Merge pull request 'Qubasa-hsjobeki/bump-nixpkgs' (#4205) from Qubasa-hsjobeki/bump-nixpkgs into main

Reviewed-on: https://git.clan.lol/clan/clan-core/pulls/4205

flake.lock

@@ -164,10 +164,10 @@
     "nixpkgs": {
       "locked": {
         "lastModified": 315532800,
-        "narHash": "sha256-VgDAFPxHNhCfC7rI5I5wFqdiVJBH43zUefVo8hwo7cI=",
-        "rev": "41da1e3ea8e23e094e5e3eeb1e6b830468a7399e",
+        "narHash": "sha256-0HRxGUoOMtOYnwlMWY0AkuU88WHaI3Q5GEILmsWpI8U=",
+        "rev": "a48741b083d4f36dd79abd9f760c84da6b4dc0e5",
         "type": "tarball",
-        "url": "https://releases.nixos.org/nixpkgs/nixpkgs-25.11pre814815.41da1e3ea8e2/nixexprs.tar.xz"
+        "url": "https://releases.nixos.org/nixpkgs/nixpkgs-25.11pre823094.a48741b083d4/nixexprs.tar.xz"
       },
       "original": {
         "type": "tarball",

lib/test/container-test-driver/pyproject.toml

@@ -15,7 +15,7 @@ find = {}
 [tool.setuptools.package-data]
 test_driver = ["py.typed"]
 [tool.mypy]
-python_version = "3.12"
+python_version = "3.13"
 warn_redundant_casts = true
 disallow_untyped_calls = true
 disallow_untyped_defs = true

pkgs/clan-app/clan_app/api/file_gtk.py

@@ -1,4 +1,3 @@
-# ruff: noqa: N801
 import gi
 
 gi.require_version("Gtk", "4.0")

pkgs/clan-app/pyproject.toml

@@ -30,7 +30,7 @@ norecursedirs = "tests/helpers"
 markers = ["impure"]
 
 [tool.mypy]
-python_version = "3.12"
+python_version = "3.13"
 warn_redundant_casts = true
 disallow_untyped_calls = true
 disallow_untyped_defs = true

pkgs/clan-app/tests/wayland.py

@@ -7,7 +7,7 @@ import pytest
 
 
 @pytest.fixture(scope="session")
-def wayland_compositor() -> Generator[Popen, None, None]:
+def wayland_compositor() -> Generator[Popen]:
     # Start the Wayland compositor (e.g., Weston)
     # compositor = Popen(["weston", "--backend=headless-backend.so"])
     compositor = Popen(["weston"])
@@ -20,7 +20,7 @@ GtkProc = NewType("GtkProc", Popen)
 
 
 @pytest.fixture
-def app() -> Generator[GtkProc, None, None]:
+def app() -> Generator[GtkProc]:
     cmd = [sys.executable, "-m", "clan_app"]
     print(f"Running: {cmd}")
     rapp = Popen(

pkgs/clan-cli/clan_cli/tests/fixtures_flakes.py

@@ -5,9 +5,9 @@ import shutil
 import subprocess as sp
 import tempfile
 from collections import defaultdict
-from collections.abc import Callable, Iterator
+from collections.abc import Iterator
 from pathlib import Path
-from typing import Any, NamedTuple
+from typing import NamedTuple
 
 import pytest
 from clan_cli.tests import age_keys
@@ -38,7 +38,12 @@ def def_value() -> defaultdict:
     return defaultdict(def_value)
 
 
-nested_dict: Callable[[], dict[str, Any]] = lambda: defaultdict(def_value)
+def nested_dict() -> defaultdict:
+    """
+    Creates a defaultdict that allows for arbitrary levels of nesting.
+    For example: d['a']['b']['c'] = value
+    """
+    return defaultdict(def_value)
 
 
 # Substitutes strings in a file.

pkgs/clan-cli/clan_cli/tests/helpers/nixos_config.py

@@ -1,11 +0,0 @@
-from collections import defaultdict
-from collections.abc import Callable
-from typing import Any
-
-
-def def_value() -> defaultdict:
-    return defaultdict(def_value)
-
-
-# allows defining nested dictionary in a single line
-nested_dict: Callable[[], dict[str, Any]] = lambda: defaultdict(def_value)

pkgs/clan-cli/clan_cli/vars/check.py

@@ -4,14 +4,13 @@ import logging
 from clan_cli.completions import add_dynamic_completer, complete_machines
 from clan_lib.errors import ClanError
 from clan_lib.machines.machines import Machine
-
-log = logging.getLogger(__name__)
-
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
     from .generate import Var
 
+log = logging.getLogger(__name__)
+
 
 class VarStatus:
     def __init__(

pkgs/clan-cli/clan_lib/api/__init__.py

@@ -16,14 +16,14 @@ from typing import (
 )
 
 from clan_lib.api.util import JSchemaTypeError
+from clan_lib.errors import ClanError
+from .serde import dataclass_to_dict, from_dict, sanitize_string
 
 log = logging.getLogger(__name__)
 
-from .serde import dataclass_to_dict, from_dict, sanitize_string
 
 __all__ = ["dataclass_to_dict", "from_dict", "sanitize_string"]
 
-from clan_lib.errors import ClanError
 
 T = TypeVar("T")
 

pkgs/clan-cli/clan_lib/api/serde.py

@@ -146,8 +146,31 @@ def is_union_type(type_hint: type | UnionType) -> bool:
 
 
 def is_type_in_union(union_type: type | UnionType, target_type: type) -> bool:
-    if get_origin(union_type) is UnionType:
-        return any(issubclass(arg, target_type) for arg in get_args(union_type))
+    # Check for Union from typing module (Union[str, None]) or UnionType (str | None)
+    if get_origin(union_type) in (Union, UnionType):
+        args = get_args(union_type)
+        for arg in args:
+            # Handle None type specially since it's not a class
+            if arg is None or arg is type(None):
+                if target_type is type(None):
+                    return True
+            # For generic types like dict[str, str], check their origin
+            elif get_origin(arg) is not None:
+                if get_origin(arg) == target_type:
+                    return True
+                # Also check if target_type is a generic with same origin
+                elif get_origin(target_type) is not None and get_origin(
+                    arg
+                ) == get_origin(target_type):
+                    return True
+            # For actual classes, use issubclass
+            elif inspect.isclass(arg) and inspect.isclass(target_type):
+                if issubclass(arg, target_type):
+                    return True
+            # For non-class types, use direct comparison
+            elif arg == target_type:
+                return True
+        return False
     return union_type == target_type
 
 

pkgs/clan-cli/clan_lib/api/serde_deserialize_test.py

@@ -8,6 +8,7 @@ import pytest
 from clan_lib.api import dataclass_to_dict, from_dict
 from clan_lib.errors import ClanError
 from clan_lib.machines import machines
+from clan_lib.api.serde import is_type_in_union
 
 
 def test_simple() -> None:
@@ -216,6 +217,44 @@ def test_none_or_string() -> None:
     assert checked3 is None
 
 
+def test_union_with_none_edge_cases() -> None:
+    """
+    Test various union types with None to ensure issubclass() error is avoided.
+    This specifically tests the fix for the TypeError in is_type_in_union.
+    """
+    # Test basic types with None
+    assert from_dict(str | None, None) is None
+    assert from_dict(str | None, "hello") == "hello"
+
+    # Test dict with None - this was the specific case that failed
+    assert from_dict(dict[str, str] | None, None) is None
+    assert from_dict(dict[str, str] | None, {"key": "value"}) == {"key": "value"}
+
+    # Test list with None
+    assert from_dict(list[str] | None, None) is None
+    assert from_dict(list[str] | None, ["a", "b"]) == ["a", "b"]
+
+    # Test dataclass with None
+    @dataclass
+    class TestClass:
+        value: str
+
+    assert from_dict(TestClass | None, None) is None
+    assert from_dict(TestClass | None, {"value": "test"}) == TestClass(value="test")
+
+    # Test Path with None (since it's used in the original failing test)
+    assert from_dict(Path | None, None) is None
+    assert from_dict(Path | None, "/home/test") == Path("/home/test")
+
+    # Test that the is_type_in_union function works correctly
+    # This is the core of what was fixed - ensuring None doesn't cause issubclass error
+    # These should not raise TypeError anymore
+    assert is_type_in_union(str | None, type(None)) is True
+    assert is_type_in_union(dict[str, str] | None, type(None)) is True
+    assert is_type_in_union(list[str] | None, type(None)) is True
+    assert is_type_in_union(Path | None, type(None)) is True
+
+
 def test_roundtrip_escape() -> None:
     assert from_dict(str, "\n") == "\n"
     assert dataclass_to_dict("\n") == "\n"

pkgs/clan-cli/clan_lib/cmd/__init__.py

@@ -179,6 +179,7 @@ def terminate_process_group(process: subprocess.Popen) -> Iterator[None]:
     try:
         process_group = os.getpgid(process.pid)
     except ProcessLookupError:
+        yield
         return
     if process_group == os.getpgid(os.getpid()):
         msg = "Bug! Refusing to terminate the current process group"

pkgs/clan-cli/clan_lib/machines/delete.py

@@ -42,7 +42,10 @@ def delete_machine(machine: Machine) -> None:
 
     # louis@(2025-02-04): clean-up legacy (pre-vars) secrets:
     sops_folder = sops_secrets_folder(machine.flake.path)
-    filter_fn = lambda secret_name: secret_name.startswith(f"{machine.name}-")
+
+    def filter_fn(secret_name: str) -> bool:
+        return secret_name.startswith(f"{machine.name}-")
+
     for secret_name in list_secrets(machine.flake.path, filter_fn):
         secret_path = sops_folder / secret_name
         changed_paths.append(secret_path)

pkgs/clan-cli/clan_lib/ssh/remote.py

@@ -1,4 +1,3 @@
-# ruff: noqa: SLF001
 import ipaddress
 import logging
 import os

pkgs/clan-cli/docs.py

@@ -1,5 +1,6 @@
 import argparse
 import sys
+import re
 from dataclasses import dataclass
 from pathlib import Path
 
@@ -118,9 +119,6 @@ def epilog_to_md(text: str) -> str:
     return md
 
 
-import re
-
-
 def contains_https_link(line: str) -> bool:
     pattern = r"https://\S+"
     return re.search(pattern, line) is not None

pkgs/clan-cli/pyproject.toml

@@ -49,9 +49,12 @@ filterwarnings = "default::ResourceWarning"
 python_files = ["test_*.py", "*_test.py"]
 
 [tool.mypy]
-python_version = "3.12"
+python_version = "3.13"
 warn_redundant_casts = true
 disallow_untyped_calls = true
 disallow_untyped_defs = true
 no_implicit_optional = true
 exclude = "clan_lib.nixpkgs"
+
+[tool.ruff]
+target-version = "py313"

pkgs/clan-vm-manager/clan_vm_manager/components/gkvstore.py

@@ -1,6 +1,6 @@
 import logging
 from collections.abc import Callable
-from typing import Any, Generic, TypeVar
+from typing import Any, TypeVar
 
 import gi
 
@@ -22,7 +22,7 @@ V = TypeVar(
 # clan_vm_manager/components/gkvstore.py:21: error: Definition of "newv" in base class "Object" is incompatible with definition in base class "GInterface"  [misc]
 # clan_vm_manager/components/gkvstore.py:21: error: Definition of "install_properties" in base class "Object" is incompatible with definition in base class "GInterface"  [misc]
 # clan_vm_manager/components/gkvstore.py:21: error: Definition of "getv" in base class "Object" is incompatible with definition in base class "GInterface"  [misc]
-class GKVStore(GObject.GObject, Gio.ListModel, Generic[K, V]):  # type: ignore[misc]
+class GKVStore[K, V: GObject.Object](GObject.GObject, Gio.ListModel):  # type: ignore[misc]
     """
     A simple key-value store that implements the Gio.ListModel interface, with generic types for keys and values.
     Only use self[key] and del self[key] for accessing the items for better performance.

pkgs/clan-vm-manager/clan_vm_manager/components/vmobj.py

@@ -143,7 +143,7 @@ class VMObject(GObject.Object):
     # We use a context manager to create the machine object
     # and make sure it is destroyed when the context is exited
     @contextmanager
-    def _create_machine(self) -> Generator[Machine, None, None]:
+    def _create_machine(self) -> Generator[Machine]:
         uri = ClanURI.from_str(
             url=str(self.data.flake.flake_url), machine_name=self.data.flake.flake_attr
         )

pkgs/clan-vm-manager/clan_vm_manager/views/details.py

@@ -12,7 +12,7 @@ from gi.repository import Adw, Gio, GObject, Gtk
 ListItem = TypeVar("ListItem", bound=GObject.Object)
 
 
-def create_details_list(
+def create_details_list[ListItem: GObject.Object](
     model: Gio.ListStore, render_row: Callable[[Gtk.ListBox, ListItem], Gtk.Widget]
 ) -> Gtk.ListBox:
     boxed_list = Gtk.ListBox()

pkgs/clan-vm-manager/clan_vm_manager/views/list.py

@@ -32,7 +32,7 @@ ListItem = TypeVar("ListItem", bound=GObject.Object)
 CustomStore = TypeVar("CustomStore", bound=Gio.ListModel)
 
 
-def create_boxed_list(
+def create_boxed_list[CustomStore: Gio.ListModel, ListItem: GObject.Object](
     model: CustomStore,
     render_row: Callable[[Gtk.ListBox, ListItem], Gtk.Widget],
 ) -> Gtk.ListBox:

pkgs/clan-vm-manager/pyproject.toml

@@ -30,7 +30,7 @@ norecursedirs = "tests/helpers"
 markers = ["impure"]
 
 [tool.mypy]
-python_version = "3.12"
+python_version = "3.13"
 warn_redundant_casts = true
 disallow_untyped_calls = true
 disallow_untyped_defs = true

pkgs/clan-vm-manager/tests/wayland.py

@@ -7,7 +7,7 @@ import pytest
 
 
 @pytest.fixture(scope="session")
-def wayland_compositor() -> Generator[Popen, None, None]:
+def wayland_compositor() -> Generator[Popen]:
     # Start the Wayland compositor (e.g., Weston)
     # compositor = Popen(["weston", "--backend=headless-backend.so"])
     compositor = Popen(["weston"])
@@ -20,7 +20,7 @@ GtkProc = NewType("GtkProc", Popen)
 
 
 @pytest.fixture
-def app() -> Generator[GtkProc, None, None]:
+def app() -> Generator[GtkProc]:
     rapp = Popen([sys.executable, "-m", "clan_vm_manager"], text=True)
     yield GtkProc(rapp)
     # Cleanup: Terminate your application

pkgs/classgen/main.py

@@ -1,4 +1,3 @@
-# ruff: noqa: RUF001
 import argparse
 import json
 import logging

pkgs/generate-test-vars/pyproject.toml

@@ -26,7 +26,7 @@ addopts = "--durations 5 --color=yes --new-first" # Add --pdb for debugging
 norecursedirs = "tests/helpers"
 
 [tool.mypy]
-python_version = "3.12"
+python_version = "3.13"
 warn_redundant_casts = true
 disallow_untyped_calls = true
 disallow_untyped_defs = true

pkgs/zerotierone/default.nix

@@ -1,7 +1,14 @@
-{ zerotierone, lib }:
+{
+  zerotierone,
+  stdenv,
+  lib,
+}:
 # halalify zerotierone
-zerotierone.overrideAttrs (_old: {
-  meta = _old.meta // {
+zerotierone.overrideAttrs (old: {
+  # Maybe a sandbox issue?
+  # zerotierone> [phy] Binding UDP listen socket to 127.0.0.1/60002... FAILED.
+  doCheck = old.doCheck && !stdenv.hostPlatform.isDarwin;
+  meta = old.meta // {
     license = lib.licenses.apsl20;
   };
 })

pyproject.toml

@@ -1,5 +1,5 @@
 [tool.mypy]
-python_version = "3.12"
+python_version = "3.13"
 pretty = true
 warn_redundant_casts = true
 disallow_untyped_calls = true
@@ -8,7 +8,7 @@ no_implicit_optional = true
 exclude = "clan_cli.nixpkgs"
 
 [tool.ruff]
-target-version = "py311"
+target-version = "py313"
 line-length = 88
 lint.select = [
   "A",