nix updates for pyopensci review (#2975)

Fix #2905 #2907 

- Use `DeterminateSystems/nix-installer-action` and
`DeterminateSystems/magic-nix-cache-action` for installing nix and
caching
- Also run nix on macos-14 (arm64)
- run `nix develop` instead of `nix-shell` to mirror direnv

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Pre-commit updates (#2427)
+fee62922d8857ce93f1d4e90fd7240629d606997

.github/workflows/dev_envs.yml

@@ -5,25 +5,23 @@ on:
     branches: [latest]
 jobs:
   nix:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-14]
     steps:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
 
-    - uses: cachix/install-nix-action@v25
-      with:
-        extra_nix_config: |
-          access-tokens = github.com=${{ secrets.GITHUB_TOKEN }}
-
-    - uses: cachix/cachix-action@v14
-      with:
-        name: sourmash-bio
-        authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
+    - name: Install Nix
+      uses: DeterminateSystems/nix-installer-action@v4
+    - name: Run the Magic Nix Cache
+      uses: DeterminateSystems/magic-nix-cache-action@v1
 
     - run: nix run .# -- --version
 
-    - run: nix-shell --command "tox -e py310"
+    - run: nix develop --command bash -c "tox -e py310"
 
   mamba:
     runs-on: ubuntu-latest

flake.nix

@@ -30,40 +30,55 @@
           rustc = rustVersion;
         };
 
+        inherit (pkgs) lib;
+
         python = pkgs.python311Packages;
 
+        stdenv = if pkgs.stdenv.isDarwin then pkgs.overrideSDK pkgs.stdenv "11.0" else pkgs.stdenv;
+
+        commonArgs = {
+          src = ./.;
+          stdenv = stdenv;
+          preConfigure = lib.optionalString stdenv.isDarwin ''
+            export MACOSX_DEPLOYMENT_TARGET=10.14
+          '';
+
+          # Work around https://github.com/NixOS/nixpkgs/issues/166205.
+          env = lib.optionalAttrs stdenv.cc.isClang {
+            NIX_LDFLAGS = "-l${stdenv.cc.libcxx.cxxabi.libName}";
+          };
+
+          buildInputs = lib.optionals stdenv.isDarwin [ pkgs.libiconv pkgs.darwin.apple_sdk.frameworks.Security ];
+
+          nativeBuildInputs = with rustPlatform; [ cargoSetupHook maturinBuildHook bindgenHook ];
+        };
+
       in
 
       with pkgs;
       {
         packages = {
 
-          lib = rustPlatform.buildRustPackage {
+          lib = rustPlatform.buildRustPackage ( commonArgs // {
             name = "libsourmash";
-            src = lib.cleanSource ./.;
             copyLibs = true;
             cargoLock.lockFile = ./Cargo.lock;
             nativeBuildInputs = with rustPlatform; [ bindgenHook ];
-          };
+          });
 
-          sourmash = python.buildPythonPackage rec {
+          sourmash = python.buildPythonPackage ( commonArgs // rec {
             pname = "sourmash";
             version = "4.8.6-dev";
             format = "pyproject";
 
-            src = ./.;
-
             cargoDeps = rustPlatform.importCargoLock {
               lockFile = ./Cargo.lock;
             };
 
-            nativeBuildInputs = with rustPlatform; [ cargoSetupHook maturinBuildHook bindgenHook ];
-
-            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";
-          };
+          });
 
           docker =
             let
@@ -83,7 +98,7 @@
 
         defaultPackage = self.packages.${system}.sourmash;
 
-        devShell = mkShell {
+        devShells.default = pkgs.mkShell.override { stdenv = stdenv; } (commonArgs // {
           nativeBuildInputs = with rustPlatform; [ bindgenHook ];
 
           buildInputs = [
@@ -113,15 +128,19 @@
             cargo-outdated
             cargo-udeps
             cargo-deny
-            cargo-semver-checks
+            #cargo-semver-checks
             nixpkgs-fmt
           ];
 
+          shellHook = ''
+              export MACOSX_DEPLOYMENT_TARGET=10.14
+            '';
+
           # Needed for matplotlib
           LD_LIBRARY_PATH = lib.makeLibraryPath [ pkgs.stdenv.cc.cc.lib ];
 
           # workaround for https://github.com/NixOS/nixpkgs/blob/48dfc9fa97d762bce28cc8372a2dd3805d14c633/doc/languages-frameworks/python.section.md#python-setuppy-bdist_wheel-cannot-create-whl
           SOURCE_DATE_EPOCH = 315532800; # 1980
-        };
+        });
       });
 }

tox.ini

@@ -56,6 +56,7 @@ wheel_build_env = .pkg
 pass_env =
     LIBCLANG_PATH
     BINDGEN_EXTRA_CLANG_ARGS
+    NIX_*
 
 [testenv:pypy3]
 deps =