Moving loading and save sigs to rust

move json parsing and init to rust
working on loading sigs
enable pickling for signatures
sort mins and abunds
remove dead code
remove refs

include/sourmash.h

@@ -109,6 +109,8 @@ uint32_t kmerminhash_ksize(KmerMinHash *ptr);
 
 uint64_t kmerminhash_max_hash(KmerMinHash *ptr);
 
+SourmashStr kmerminhash_md5sum(KmerMinHash *ptr);
+
 void kmerminhash_merge(KmerMinHash *ptr, const KmerMinHash *other);
 
 bool kmerminhash_is_compatible(const KmerMinHash *ptr, const KmerMinHash *other);

setup.py

@@ -62,8 +62,7 @@ def build_native(spec):
         'sourmash = sourmash.__main__:main'
         ]
     },
-    "install_requires": ["screed>=0.9", "ijson>=2.5.1", "khmer>=2.1", 'numpy',
-                         "cffi",
+    "install_requires": ["screed>=0.9", "khmer>=2.1", "cffi", 'numpy',
                          'matplotlib', 'scipy', "deprecation>=2.0.6"],
     "setup_requires": [
         "setuptools>=38.6.0",

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:

sourmash/commands.py

@@ -1036,14 +1036,14 @@ def watch(args):
         ksize = tree_mh.ksize
 
     E = MinHash(ksize=ksize, n=args.num_hashes, is_protein=is_protein, dayhoff=dayhoff, hp=hp)
-    streamsig = sig.SourmashSignature(E, filename='stdin', name=args.name)
 
     notify('Computing signature for k={}, {} from stdin', ksize, moltype)
 
     def do_search():
         search_fn = SearchMinHashesFindBest().search
 
         results = []
+        streamsig = sig.SourmashSignature(E, filename='stdin', name=args.name)
         for leaf in tree.find(search_fn, streamsig, args.threshold):
             results.append((streamsig.similarity(leaf.data),
                             leaf.data))
@@ -1081,6 +1081,7 @@ def do_search():
 
     if args.output:
         notify('saving signature to {}', args.output.name)
+        streamsig = sig.SourmashSignature(E, filename='stdin', name=args.name)
         sig.save_signatures([streamsig], args.output)
 
 

sourmash/sig/__main__.py

@@ -121,8 +121,8 @@ def describe(args):
             with_abundance = 1
         md5 = sig.md5sum()
         name = sig.name()
-        filename = sig.d.get('filename', '')
-        license = sig.d['license']
+        filename = sig.filename
+        license = sig.license
 
         if w:
             w.writerow(locals())
@@ -454,7 +454,7 @@ def rename(args):
                                            select_moltype=moltype)
 
         for sigobj in siglist:
-            sigobj.d['name'] = args.name
+            sigobj._name = args.name
             outlist.append(sigobj)
 
     if args.output: