clan-cli: fix PATH not correctly including runtime dependencies

pkgs/clan-cli/default.nix

@@ -1,7 +1,6 @@
 {
   # callPackage args
   argcomplete,
-  gitMinimal,
   gnupg,
   installShellFiles,
   lib,
@@ -34,11 +33,17 @@ let
   # load nixpkgs runtime dependencies from a json file
   # This file represents an allow list at the same time that is checked by the run_cmd
   #   implementation in nix.py
-  runtimeDependenciesAsSet = lib.filterAttrs (_name: pkg: !pkg.meta.unsupported or false) (
-    lib.genAttrs (lib.importJSON ./clan_cli/nix/allowed-programs.json) (name: pkgs.${name})
-  );
+  allDependencies = lib.importJSON ./clan_cli/nix/allowed-programs.json;
 
-  runtimeDependencies = lib.attrValues runtimeDependenciesAsSet;
+  generateRuntimeDependenciesMap =
+    deps:
+    lib.filterAttrs (_: pkg: !pkg.meta.unsupported or false) (lib.genAttrs deps (name: pkgs.${name}));
+
+  runtimeDependenciesMap = generateRuntimeDependenciesMap allDependencies;
+
+  runtimeDependencies = lib.attrValues runtimeDependenciesMap;
+
+  includedRuntimeDependenciesMap = generateRuntimeDependenciesMap includedRuntimeDeps;
 
   testDependencies =
     runtimeDependencies
@@ -102,29 +107,20 @@ python3.pkgs.buildPythonApplication {
   format = "pyproject";
 
   # Arguments for the wrapper to unset LD_LIBRARY_PATH to avoid glibc version issues
-  makeWrapperArgs =
-    [
-      "--unset LD_LIBRARY_PATH"
-      "--unset PYTHONPATH"
+  makeWrapperArgs = [
+    "--unset LD_LIBRARY_PATH"
+    "--unset PYTHONPATH"
 
-      # TODO: remove gitMinimal here and use the one from runtimeDependencies
-      "--suffix"
-      "PATH"
-      ":"
-      "${gitMinimal}/bin/git"
-    ]
     # include selected runtime dependencies in the PATH
-    ++ lib.concatMap (p: [
-      "--prefix"
-      "PATH"
-      ":"
-      p
-    ]) includedRuntimeDeps
-    ++ [
-      "--set"
-      "CLAN_STATIC_PROGRAMS"
-      (lib.concatStringsSep ":" includedRuntimeDeps)
-    ];
+    "--prefix"
+    "PATH"
+    ":"
+    (lib.makeBinPath (lib.attrValues includedRuntimeDependenciesMap))
+
+    "--set"
+    "CLAN_STATIC_PROGRAMS"
+    (lib.concatStringsSep ":" (lib.attrNames includedRuntimeDependenciesMap))
+  ];
 
   nativeBuildInputs = [
     setuptools
@@ -134,65 +130,63 @@ python3.pkgs.buildPythonApplication {
   propagatedBuildInputs = pythonDependencies;
 
   # Define and expose the tests and checks to run in CI
-  passthru.tests =
-    (lib.mapAttrs' (n: lib.nameValuePair "clan-dep-${n}") runtimeDependenciesAsSet)
-    // {
-      clan-pytest-without-core =
-        runCommand "clan-pytest-without-core"
-          { nativeBuildInputs = [ pythonWithTestDeps ] ++ testDependencies; }
-          ''
-            cp -r ${source} ./src
-            chmod +w -R ./src
-            cd ./src
+  passthru.tests = (lib.mapAttrs' (n: lib.nameValuePair "clan-dep-${n}") runtimeDependenciesMap) // {
+    clan-pytest-without-core =
+      runCommand "clan-pytest-without-core"
+        { nativeBuildInputs = [ pythonWithTestDeps ] ++ testDependencies; }
+        ''
+          cp -r ${source} ./src
+          chmod +w -R ./src
+          cd ./src
 
-            export NIX_STATE_DIR=$TMPDIR/nix IN_NIX_SANDBOX=1 PYTHONWARNINGS=error
-            ${pythonWithTestDeps}/bin/python -m pytest -m "not impure and not with_core" ./tests
-            touch $out
-          '';
-      clan-pytest-with-core =
-        runCommand "clan-pytest-with-core"
-          {
-            nativeBuildInputs = [ pythonWithTestDeps ] ++ testDependencies;
-            buildInputs = [
+          export NIX_STATE_DIR=$TMPDIR/nix IN_NIX_SANDBOX=1 PYTHONWARNINGS=error
+          ${pythonWithTestDeps}/bin/python -m pytest -m "not impure and not with_core" ./tests
+          touch $out
+        '';
+    clan-pytest-with-core =
+      runCommand "clan-pytest-with-core"
+        {
+          nativeBuildInputs = [ pythonWithTestDeps ] ++ testDependencies;
+          buildInputs = [
+            pkgs.bash
+            pkgs.coreutils
+            pkgs.nix
+          ];
+          closureInfo = pkgs.closureInfo {
+            rootPaths = [
               pkgs.bash
               pkgs.coreutils
-              pkgs.nix
+              pkgs.jq.dev
+              pkgs.stdenv
+              pkgs.stdenvNoCC
             ];
-            closureInfo = pkgs.closureInfo {
-              rootPaths = [
-                pkgs.bash
-                pkgs.coreutils
-                pkgs.jq.dev
-                pkgs.stdenv
-                pkgs.stdenvNoCC
-              ];
-            };
-          }
-          ''
-            cp -r ${source} ./src
-            chmod +w -R ./src
-            cd ./src
+          };
+        }
+        ''
+          cp -r ${source} ./src
+          chmod +w -R ./src
+          cd ./src
 
-            export CLAN_CORE=${clan-core-path}
-            export NIX_STATE_DIR=$TMPDIR/nix
-            export IN_NIX_SANDBOX=1
-            export PYTHONWARNINGS=error
-            export CLAN_TEST_STORE=$TMPDIR/store
-            # required to prevent concurrent 'nix flake lock' operations
-            export LOCK_NIX=$TMPDIR/nix_lock
-            mkdir -p "$CLAN_TEST_STORE/nix/store"
-            xargs cp --recursive --target "$CLAN_TEST_STORE/nix/store"  < "$closureInfo/store-paths"
-            nix-store --load-db --store "$CLAN_TEST_STORE" < "$closureInfo/registration"
-            ${pythonWithTestDeps}/bin/python -m pytest -m "not impure and with_core" ./tests
-            touch $out
-          '';
-    };
+          export CLAN_CORE=${clan-core-path}
+          export NIX_STATE_DIR=$TMPDIR/nix
+          export IN_NIX_SANDBOX=1
+          export PYTHONWARNINGS=error
+          export CLAN_TEST_STORE=$TMPDIR/store
+          # required to prevent concurrent 'nix flake lock' operations
+          export LOCK_NIX=$TMPDIR/nix_lock
+          mkdir -p "$CLAN_TEST_STORE/nix/store"
+          xargs cp --recursive --target "$CLAN_TEST_STORE/nix/store"  < "$closureInfo/store-paths"
+          nix-store --load-db --store "$CLAN_TEST_STORE" < "$closureInfo/registration"
+          ${pythonWithTestDeps}/bin/python -m pytest -m "not impure and with_core" ./tests
+          touch $out
+        '';
+  };
 
   passthru.nixpkgs = nixpkgs';
   passthru.testDependencies = testDependencies;
   passthru.pythonWithTestDeps = pythonWithTestDeps;
   passthru.runtimeDependencies = runtimeDependencies;
-  passthru.runtimeDependenciesAsSet = runtimeDependenciesAsSet;
+  passthru.runtimeDependenciesMap = runtimeDependenciesMap;
 
   postInstall = ''
     cp -r ${nixpkgs'} $out/${python3.sitePackages}/clan_cli/nixpkgs

pkgs/clan-cli/shell.nix

@@ -28,7 +28,7 @@ mkShell {
   inputsFrom = [ self'.devShells.default ];
 
   CLAN_STATIC_PROGRAMS = lib.concatStringsSep ":" (
-    lib.attrNames clan-cli-full.passthru.runtimeDependenciesAsSet
+    lib.attrNames clan-cli-full.passthru.runtimeDependenciesMap
   );
 
   shellHook = ''