Update dependencies

.github/workflows/nightly.yml

@@ -70,7 +70,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: khanlab/actions/.github/actions/[email protected]
         id: setup

.github/workflows/test.yml

@@ -15,6 +15,7 @@ on:
     paths:
       - snakebids/**
       - scripts/**
+      - poetry.lock
 
 jobs:
   quality:
@@ -67,7 +68,7 @@ jobs:
     needs: [ 'build-cache-env'  ]
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
         split: ['1', '2', '3', '4', '5']
       fail-fast: false
     steps:

.readthedocs.yml

@@ -20,7 +20,7 @@ formats:
 build:
   os: 'ubuntu-22.04'
   tools:
-    python: '3.11'
+    python: '3.12'
   jobs:
     post_checkout:
       - (git fetch --tags) || exit 183

pyproject.toml

@@ -34,7 +34,7 @@ patterns = [
 python = ">=3.8,<4.0"
 # core dep with high breakage potential given plans for redesign, so
 # keep upper limit
-pybids = ">=0.16.0,<0.17"
+pybids = ">=0.16.0,<0.18"
 snakemake = [
     { version = ">=5.28.0,<8", python = "<3.11" },
     { version = ">=7.18.2", python = ">=3.11" },
@@ -81,7 +81,7 @@ pluggy = ">=1.3"
 [tool.poetry.group.dev.dependencies]
 pytest = "^8"
 pytest-mock = "^3.7.0"
-poethepoet = "^0.27"
+poethepoet = "^0.29"
 pre-commit = "^3.0.0"
 # a mkinit dep has the 'platform_system == "Windows"' as a marker on an incompatible dependency
 #   (pydantic<2.0 cf copier), so set the inverse as a marker here so mkinit can
@@ -92,8 +92,9 @@ pytest-benchmark = "^4.0.0"
 pyfakefs = "^5.1.0"
 pyparsing = "^3.0.9"
 pathvalidate = "^3.0.0"
-pyright = "^1.1.370"
-ruff = "^0.5"
+# Avoid bug in 1.1.388 (see https://github.com/microsoft/pyright/issues/9136)
+pyright = "1.1.377"
+ruff = "^0.6"
 pytest-xdist = "^3.3.1"
 pytest-split = [
     { version = "^0.8.1", python = "3.8" },
@@ -106,21 +107,16 @@ docstring-parser = "^0.16"
 
 
 [tool.poetry.group.docs.dependencies]
-sphinx = "^7"
-sphinx-argparse = "^0.4.0"
-sphinxcontrib-asciinema = "^0.4"
-myst-parser = "^3"
-furo = "^2024.4.27"
-sphinx-copybutton = "^0.5.2"
-sphinx-reredirects = "^0.1.3"
-sphinx-design = [
-    { version = "^0.5.0", python = "3.8" },
-    { version = "^0.6", python = ">=3.9" },
-]
-sphinx-autobuild = [
-    { version = "^2021.03.14", python = "3.8" },
-    { version = "^2024.02.04", python = ">=3.9" },
-]
+sphinx = { version = "^8", python = ">=3.10" }
+sphinx-argparse = { version = "^0.4.0", python = ">=3.10" }
+sphinxcontrib-asciinema = { version = "^0.4", python = ">=3.10" }
+myst-parser = { version = "^4", python = ">=3.10" }
+furo = { version = "^2024.4.27", python = ">=3.10" }
+sphinx-copybutton = { version = "^0.5.2", python = ">=3.10" }
+sphinx-reredirects = { version = "^0.1.3", python = ">=3.10" }
+sphinx-design = { version = "^0.6", python = ">=3.10" }
+sphinx-autobuild = { version = "^2024.02.04", python = ">=3.10" }
+
 
 [tool.poetry.scripts]
 snakebids = "snakebids.admin:main"

snakebids/plugins/cli_config.py

@@ -3,7 +3,7 @@
 import argparse
 import re
 from pathlib import Path
-from typing import Any
+from typing import Any, Callable
 
 import attrs
 
@@ -38,7 +38,7 @@ def _make_underscore_dash_aliases(name: str) -> set[str]:
     return {name}
 
 
-def _find_type(name: str, *, yamlsafe: bool = True) -> type[Any]:
+def _find_type(name: str, *, yamlsafe: bool = True) -> Callable[[Any], Any]:
     import importlib
 
     if name == "Path":

snakebids/tests/test_generate_inputs.py

@@ -13,7 +13,16 @@
 import warnings
 from collections import defaultdict
 from pathlib import Path, PosixPath
-from typing import Any, Iterable, Literal, NamedTuple, TypedDict, TypeVar, cast
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Iterable,
+    Literal,
+    NamedTuple,
+    TypedDict,
+    TypeVar,
+    cast,
+)
 
 import attrs
 import more_itertools as itx
@@ -56,6 +65,9 @@
 from snakebids.utils.containers import MultiSelectDict
 from snakebids.utils.utils import DEPRECATION_FLAG, BidsEntity, BidsParseError
 
+if TYPE_CHECKING:
+    from _typeshed import StrPath, Unused
+
 T = TypeVar("T")
 
 
@@ -1666,7 +1678,7 @@ def test_path_subclassing(self, path: str, path_type: str):
         # Google cloud is not posix, for mocking purpose however we just
         # need a class that is a subclass of Path
         class MockGCSPath(PosixPath):
-            def __init__(self, *pathsegments: str):
+            def __init__(self, *pathsegments: StrPath, **kwargs: Unused):
                 super().__init__(*pathsegments)
 
             def __str__(self):  # __fspath__ calls __str__ by default

typings/pyfakefs/fake_filesystem.pyi

@@ -6,7 +6,7 @@ import sys
 from enum import Enum
 from typing import Any, AnyStr, Callable, NoReturn
 
-from pyfakefs.fake_file import AnyFile, AnyFileWrapper, FakeFile
+from pyfakefs.fake_file import AnyFile, AnyFileWrapper, FakeFile, FakeDirectory
 from pyfakefs.helpers import AnyPath, AnyString
 
 """A fake filesystem implementation for unit testing.
@@ -91,7 +91,6 @@ class OSType(Enum):
 
 FakeNullFile = ...
 FakeFileFromRealFile = ...
-FakeDirectory = ...
 FakeDirectoryFromRealDirectory = ...
 FakeFileWrapper = ...
 StandardStreamWrapper = ...