Indexing in Rust

.github/actions-rs/grcov.yml

@@ -0,0 +1,7 @@
+branch: true
+ignore-not-existing: true
+llvm: true
+filter: covered
+output-type: lcov
+output-file: ./lcov.info
+prefix-dir: /home/user/build/

.github/workflows/rust.yml

@@ -0,0 +1,231 @@
+name: Rust checks
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  check:
+    name: Check
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v1
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+
+      - name: Run cargo check
+        uses: actions-rs/cargo@v1
+        with:
+          command: check
+
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        build: [beta, stable, windows, macos]
+        include:
+          - build: macos
+            os: macos-latest
+            rust: stable
+          - build: windows
+            os: windows-latest
+            rust: stable
+          - build: beta
+            os: ubuntu-latest
+            rust: beta
+          - build: stable
+            os: ubuntu-latest
+            rust: stable
+    steps:
+      - uses: actions/checkout@v1
+
+      - uses: actions-rs/toolchain@v1
+        with:
+          toolchain: ${{ matrix.rust }}
+          override: true
+
+      - name: Set up Python 3.8
+        if: matrix.os != 'windows-latest'
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.8"
+
+      - name: Install dependencies
+        if: matrix.os != 'windows-latest'
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .
+
+      - name: Run tests
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --no-fail-fast
+
+  test_all_features:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+
+      - uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.8"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .
+
+      - name: Run tests
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --no-fail-fast --all --all-features
+
+  coverage:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+
+      - uses: actions-rs/toolchain@v1
+        with:
+          toolchain: nightly
+          override: true
+
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.8"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .
+
+      - name: Run tests
+        uses: actions-rs/cargo@v1
+        with:
+          command: test
+          args: --no-fail-fast --all --all-features
+        env:
+          'CARGO_INCREMENTAL': '0'
+          'RUSTFLAGS': '-Zprofile -Ccodegen-units=1 -Cinline-threshold=0 -Clink-dead-code -Coverflow-checks=off -Zno-landing-pads'
+
+      - name: Collect coverage and generate report with grcov
+        uses: actions-rs/[email protected]
+        id: coverage
+
+      - name: Upload coverage to codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ${{ steps.coverage.outputs.report }}
+
+  lints:
+    name: Lints
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v1
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+          components: rustfmt, clippy
+
+      - name: Run cargo fmt
+        uses: actions-rs/cargo@v1
+        with:
+          command: fmt
+          args: --all -- --check
+
+      - name: Run cargo clippy
+        uses: actions-rs/cargo@v1
+        with:
+          command: clippy
+          args: -- -D warnings
+
+  wasm-pack:
+    name: Check if wasm-pack builds a valid package
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          target: wasm32-unknown-unknown
+      - uses: actions-rs/cargo@v1
+        with:
+          command: install
+          args: --force wasm-pack
+      - name: run wasm-pack
+        run: wasm-pack build
+
+  wasm32-wasi:
+    name: Run tests under wasm32-wasi
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - name: Install wasm32-wasi target
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          target: wasm32-wasi
+      - name: Install wasmtime
+        run: "curl https://wasmtime.dev/install.sh -sSf | bash"
+      - name: Add wasmtime to PATH
+        run: echo "::add-path::$HOME/.wasmtime/bin"
+      - name: Install cargo-wasi command
+        uses: actions-rs/cargo@v1
+        with:
+          command: install
+          args: --force cargo-wasi
+      - name: Build code with cargo-wasi
+        uses: actions-rs/cargo@v1
+        with:
+          command: wasi
+          args: build
+      - name: Run tests under wasm32-wasi
+        uses: actions-rs/cargo@v1
+        continue-on-error: true  ## TODO: remove this when tests work...
+        with:
+          command: wasi
+          args: test
+
+  publish:
+    name: Publish (dry-run)
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v1
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+
+      - name: Make sure we can publish the crate
+        uses: actions-rs/cargo@v1
+        with:
+          command: publish
+          args: --dry-run

.gitignore

@@ -24,4 +24,12 @@ sourmash/_minhash.cpp
 .pytest_cache
 .python-version
 sourmash/version.py
-*.DS_Store
+*.DS_Store
+.tox
+sourmash/_lowlevel*.py
+.env
+Pipfile
+Pipfile.lock
+ocf/target/
+target/
+Cargo.lock

.travis.yml

@@ -48,26 +48,6 @@ jobs:
       python: 3.6
     - <<: *test
       python: 3.5
-    - <<: *test
-      name: wasm-pack
-      language: rust
-      rust: stable
-      before_script: skip
-      install: skip
-      script:
-        - rustup target add wasm32-unknown-unknown
-        - cargo install --force wasm-pack
-        - wasm-pack build
-    - <<: *test
-      name: wasi target
-      language: rust
-      rust: stable
-      before_script: skip
-      install: skip
-      script:
-        - rustup target add wasm32-wasi
-        - cargo install --force cargo-wasi
-        - cargo wasi build
 
     - &wheel
       stage: build wheel and send to github releases

Cargo.toml

@@ -8,6 +8,9 @@ keywords = ["minhash", "bioinformatics"]
 categories = ["science", "algorithms", "data-structures"]
 license = "BSD-3-Clause"
 edition = "2018"
+default-run = "smrs"
+autoexamples = false
+autobins = false
 
 [lib]
 name = "sourmash"
@@ -18,61 +21,67 @@ bench = false
 lto=true
 
 [features]
-from-finch = ["finch", "needletail"]
+from-finch = ["finch"]
 
 [workspace]
 
 #[build-dependencies]
 #cbindgen = "~0.6.7"
 
 [dependencies]
-byteorder = "^1.2"
-cfg-if = "0.1"
-clap = { version = "~2.32", features = ["yaml"] }
-env_logger = "0.6.0"
+byteorder = "1.3.2"
+cfg-if = "0.1.10"
+clap = { version = "2.33.0", features = ["yaml"] }
+env_logger = "0.7.1"
 exitfailure = "0.5.1"
-failure = "0.1.3"
-failure_derive = "0.1.3"
-finch = { version = "~0.1.6", optional = true }
-fixedbitset = "^0.1.9"
-human-panic = "1.0.1"
-lazy_static = "1.0.0"
+failure = "0.1.6"
+failure_derive = "0.1.6"
+finch = { version = "0.3.0", optional = true }
+fixedbitset = "0.2.0"
+lazy_static = "1.4.0"
 lazy-init = "0.3.0"
-log = "0.4.0"
-md5 = "0.6.0"
-murmurhash3 = "~0.0.5"
-needletail = { version = "~0.2.1", optional = true }
-serde = "1.0"
-serde_derive = "~1.0.58"
-serde_json = "1.0.2"
-ukhs = { git = "https://github.com/luizirber/ukhs", branch = "feature/alternative_backends", features = ["boomphf_mphf"], default-features = false}
-bio = { git = "https://github.com/luizirber/rust-bio", branch = "feature/fastx_reader" }
+log = "0.4.8"
+md5 = "0.7.0"
+murmurhash3 = "0.0.5"
+serde = "1.0.103"
+serde_derive = "1.0.103"
+serde_json = "1.0.44"
+#ukhs = { git = "https://github.com/luizirber/ukhs", branch = "feature/alternative_backends", features = ["boomphf_mphf"], default-features = false}
 primal = "0.2.3"
-pdatastructs = { git = "https://github.com/luizirber/pdatastructs.rs", branch = "succinct_wasm" }
-itertools = "0.8.0"
-typed-builder = "0.3.0"
-csv = "1.0.7"
+#pdatastructs = { git = "https://github.com/luizirber/pdatastructs.rs", branch = "succinct_wasm" }
+itertools = "0.8.2"
+typed-builder = "0.4.0"
+csv = "1.1.1"
 tempfile = "3.1.0"
 
+[dependencies.needletail]
+version = "0.3.2"
+default-features = false
+#features = ["compression"]
+
 [target.'cfg(all(target_arch = "wasm32", target_vendor="unknown"))'.dependencies.wasm-bindgen]
-version = "^0.2"
+version = "0.2.55"
 features = ["serde-serialize"]
 
-[target.'cfg(not(all(target_arch = "wasm32", target_vendor="unknown")))'.dependencies.ocf]
-version = "0.1"
-path = "ocf"
+[target.'cfg(not(all(target_arch = "wasm32", target_vendor="unknown")))'.dependencies.niffler]
+version = "1.0"
 default-features = false
 
-[target.'cfg(not(target_arch = "wasm32"))'.dependencies.mqf]
-version = "1.0.0"
+[target.'cfg(not(target_arch = "wasm32"))'.dev-dependencies]
+proptest = "0.9.4"
 
 [dev-dependencies]
-proptest = "^0.8"
-criterion = "^0.2"
-rand = "^0.5"
-tempfile = "3"
-assert_matches = "1.2"
+criterion = "0.3.0"
+rand = "0.7.2"
+tempfile = "3.1.0"
+assert_matches = "1.3.0"
+assert_cmd = "0.12.0"
+predicates = "1.0.2"
 
 [[bench]]
 name = "index"
 harness = false
+
+[[bin]]
+name = "smrs"
+path = "src/bin/smrs.rs"