Wasm implementation is now more similar to how FFI is implemented

src/core/CHANGELOG.md

@@ -0,0 +1,160 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.11.0] - 2021-07-07
+
+Added:
+
+- Add HyperLogLog implementation (#1223)
+
+Changed:
+
+- Update `MinHash.set_abundances` to remove hash if 0 abund; handle negative abundances. (#1575)
+- Improving `MinHash.remove_many(...)` performance (#1571)
+- Improved intersection and union calculations (#1475)
+- Bump MSRV to 1.42 (and other dep fixes) (#1461)
+- Rework the `find` functionality for `Index` classes (#1392)
+- Rationalize `SourmashSignature.name` and `str(sig)` (#1179)
+
+Fixed:
+
+- Fix needless borrows as suggested by clippy (#1636)
+- Fix Rust 1.59 lints (#1600)
+- Clean up clippy lints from 1.52 (#1505)
+- Fix clippy lints introduced in 1.51 (#1407)
+- CI/Rust: update and fix cbindgen config (#1473)
+- pin needletail version to keep MSRV at 1.37 (#1393)
+- Update proptest requirement from 0.9.6 to 1.0.0 (#1344)
+- Fix clippy lints introduced in 1.50 and update nix configs (#1332)
+- Update finch requirement from 0.3.0 to 0.4.1 (#1290)
+- update rand for test, and activate "js" feature for getrandom (#1275)
+- Fix new clippy warnings from Rust 1.49 (#1267)
+- CI: small build fixes (#1252)
+
+Removed:
+
+- Remove 10x support in compute (#1229)
+
+## [0.10.0] - 2020-10-08
+
+Added:
+
+- Add `clear` option to set_abundances(...) method (#1046)
+
+Changed:
+
+- Replace mx by scaled (#1139)
+
+Fixed:
+
+- Fix Rust panic error in signature creation (#1172)
+- Update typed-builder requirement from 0.6.0 to 0.7.0 (#1121)
+- update CI for latest branch name change (#1150)
+- Update typed-builder requirement from 0.6.0 to 0.7.0 (#1121)
+
+## [0.9.0] - 2020-07-13
+
+Added:
+
+- Cache md5sum calculation (#1058)
+- Expose more of the API for wasm (signature and ComputeParameters) (#1058)
+- Getters and setters for ComputeParameters (#1058)
+
+Changed: 
+
+- Migrate from failure to thiserror (#1058)
+- Bump MSRV to 1.37 (#1058)
+
+Fixed: 
+
+- Use the derive feature in serde instead of serde_derive (#1058)
+- Use nohash-hasher crate instead of previous NoHashHasher from finch.
+- Update typed-builder to 0.6.0 (#1058)
+- stricter niffler versions and add new gz feature to it (#1070)
+
+## [0.8.0] - 2020-06-26
+
+Added:
+
+- compute-optimized MinHash (for small scaled or large cardinalities) (#1045)
+
+## [0.7.0] - 2020-05-12
+
+Changed:
+
+- Hide internal representation in core (#986)
+
+Fixed: 
+
+- update FFI and cbindgen (#986)
+
+## [0.6.0] - 2020-04-28
+
+Added:
+
+- Nodegraph implementation based on khmer.Nodegraph (#799)
+
+## [0.5.0] - 2020-02-08
+
+Added:
+
+- add_hash_with_abundance method in core library (#892)
+
+Changed:
+
+- More refactoring of MinHash comparison code (#882)
+- Replace mins_push and abunds_push with set_abundances (#887)
+
+Fixed:
+
+- add_hash with num doesn't set abundances properly (#891)
+
+## [0.4.0] - 2020-01-26
+
+Added:
+
+- Compute improvements: Parameter sets for defining signatures, add_protein implemented (#845)
+- add_many for faster insertion of multiple hashes (#826)
+
+Changed:
+
+- Compare/similarity now have a downsample argument (#856)
+
+Fixed:
+
+- Improve sketching performance with lookup tables for complement and DNA validation (#861) (#865)
+- Use tarpaulin instead of grcov (#862)
+- set up publishing workflow for NPM and crates.io (#824)
+
+## [0.3.0] - 2020-01-05
+
+Added:
+
+- Similarity with abundance method for MinHash (#808)
+- Experimental support for indices in Rust (#773)
+- Experimental SBT with MQF internal nodes in Rust (#772)
+
+Changed:
+
+- Make the sourmash crate library-only (#812)
+
+Fixed:
+
+- Use once_cell instead of lazy_static and lazy-init (#815)
+- Fix mem leak in get_mins (#807)
+- Fixes for WASI and WASM compilation (#771) (#723)
+
+[unreleased]: https://github.com/sourmash-bio/sourmash/compare/r0.11.0...HEAD
+[0.11.0]: https://github.com/sourmash-bio/sourmash/compare/r0.10.0...r0.11.0
+[0.10.0]: https://github.com/sourmash-bio/sourmash/compare/r0.9.0...r0.10.0
+[0.9.0]: https://github.com/sourmash-bio/sourmash/compare/r0.9.0...r0.10.0
+[0.8.0]: https://github.com/sourmash-bio/sourmash/compare/r0.8.0...r0.9.0
+[0.7.0]: https://github.com/sourmash-bio/sourmash/compare/r0.7.0...r0.8.0
+[0.6.0]: https://github.com/sourmash-bio/sourmash/compare/r0.6.0...r0.7.0
+[0.5.0]: https://github.com/sourmash-bio/sourmash/compare/r0.5.0...r0.6.0
+[0.4.0]: https://github.com/sourmash-bio/sourmash/compare/r0.4.0...r0.5.0
+[0.3.0]: https://github.com/sourmash-bio/sourmash/compare/r0.3.0...r0.4.0

src/core/Cargo.toml

@@ -54,9 +54,6 @@ wasm-bindgen-test = "0.3.0"
 [target.'cfg(not(target_arch = "wasm32"))'.dev-dependencies.assert_cmd]
 version = "1.0.1"
 
-[package.metadata.wasm-pack.profile.release]
-wasm-opt = false # https://github.com/rustwasm/wasm-pack/issues/886
-
 [dev-dependencies]
 assert_matches = "1.3.0"
 criterion = "0.3.2"

src/core/src/cmd.rs

@@ -1,6 +1,3 @@
-#[cfg(all(target_arch = "wasm32", target_vendor = "unknown"))]
-use wasm_bindgen::prelude::*;
-
 use getset::{CopyGetters, Getters, Setters};
 use typed_builder::TypedBuilder;
 
@@ -36,7 +33,6 @@ impl Signature {
 }
 
 #[allow(dead_code)]
-#[cfg_attr(all(target_arch = "wasm32", target_vendor = "unknown"), wasm_bindgen)]
 #[derive(TypedBuilder, CopyGetters, Getters, Setters)]
 pub struct ComputeParameters {
     #[getset(get = "pub", set = "pub")]

src/core/src/encodings.rs

@@ -4,12 +4,9 @@ use std::iter::Iterator;
 use std::str;
 
 use once_cell::sync::Lazy;
-#[cfg(all(target_arch = "wasm32", target_vendor = "unknown"))]
-use wasm_bindgen::prelude::*;
 
 use crate::Error;
 
-#[cfg_attr(all(target_arch = "wasm32", target_vendor = "unknown"), wasm_bindgen)]
 #[allow(non_camel_case_types)]
 #[derive(Debug, Clone, Copy, PartialEq)]
 #[repr(u32)]

src/core/src/signature.rs

@@ -14,9 +14,6 @@ use rayon::prelude::*;
 use serde::{Deserialize, Serialize};
 use typed_builder::TypedBuilder;
 
-#[cfg(all(target_arch = "wasm32", target_vendor = "unknown"))]
-use wasm_bindgen::prelude::*;
-
 use crate::encodings::{aa_to_dayhoff, aa_to_hp, revcomp, to_aa, HashFunctions, VALID};
 use crate::index::storage::ToWriter;
 use crate::sketch::Sketch;
@@ -242,7 +239,6 @@ impl SigsTrait for Sketch {
     }
 }
 
-#[cfg_attr(all(target_arch = "wasm32", target_vendor = "unknown"), wasm_bindgen)]
 #[derive(Serialize, Deserialize, Debug, Clone, TypedBuilder)]
 pub struct Signature {
     #[serde(default = "default_class")]

src/core/src/sketch/minhash.rs

@@ -17,9 +17,6 @@ use crate::signature::SigsTrait;
 use crate::sketch::hyperloglog::HyperLogLog;
 use crate::Error;
 
-#[cfg(all(target_arch = "wasm32", target_vendor = "unknown"))]
-use wasm_bindgen::prelude::*;
-
 pub fn max_hash_for_scaled(scaled: u64) -> u64 {
     match scaled {
         0 => 0,
@@ -35,7 +32,6 @@ pub fn scaled_for_max_hash(max_hash: u64) -> u64 {
     }
 }
 
-#[cfg_attr(all(target_arch = "wasm32", target_vendor = "unknown"), wasm_bindgen)]
 #[derive(Debug, TypedBuilder)]
 pub struct KmerMinHash {
     num: u32,
@@ -939,7 +935,6 @@ mod test {
 //#############
 // A MinHash implementation for low scaled or large cardinalities
 
-#[cfg_attr(all(target_arch = "wasm32", target_vendor = "unknown"), wasm_bindgen)]
 #[derive(Debug, TypedBuilder)]
 pub struct KmerMinHashBTree {
     num: u32,

src/core/src/wasm.rs

@@ -1,11 +1,25 @@
+// When the `wee_alloc` feature is enabled, use `wee_alloc` as the global
+// allocator.
+#[cfg(feature = "wee_alloc")]
+#[global_allocator]
+static ALLOC: wee_alloc::WeeAlloc = wee_alloc::WeeAlloc::INIT;
+
 use wasm_bindgen::prelude::*;
 
-use serde_json;
+use sourmash::cmd::ComputeParameters as _ComputeParameters;
+use sourmash::encodings::HashFunctions;
+use sourmash::signature::Signature as _Signature;
+use sourmash::signature::SigsTrait;
+use sourmash::sketch::minhash::KmerMinHash as _KmerMinHash;
+
+#[wasm_bindgen]
+pub struct KmerMinHash(_KmerMinHash);
 
-use crate::cmd::ComputeParameters;
-use crate::encodings::HashFunctions;
-use crate::signature::{Signature, SigsTrait};
-use crate::sketch::minhash::KmerMinHash;
+#[wasm_bindgen]
+pub struct Signature(_Signature);
+
+#[wasm_bindgen]
+pub struct ComputeParameters(_ComputeParameters);
 
 #[wasm_bindgen]
 impl KmerMinHash {
@@ -32,34 +46,40 @@ impl KmerMinHash {
             HashFunctions::murmur64_DNA
         };
 
-        KmerMinHash::new(
+        KmerMinHash(_KmerMinHash::new(
             scaled as u64,
             ksize,
             hash_function,
             seed as u64,
             track_abundance,
             num,
-        )
+        ))
     }
 
     #[wasm_bindgen]
     pub fn add_sequence_js(&mut self, buf: &str) {
-        self.add_sequence(buf.as_bytes(), true)
+        self.0
+            .add_sequence(buf.as_bytes(), true)
             .expect("Error adding sequence");
     }
 
     #[wasm_bindgen]
     pub fn to_json(&mut self) -> String {
-        serde_json::to_string(self).unwrap()
+        serde_json::to_string(&self.0).unwrap()
     }
 }
 
 #[wasm_bindgen]
 impl ComputeParameters {
     #[wasm_bindgen(constructor)]
     pub fn new_with_params() -> ComputeParameters {
-        let params = ComputeParameters::default();
-        params
+        let params = _ComputeParameters::default();
+        ComputeParameters(params)
+    }
+
+    #[wasm_bindgen]
+    pub fn set_ksizes(&mut self, ksizes: Vec<u32>) {
+        self.0.set_ksizes(ksizes);
     }
 }
 
@@ -69,18 +89,28 @@ impl Signature {
     pub fn new_from_params(params: &ComputeParameters) -> Signature {
         //let params = ComputeParameters::default();
 
-        Signature::from_params(&params)
+        Signature(_Signature::from_params(&params.0))
     }
 
     #[wasm_bindgen]
     pub fn add_sequence_js(&mut self, buf: &str) {
-        self.add_sequence(buf.as_bytes(), true)
+        self.0
+            .add_sequence(buf.as_bytes(), true)
             .expect("Error adding sequence");
     }
 
+    #[wasm_bindgen]
+    pub fn add_from_file(&mut self, fp: web_sys::File) {
+        unimplemented!()
+    }
+
     #[wasm_bindgen]
     pub fn to_json(&mut self) -> String {
-        serde_json::to_string(self).unwrap()
+        serde_json::to_string(&self.0).unwrap()
+    }
+
+    pub fn size(&self) -> usize {
+        self.0.size()
     }
 }