diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
index 332b443f76..c156659b33 100644
--- a/.github/workflows/build_wheel.yml
+++ b/.github/workflows/build_wheel.yml
@@ -31,7 +31,7 @@ jobs:
           - build: macos-arm64
             os: macos-latest
             arch: arm64
-            macos_target: 'MACOSX_DEPLOYMENT_TARGET=11 CARGO_BUILD_TARGET=aarch64-apple-darwin'
+            macos_target: 'MACOSX_DEPLOYMENT_TARGET=11.0 CARGO_BUILD_TARGET=aarch64-apple-darwin'
       fail-fast: false
 
     steps:
diff --git a/.github/workflows/dev_envs.yml b/.github/workflows/dev_envs.yml
index c53aa38695..1cdf1fffb8 100644
--- a/.github/workflows/dev_envs.yml
+++ b/.github/workflows/dev_envs.yml
@@ -11,25 +11,14 @@ jobs:
       with:
         fetch-depth: 0
 
-    - name: Cache nix store
-      id: cache-nix
-      uses: actions/cache@v3
+    - uses: cachix/install-nix-action@v18
       with:
-        path: |
-          ~/.nix-portable/store
-          ~/bin/nix-portable
-        key: nix-${{ hashFiles('shell.nix') }}-${{ hashFiles('nix/**') }}-v009
-
-    - name: Install nix-portable
-      if: steps.cache-nix.outputs.cache-hit != 'true'
-      run: |
-        mkdir ~/bin
-        wget -qO ~/bin/nix-portable https://github.com/DavHau/nix-portable/releases/download/v009/nix-portable
-        chmod +x ~/bin/nix-portable
+        extra_nix_config: |
+          access-tokens = github.com=${{ secrets.GITHUB_TOKEN }}
 
-    - run: ~/bin/nix-portable nix-shell --command "tox -e py39"
+    - run: nix run .# -- --version
 
-    - run: ~/bin/nix-portable nix run . -- --version
+    - run: nix-shell --command "tox -e py39"
 
   mamba:
     runs-on: ubuntu-latest
diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
index c97a62e6bf..a67a75c130 100644
--- a/.github/workflows/python.yml
+++ b/.github/workflows/python.yml
@@ -1,4 +1,4 @@
-# note: to invalidate caches, adjust the pip-v? and tox-v? numbers below.
+# note: to invalidate caches, adjust the pip-v? number below.
 name: Python tests
 
 on:
@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, macos-latest]
-        py: ["3.10", "3.9", "3.8"]
+        py: ["3.11", "3.10", "3.9", "3.8"]
       fail-fast: false
 
     steps:
@@ -36,7 +36,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ steps.pip-cache.outputs.dir }}
-          key: ${{ runner.os }}-pip-v4-${{ hashFiles('**/setup.cfg') }}
+          key: ${{ runner.os }}-pip-v4-${{ hashFiles('**/pyproject.toml') }}
           restore-keys: |
             ${{ runner.os }}-pip-v4-
 
@@ -65,7 +65,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: .tox/
-          key: ${{ runner.os }}-tox-v4-${{ hashFiles('**/setup.cfg') }}
+          key: ${{ runner.os }}-tox-v4-${{ hashFiles('**/pyproject.toml') }}
           restore-keys: |
             ${{ runner.os }}-tox-v4-
 
diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 32bf8e195a..2cb8c93feb 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -268,26 +268,17 @@ jobs:
 
       - uses: actions-rs/toolchain@v1
         with:
-          toolchain: 1.48.0
+          toolchain: 1.56.1
           override: true
 
       - name: check if README matches MSRV defined here
-        run: grep '1.48.0' src/core/README.md
-
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.8"
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install -e .
+        run: grep '1.56.1' src/core/README.md
 
       - name: Check if it builds properly
         uses: actions-rs/cargo@v1
         with:
           command: build
+          args: --all-features
 
   check_cbindgen:
     name: "Check if cbindgen runs cleanly for generating the C headers"
diff --git a/.gitignore b/.gitignore
index 968cc71d2e..23035e78c9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,7 +26,6 @@ src/sourmash/_lowlevel*.py
 Pipfile
 Pipfile.lock
 target/
-Cargo.lock
 .eggs
 .asv
 pkg/
diff --git a/asv.conf.json b/asv.conf.json
index d5687509ba..4b6770bc35 100644
--- a/asv.conf.json
+++ b/asv.conf.json
@@ -11,8 +11,7 @@
     "html_dir": ".asv/html",
     "build_cache_size": 8,
     "build_command": [
-      "python -m pip install 'setuptools_scm[toml]>=4,<6' milksnake",
-      "python setup.py build",
+      "python -m pip install 'setuptools_scm[toml]>=4,<6' milksnake maturin",
       "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}"
     ]
 }
diff --git a/flake.lock b/flake.lock
index a84e6788de..766da3bb24 100644
--- a/flake.lock
+++ b/flake.lock
@@ -1,47 +1,5 @@
 {
   "nodes": {
-    "flake-utils": {
-      "locked": {
-        "lastModified": 1642700792,
-        "narHash": "sha256-XqHrk7hFb+zBvRg6Ghl+AZDq03ov6OshJLiSWOoX5es=",
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "rev": "846b2ae0fc4cc943637d3d1def4454213e203cba",
-        "type": "github"
-      },
-      "original": {
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "type": "github"
-      }
-    },
-    "mach-nix": {
-      "inputs": {
-        "flake-utils": [
-          "utils"
-        ],
-        "nixpkgs": [
-          "nixpkgs"
-        ],
-        "pypi-deps-db": [
-          "pypi-deps-db"
-        ]
-      },
-      "locked": {
-        "lastModified": 1654084003,
-        "narHash": "sha256-j/XrVVistvM+Ua+0tNFvO5z83isL+LBgmBi9XppxuKA=",
-        "owner": "DavHau",
-        "repo": "mach-nix",
-        "rev": "7e14360bde07dcae32e5e24f366c83272f52923f",
-        "type": "github"
-      },
-      "original": {
-        "owner": "DavHau",
-        "ref": "3.5.0",
-        "repo": "mach-nix",
-        "type": "github"
-      }
-    },
     "naersk": {
       "inputs": {
         "nixpkgs": [
@@ -49,11 +7,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1662220400,
-        "narHash": "sha256-9o2OGQqu4xyLZP9K6kNe1pTHnyPz0Wr3raGYnr9AIgY=",
+        "lastModified": 1671096816,
+        "narHash": "sha256-ezQCsNgmpUHdZANDCILm3RvtO1xH8uujk/+EqNvzIOg=",
         "owner": "nix-community",
         "repo": "naersk",
-        "rev": "6944160c19cb591eb85bbf9b2f2768a935623ed3",
+        "rev": "d998160d6a076cfe8f9741e56aeec7e267e3e114",
         "type": "github"
       },
       "original": {
@@ -64,11 +22,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1664028844,
-        "narHash": "sha256-wwGqnvROHW54ma0h4q6GL5toKxTVVKvAypv0CcJkraU=",
+        "lastModified": 1671458120,
+        "narHash": "sha256-2+k/OONN4OF21TeoNjKB5sXVZv6Zvm/uEyQIW9OYCg8=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "72bdd03f0d5696412b25a93218acaad530570d30",
+        "rev": "e37ef84b478fa8da0ced96522adfd956fde9047a",
         "type": "github"
       },
       "original": {
@@ -78,64 +36,10 @@
         "type": "github"
       }
     },
-    "nixpkgs_2": {
-      "locked": {
-        "lastModified": 1643805626,
-        "narHash": "sha256-AXLDVMG+UaAGsGSpOtQHPIKB+IZ0KSd9WS77aanGzgc=",
-        "owner": "NixOS",
-        "repo": "nixpkgs",
-        "rev": "554d2d8aa25b6e583575459c297ec23750adb6cb",
-        "type": "github"
-      },
-      "original": {
-        "id": "nixpkgs",
-        "ref": "nixos-unstable",
-        "type": "indirect"
-      }
-    },
-    "pypi-deps-db": {
-      "inputs": {
-        "flake-utils": "flake-utils",
-        "nixpkgs": "nixpkgs_2",
-        "pypi-deps-db": "pypi-deps-db_2"
-      },
-      "locked": {
-        "lastModified": 1654084003,
-        "narHash": "sha256-j/XrVVistvM+Ua+0tNFvO5z83isL+LBgmBi9XppxuKA=",
-        "owner": "DavHau",
-        "repo": "mach-nix",
-        "rev": "7e14360bde07dcae32e5e24f366c83272f52923f",
-        "type": "github"
-      },
-      "original": {
-        "owner": "DavHau",
-        "ref": "3.5.0",
-        "repo": "mach-nix",
-        "type": "github"
-      }
-    },
-    "pypi-deps-db_2": {
-      "flake": false,
-      "locked": {
-        "lastModified": 1643877077,
-        "narHash": "sha256-jv8pIvRFTP919GybOxXE5TfOkrjTbdo9QiCO1TD3ZaY=",
-        "owner": "DavHau",
-        "repo": "pypi-deps-db",
-        "rev": "da53397f0b782b0b18deb72ef8e0fb5aa7c98aa3",
-        "type": "github"
-      },
-      "original": {
-        "owner": "DavHau",
-        "repo": "pypi-deps-db",
-        "type": "github"
-      }
-    },
     "root": {
       "inputs": {
-        "mach-nix": "mach-nix",
         "naersk": "naersk",
         "nixpkgs": "nixpkgs",
-        "pypi-deps-db": "pypi-deps-db",
         "rust-overlay": "rust-overlay",
         "utils": "utils"
       }
@@ -150,11 +54,11 @@
         ]
       },
       "locked": {
-        "lastModified": 1664074880,
-        "narHash": "sha256-/V1TX4HLADElvi3MuuIbNdvzR/HmNzbYRemKBjX/5YY=",
+        "lastModified": 1671503041,
+        "narHash": "sha256-PJdh3q1zzzaMzk3M6yZHUVqQSBPiF46EVfMh7L+jtEI=",
         "owner": "oxalica",
         "repo": "rust-overlay",
-        "rev": "45140fa526b1cb85498f717e355c79a54367cb1d",
+        "rev": "e4e129cf743b49b663d99abe81142d6bd213ac91",
         "type": "github"
       },
       "original": {
@@ -165,11 +69,11 @@
     },
     "utils": {
       "locked": {
-        "lastModified": 1659877975,
-        "narHash": "sha256-zllb8aq3YO3h8B/U0/J1WBgAL8EX5yWf5pMj3G0NAmc=",
+        "lastModified": 1667395993,
+        "narHash": "sha256-nuEHfE/LcWyuSWnS8t12N1wc105Qtau+/OdUAjtQ0rA=",
         "owner": "numtide",
         "repo": "flake-utils",
-        "rev": "c0e246b9b83f637f4681389ecabcb2681b4f3af0",
+        "rev": "5aed5285a952e0b949eb3ba02c12fa4fcfef535f",
         "type": "github"
       },
       "original": {
diff --git a/flake.nix b/flake.nix
index c70f48ca34..745fcbb0cc 100644
--- a/flake.nix
+++ b/flake.nix
@@ -16,28 +16,32 @@
       url = "github:nix-community/naersk";
       inputs = {
         nixpkgs.follows = "nixpkgs";
-        flake-utils.follows = "utils";
       };
     };
-
-    mach-nix = {
-      url = "github:DavHau/mach-nix/3.5.0";
-      inputs.nixpkgs.follows = "nixpkgs";
-      inputs.flake-utils.follows = "utils";
-      inputs.pypi-deps-db.follows = "pypi-deps-db";
-    };
-
-    pypi-deps-db = {
-      url = "github:DavHau/mach-nix/3.5.0";
-    };
   };
 
-  outputs = { self, nixpkgs, naersk, rust-overlay, mach-nix, pypi-deps-db, utils }:
+  outputs = { self, nixpkgs, naersk, rust-overlay, utils }:
     utils.lib.eachDefaultSystem (system:
       let
         overlays = [ (import rust-overlay) ];
         pkgs = import nixpkgs {
           inherit system overlays;
+          config.packageOverrides = pkgs:
+            {
+              maturin = pkgs.rustPlatform.buildRustPackage rec {
+                pname = "maturin";
+                version = "0.14.7";
+                src = pkgs.fetchFromGitHub {
+                  owner = "PyO3";
+                  repo = "maturin";
+                  rev = "v0.14.7";
+                  hash = "sha256-PCE4SvUrS8ass8UPc+t5Ix126Q4tB2yCMU2kWuCfr5Q=";
+                };
+                cargoHash = "sha256-ODMOJOoyra29ZeaG0yKnjPRwcjh/20VsgOz+IGZbQ/s=";
+                nativeBuildInputs = [ pkgs.pkg-config ];
+                doCheck = false;
+              };
+            };
         };
         rustVersion = pkgs.rust-bin.stable.latest.default.override {
           #extensions = [ "rust-src" ];
@@ -53,42 +57,58 @@
           rustc = rustPlatform.rust.rustc;
         };
 
-        python = "python39";
-        mach-nix-wrapper = import mach-nix { inherit pkgs python; };
+        python = pkgs.python310Packages;
+
+        screed = python.buildPythonPackage rec {
+          pname = "screed";
+          version = "1.1";
+          #format = "pyproject";
+
+          src = pkgs.fetchFromGitHub {
+            owner = "dib-lab";
+            repo = "screed";
+            rev = "v1.1";
+            hash = "sha256-g1FZJx94RGBPoTiLfwttdYqCJ02pxtOKK708WA63kHE=";
+          };
+
+          SETUPTOOLS_SCM_PRETEND_VERSION = "1.1";
+          propagatedBuildInputs = with python; [ setuptools bz2file setuptools_scm ];
+          doCheck = false;
+        };
+
       in
 
       with pkgs;
       {
         packages = {
+
           lib = naersk-lib.buildPackage {
             pname = "libsourmash";
             root = ./.;
             copyLibs = true;
           };
-          sourmash = mach-nix-wrapper.buildPythonPackage {
-            src = ./.;
+
+          sourmash = python.buildPythonPackage rec {
             pname = "sourmash";
-            version = "4.4.2";
-            requirements = ''
-              screed>=1.0.5
-              cffi>=1.14.0
-              numpy
-              matplotlib
-              scipy
-              deprecation>=2.0.6
-              cachetools<6,>=4
-              bitstring<5,>=3.1.9
-            '';
-            requirementsExtra = ''
-              setuptools >= 61
-              milksnake
-              setuptools_scm[toml] >= 4, <6
-              wheel >= 0.29.0
-            '';
-            SETUPTOOLS_SCM_PRETEND_VERSION = "4.4.2";
+            version = "4.6.1";
+            format = "pyproject";
+
+            src = ./.;
+
+            cargoDeps = rustPlatform.fetchCargoTarball {
+              inherit src;
+              name = "${pname}-${version}";
+              hash = "sha256-IaIX4RdXEhLQhne+QiSfdP1KiIwZUqxRg14uWknS+0o=";
+            };
+
+            nativeBuildInputs = with rustPlatform; [ cargoSetupHook maturinBuildHook ];
+
+            buildInputs = lib.optionals stdenv.isDarwin [ libiconv ];
+            propagatedBuildInputs = with python; [ cffi deprecation cachetools bitstring numpy scipy matplotlib screed ];
+
             DYLD_LIBRARY_PATH = "${self.packages.${system}.lib}/lib";
-            NO_BUILD = "1";
           };
+
           docker =
             let
               bin = self.defaultPackage.${system};
@@ -119,11 +139,13 @@
 
             git
             stdenv.cc.cc.lib
-            (python310.withPackages (ps: with ps; [ virtualenv tox setuptools ]))
-            (python39.withPackages (ps: with ps; [ virtualenv setuptools ]))
-            (python38.withPackages (ps: with ps; [ virtualenv setuptools ]))
+            (python310.withPackages (ps: with ps; [ virtualenv tox cffi ]))
+            (python311.withPackages (ps: with ps; [ virtualenv ]))
+            (python39.withPackages (ps: with ps; [ virtualenv ]))
+            (python38.withPackages (ps: with ps; [ virtualenv ]))
 
             rust-cbindgen
+            maturin
 
             wasmtime
             wasm-pack
diff --git a/pyproject.toml b/pyproject.toml
index 6a8b247f82..8f87a4ca5d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,17 +1,15 @@
 [build-system]
 requires = [
-    "setuptools >= 61",
-    "setuptools_scm[toml] >= 4, <6",
-    "setuptools_scm_git_archive",
-    "milksnake",
-    "wheel >= 0.29.0",
+    "maturin>=0.14.7,<0.15",
+    "cffi",
 ]
-build-backend = 'setuptools.build_meta'
+build-backend = 'maturin'
 
 [project]
 name = "sourmash"
 description = "tools for comparing biological sequences with k-mer sketches"
 readme = "README.md"
+version = "4.6.1"
 
 authors = [
   { name="Luiz Irber", orcid="0000-0003-4371-9659" },
@@ -83,7 +81,6 @@ dependencies = [
 ]
 
 requires-python = ">=3.8"
-dynamic = ["version"]
 
 [metadata]
 license = { text = "BSD 3-Clause License" }
@@ -130,19 +127,15 @@ storage = [
 # https://github.com/pypa/pip/issues/10393#issuecomment-941885429
 all = ["sourmash[test,demo,doc,storage]"]
 
-[tool.setuptools]
-zip-safe = false
-platforms = ["any"]
-
-[tool.setuptools.packages.find]
-where = ["src"]
-
-[tool.setuptools.dynamic]
-version = {attr = "sourmash.version.version"}
-
-[tool.setuptools_scm]
-write_to = "src/sourmash/version.py"
-git_describe_command = "git describe --dirty --tags --long --match v* --first-parent"
+[tool.maturin]
+python-source = "src"
+manifest-path = "src/core/Cargo.toml"
+bindings = "cffi"
+include = [
+  { path = "include/sourmash.h", format = ["sdist","wheel"] },
+]
+features = ["maturin"]
+locked = true
 
 [tool.isort]
 known_third_party = ["deprecation", "hypothesis", "mmh3", "numpy", "pkg_resources", "pytest", "screed", "setuptools", "sourmash_tst_utils"]
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 8d3cb339bd..0000000000
--- a/setup.py
+++ /dev/null
@@ -1,69 +0,0 @@
-import os
-import sys
-
-from setuptools import setup
-
-
-DEBUG_BUILD = os.environ.get("SOURMASH_DEBUG") == "1"
-NO_BUILD = os.environ.get("NO_BUILD") == "1"
-
-
-def find_dylib_no_build(name, paths):
-    to_find = None
-    if sys.platform == 'darwin':
-        to_find = f'lib{name}.dylib'
-    elif sys.platform == 'win32':
-        to_find = f'{name}.dll'
-    else:
-        to_find = f'lib{name}.so'
-
-    for path in paths.split(":"):
-        for filename in os.listdir(path):
-            if filename == to_find:
-                return os.path.join(path, filename)
-
-        raise LookupError('dylib %r not found' % name)
-
-
-def find_dylib(build, target):
-    cargo_target = os.environ.get("CARGO_BUILD_TARGET")
-    if cargo_target:
-        in_path = "target/%s/%s" % (cargo_target, target)
-    else:
-        in_path = "target/%s" % target
-    return build.find_dylib("sourmash", in_path=in_path)
-
-
-def build_native(spec):
-    cmd = ["cargo", "build",
-           "--manifest-path", "src/core/Cargo.toml",
-            # "--features", "parallel",
-           "--lib"]
-
-    target = "debug"
-    if not DEBUG_BUILD:
-        cmd.append("--release")
-        target = "release"
-
-    if NO_BUILD:
-        dylib = lambda: find_dylib_no_build("sourmash", os.environ["DYLD_LIBRARY_PATH"])
-        header_filename = lambda: "include/sourmash.h"
-    else:
-        build = spec.add_external_build(cmd=cmd, path=".")
-        dylib = lambda: find_dylib(build, target)
-        header_filename=lambda: build.find_header("sourmash.h", in_path="include")
-
-    rtld_flags = ["NOW"]
-    if sys.platform == "darwin":
-        rtld_flags.append("NODELETE")
-    spec.add_cffi_module(
-        module_path="sourmash._lowlevel",
-        dylib=dylib,
-        header_filename=header_filename,
-        rtld_flags=rtld_flags,
-    )
-
-setup(
-  milksnake_tasks=[build_native],
-  package_dir={"": "src"},
-)
diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml
index b9742b1372..820a60868e 100644
--- a/src/core/Cargo.toml
+++ b/src/core/Cargo.toml
@@ -7,10 +7,11 @@ repository = "https://github.com/sourmash-bio/sourmash"
 keywords = ["minhash", "bioinformatics"]
 categories = ["science", "algorithms", "data-structures"]
 license = "BSD-3-Clause"
-edition = "2018"
+edition = "2021"
 readme = "README.md"
 autoexamples = false
 autobins = false
+rust-version = "1.56.1"
 
 [lib]
 name = "sourmash"
@@ -20,6 +21,7 @@ bench = false
 [features]
 from-finch = ["finch"]
 parallel = ["rayon"]
+maturin = []
 
 [dependencies]
 az = "1.0.0"
@@ -89,3 +91,6 @@ wasm-bindgen-test = "0.3.31"
 
 ### These crates don't compile on wasm
 [target.'cfg(not(all(target_arch = "wasm32", target_vendor="unknown")))'.dependencies]
+
+[package.metadata.maturin]
+name = "sourmash._lowlevel"
diff --git a/src/core/README.md b/src/core/README.md
index 005d3334e5..0aee799654 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 1.48.0.
+Currently the minimum supported Rust version is 1.56.1.
diff --git a/src/core/build.rs b/src/core/build.rs
new file mode 100644
index 0000000000..a22396c25a
--- /dev/null
+++ b/src/core/build.rs
@@ -0,0 +1,75 @@
+use std::env;
+
+fn main() {
+    let crate_dir = env::var("CARGO_MANIFEST_DIR").unwrap();
+    copy_c_bindings(&crate_dir);
+}
+
+#[cfg(not(feature = "maturin"))]
+fn copy_c_bindings(_crate_dir: &str) {}
+
+#[cfg(feature = "maturin")]
+fn copy_c_bindings(crate_dir: &str) {
+    use std::path::{Path, PathBuf};
+
+    fn find_root_dir(crate_dir: &str) -> &Path {
+        let root_dir = Path::new(crate_dir);
+
+        if root_dir.join("pyproject.toml").is_file() {
+            return root_dir;
+        }
+
+        let root_dir = Path::new(crate_dir).parent().unwrap().parent().unwrap();
+        if root_dir.join("pyproject.toml").is_file() {
+            return root_dir;
+        }
+
+        panic!("Couldn't find pyproject.toml to determine root dir");
+    }
+
+    fn find_target_dir(out_dir: &str) -> PathBuf {
+        use std::ffi::OsStr;
+
+        let mut components = Path::new(out_dir).iter();
+
+        while let Some(dir) = components.next_back() {
+            if dir == OsStr::new("target") {
+                break;
+            }
+        }
+        let mut dir: PathBuf = components.collect();
+
+        if dir.as_os_str().is_empty() {
+            panic!("Couldn't find target dir based on OUT_DIR");
+        } else {
+            dir.push("target");
+            dir
+        }
+    }
+
+    let root_dir = find_root_dir(crate_dir);
+    let header_path = root_dir.join("include").join("sourmash.h");
+    let header = std::fs::read_to_string(header_path).expect("error reading header");
+
+    // strip directives, not supported by the cffi C parser
+    let new_header: String = header
+        .lines()
+        .filter_map(|s| {
+            if s.starts_with("#") {
+                None
+            } else {
+                Some({
+                    let mut s = s.to_owned();
+                    s.push_str("\n");
+                    s
+                })
+            }
+        })
+        .collect();
+
+    let out_dir = env::var("OUT_DIR").unwrap();
+    let target_dir = find_target_dir(&out_dir);
+    std::fs::create_dir_all(&target_dir).expect("error creating target dir");
+    let out_path = target_dir.join("header.h");
+    std::fs::write(out_path, &new_header).expect("error writing header");
+}
diff --git a/src/sourmash/cli/sbt_combine.py b/src/sourmash/cli/sbt_combine.py
index 2e708b928d..1b5ce0febf 100644
--- a/src/sourmash/cli/sbt_combine.py
+++ b/src/sourmash/cli/sbt_combine.py
@@ -11,16 +11,6 @@ def subparser(subparsers):
         '-x', '--bf-size', metavar='S', type=float, default=1e5
     )
 
-    subparser = subparsers.add_parser('sbt_combine')
-    subparser.add_argument('sbt_name', help='name to save SBT into')
-    subparser.add_argument(
-        'sbts', nargs='+',
-        help='SBTs to combine to form a new SBT'
-    )
-    subparser.add_argument(
-        '-x', '--bf-size', metavar='S', type=float, default=1e5
-    )
-
 
 def main(args):
     import sourmash
diff --git a/src/sourmash/cli/tax/metagenome.py b/src/sourmash/cli/tax/metagenome.py
index 0bc7ab7c4e..df81789360 100644
--- a/src/sourmash/cli/tax/metagenome.py
+++ b/src/sourmash/cli/tax/metagenome.py
@@ -27,7 +27,6 @@
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('metagenome',
-                                      aliases=['summarize'],
                                       usage=usage)
     subparser.add_argument(
         '-g', '--gather-csv', action="extend", nargs='*', default = [],
diff --git a/tox.ini b/tox.ini
index 6a8d681ad8..87e4330004 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,6 +1,7 @@
 [tox]
 envlist =
   py310,
+  py311,
   py39,
   coverage,
   codecov,
@@ -209,6 +210,7 @@ source = src/sourmash/
 [gh-actions]
 python =
   3.10: py310, docs, package_description, coverage, codecov
+  3.11: py311, coverage, codecov
   3.9: py39, coverage, codecov
   3.8: py38, coverage, codecov