Merge branch 'latest' into ctb_hacky_rocksdb

.github/workflows/asv.yml

@@ -27,10 +27,9 @@ jobs:
       with:
         python-version: "3.10"
 
-    - uses: actions-rs/toolchain@v1
-      with:
-        toolchain: stable
-        override: true
+    - uses: dtolnay/rust-toolchain@stable
+
+    - uses: Swatinem/rust-cache@v2
 
     - name: Install dependencies
       run: |

.github/workflows/dev_envs.yml

@@ -24,7 +24,7 @@ jobs:
 
     - run: nix run .# -- --version
 
-    - run: nix develop --command bash -c "tox -e py310"
+    - run: nix develop --command bash -c "tox -e py311"
 
   pixi:
     runs-on: ${{ matrix.os }}
@@ -39,7 +39,7 @@ jobs:
     - name: set up pixi
       uses: prefix-dev/[email protected]
       with:
-        pixi-version: v0.26.1
+        pixi-version: v0.39.5
         cache: true
         frozen: true
 
@@ -67,7 +67,7 @@ jobs:
           ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
 
     - name: setup conda
-      uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d
+      uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830
       with:
         python-version: "3.10"
         miniforge-version: latest

.github/workflows/python.yml

@@ -40,6 +40,9 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-pip-v4-
 
+      - uses: dtolnay/rust-toolchain@stable
+      - uses: Swatinem/rust-cache@v2
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.github/workflows/rust.yml

@@ -15,17 +15,13 @@ jobs:
       - name: Checkout sources
         uses: actions/checkout@v4
 
-      - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1
-        with:
-          profile: minimal
-          toolchain: stable
-          override: true
+      - uses: dtolnay/rust-toolchain@stable
+
+      - uses: Swatinem/rust-cache@v2
 
       - name: Run cargo check
-        uses: actions-rs/cargo@v1
-        with:
-          command: check
+        run: |
+          cargo check
 
   test:
     runs-on: ${{ matrix.os }}
@@ -53,32 +49,30 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions-rs/toolchain@v1
+      - uses: dtolnay/rust-toolchain@master
         with:
           toolchain: ${{ matrix.rust }}
-          override: true
+
+      - uses: Swatinem/rust-cache@v2
+
+      - uses: taiki-e/install-action@nextest
 
       - name: Run tests
-        uses: actions-rs/cargo@v1
-        with:
-          command: test
-          args: --no-fail-fast
+        run: |
+          cargo nextest run
 
   test_all_features:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions-rs/toolchain@v1
-        with:
-          toolchain: stable
-          override: true
+      - uses: dtolnay/rust-toolchain@stable
+
+      - uses: Swatinem/rust-cache@v2
 
-      - uses: actions-rs/install@v0.1
+      - uses: taiki-e/install-action@v2
         with:
-          crate: cargo-all-features
-          version: latest
-          use-tool-cache: true
+          tool: cargo-all-features
 
       - name: Run tests for all feature combinations
         run: cargo test-all-features --no-fail-fast --all
@@ -88,29 +82,23 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions-rs/toolchain@v1
+      - uses: dtolnay/rust-toolchain@stable
         with:
-          toolchain: stable
-          override: true
+          components: llvm-tools-preview
+      - uses: Swatinem/rust-cache@v2
 
-      - name: Install cargo-binstall
-        run: |
-          wget https://github.com/ryankurte/cargo-binstall/releases/latest/download/cargo-binstall-x86_64-unknown-linux-gnu.tgz
-          tar xf cargo-binstall-x86_64-unknown-linux-gnu.tgz
-          chmod +x cargo-binstall
-          mv cargo-binstall "$HOME/.cargo/bin"
-
-      - name: Install cargo-tarpaulin
-        run: cargo binstall --no-confirm cargo-tarpaulin
+      - uses: taiki-e/install-action@cargo-llvm-cov
+      - uses: taiki-e/install-action@nextest
 
-      - name: Coverage with tarpaulin
-        run: cargo tarpaulin --all --all-features --timeout 600 --out xml -- --test-threads 1
+      - name: Collect coverage data
+        run: cargo llvm-cov nextest --all-features --lcov --output-path lcov.info
 
       - name: Upload Rust coverage to codecov
         uses: codecov/codecov-action@v3
         with:
           flags: rust
           fail_ci_if_error: true
+          files: lcov.info
 
   lints:
     name: Lints
@@ -129,36 +117,33 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install Rust toolchain
-        uses: actions-rs/toolchain@v1
+        uses: dtolnay/rust-toolchain@master
         with:
-          profile: minimal
           toolchain: ${{ matrix.rust }}
-          override: true
-          components: rustfmt, clippy
+          components: "clippy, rustfmt"
+
+      - uses: Swatinem/rust-cache@v2
 
       - name: Run cargo fmt
-        uses: actions-rs/cargo@v1
-        with:
-          command: fmt
-          args: --all -- --check
+        run: |
+          cargo fmt --all -- --check
 
       - name: Run cargo clippy
-        uses: actions-rs/cargo@v1
-        with:
-          command: clippy
-          args: --all -- -D warnings
+        run: |
+          cargo clippy --all -- -D warnings
 
   wasm-pack:
     name: Check if wasm-pack builds a valid package for the sourmash crate
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions-rs/toolchain@v1
+      - uses: dtolnay/rust-toolchain@stable
         with:
-          toolchain: stable
           target: wasm32-unknown-unknown
 
+      - uses: Swatinem/rust-cache@v2
+
       - name: Install wasm-pack
         run: "curl https://rustwasm.github.io/wasm-pack/installer/init.sh -sSf | sh"
 
@@ -190,51 +175,16 @@ jobs:
         with:
           path: 'pkg/sourmash*.tgz'
 
-  wasm32-wasi:
-    name: Run tests under wasm32-wasi
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - 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 "$HOME/.wasmtime/bin" >> $GITHUB_PATH
-      - 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
-        continue-on-error: true  ## TODO: remove this when build works...
-        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 (on tags, dry-run otherwise)
     runs-on: ubuntu-latest
     steps:
       - name: Checkout sources
         uses: actions/checkout@v4
 
-      - name: Install stable toolchain
-        uses: actions-rs/toolchain@v1
-        with:
-          profile: minimal
-          toolchain: stable
-          override: true
+      - uses: dtolnay/rust-toolchain@stable
+
+      - uses: Swatinem/rust-cache@v2
 
       - name: Check semver
         uses: obi1kenobi/cargo-semver-checks-action@v2
@@ -245,62 +195,52 @@ jobs:
           features: branchwater
 
       - name: Make sure we can publish the sourmash crate
-        uses: actions-rs/cargo@v1
-        with:
-          command: publish
-          args: --dry-run --manifest-path src/core/Cargo.toml
+        run: |
+          cargo publish --dry-run --manifest-path src/core/Cargo.toml
 
       # Login to crates.io on tags
       - name: login to crates.io
-        uses: actions-rs/cargo@v1
         if: startsWith(github.ref, 'refs/tags/r')
-        with:
-          command: login
-          args: ${{ secrets.CRATES_IO_TOKEN }}
+        run: |
+          cargo login ${{ secrets.CRATES_IO_TOKEN }}
 
       # Publish to crates.io on tags
       - name: Publish to crates.io
         if: startsWith(github.ref, 'refs/tags/r')
-        uses: actions-rs/cargo@v1
-        with:
-          command: publish
-          args: --manifest-path src/core/Cargo.toml
+        run: |
+          cargo publish --manifest-path src/core/Cargo.toml
 
   minimum_rust_version:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions-rs/toolchain@v1
+      - uses: dtolnay/rust-toolchain@master
         with:
-          toolchain: "1.66.0"
-          override: true
+          toolchain: "1.71.1"
+
+      - uses: Swatinem/rust-cache@v2
 
       - name: check if README matches MSRV defined here
-        run: grep '1.66.0' src/core/README.md
+        run: grep '1.71.1' src/core/README.md
 
       - name: Check if it builds properly
-        uses: actions-rs/cargo@v1
-        with:
-          command: build
-          args: --all-features
+        run: |
+          cargo build --all-features
 
   check_cbindgen:
     name: "Check if cbindgen runs cleanly for generating the C headers"
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions-rs/toolchain@v1
-        with:
-          toolchain: stable
-          override: true
+      - uses: dtolnay/rust-toolchain@stable
+
+      - uses: Swatinem/rust-cache@v2
 
-      - uses: actions-rs/install@v0.1
+      - uses: taiki-e/install-action@v2
         with:
-          crate: cbindgen
-          version: 0.20.0
-          use-tool-cache: true
+          tool: [email protected]
 
       - run: make include/sourmash.h
 

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
       - id: check-toml
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.4
+    rev: v0.9.3
     hooks:
       - id: ruff-format
       - id: ruff

.readthedocs.yml

@@ -8,7 +8,7 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.10"
-    rust: "1.70"
+    rust: "1.75"
   apt_packages:
     - llvm-dev
     - libclang-dev