diff --git a/lib/clanTest/flake-module.nix b/lib/clanTest/flake-module.nix
index 4e140a251..214615981 100644
--- a/lib/clanTest/flake-module.nix
+++ b/lib/clanTest/flake-module.nix
@@ -158,14 +158,26 @@ in
           '';
 
       # the test's flake.nix with locked clan-core input
-      flakeForSandbox = hostPkgs.runCommand "offline-flake-for-test-${config.name}" { } ''
-        cp -r ${config.clan.directory} $out
-        chmod +w -R $out
-        substituteInPlace $out/flake.nix \
-          --replace-fail \
-            "https://git.clan.lol/clan/clan-core/archive/main.tar.gz" \
-            "${clan-core.packages.${hostPkgs.system}.clan-core-flake}"
-      '';
+      flakeForSandbox =
+        hostPkgs.runCommand "offline-flake-for-test-${config.name}"
+          {
+            nativeBuildInputs = [ hostPkgs.nix ];
+          }
+          ''
+            cp -r ${config.clan.directory} $out
+            chmod +w -R $out
+            substituteInPlace $out/flake.nix \
+              --replace-fail \
+                "https://git.clan.lol/clan/clan-core/archive/main.tar.gz" \
+                "${clan-core.packages.${hostPkgs.system}.clan-core-flake}"
+
+            # Create a proper lock file for the test flake
+            export HOME=$(mktemp -d)
+            nix flake lock $out \
+              --extra-experimental-features 'nix-command flakes' \
+              --override-input clan-core ${clan-core.packages.${hostPkgs.system}.clan-core-flake} \
+              --override-input nixpkgs ${clan-core.inputs.nixpkgs}
+          '';
     in
     {
       imports = [
diff --git a/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py b/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py
index 62b77f5ea..fefd8a262 100644
--- a/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py
+++ b/pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py
@@ -14,6 +14,7 @@ from clan_cli.tests import age_keys
 from clan_cli.tests.fixture_error import FixtureError
 from clan_cli.tests.root import CLAN_CORE
 from clan_cli.tests.temporary_dir import TEMPDIR
+from clan_lib import cmd
 from clan_lib.dirs import (
     TemplateType,
     clan_templates,
@@ -23,7 +24,7 @@ from clan_lib.dirs import (
 from clan_lib.flake import Flake
 from clan_lib.locked_open import locked_open
 from clan_lib.machines.machines import Machine
-from clan_lib.nix import nix_test_store
+from clan_lib.nix import nix_command, nix_test_store
 
 log = logging.getLogger(__name__)
 
@@ -86,6 +87,11 @@ def substitute(
     print(f"flake: {flake}")
     file.write_text(buf)
 
+    # Lock the flake after substitution if clan_core was replaced
+    if clan_core_flake:
+        flake_dir = file.parent
+        cmd.run(nix_command(["flake", "lock"]), cmd.RunOpts(cwd=flake_dir))
+
 
 class FlakeForTest(NamedTuple):
     path: Path
diff --git a/pkgs/clan-cli/clan_lib/flake/flake.py b/pkgs/clan-cli/clan_lib/flake/flake.py
index b84cd07e4..ed3b33375 100644
--- a/pkgs/clan-cli/clan_lib/flake/flake.py
+++ b/pkgs/clan-cli/clan_lib/flake/flake.py
@@ -720,7 +720,7 @@ class Flake:
             AssertionError: If the cache or flake cache path is not properly initialized.
         """
         from clan_lib.cmd import Log, RunOpts, run
-        from clan_lib.dirs import nixpkgs_source, select_source
+        from clan_lib.dirs import select_source
         from clan_lib.nix import (
             nix_build,
             nix_config,
@@ -731,7 +731,7 @@ class Flake:
             self.invalidate_cache()
         assert self._cache is not None
 
-        nix_options = self.nix_options if self.nix_options is not None else []
+        nix_options = self.nix_options[:] if self.nix_options is not None else []
 
         str_selectors: list[str] = []
         for selector in selectors:
@@ -739,23 +739,9 @@ class Flake:
 
         config = nix_config()
 
-        # these hashes should be filled in by `nix build`
-        # if we run this Python code directly then we use a fallback
-        # method to getting the NAR hash
-        fallback_nixpkgs_hash = "@fallback_nixpkgs_hash@"
-        if not fallback_nixpkgs_hash.startswith("sha256-"):
-            fallback_nixpkgs = Flake(
-                str(nixpkgs_source()), nix_options=self.nix_options
-            )
-            fallback_nixpkgs.invalidate_cache()
-            assert fallback_nixpkgs.hash is not None, (
-                "this should be impossible as invalidate_cache() should always set `hash`"
-            )
-            fallback_nixpkgs_hash = fallback_nixpkgs.hash
-
         select_hash = "@select_hash@"
         if not select_hash.startswith("sha256-"):
-            select_flake = Flake(str(select_source()), nix_options=self.nix_options)
+            select_flake = Flake(str(select_source()), nix_options=nix_options)
             select_flake.invalidate_cache()
             assert select_flake.hash is not None, (
                 "this should be impossible as invalidate_cache() should always set `hash`"
@@ -800,12 +786,6 @@ class Flake:
               }}
         """
         # fmt: on
-        if tmp_store := nix_test_store():
-            nix_options.append("--impure")
-
-        # build_output = Path(
-        #     run(nix_build(["--expr", nix_code, *nix_options])).stdout.strip()
-        # )
 
         build_output = Path(
             run(
@@ -813,7 +793,7 @@ class Flake:
             ).stdout.strip()
         )
 
-        if tmp_store:
+        if tmp_store := nix_test_store():
             build_output = tmp_store.joinpath(*build_output.parts[1:])
         outputs = json.loads(build_output.read_bytes())
         if len(outputs) != len(selectors):
diff --git a/pkgs/clan-cli/default.nix b/pkgs/clan-cli/default.nix
index d35dd7a6c..81820c858 100644
--- a/pkgs/clan-cli/default.nix
+++ b/pkgs/clan-cli/default.nix
@@ -43,7 +43,10 @@ let
     deps:
     lib.filterAttrs (_: pkg: !pkg.meta.unsupported or false) (lib.genAttrs deps (name: pkgs.${name}));
   testRuntimeDependenciesMap = generateRuntimeDependenciesMap allDependencies;
-  testRuntimeDependencies = (lib.attrValues testRuntimeDependenciesMap);
+  # Filter out virt-viewer from test dependencies since it pulls quiet a lot of other packages, we don't run virt-viewer in tests.
+  testRuntimeDependencies = lib.filter (pkg: pkg.pname or "" != "virt-viewer") (
+    lib.attrValues testRuntimeDependenciesMap
+  );
   bundledRuntimeDependenciesMap = generateRuntimeDependenciesMap includedRuntimeDeps;
   bundledRuntimeDependencies = lib.attrValues bundledRuntimeDependenciesMap;
 
@@ -70,7 +73,6 @@ let
         rm -f $out/clan_lib/select
 
         substituteInPlace $out/clan_lib/flake/flake.py \
-          --replace-fail '@fallback_nixpkgs_hash@' "$(jq -r '.nodes.nixpkgs.locked.narHash' ${nixpkgs'}/flake.lock)" \
           --replace-fail '@select_hash@' "$(jq -r '.nodes."nix-select".locked.narHash' ${../../flake.lock})"
         ln -sf ${nixpkgs'} $out/clan_lib/nixpkgs
         ln -sf ${nix-select} $out/clan_lib/select
@@ -193,48 +195,6 @@ pythonRuntime.pkgs.buildPythonApplication {
               pkgs.coreutils
               pkgs.nix
             ];
-            closureInfo = pkgs.closureInfo {
-              rootPaths = [
-                templateDerivation
-                pkgs.bash
-                pkgs.coreutils
-                pkgs.jq.dev
-                pkgs.stdenv
-                pkgs.stdenvNoCC
-                pkgs.shellcheck-minimal
-              ];
-            };
-          }
-          ''
-            set -euo pipefail
-            cp -r ${sourceWithTests} ./src
-            chmod +w -R ./src
-            cd ./src
-
-            ${setupNixInNix}
-
-            export CLAN_CORE_PATH=${clan-core-path}
-            export PYTHONWARNINGS=error
-
-            # limit build cores to 16
-            jobs="$((NIX_BUILD_CORES>16 ? 16 : NIX_BUILD_CORES))"
-
-            python -m pytest -m "not impure and with_core" ./clan_cli -n $jobs
-            touch $out
-          '';
-    }
-    // lib.optionalAttrs (!stdenv.isDarwin) {
-      # disabled on macOS until we fix all remaining issues
-      clan-lib-pytest =
-        runCommand "clan-lib-pytest"
-          {
-            nativeBuildInputs = testDependencies;
-            buildInputs = [
-              pkgs.bash
-              pkgs.coreutils
-              pkgs.nix
-
-            ];
             closureInfo = pkgs.closureInfo {
               rootPaths = [
                 templateDerivation
@@ -266,10 +226,11 @@ pythonRuntime.pkgs.buildPythonApplication {
             export NIXPKGS=${nixpkgs}
             export NIX_SELECT=${nix-select}
 
-            # limit build cores to 4
-            jobs="$((NIX_BUILD_CORES>4 ? 4 : NIX_BUILD_CORES))"
+            # limit build cores to 16
+            jobs="$((NIX_BUILD_CORES>16 ? 16 : NIX_BUILD_CORES))"
 
-            python -m pytest -m "with_core" ./clan_lib -n $jobs
+            # Run all tests with core marker
+            python -m pytest -m "not impure and with_core" -n $jobs ./clan_cli ./clan_lib
             touch $out
           '';
     };
diff --git a/pkgs/generate-test-vars/pyproject.toml b/pkgs/generate-test-vars/pyproject.toml
index 3347a9efa..aede95ecb 100644
--- a/pkgs/generate-test-vars/pyproject.toml
+++ b/pkgs/generate-test-vars/pyproject.toml
@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 name = "generate-test-vars"
 description = "vars generate"
 dynamic = ["version"]
-scripts = { generate-test-vars = "generate_test_vars:cli.main" }
+scripts = { generate-test-vars = "generate_test_vars.cli:main" }
 
 [project.urls]
 Homepage = "https://clan.lol/"