Initial support for custom hash function

.github/workflows/rust.yml

@@ -109,7 +109,7 @@ jobs:
         run: cargo binstall --no-confirm cargo-tarpaulin
 
       - name: Coverage with tarpaulin
-        run: cargo tarpaulin --all --all-features --timeout 600 --out Xml -- --test-threads 1
+        run: cargo tarpaulin --all --all-features --timeout 600 --out xml -- --test-threads 1
 
       - name: Upload Rust coverage to codecov
         uses: codecov/codecov-action@v3

src/core/src/encodings.rs

@@ -22,16 +22,18 @@ pub type Idx = u32;
 type IdxTracker = (vec_collections::VecSet<[Idx; 8]>, u64);
 type ColorToIdx = HashMap<Color, IdxTracker, BuildNoHashHasher<Color>>;
 
-#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+#[derive(Debug, Clone, PartialEq, Eq)]
 #[cfg_attr(
     feature = "rkyv",
     derive(rkyv::Serialize, rkyv::Deserialize, rkyv::Archive)
 )]
+#[non_exhaustive]
 pub enum HashFunctions {
     Murmur64Dna,
     Murmur64Protein,
     Murmur64Dayhoff,
     Murmur64Hp,
+    Custom(String),
 }
 
 impl HashFunctions {
@@ -62,6 +64,7 @@ impl std::fmt::Display for HashFunctions {
                 HashFunctions::Murmur64Protein => "protein",
                 HashFunctions::Murmur64Dayhoff => "dayhoff",
                 HashFunctions::Murmur64Hp => "hp",
+                HashFunctions::Custom(v) => v,
             }
         )
     }

src/core/src/ffi/mod.rs

@@ -1,6 +1,6 @@
 //! # Foreign Function Interface for calling sourmash from a C API
 //!
-//! Primary client for now is the Python version, using CFFI and milksnake.
+//! Primary client for now is the Python version, using CFFI and maturin.
 #![allow(clippy::missing_safety_doc)]
 
 #[macro_use]
@@ -62,6 +62,7 @@ impl From<crate::encodings::HashFunctions> for HashFunctions {
             Murmur64Protein => HashFunctions::Murmur64Protein,
             Murmur64Dayhoff => HashFunctions::Murmur64Dayhoff,
             Murmur64Hp => HashFunctions::Murmur64Hp,
+            _ => todo!("Not supported, probably custom"),
         }
     }
 }

src/core/src/from.rs

@@ -17,7 +17,7 @@ impl From<MashSketcher> for KmerMinHash {
         let mut new_mh = KmerMinHash::new(
             0,
             values.get(0).unwrap().kmer.len() as u32,
-            HashFunctions::murmur64_DNA,
+            HashFunctions::Murmur64Dna,
             42,
             true,
             values.len() as u32,
@@ -51,7 +51,7 @@ mod test {
 
     #[test]
     fn finch_behavior() {
-        let mut a = KmerMinHash::new(0, 10, HashFunctions::murmur64_DNA, 42, true, 20);
+        let mut a = KmerMinHash::new(0, 10, HashFunctions::Murmur64Dna, 42, true, 20);
         let mut b = MashSketcher::new(20, 10, 42);
 
         let seq = b"TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGA";
@@ -87,7 +87,7 @@ mod test {
 
     #[test]
     fn from_finch() {
-        let mut a = KmerMinHash::new(0, 10, HashFunctions::murmur64_DNA, 42, true, 20);
+        let mut a = KmerMinHash::new(0, 10, HashFunctions::Murmur64Dna, 42, true, 20);
         let mut b = MashSketcher::new(20, 10, 42);
 
         let seq = b"TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGA";

src/core/src/selection.rs

@@ -104,7 +104,7 @@ impl Selection {
     }
 
     pub fn moltype(&self) -> Option<HashFunctions> {
-        self.moltype
+        self.moltype.clone()
     }
 
     pub fn set_moltype(&mut self, value: HashFunctions) {

src/core/src/signature.rs

@@ -371,7 +371,7 @@ impl Iterator for SeqToHashes {
                     Some(Ok(hash))
                 } else {
                     if !self.prot_configured {
-                        self.aa_seq = match self.hash_function {
+                        self.aa_seq = match &self.hash_function {
                             HashFunctions::Murmur64Dayhoff => {
                                 self.sequence.iter().cloned().map(aa_to_dayhoff).collect()
                             }
@@ -584,9 +584,9 @@ impl Signature {
                                 }
                             };
 
-                            match moltype {
+                            match &moltype {
                                 Some(x) => {
-                                    if mh.hash_function() == x {
+                                    if mh.hash_function() == *x {
                                         return true;
                                     }
                                 }
@@ -600,9 +600,9 @@ impl Signature {
                                 }
                             };
 
-                            match moltype {
+                            match &moltype {
                                 Some(x) => {
-                                    if mh.hash_function() == x {
+                                    if mh.hash_function() == *x {
                                         return true;
                                     }
                                 }

src/core/src/sketch/minhash.rs

@@ -74,7 +74,7 @@ impl Clone for KmerMinHash {
         KmerMinHash {
             num: self.num,
             ksize: self.ksize,
-            hash_function: self.hash_function,
+            hash_function: self.hash_function.clone(),
             seed: self.seed,
             max_hash: self.max_hash,
             mins: self.mins.clone(),
@@ -579,7 +579,7 @@ impl KmerMinHash {
             let mut combined_mh = KmerMinHash::new(
                 self.scaled(),
                 self.ksize,
-                self.hash_function,
+                self.hash_function.clone(),
                 self.seed,
                 self.abunds.is_some(),
                 self.num,
@@ -612,7 +612,7 @@ impl KmerMinHash {
             let mut combined_mh = KmerMinHash::new(
                 self.scaled(),
                 self.ksize,
-                self.hash_function,
+                self.hash_function.clone(),
                 self.seed,
                 self.abunds.is_some(),
                 self.num,
@@ -741,7 +741,7 @@ impl KmerMinHash {
         let mut new_mh = KmerMinHash::new(
             scaled,
             self.ksize,
-            self.hash_function,
+            self.hash_function.clone(),
             self.seed,
             self.abunds.is_some(),
             self.num,
@@ -805,7 +805,7 @@ impl SigsTrait for KmerMinHash {
     }
 
     fn hash_function(&self) -> HashFunctions {
-        self.hash_function
+        self.hash_function.clone()
     }
 
     fn add_hash(&mut self, hash: u64) {
@@ -979,7 +979,7 @@ impl Clone for KmerMinHashBTree {
         KmerMinHashBTree {
             num: self.num,
             ksize: self.ksize,
-            hash_function: self.hash_function,
+            hash_function: self.hash_function.clone(),
             seed: self.seed,
             max_hash: self.max_hash,
             mins: self.mins.clone(),
@@ -1372,7 +1372,7 @@ impl KmerMinHashBTree {
             let mut combined_mh = KmerMinHashBTree::new(
                 self.scaled(),
                 self.ksize,
-                self.hash_function,
+                self.hash_function.clone(),
                 self.seed,
                 self.abunds.is_some(),
                 self.num,
@@ -1404,7 +1404,7 @@ impl KmerMinHashBTree {
             let mut combined_mh = KmerMinHashBTree::new(
                 self.scaled(),
                 self.ksize,
-                self.hash_function,
+                self.hash_function.clone(),
                 self.seed,
                 self.abunds.is_some(),
                 self.num,
@@ -1500,7 +1500,7 @@ impl KmerMinHashBTree {
     }
 
     pub fn hash_function(&self) -> HashFunctions {
-        self.hash_function
+        self.hash_function.clone()
     }
 
     pub fn mins(&self) -> Vec<u64> {
@@ -1524,7 +1524,7 @@ impl KmerMinHashBTree {
         let mut new_mh = KmerMinHashBTree::new(
             scaled,
             self.ksize,
-            self.hash_function,
+            self.hash_function.clone(),
             self.seed,
             self.abunds.is_some(),
             self.num,
@@ -1574,7 +1574,7 @@ impl SigsTrait for KmerMinHashBTree {
     }
 
     fn hash_function(&self) -> HashFunctions {
-        self.hash_function
+        self.hash_function.clone()
     }
 
     fn add_hash(&mut self, hash: u64) {

src/core/src/wasm.rs

@@ -37,13 +37,13 @@ impl KmerMinHash {
         // TODO: at most one of (prot, dayhoff, hp) should be true
 
         let hash_function = if dayhoff {
-            HashFunctions::murmur64_dayhoff
+            HashFunctions::Murmur64Dayhoff
         } else if hp {
-            HashFunctions::murmur64_hp
+            HashFunctions::Murmur64Hp
         } else if is_protein {
-            HashFunctions::murmur64_protein
+            HashFunctions::Murmur64Protein
         } else {
-            HashFunctions::murmur64_DNA
+            HashFunctions::Murmur64Dna
         };
 
         KmerMinHash(_KmerMinHash::new(