Prepare new core release (and upload to NPM) (#1643)

* Bump rust version
* Wasm implementation is now more similar to how FFI is implemented
* wasm-pack 0.10.0 does not needed the patch for adding sourmash_bg.js

.github/workflows/rust.yml

@@ -180,10 +180,10 @@ jobs:
           toolchain: stable
           target: wasm32-unknown-unknown
 
-      - uses: actions-rs/install@v0.1
+      - uses: actions-rs/cargo@v1
         with:
-          crate: wasm-pack
-          version: latest
+          command: install
+          args: --force wasm-pack --version 0.10.0
 
       - name: Prepare node for running tests
         uses: actions/setup-node@v1
@@ -197,6 +197,14 @@ jobs:
       - name: run wasm-pack build
         run: wasm-pack build src/core -d ../../pkg
 
+      - name: Prepare package for NPM publishing
+        working-directory: pkg
+        run: npm pack
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: 'pkg/sourmash*.tgz'
+
   wasm32-wasi:
     name: Run tests under wasm32-wasi
     runs-on: ubuntu-latest

.github/workflows/rust_publish.yml

@@ -18,9 +18,10 @@ jobs:
       - uses: actions-rs/cargo@v1
         with:
           command: install
-          args: --force wasm-pack --version 0.8.1
+          args: --force wasm-pack --version 0.10.0
       - name: run wasm-pack
-        run: wasm-pack build src/core -d ../../pkg
+        run: |
+          wasm-pack build src/core -d ../../pkg
 
       - name: Prepare node for NPM publishing
         uses: actions/setup-node@v1
@@ -29,7 +30,8 @@ jobs:
           registry-url: https://registry.npmjs.org/
 
       - name: Publish to NPM
-        run: '(cd pkg && npm publish)'
+        working-directory: pkg
+        run: npm publish
         env:
           NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
 

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

@@ -1,6 +1,6 @@
 [package]
 name = "sourmash"
-version = "0.10.0"
+version = "0.11.0"
 authors = ["Luiz Irber <luiz.irber@gmail.com>"]
 description = "MinHash sketches for genomic data"
 repository = "https://github.com/dib-lab/sourmash"
@@ -44,19 +44,6 @@ primal-check = "0.3.1"
 thiserror = "1.0"
 typed-builder = "0.9.0"
 
-[target.'cfg(all(target_arch = "wasm32", target_vendor="unknown"))'.dependencies.wasm-bindgen]
-version = "0.2.62"
-features = ["serde-serialize"]
-
-[target.'cfg(all(target_arch = "wasm32", target_vendor="unknown"))'.dev-dependencies]
-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"
@@ -82,3 +69,19 @@ harness = false
 [[bench]]
 name = "minhash"
 harness = false
+
+## Wasm section. Crates only used for WASM, as well as specific configurations
+
+[target.'cfg(all(target_arch = "wasm32", target_vendor="unknown"))'.dependencies.wasm-bindgen]
+version = "0.2.62"
+features = ["serde-serialize"]
+
+[target.'cfg(all(target_arch = "wasm32", target_vendor="unknown"))'.dependencies.web-sys]
+version = "0.3.51"
+features = ["console", "File"]
+
+[target.'cfg(all(target_arch = "wasm32", target_vendor="unknown"))'.dev-dependencies]
+wasm-bindgen-test = "0.3.0"
+
+[target.'cfg(not(target_arch = "wasm32"))'.dev-dependencies.assert_cmd]
+version = "1.0.1"

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,