diff --git a/.github/workflows/asv.yml b/.github/workflows/asv.yml
index aca239e935..3b3167a6c4 100644
--- a/.github/workflows/asv.yml
+++ b/.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: |
diff --git a/.github/workflows/dev_envs.yml b/.github/workflows/dev_envs.yml
index 24ef7112e8..11371ae3ce 100644
--- a/.github/workflows/dev_envs.yml
+++ b/.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/setup-pixi@v0.8.1
       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
diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index 0805449e48..055e804da1 100644
--- a/.github/workflows/python.yml
+++ b/.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
diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 459f29ece2..9324699e67 100644
--- a/.github/workflows/rust.yml
+++ b/.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
@@ -129,24 +117,20 @@ 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
@@ -154,11 +138,12 @@ jobs:
     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"
 
@@ -190,38 +175,6 @@ 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
@@ -229,12 +182,9 @@ 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: Check semver
         uses: obi1kenobi/cargo-semver-checks-action@v2
@@ -245,45 +195,38 @@ 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"
@@ -291,16 +234,13 @@ jobs:
     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: cbindgen@0.26.0
 
       - run: make include/sourmash.h
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3aec96f877..fdc2bd5453 100644
--- a/.pre-commit-config.yaml
+++ b/.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
diff --git a/.readthedocs.yml b/.readthedocs.yml
index e5d525f014..f36f0afdad 100644
--- a/.readthedocs.yml
+++ b/.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
diff --git a/Cargo.lock b/Cargo.lock
index a98f3c87d3..9cd80dbfad 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -14,7 +14,7 @@ version = "0.7.8"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "891477e0c6a8957309ee5c45a6368af3ae14bb510732d2684ffa19af310920f9"
 dependencies = [
- "getrandom",
+ "getrandom 0.2.15",
  "once_cell",
  "version_check",
 ]
@@ -178,9 +178,9 @@ checksum = "e1e5f035d16fc623ae5f74981db80a439803888314e3a555fd6f04acd51a3205"
 
 [[package]]
 name = "bytemuck"
-version = "1.16.1"
+version = "1.21.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b236fc92302c97ed75b38da1f4917b5cdda4984745740f153a5d3059e48d725e"
+checksum = "ef657dfab802224e671f5818e9a4935f9b1957ed18e58292690cc39e7a4092a3"
 
 [[package]]
 name = "byteorder"
@@ -642,15 +642,27 @@ dependencies = [
  "cfg-if",
  "js-sys",
  "libc",
- "wasi",
+ "wasi 0.11.0+wasi-snapshot-preview1",
  "wasm-bindgen",
 ]
 
+[[package]]
+name = "getrandom"
+version = "0.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "43a49c392881ce6d5c3b8cb70f98717b7c07aabbdff06687b9030dbfbe2725f8"
+dependencies = [
+ "cfg-if",
+ "libc",
+ "wasi 0.13.3+wasi-0.2.2",
+ "windows-targets 0.52.6",
+]
+
 [[package]]
 name = "getset"
-version = "0.1.3"
+version = "0.1.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f636605b743120a8d32ed92fc27b6cde1a769f8f936c065151eb66f88ded513c"
+checksum = "eded738faa0e88d3abc9d1a13cb11adc2073c400969eeb8793cf7132589959fc"
 dependencies = [
  "proc-macro-error2",
  "proc-macro2",
@@ -693,9 +705,9 @@ checksum = "443144c8cdadd93ebf52ddb4056d257f5b52c04d3c804e657d19eb73fc33668b"
 
 [[package]]
 name = "histogram"
-version = "0.11.1"
+version = "0.11.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "58cf6b99a250776d813cdf2f0b478a053a822d078e7a2baf5cb36afc88c41a7c"
+checksum = "e1afb38a8df06a3145793cc0bd7d7b929211de1fcee50a89fa4bc0f5cd9bf0ca"
 dependencies = [
  "thiserror 1.0.69",
 ]
@@ -776,9 +788,9 @@ dependencies = [
 
 [[package]]
 name = "itertools"
-version = "0.13.0"
+version = "0.14.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "413ee7dfc52ee1a4949ceeb7dbc8a33f2d6c088194d9f922fb8318faf1f01186"
+checksum = "2b192c782037fadd9cfa75548310488aabdbf3d2da73885b31bd0abd03351285"
 dependencies = [
  "either",
 ]
@@ -844,17 +856,15 @@ checksum = "348108ab3fba42ec82ff6e9564fc4ca0247bdccdc68dd8af9764bbc79c3c8ffb"
 
 [[package]]
 name = "librocksdb-sys"
-version = "0.16.0+8.10.0"
+version = "0.17.1+9.9.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ce3d60bc059831dc1c83903fb45c103f75db65c5a7bf22272764d9cc683e348c"
+checksum = "2b7869a512ae9982f4d46ba482c2a304f1efd80c6412a3d4bf57bb79a619679f"
 dependencies = [
  "bindgen",
  "bzip2-sys",
  "cc",
- "glob",
  "libc",
  "libz-sys",
- "lz4-sys",
  "zstd-sys",
 ]
 
@@ -892,19 +902,9 @@ checksum = "78b3ae25bc7c8c38cec158d1f2757ee79e9b3740fbc7ccf0e59e4b08d793fa89"
 
 [[package]]
 name = "log"
-version = "0.4.22"
+version = "0.4.25"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a7a70ba024b9dc04c27ea2f0c0548feb474ec5c54bba33a7f72f873a39d07b24"
-
-[[package]]
-name = "lz4-sys"
-version = "1.9.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "57d27b317e207b10f69f5e75494119e391a96f48861ae870d1da6edac98ca900"
-dependencies = [
- "cc",
- "libc",
-]
+checksum = "04cbf5b083de1c7e0222a7a51dbfdba1cbe1c6ab0b15e29fff3f6c077fd9cd9f"
 
 [[package]]
 name = "lzma-sys"
@@ -1000,7 +1000,7 @@ dependencies = [
  "num-complex",
  "num-rational",
  "num-traits",
- "rand",
+ "rand 0.8.5",
  "rand_distr",
  "simba",
  "typenum",
@@ -1122,9 +1122,9 @@ checksum = "0ab1bc2a289d34bd04a330323ac98a1b4bc82c9d9fcb1e66b63caa84da26b575"
 
 [[package]]
 name = "ouroboros"
-version = "0.18.4"
+version = "0.18.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "944fa20996a25aded6b4795c6d63f10014a7a83f8be9828a11860b08c5fc4a67"
+checksum = "1e0f050db9c44b97a94723127e6be766ac5c340c48f2c4bb3ffa11713744be59"
 dependencies = [
  "aliasable",
  "ouroboros_macro",
@@ -1133,12 +1133,11 @@ dependencies = [
 
 [[package]]
 name = "ouroboros_macro"
-version = "0.18.4"
+version = "0.18.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "39b0deead1528fd0e5947a8546a9642a9777c25f6e1e26f34c97b204bbb465bd"
+checksum = "3c7028bdd3d43083f6d8d4d5187680d0d3560d54df4cc9d752005268b41e64d0"
 dependencies = [
  "heck",
- "itertools 0.12.1",
  "proc-macro2",
  "proc-macro2-diagnostics",
  "quote",
@@ -1269,8 +1268,8 @@ dependencies = [
  "bitflags 2.4.1",
  "lazy_static",
  "num-traits",
- "rand",
- "rand_chacha",
+ "rand 0.8.5",
+ "rand_chacha 0.3.1",
  "rand_xorshift",
  "regex-syntax 0.8.2",
  "unarray",
@@ -1318,8 +1317,19 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404"
 dependencies = [
  "libc",
- "rand_chacha",
- "rand_core",
+ "rand_chacha 0.3.1",
+ "rand_core 0.6.3",
+]
+
+[[package]]
+name = "rand"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3779b94aeb87e8bd4e834cee3650289ee9e0d5677f976ecdb6d219e5f4f6cd94"
+dependencies = [
+ "rand_chacha 0.9.0",
+ "rand_core 0.9.0",
+ "zerocopy",
 ]
 
 [[package]]
@@ -1329,7 +1339,17 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88"
 dependencies = [
  "ppv-lite86",
- "rand_core",
+ "rand_core 0.6.3",
+]
+
+[[package]]
+name = "rand_chacha"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d3022b5f1df60f26e1ffddd6c66e8aa15de382ae63b3a0c1bfc0e4d3e3f325cb"
+dependencies = [
+ "ppv-lite86",
+ "rand_core 0.9.0",
 ]
 
 [[package]]
@@ -1338,7 +1358,17 @@ version = "0.6.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d34f1408f55294453790c48b2f1ebbb1c5b4b7563eb1f418bcfcfdbb06ebb4e7"
 dependencies = [
- "getrandom",
+ "getrandom 0.2.15",
+]
+
+[[package]]
+name = "rand_core"
+version = "0.9.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b08f3c9802962f7e1b25113931d94f43ed9725bebc59db9d0c3e9a23b67e15ff"
+dependencies = [
+ "getrandom 0.3.1",
+ "zerocopy",
 ]
 
 [[package]]
@@ -1348,7 +1378,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32cb0b9bc82b0a0876c2dd994a7e7a2683d3e7390ca40e6886785ef0c7e3ee31"
 dependencies = [
  "num-traits",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -1357,7 +1387,7 @@ version = "0.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d25bf25ec5ae4a3f1b92f929810509a2f53d7dca2f50b794ff57e3face536c8f"
 dependencies = [
- "rand_core",
+ "rand_core 0.6.3",
 ]
 
 [[package]]
@@ -1447,9 +1477,9 @@ dependencies = [
 
 [[package]]
 name = "roaring"
-version = "0.10.9"
+version = "0.10.10"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "41589aba99537475bf697f2118357cad1c31590c5a1b9f6d9fc4ad6d07503661"
+checksum = "a652edd001c53df0b3f96a36a8dc93fce6866988efc16808235653c6bcac8bf2"
 dependencies = [
  "bytemuck",
  "byteorder",
@@ -1457,9 +1487,9 @@ dependencies = [
 
 [[package]]
 name = "rocksdb"
-version = "0.22.0"
+version = "0.23.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "6bd13e55d6d7b8cd0ea569161127567cd587676c99f4472f779a0279aa60a7a7"
+checksum = "26ec73b20525cb235bad420f911473b69f9fe27cc856c5461bccd7e4af037f43"
 dependencies = [
  "libc",
  "librocksdb-sys",
@@ -1580,9 +1610,9 @@ dependencies = [
 
 [[package]]
 name = "serde_json"
-version = "1.0.134"
+version = "1.0.137"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d00f4175c42ee48b15416f6193a959ba3a0d67fc699a0db9ad12df9f83991c7d"
+checksum = "930cfb6e6abf99298aaad7d29abbef7a9999a9a8806a40088f55f0dcec03146b"
 dependencies = [
  "itoa",
  "memchr",
@@ -1643,10 +1673,10 @@ dependencies = [
  "enum_dispatch",
  "finch",
  "fixedbitset",
- "getrandom",
+ "getrandom 0.2.15",
  "getset",
  "histogram",
- "itertools 0.13.0",
+ "itertools 0.14.0",
  "js-sys",
  "log",
  "md5",
@@ -1661,7 +1691,7 @@ dependencies = [
  "piz",
  "primal-check",
  "proptest",
- "rand",
+ "rand 0.9.0",
  "rayon",
  "rkyv",
  "roaring",
@@ -1672,7 +1702,7 @@ dependencies = [
  "statrs",
  "streaming-stats",
  "tempfile",
- "thiserror 2.0.9",
+ "thiserror 2.0.11",
  "twox-hash",
  "typed-builder",
  "vec-collections",
@@ -1696,7 +1726,7 @@ dependencies = [
  "approx",
  "nalgebra",
  "num-traits",
- "rand",
+ "rand 0.8.5",
 ]
 
 [[package]]
@@ -1738,12 +1768,13 @@ checksum = "55937e1799185b12863d447f42597ed69d9928686b8d88a1df17376a097d8369"
 
 [[package]]
 name = "tempfile"
-version = "3.14.0"
+version = "3.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "28cce251fcbc87fac86a866eeb0d6c2d536fc16d06f184bb61aeae11aa4cee0c"
+checksum = "9a8a559c81686f576e8cd0290cd2a24a2a9ad80c98b3478856500fcbd7acd704"
 dependencies = [
  "cfg-if",
  "fastrand",
+ "getrandom 0.2.15",
  "once_cell",
  "rustix 0.38.40",
  "windows-sys 0.59.0",
@@ -1769,11 +1800,11 @@ dependencies = [
 
 [[package]]
 name = "thiserror"
-version = "2.0.9"
+version = "2.0.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "f072643fd0190df67a8bab670c20ef5d8737177d6ac6b2e9a236cb096206b2cc"
+checksum = "d452f284b73e6d76dd36758a0c8684b1d5be31f92b89d07fd5822175732206fc"
 dependencies = [
- "thiserror-impl 2.0.9",
+ "thiserror-impl 2.0.11",
 ]
 
 [[package]]
@@ -1789,9 +1820,9 @@ dependencies = [
 
 [[package]]
 name = "thiserror-impl"
-version = "2.0.9"
+version = "2.0.11"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7b50fa271071aae2e6ee85f842e2e28ba8cd2c5fb67f11fcb1fd70b276f9e7d4"
+checksum = "26afc1baea8a989337eeb52b6e72a039780ce45c3edfcc9c5b9d112feeb173c2"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1830,7 +1861,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "97fee6b57c6a41524a810daee9286c02d7752c4253064d0b05472833a438f675"
 dependencies = [
  "cfg-if",
- "rand",
+ "rand 0.8.5",
  "static_assertions",
 ]
 
@@ -1928,6 +1959,15 @@ version = "0.11.0+wasi-snapshot-preview1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
+[[package]]
+name = "wasi"
+version = "0.13.3+wasi-0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "26816d2e1a4a36a2940b96c5296ce403917633dff8f3440e9b236ed6f6bacad2"
+dependencies = [
+ "wit-bindgen-rt",
+]
+
 [[package]]
 name = "wasm-bindgen"
 version = "0.2.97"
@@ -2219,6 +2259,15 @@ version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
 
+[[package]]
+name = "wit-bindgen-rt"
+version = "0.33.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3268f3d866458b787f390cf61f4bbb563b922d091359f9608842999eaee3943c"
+dependencies = [
+ "bitflags 2.4.1",
+]
+
 [[package]]
 name = "wyz"
 version = "0.5.1"
@@ -2243,6 +2292,26 @@ version = "1.0.0-rc.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1367295b8f788d371ce2dbc842c7b709c73ee1364d30351dd300ec2203b12377"
 
+[[package]]
+name = "zerocopy"
+version = "0.8.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a367f292d93d4eab890745e75a778da40909cab4d6ff8173693812f79c4a2468"
+dependencies = [
+ "zerocopy-derive",
+]
+
+[[package]]
+name = "zerocopy-derive"
+version = "0.8.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d3931cb58c62c13adec22e38686b559c86a30565e16ad6e8510a337cedc611e1"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.87",
+]
+
 [[package]]
 name = "zstd-sys"
 version = "2.0.7+zstd.1.5.4"
diff --git a/README.md b/README.md
index b62f0534fa..6244a56df2 100644
--- a/README.md
+++ b/README.md
@@ -13,6 +13,7 @@ Quickly search, compare, and analyze genomic and metagenomic data sets.
 [![Bioconda install](https://img.shields.io/conda/dn/bioconda/sourmash.svg?style=flag&label=Bioconda)](https://anaconda.org/bioconda/sourmash)
 <a href="https://pypi.org/project/sourmash/"><img alt="PyPI" src="https://badge.fury.io/py/sourmash.svg"></a>
 [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/sourmash-minimal.svg)](https://anaconda.org/conda-forge/sourmash-minimal)
+[![Debian Testing](https://badges.debian.net/badges/debian/testing/sourmash/version.svg)](https://packages.debian.org/testing/sourmash) [![Debian Unstable](https://badges.debian.net/badges/debian/unstable/sourmash/version.svg)](https://packages.debian.org/unstable/sourmash)
 
 ![Python 3.10](https://img.shields.io/badge/python-3.10-blue.svg)
 ![Python 3.11](https://img.shields.io/badge/python-3.11-blue.svg)
diff --git a/doc/release.md b/doc/release.md
index f3f19dcec9..b2cf777ee1 100644
--- a/doc/release.md
+++ b/doc/release.md
@@ -11,14 +11,14 @@ Here's a checklist to copy/paste into an issue:
 
 Release candidate testing:
 - [ ] Command line tests pass for a release candidate
-- [ ] All eight release candidate wheels are built
+- [ ] All six release candidate wheels are built
 
 Releasing to PyPI:
 
 - [ ] RC tag(s)s deleted on github
 - [ ] Release tag cut
 - [ ] Release notes written
-- [ ] All eight release wheels built
+- [ ] All six release wheels built
 - [ ] Release wheels uploaded to pypi
 - [ ] tar.gz distribution uploaded to pypi
 
@@ -46,7 +46,7 @@ conda version with `conda --version` and update with `conda update conda`.
 Create the basic build environment:
 
 ```
-mamba create -y -n sourmash-rc python=3.10 pip \
+mamba create -y -n sourmash-rc python=3.12 pip \
     cxx-compiler make twine tox tox-conda rust
 ```
 
diff --git a/flake.lock b/flake.lock
index 41f929d8e7..eb0632cfe2 100644
--- a/flake.lock
+++ b/flake.lock
@@ -2,11 +2,11 @@
   "nodes": {
     "nixpkgs": {
       "locked": {
-        "lastModified": 1728979988,
-        "narHash": "sha256-GBJRnbFLDg0y7ridWJHAP4Nn7oss50/VNgqoXaf/RVk=",
+        "lastModified": 1736241350,
+        "narHash": "sha256-CHd7yhaDigUuJyDeX0SADbTM9FXfiWaeNyY34FL1wQU=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "7881fbfd2e3ed1dfa315fca889b2cfd94be39337",
+        "rev": "8c9fd3e564728e90829ee7dbac6edc972971cd0f",
         "type": "github"
       },
       "original": {
@@ -30,11 +30,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1729184663,
-        "narHash": "sha256-uNyi5vQrzaLkt4jj6ZEOs4+4UqOAwP6jFG2s7LIDwIk=",
+        "lastModified": 1736303309,
+        "narHash": "sha256-IKrk7RL+Q/2NC6+Ql6dwwCNZI6T6JH2grTdJaVWHF0A=",
         "owner": "oxalica",
         "repo": "rust-overlay",
-        "rev": "16fb78d443c1970dda9a0bbb93070c9d8598a925",
+        "rev": "a0b81d4fa349d9af1765b0f0b4a899c13776f706",
         "type": "github"
       },
       "original": {
@@ -63,11 +63,11 @@
         "systems": "systems"
       },
       "locked": {
-        "lastModified": 1726560853,
-        "narHash": "sha256-X6rJYSESBVr3hBoH0WbKE5KvhPU5bloyZ2L4K60/fPQ=",
+        "lastModified": 1731533236,
+        "narHash": "sha256-l0KFg5HjrsfsO/JpG+r7fRrqm12kzFHyUHqHCVpMMbI=",
         "owner": "numtide",
         "repo": "flake-utils",
-        "rev": "c1dfcf08411b08f6b8615f7d8971a2bfa81d5e8a",
+        "rev": "11707dc2f618dd54ca8739b309ec4fc024de578b",
         "type": "github"
       },
       "original": {
diff --git a/flake.nix b/flake.nix
index 732f4b59de..0a254e1016 100644
--- a/flake.nix
+++ b/flake.nix
@@ -21,8 +21,9 @@
         };
         rustVersion = pkgs.rust-bin.stable.latest.default.override {
           #extensions = [ "rust-src" ];
+          extensions = [ "llvm-tools-preview" ];
           #targets = [ "x86_64-unknown-linux-musl" ];
-          targets = [ "wasm32-wasi" "wasm32-unknown-unknown" "wasm32-unknown-emscripten" ];
+          targets = [ "wasm32-unknown-unknown" "wasm32-unknown-emscripten" ];
         };
         rustPlatform = pkgs.makeRustPlatform {
           cargo = rustVersion;
@@ -62,7 +63,7 @@
 
           sourmash = python.buildPythonPackage ( commonArgs // rec {
             pname = "sourmash";
-            version = "4.8.12";
+            version = "4.8.14";
             format = "pyproject";
 
             cargoDeps = rustPlatform.importCargoLock {
@@ -106,7 +107,7 @@
             (python311.withPackages (ps: with ps; [ virtualenv tox cffi ]))
             (python310.withPackages (ps: with ps; [ virtualenv ]))
 
-            rust-cbindgen
+            #rust-cbindgen
             maturin
 
             wasmtime
@@ -122,9 +123,11 @@
             cargo-outdated
             cargo-udeps
             cargo-deny
-            cargo-wasi
+            cargo-nextest
+            #cargo-llvm-cov
+            cargo-component
             cargo-codspeed
-            cargo-semver-checks
+            #cargo-semver-checks
             nixpkgs-fmt
           ];
 
diff --git a/pyproject.toml b/pyproject.toml
index c9d5c84615..54555b8aa7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ build-backend = 'maturin'
 name = "sourmash"
 description = "tools for comparing biological sequences with k-mer sketches"
 readme = "README.md"
-version = "4.8.12"
+version = "4.8.15-dev"
 
 authors = [
   { name="Luiz Irber" },
diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml
index 5bf4bf6fa1..7802b137d5 100644
--- a/src/core/Cargo.toml
+++ b/src/core/Cargo.toml
@@ -11,7 +11,7 @@ edition = "2021"
 readme = "README.md"
 autoexamples = false
 autobins = false
-rust-version = "1.66.0"
+rust-version = "1.71.1"
 
 [lib]
 name = "sourmash"
@@ -36,10 +36,10 @@ csv = "1.3.1"
 enum_dispatch = "0.3.13"
 finch = { version = "0.6.0", optional = true }
 fixedbitset = "0.4.0"
-getset = "0.1.3"
-histogram = "0.11.1"
-itertools = "0.13.0"
-log = "0.4.22"
+getset = "0.1.4"
+histogram = "0.11.2"
+itertools = "0.14.0"
+log = "0.4.25"
 md5 = "0.7.0"
 memmap2 = "0.9.5"
 murmurhash3 = "0.0.5"
@@ -48,15 +48,15 @@ niffler = { version = "2.4.0", default-features = false, features = [ "gz" ] }
 nohash-hasher = "0.2.0"
 num-iter = "0.1.45"
 once_cell = "1.18.0"
-ouroboros = "0.18.4"
+ouroboros = "0.18.5"
 piz = "0.5.0"
 primal-check = "0.3.4"
 rayon = { version = "1.10.0", optional = true }
 rkyv = { version = "0.7.44", optional = true }
-roaring = "0.10.9"
+roaring = "0.10.10"
 roots = "0.0.8"
 serde = { version = "1.0.217", features = ["derive"] }
-serde_json = "1.0.134"
+serde_json = "1.0.137"
 statrs = "0.18.0"
 streaming-stats = "0.2.3"
 thiserror = "2.0"
@@ -67,8 +67,8 @@ vec-collections = "0.4.3"
 [dev-dependencies]
 codspeed-criterion-compat = "2.7.2"
 proptest = { version = "1.6.0", default-features = false, features = ["std"]}
-rand = "0.8.2"
-tempfile = "3.14.0"
+rand = "0.9.0"
+tempfile = "3.15.0"
 
 [[bench]]
 name = "compute"
@@ -108,7 +108,11 @@ chrono = { version = "0.4.32", features = ["wasmbind"] }
 wasm-bindgen-test = "0.3.42"
 
 ### These crates don't compile on wasm
-[target.'cfg(not(target_arch = "wasm32"))'.dependencies]
-rocksdb = { version = "0.22.0", optional = true }
+[target.'cfg(not(target_arch = "wasm32"))'.dependencies.rocksdb]
+version = "0.23.0"
+optional = true
+default-features = false
+features = [ "bindgen-runtime", "snappy", "zstd" ]
+
 [target.'cfg(not(target_arch = "wasm32"))'.dev-dependencies]
 criterion = "0.5.1"
diff --git a/src/core/README.md b/src/core/README.md
index 0fa56ad29b..64594342f5 100644
--- a/src/core/README.md
+++ b/src/core/README.md
@@ -38,4 +38,4 @@ Development happens on github at
 
 ## Minimum supported Rust version
 
-Currently the minimum supported Rust version is 1.66.0.
+Currently the minimum supported Rust version is 1.71.1.
diff --git a/src/core/src/encodings.rs b/src/core/src/encodings.rs
index 06af5d03c1..e55977c5bc 100644
--- a/src/core/src/encodings.rs
+++ b/src/core/src/encodings.rs
@@ -1,6 +1,6 @@
 use serde::{Deserialize, Serialize};
 use std::collections::HashMap;
-use std::hash::{BuildHasher, BuildHasherDefault, Hash, Hasher};
+use std::hash::{BuildHasher, BuildHasherDefault, Hash};
 use std::str;
 
 use nohash_hasher::BuildNoHashHasher;
@@ -469,9 +469,7 @@ impl Colors {
 
     fn compute_color(idxs: &IdxTracker) -> Color {
         let s = BuildHasherDefault::<twox_hash::Xxh3Hash128>::default();
-        let mut hasher = s.build_hasher();
-        idxs.0.hash(&mut hasher);
-        hasher.finish()
+        s.hash_one(&idxs.0)
     }
 
     pub fn len(&self) -> usize {
diff --git a/src/core/src/index/revindex/disk_revindex.rs b/src/core/src/index/revindex/disk_revindex.rs
index dbc2b50ba7..e534a4f636 100644
--- a/src/core/src/index/revindex/disk_revindex.rs
+++ b/src/core/src/index/revindex/disk_revindex.rs
@@ -1,5 +1,5 @@
 use std::cmp::max;
-use std::hash::{BuildHasher, BuildHasherDefault, Hash, Hasher};
+use std::hash::{BuildHasher, BuildHasherDefault};
 use std::path::Path;
 use std::sync::atomic::{AtomicUsize, Ordering};
 use std::sync::{Arc, RwLock};
@@ -30,9 +30,7 @@ const DB_VERSION: u8 = 1;
 
 fn compute_color(idxs: &Datasets) -> Color {
     let s = BuildHasherDefault::<twox_hash::Xxh3Hash128>::default();
-    let mut hasher = s.build_hasher();
-    idxs.hash(&mut hasher);
-    hasher.finish()
+    s.hash_one(idxs)
 }
 
 #[derive(Clone)]
@@ -354,8 +352,7 @@ impl RevIndexOps for RevIndex {
 
                     let name = [row.name(), row.filename(), row.md5()]
                         .into_iter()
-                        .skip_while(|v| v.is_empty())
-                        .next()
+                        .find(|v| !v.is_empty())
                         .unwrap(); // guaranteed to succeed because `md5` always exists
 
                     Some((name.into(), size))
diff --git a/src/sourmash/cli/compare.py b/src/sourmash/cli/compare.py
index 45844aaa1d..aca5863c78 100644
--- a/src/sourmash/cli/compare.py
+++ b/src/sourmash/cli/compare.py
@@ -92,7 +92,7 @@ def subparser(subparsers):
     subparser.add_argument(
         "--csv",
         metavar="F",
-        help="write matrix to specified file in CSV format (with column " "headers)",
+        help="write matrix to specified file in CSV format (with column headers)",
     )
     subparser.add_argument(
         "--labels-to",
diff --git a/src/sourmash/cli/compute.py b/src/sourmash/cli/compute.py
index cfdb48f42a..f5f20647c1 100644
--- a/src/sourmash/cli/compute.py
+++ b/src/sourmash/cli/compute.py
@@ -105,7 +105,7 @@ def subparser(subparsers):
         type=str,
         default="",
         metavar="FILE",
-        help="merge all input files into one signature file with the " "specified name",
+        help="merge all input files into one signature file with the specified name",
     )
     file_args.add_argument(
         "--name-from-first",
diff --git a/src/sourmash/cli/gather.py b/src/sourmash/cli/gather.py
index 159d8c2c0e..2f449aca7f 100644
--- a/src/sourmash/cli/gather.py
+++ b/src/sourmash/cli/gather.py
@@ -100,8 +100,7 @@ def subparser(subparsers):
     subparser.add_argument(
         "--save-matches",
         metavar="FILE",
-        help="save gather matched signatures from the database to the "
-        "specified file",
+        help="save gather matched signatures from the database to the specified file",
     )
     subparser.add_argument(
         "--save-prefetch",
diff --git a/src/sourmash/cli/prefetch.py b/src/sourmash/cli/prefetch.py
index 55ee063d0b..30d7fcc96d 100644
--- a/src/sourmash/cli/prefetch.py
+++ b/src/sourmash/cli/prefetch.py
@@ -58,12 +58,12 @@ def subparser(subparsers):
     subparser.add_argument(
         "--save-unmatched-hashes",
         metavar="FILE",
-        help="output unmatched query hashes as a signature to the " "specified file",
+        help="output unmatched query hashes as a signature to the specified file",
     )
     subparser.add_argument(
         "--save-matching-hashes",
         metavar="FILE",
-        help="output matching query hashes as a signature to the " "specified file",
+        help="output matching query hashes as a signature to the specified file",
     )
     subparser.add_argument(
         "--md5", default=None, help="select the signature with this md5 as query"
diff --git a/src/sourmash/command_compute.py b/src/sourmash/command_compute.py
index 78edc8dcaa..e3eede0715 100644
--- a/src/sourmash/command_compute.py
+++ b/src/sourmash/command_compute.py
@@ -78,10 +78,10 @@ def compute(args):
         notify("Computing both nucleotide and protein signatures.")
         num_sigs = 2 * len(ksizes)
     elif args.dna and args.dayhoff:
-        notify("Computing both nucleotide and Dayhoff-encoded protein " "signatures.")
+        notify("Computing both nucleotide and Dayhoff-encoded protein signatures.")
         num_sigs = 2 * len(ksizes)
     elif args.dna and args.hp:
-        notify("Computing both nucleotide and hp-encoded protein " "signatures.")
+        notify("Computing both nucleotide and hp-encoded protein signatures.")
         num_sigs = 2 * len(ksizes)
     elif args.dna:
         notify("Computing only nucleotide (and not protein) signatures.")
@@ -91,11 +91,11 @@ def compute(args):
         num_sigs = len(ksizes)
     elif args.dayhoff:
         notify(
-            "Computing only Dayhoff-encoded protein (and not nucleotide) " "signatures."
+            "Computing only Dayhoff-encoded protein (and not nucleotide) signatures."
         )
         num_sigs = len(ksizes)
     elif args.hp:
-        notify("Computing only hp-encoded protein (and not nucleotide) " "signatures.")
+        notify("Computing only hp-encoded protein (and not nucleotide) signatures.")
         num_sigs = len(ksizes)
 
     if args.protein or args.dayhoff or args.hp:
@@ -269,7 +269,7 @@ def _compute_individual(args, signatures_factory):
                 save_sigs_to_location(sigs, save_sigs)
 
                 notify(
-                    f"calculated {len(sigs)} signatures for {n+1} sequences in {filename}"
+                    f"calculated {len(sigs)} signatures for {n + 1} sequences in {filename}"
                 )
 
         # if not args.output, close output for every input filename.
@@ -443,7 +443,7 @@ def to_param_str(self):
             kstr = [f"k={k}" for k in self.ksizes]
         else:
             # for protein, divide ksize by three.
-            kstr = [f"k={k//3}" for k in self.ksizes]
+            kstr = [f"k={k // 3}" for k in self.ksizes]
         assert kstr
         pi.extend(kstr)
 
diff --git a/src/sourmash/command_sketch.py b/src/sourmash/command_sketch.py
index d962d2ec77..d7aeba3588 100644
--- a/src/sourmash/command_sketch.py
+++ b/src/sourmash/command_sketch.py
@@ -207,7 +207,7 @@ def _execute_sketch(args, signatures_factory):
         error("error: sourmash only supports CC0-licensed signatures. sorry!")
         sys.exit(-1)
 
-    notify(f'computing signatures for files: {", ".join(args.filenames)}')
+    notify(f"computing signatures for files: {', '.join(args.filenames)}")
 
     if args.merge and not args.output:
         error("ERROR: must specify -o with --merge")
@@ -353,7 +353,7 @@ def _compute_sigs(to_build, output, *, check_sequence=False):
                 save_sigs.add(sig)
 
             notify(
-                f"calculated {len(sigs)} signatures for {n+1} sequences in {filename}"
+                f"calculated {len(sigs)} signatures for {n + 1} sequences in {filename}"
             )
 
     save_sigs.close()
@@ -768,7 +768,7 @@ def _compute_individual(args, signatures_factory):
                 save_sigs_to_location(sigs, save_sigs)
 
                 notify(
-                    f"calculated {len(sigs)} signatures for {n+1} sequences in {filename}"
+                    f"calculated {len(sigs)} signatures for {n + 1} sequences in {filename}"
                 )
 
         # if not args.output, close output for every input filename.
@@ -942,7 +942,7 @@ def to_param_str(self):
             kstr = [f"k={k}" for k in self.ksizes]
         else:
             # for protein, divide ksize by three.
-            kstr = [f"k={k//3}" for k in self.ksizes]
+            kstr = [f"k={k // 3}" for k in self.ksizes]
         assert kstr
         pi.extend(kstr)
 
diff --git a/src/sourmash/commands.py b/src/sourmash/commands.py
index 26661f4317..147de9fb3f 100644
--- a/src/sourmash/commands.py
+++ b/src/sourmash/commands.py
@@ -1077,7 +1077,7 @@ def gather(args):
             )
 
         print_results(
-            f"the recovered matches hit {sum_f_uniq_found*100:.1f}% of the query k-mers (unweighted)."
+            f"the recovered matches hit {sum_f_uniq_found * 100:.1f}% of the query k-mers (unweighted)."
         )
 
     print_results("")
@@ -1345,7 +1345,7 @@ def multigather(args):
                 )
 
             print_results(
-                f"the recovered matches hit {sum_f_uniq_found*100:.1f}% of the query k-mers (unweighted)."
+                f"the recovered matches hit {sum_f_uniq_found * 100:.1f}% of the query k-mers (unweighted)."
             )
             print_results("")
 
diff --git a/src/sourmash/distance_utils.py b/src/sourmash/distance_utils.py
index ad267bd0fe..41c325ccfa 100644
--- a/src/sourmash/distance_utils.py
+++ b/src/sourmash/distance_utils.py
@@ -16,7 +16,7 @@
 
 def check_distance(dist):
     if not 0 <= dist <= 1:
-        raise ValueError(f"Error: distance value {dist :.4f} is not between 0 and 1!")
+        raise ValueError(f"Error: distance value {dist:.4f} is not between 0 and 1!")
     else:
         return dist
 
diff --git a/src/sourmash/minhash.py b/src/sourmash/minhash.py
index c036fa6c3d..448f64c00d 100644
--- a/src/sourmash/minhash.py
+++ b/src/sourmash/minhash.py
@@ -742,6 +742,8 @@ def downsample(self, *, num=None, scaled=None):
             is_protein=self.is_protein,
             dayhoff=self.dayhoff,
             hp=self.hp,
+            skipm1n3=self.skipm1n3,
+            skipm2n3=self.skipm2n3,
             track_abundance=self.track_abundance,
             seed=self.seed,
             max_hash=max_hash,
@@ -764,6 +766,8 @@ def flatten(self):
                 is_protein=self.is_protein,
                 dayhoff=self.dayhoff,
                 hp=self.hp,
+                skipm1n3=self.skipm1n3,
+                skipm2n3=self.skipm2n3,
                 track_abundance=False,
                 seed=self.seed,
                 max_hash=self._max_hash,
diff --git a/src/sourmash/plugins.py b/src/sourmash/plugins.py
index 0871154f2d..fe9b073563 100644
--- a/src/sourmash/plugins.py
+++ b/src/sourmash/plugins.py
@@ -198,7 +198,7 @@ def list_all_plugins():
     notify(
         f"{'plugin type':<20s} {'from python module':<30s} {'v':<5s} {'entry point name':<20s}"
     )
-    notify(f"{'-'*20} {'-'*30} {'-'*5} {'-'*20}")
+    notify(f"{'-' * 20} {'-' * 30} {'-' * 5} {'-' * 20}")
 
     for plugin in plugins:
         name = plugin.name
diff --git a/src/sourmash/sbt.py b/src/sourmash/sbt.py
index 21e6b25c16..6ca4a746d7 100644
--- a/src/sourmash/sbt.py
+++ b/src/sourmash/sbt.py
@@ -763,7 +763,9 @@ def save(self, path, storage=None, sparseness=0.0, structure_only=False):
                     manifest_rows.append(row)
 
             if n % 100 == 0:
-                notify(f"{format(n+1)} of {format(total_nodes)} nodes saved", end="\r")
+                notify(
+                    f"{format(n + 1)} of {format(total_nodes)} nodes saved", end="\r"
+                )
 
         # now, save the index file and manifests.
         #
diff --git a/src/sourmash/sig/__main__.py b/src/sourmash/sig/__main__.py
index e63fc433a4..dcc166f701 100644
--- a/src/sourmash/sig/__main__.py
+++ b/src/sourmash/sig/__main__.py
@@ -1298,7 +1298,7 @@ def kmers(args):
     found_hashes = set(found_mh.hashes)
     cont = len(query_hashes.intersection(found_hashes)) / len(query_hashes)
 
-    notify(f"found {len(found_mh)} distinct matching hashes ({cont*100:.1f}%)")
+    notify(f"found {len(found_mh)} distinct matching hashes ({cont * 100:.1f}%)")
 
     if not kmer_w and not save_seqs:
         notify("NOTE: see --save-kmers or --save-sequences for output options.")
diff --git a/src/sourmash/tax/__main__.py b/src/sourmash/tax/__main__.py
index c4e22d07fa..8d3692011e 100644
--- a/src/sourmash/tax/__main__.py
+++ b/src/sourmash/tax/__main__.py
@@ -93,7 +93,7 @@ def metagenome(args):
 
     if not tax_assign:
         error(
-            f'ERROR: No taxonomic assignments loaded from {",".join(args.taxonomy_csv)}. Exiting.'
+            f"ERROR: No taxonomic assignments loaded from {','.join(args.taxonomy_csv)}. Exiting."
         )
         sys.exit(-1)
 
@@ -284,7 +284,7 @@ def genome(args):
 
     if not tax_assign:
         error(
-            f'ERROR: No taxonomic assignments loaded from {",".join(args.taxonomy_csv)}. Exiting.'
+            f"ERROR: No taxonomic assignments loaded from {','.join(args.taxonomy_csv)}. Exiting."
         )
         sys.exit(-1)
 
@@ -345,7 +345,7 @@ def genome(args):
     else:
         classif_perc = (float(n_classified) / float(n_total)) * 100
         notify(
-            f"classified {n_classified}/{n_total} queries ({classif_perc :.2f}%). Writing results"
+            f"classified {n_classified}/{n_total} queries ({classif_perc:.2f}%). Writing results"
         )
 
     # write outputs
@@ -442,7 +442,7 @@ def annotate(args):
 
     if not tax_assign:
         error(
-            f'ERROR: No taxonomic assignments loaded from {",".join(args.taxonomy_csv)}. Exiting.'
+            f"ERROR: No taxonomic assignments loaded from {','.join(args.taxonomy_csv)}. Exiting."
         )
         sys.exit(-1)
 
@@ -518,7 +518,7 @@ def annotate(args):
                         )
                     else:
                         notify(
-                            f"Annotated {rows_annotated} of {n+1} total rows from '{in_csv}'."
+                            f"Annotated {rows_annotated} of {n + 1} total rows from '{in_csv}'."
                         )
 
         except ValueError as exc:
diff --git a/src/sourmash/tax/tax_utils.py b/src/sourmash/tax/tax_utils.py
index 60a967c6b4..8ad43c3b36 100644
--- a/src/sourmash/tax/tax_utils.py
+++ b/src/sourmash/tax/tax_utils.py
@@ -22,8 +22,8 @@
     "ascending_taxlist",
     "collect_gather_csvs",
     "load_gather_results",
-    "check_and_load_gather_csvs" "report_missing_and_skipped_identities",
-    "aggregate_by_lineage_at_rank" "format_for_krona",
+    "check_and_load_gather_csvsreport_missing_and_skipped_identities",
+    "aggregate_by_lineage_at_rankformat_for_krona",
     "write_output",
     "write_bioboxes",
     "parse_lingroups",
@@ -793,7 +793,7 @@ def read_lingroups(lingroup_csv):
     if n is None:
         raise ValueError(f"No lingroups loaded from {lingroup_csv}.")
     n_lg = len(lingroupD.keys())
-    notify(f"Read {n+1} lingroup rows and found {n_lg} distinct lingroup prefixes.")
+    notify(f"Read {n + 1} lingroup rows and found {n_lg} distinct lingroup prefixes.")
     return lingroupD
 
 
@@ -978,7 +978,7 @@ def report_missing_and_skipped_identities(gather_results):
             f"of {total_taxresults} gather results, lineage assignments for {total_n_missed} results were missed."
         )
         notify(
-            f'The following are missing from the taxonomy information: {", ".join(ident_missed)}'
+            f"The following are missing from the taxonomy information: {', '.join(ident_missed)}"
         )
 
 
@@ -2106,9 +2106,9 @@ def as_summary_dict(self, query_info, limit_float=False, lingroups=None):
 
     def as_human_friendly_dict(self, query_info):
         sD = self.as_summary_dict(query_info=query_info, limit_float=True)
-        sD["f_weighted_at_rank"] = f"{self.f_weighted_at_rank*100:>4.1f}%"
+        sD["f_weighted_at_rank"] = f"{self.f_weighted_at_rank * 100:>4.1f}%"
         if self.query_ani_at_rank is not None:
-            sD["query_ani_at_rank"] = f"{self.query_ani_at_rank*100:>3.1f}%"
+            sD["query_ani_at_rank"] = f"{self.query_ani_at_rank * 100:>3.1f}%"
         else:
             sD["query_ani_at_rank"] = "-    "
         return sD
diff --git a/tests/test_sourmash_compute.py b/tests/test_sourmash_compute.py
index 35f5635237..172b520d07 100644
--- a/tests/test_sourmash_compute.py
+++ b/tests/test_sourmash_compute.py
@@ -453,8 +453,7 @@ def test_do_sourmash_compute_multik_with_hp():
             in_directory=location,
         )
         assert (
-            "Computing only hp-encoded protein (and not nucleotide) "
-            "signatures." in err
+            "Computing only hp-encoded protein (and not nucleotide) signatures." in err
         )
         outfile = os.path.join(location, "short.fa.sig")
         assert os.path.exists(outfile)
diff --git a/tests/test_tax_utils.py b/tests/test_tax_utils.py
index dfca20628a..34c4743b7c 100644
--- a/tests/test_tax_utils.py
+++ b/tests/test_tax_utils.py
@@ -2221,7 +2221,7 @@ def test_RankLineageInfo_init_lineage_str_2():
     taxinf = RankLineageInfo(lineage_str=x)
     print(taxinf.lineage)
     print(taxinf.lineage_str)
-    assert taxinf.zip_lineage() == ["a", "b", "", "c" "", "", "", "", ""]
+    assert taxinf.zip_lineage() == ["a", "b", "", "c", "", "", "", ""]
 
 
 def test_RankLineageInfo_init_lineage_str_2_truncate():