Do add_many in Rust, use it in LCA _signatures

include/sourmash.h

@@ -93,6 +93,8 @@ uint64_t kmerminhash_get_min_idx(KmerMinHash *ptr, uint64_t idx);
 
 const uint64_t *kmerminhash_get_mins(KmerMinHash *ptr);
 
+void kmerminhash_add_many(KmerMinHash *ptr, const uint64_t *hashes_ptr, uintptr_t insize);
+
 uintptr_t kmerminhash_get_mins_size(KmerMinHash *ptr);
 
 HashFunctions kmerminhash_hash_function(KmerMinHash *ptr);

sourmash/_minhash.py

@@ -68,6 +68,8 @@ def hash_murmur(kmer, seed=MINHASH_DEFAULT_SEED):
 
 
 class MinHash(RustObject):
+    __dealloc_func__ = lib.kmerminhash_free
+
     def __init__(
         self,
         n,
@@ -98,7 +100,6 @@ def __init__(
         self._objptr = lib.kmerminhash_new(
             n, ksize, is_protein, dayhoff, hp, seed, int(max_hash), track_abundance
         )
-        self.__dealloc_func__ = lib.kmerminhash_free
 
         if mins:
             if track_abundance:
@@ -191,11 +192,10 @@ def add_many(self, hashes):
         if isinstance(hashes, MinHash):
             self._methodcall(lib.kmerminhash_add_from, hashes._objptr)
         else:
-            for hash in hashes:
-                self._methodcall(lib.kmerminhash_add_hash, hash)
+            self._methodcall(lib.kmerminhash_add_many, list(hashes), len(hashes))
 
     def remove_many(self, hashes):
-        "Add many hashes in at once."
+        "Remove many hashes at once."
         self._methodcall(lib.kmerminhash_remove_many, list(hashes), len(hashes))
 
     def update(self, other):

sourmash/lca/lca_utils.py

@@ -378,10 +378,14 @@ def _signatures(self):
 
         debug('creating signatures for LCA DB...')
         sigd = defaultdict(minhash.copy_and_clear)
+        temp_vals = defaultdict(list)
 
         for (k, v) in self.hashval_to_idx.items():
             for vv in v:
-                sigd[vv].add_hash(k)
+                temp_vals[vv].append(k)
+
+        for sig, vals in temp_vals.items():
+            sigd[sig].add_many(vals)
 
         debug('=> {} signatures!', len(sigd))
         return sigd

src/core/src/ffi/minhash.rs

@@ -162,6 +162,30 @@ unsafe fn kmerminhash_get_mins(ptr: *mut KmerMinHash) -> Result<*const u64> {
 }
 }
 
+ffi_fn! {
+unsafe fn kmerminhash_add_many(
+    ptr: *mut KmerMinHash,
+    hashes_ptr: *const u64,
+    insize: usize,
+  ) -> Result<()> {
+    let mh = {
+        assert!(!ptr.is_null());
+        &mut *ptr
+    };
+
+    let hashes = {
+        assert!(!hashes_ptr.is_null());
+        slice::from_raw_parts(hashes_ptr as *mut u64, insize)
+    };
+
+    for hash in hashes {
+      mh.add_hash(*hash);
+    }
+
+    Ok(())
+}
+}
+
 ffi_fn! {
 unsafe fn kmerminhash_get_abunds(ptr: *mut KmerMinHash) -> Result<*const u64> {
     let mh = {