = [x.minhash.seed for x in siglist]
@@ -1269,11 +1271,11 @@ def test_do_sourmash_check_protein_comparisons(runtmp):
     sig2 = runtmp.output("ecoli.genes.fna.sig")
     assert os.path.exists(sig2)
 
-    # I'm not sure why load_signatures is randomizing order, but ok.
-    x = list(signature.load_signatures(sig1))
+    # I'm not sure why load_signatures_from_json is randomizing order, but ok.
+    x = list(load_signatures_from_json(sig1))
     sig1_aa, sig2_aa = sorted(x, key=lambda x: x.name)
 
-    x = list(signature.load_signatures(sig2))
+    x = list(load_signatures_from_json(sig2))
     sig1_trans, sig2_trans = sorted(x, key=lambda x: x.name)
 
     name1 = sig1_aa.name.split()[0]
@@ -1305,14 +1307,14 @@ def test_do_sourmash_check_knowngood_dna_comparisons(c):
     sig1 = c.output("ecoli.genes.fna.sig")
     assert os.path.exists(sig1)
 
-    x = list(signature.load_signatures(sig1))
+    x = list(load_signatures_from_json(sig1))
     sig1, sig2 = sorted(x, key=lambda x: x.name)
 
     print(sig1.name)
     print(sig2.name)
 
     knowngood = utils.get_test_data("benchmark.dna.sig")
-    good = list(signature.load_signatures(knowngood))[0]
+    good = list(load_signatures_from_json(knowngood))[0]
 
     assert sig2.similarity(good) == 1.0
 
@@ -1325,11 +1327,11 @@ def test_do_sourmash_check_knowngood_dna_comparisons_use_rna(c):
     sig1 = c.output("ecoli.genes.fna.sig")
     assert os.path.exists(sig1)
 
-    x = list(signature.load_signatures(sig1))
+    x = list(load_signatures_from_json(sig1))
     sig1, sig2 = sorted(x, key=lambda x: x.name)
 
     knowngood = utils.get_test_data("benchmark.dna.sig")
-    good = list(signature.load_signatures(knowngood))[0]
+    good = list(load_signatures_from_json(knowngood))[0]
 
     assert sig2.similarity(good) == 1.0
 
@@ -1344,11 +1346,11 @@ def test_do_sourmash_check_knowngood_input_protein_comparisons(runtmp):
     sig1 = runtmp.output("ecoli.faa.sig")
     assert os.path.exists(sig1)
 
-    x = list(signature.load_signatures(sig1))
+    x = list(load_signatures_from_json(sig1))
     sig1_aa, sig2_aa = sorted(x, key=lambda x: x.name)
 
     knowngood = utils.get_test_data("benchmark.input_prot.sig")
-    good_aa = list(signature.load_signatures(knowngood))[0]
+    good_aa = list(load_signatures_from_json(knowngood))[0]
 
     assert sig1_aa.similarity(good_aa) == 1.0
 
@@ -1365,11 +1367,11 @@ def test_do_sourmash_check_knowngood_protein_comparisons(runtmp):
     sig1 = runtmp.output("ecoli.genes.fna.sig")
     assert os.path.exists(sig1)
 
-    x = list(signature.load_signatures(sig1))
+    x = list(load_signatures_from_json(sig1))
     sig1_trans, sig2_trans = sorted(x, key=lambda x: x.name)
 
     knowngood = utils.get_test_data("benchmark.prot.sig")
-    good_trans = list(signature.load_signatures(knowngood))[0]
+    good_trans = list(load_signatures_from_json(knowngood))[0]
 
     assert sig2_trans.similarity(good_trans) == 1.0
 
@@ -1399,11 +1401,11 @@ def test_do_sourmash_singleton_multiple_files_no_out_specified(runtmp):
     sig2 = runtmp.output("shewanella.faa.sig")
     assert os.path.exists(sig2)
 
-    x = list(signature.load_signatures(sig1))
+    x = list(load_signatures_from_json(sig1))
     for ss in x:
         print(ss.name)
 
-    y = list(signature.load_signatures(sig2))
+    y = list(load_signatures_from_json(sig2))
     for ss in y:
         print(ss.name)
 
@@ -1447,7 +1449,7 @@ def test_do_sourmash_singleton_multiple_files_output(runtmp):
     sig1 = runtmp.output("output.sig")
     assert os.path.exists(sig1)
 
-    x = list(signature.load_signatures(sig1))
+    x = list(load_signatures_from_json(sig1))
     for ss in x:
         print(ss.name)
 
@@ -1512,7 +1514,7 @@ def test_protein_with_stop_codons(runtmp):
     sig1 = runtmp.output("ecoli.faa.sig")
     assert os.path.exists(sig1)
 
-    x = signature.load_one_signature(sig1)
+    x = load_one_signature(sig1)
     cli_mh1 = x.minhash
 
     # second, via CLI w/stop codons
@@ -1525,7 +1527,7 @@ def test_protein_with_stop_codons(runtmp):
     sig2 = runtmp.output("ecoli.stop.faa.sig")
     assert os.path.exists(sig2)
 
-    x = signature.load_one_signature(sig2)
+    x = load_one_signature(sig2)
     cli_mh2 = x.minhash
 
     # now calculate sketch with MinHash...
@@ -1578,7 +1580,7 @@ def test_hp_with_stop_codons(runtmp):
     sig1 = runtmp.output("ecoli.faa.sig")
     assert os.path.exists(sig1)
 
-    x = signature.load_one_signature(sig1)
+    x = load_one_signature(sig1)
     cli_mh1 = x.minhash
 
     # second, via CLI w/stop codons
@@ -1591,7 +1593,7 @@ def test_hp_with_stop_codons(runtmp):
     sig2 = runtmp.output("ecoli.stop.faa.sig")
     assert os.path.exists(sig2)
 
-    x = signature.load_one_signature(sig2)
+    x = load_one_signature(sig2)
     cli_mh2 = x.minhash
 
     # now calculate sketch with MinHash...
@@ -1644,7 +1646,7 @@ def test_dayhoff_with_stop_codons(runtmp):
     sig1 = runtmp.output("ecoli.faa.sig")
     assert os.path.exists(sig1)
 
-    x = signature.load_one_signature(sig1)
+    x = load_one_signature(sig1)
     cli_mh1 = x.minhash
 
     # second, via CLI w/stop codons
@@ -1657,7 +1659,7 @@ def test_dayhoff_with_stop_codons(runtmp):
     sig2 = runtmp.output("ecoli.stop.faa.sig")
     assert os.path.exists(sig2)
 
-    x = signature.load_one_signature(sig2)
+    x = load_one_signature(sig2)
     cli_mh2 = x.minhash
 
     # now calculate sketch with MinHash...