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:
@@ -51,7 +52,7 @@ jobs:
     needs: [ 'quality'  ]
     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.-rc.3']
     steps:
     - uses: khanlab/actions/.github/actions/[email protected]
       id: setup
@@ -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.-rc.3']
         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/__init__.py

@@ -3,6 +3,7 @@
 
 __submodules__ = ["core", "paths"]
 
+
 from snakebids import _warningformat  # noqa: F401
 
 # isort: split

snakebids/core/_querying.py

@@ -7,8 +7,7 @@
 
 import attrs
 import more_itertools as itx
-from bids.layout import BIDSLayout, Query
-from bids.layout.models import BIDSFile
+from bids.layout import BIDSFile, BIDSLayout, Query
 from typing_extensions import Self, TypeAlias, override
 
 from snakebids.exceptions import ConfigError, PybidsError

snakebids/core/datasets.py

@@ -11,7 +11,7 @@
 
 import attr
 import more_itertools as itx
-from bids import BIDSLayout
+from bids.layout import BIDSLayout
 from pvandyken.deprecated import deprecated
 from typing_extensions import Self, TypedDict
 

snakebids/core/input_generation.py

@@ -17,7 +17,7 @@
 )
 
 import more_itertools as itx
-from bids import BIDSLayout, BIDSLayoutIndexer
+from bids.layout import BIDSLayout, BIDSLayoutIndexer
 
 from snakebids.core._querying import (
     FilterSpecError,

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/resources/bids_tags.json

@@ -183,6 +183,12 @@
         "before": "subset-",
         "match": "[a-zA-Z0-9]+"
     },
+    "nucleus": {
+        "tag": "nucleus",
+        "before": "nuc-",
+        "match": "[a-zA-Z0-9]+"
+
+    },
     "desc": {
         "tag": "desc",
         "before": "desc-",

snakebids/tests/conftest.py

@@ -8,6 +8,7 @@
 import pytest
 from hypothesis import database, settings
 from pyfakefs.fake_filesystem import FakeFilesystem
+from upath import UPath
 
 import snakebids.paths.resources as specs
 from snakebids import resources, set_bids_spec
@@ -51,9 +52,7 @@ def fakefs(
 
 
 @pytest.fixture
-def fakefs_tmpdir(
-    request: pytest.FixtureRequest, fakefs: FakeFilesystem | None
-) -> Path:
+def tmpdir(request: pytest.FixtureRequest, fakefs: FakeFilesystem | None) -> Path:
     """Version of tmpdir compatible with fakefs
 
     If fakefs is disabled, a tmpdir is returned using the builtin tmpdir fixture.

snakebids/tests/test_generate_inputs.py

@@ -13,12 +13,21 @@
 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
 import pytest
-from bids import BIDSLayout
+from bids.layout import BIDSLayout
 from hypothesis import HealthCheck, assume, example, given, settings
 from hypothesis import strategies as st
 from pyfakefs.fake_filesystem import FakeFilesystem
@@ -46,6 +55,7 @@
     allow_function_scoped,
     create_dataset,
     create_snakebids_config,
+    debug,
     example_if,
     get_bids_path,
     get_zip_list,
@@ -56,6 +66,9 @@
 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")
 
 
@@ -196,13 +209,13 @@ def test_attribute_errors_from_pybids_qualified_and_raised():
 
 
 class TestFilterBools:
-    @pytest.fixture(autouse=True)
-    def bids_fs(self, bids_fs: FakeFilesystem | None):
-        return bids_fs
+    # @pytest.fixture(autouse=True)
+    # def bids_fs(self, bids_fs: FakeFilesystem | None):
+    #     return bids_fs
 
-    @pytest.fixture
-    def tmpdir(self, fakefs_tmpdir: Path):
-        return fakefs_tmpdir
+    # @pytest.fixture
+    # def tmpdir(self, tmpdir: Path):
+    #     return tmpdir
 
     def disambiguate_components(self, dataset: BidsDataset):
         assert len(dataset) == 2
@@ -230,7 +243,7 @@ def set_difference(set_: set[str], comp: BidsComponent) -> set[str]:
     )
     @given(dataset=sb_st.datasets())
     def test_ambiguous_paths_with_extra_entities_leads_to_error(
-        self, tmpdir: Path, dataset: BidsDataset
+        self, tmpdir: Path, dataset: BidsDataset, mocker: MockerFixture
     ):
         root = tempfile.mkdtemp(dir=tmpdir)
         create_dataset(root, dataset)
@@ -256,7 +269,7 @@ def test_ambiguous_paths_with_extra_entities_leads_to_error(
     )
     @given(dataset=sb_st.datasets())
     def test_ambiguous_paths_with_missing_entity_leads_to_error(
-        self, tmpdir: Path, dataset: BidsDataset
+        self, tmpdir: Path, dataset: BidsDataset, mocker: MockerFixture
     ):
         root = tempfile.mkdtemp(dir=tmpdir)
         create_dataset(root, dataset)
@@ -507,15 +520,27 @@ def add_entity(component: BidsComponent, entity: str, value: str):
         assert result == BidsDataset({"template": dataset["template"]})
 
 
+@pytest.mark.disable_fakefs(True)
 class TestFilterMethods:
-    @pytest.fixture(autouse=True)
-    def bids_fs(self, bids_fs: FakeFilesystem | None):
-        return bids_fs
+    # @pytest.fixture(autouse=True)
+    # def bids_fs(self, bids_fs: FakeFilesystem | None):
+    #     return bids_fs
 
-    @pytest.fixture
-    def tmpdir(self, fakefs_tmpdir: Path):
-        return fakefs_tmpdir
+    # @pytest.fixture
+    # def tmpdir(self, fakefs_tmpdir: Path):
+    #     return fakefs_tmpdir
 
+    @debug(
+        component=BidsComponent(
+            name="template",
+            path="sub-{subject}/sub-{subject}_nuc-{nucleus}",
+            zip_lists={
+                "subject": ["0"],
+                "nucleus": ["0"],
+            },
+        ),
+        data=mock_data("0"),
+    )
     @example(
         component=BidsComponent(
             name="template",
@@ -849,10 +874,8 @@ def test_filter_with_invalid_method_raises_error(self, tmpdir: Path, method: str
     max_examples=1,
 )
 @given(dataset=sb_st.datasets_one_comp(unique=True))
-def test_duplicate_wildcards_does_not_create_error(
-    dataset: BidsDataset, bids_fs: Path, fakefs_tmpdir: Path
-):
-    root = tempfile.mkdtemp(dir=fakefs_tmpdir)
+def test_duplicate_wildcards_does_not_create_error(dataset: BidsDataset, tmpdir: Path):
+    root = tempfile.mkdtemp(dir=tmpdir)
     rooted = BidsDataset.from_iterable(
         attrs.evolve(comp, path=os.path.join(root, comp.path))
         for comp in dataset.values()
@@ -1059,8 +1082,8 @@ def get_subset(of: Iterable[T]) -> list[T]:
 
 class TestCustomPaths:
     @pytest.fixture
-    def temp_dir(self, fakefs_tmpdir: Path, bids_fs: Path):
-        return fakefs_tmpdir
+    def temp_dir(self, tmpdir: Path, bids_fs: Path):
+        return tmpdir
 
     def generate_test_directory(
         self, entities: dict[str, list[str]], template: Path, tmpdir: Path
@@ -1584,13 +1607,13 @@ def test_get_lists_from_bids():
 
 
 class TestGenBidsLayout:
-    @pytest.fixture
-    def tmpdir(self, fakefs_tmpdir: Path):
-        return fakefs_tmpdir
+    # @pytest.fixture
+    # def tmpdir(self, tmpdir: Path):
+    #     return tmpdir
 
-    @pytest.fixture(autouse=True)
-    def bids_fs(self, bids_fs: FakeFilesystem | None):
-        return bids_fs
+    # @pytest.fixture(autouse=True)
+    # def bids_fs(self, bids_fs: FakeFilesystem | None):
+    #     return bids_fs
 
     @settings(
         max_examples=1, suppress_health_check=[HealthCheck.function_scoped_fixture]
@@ -1666,7 +1689,7 @@ 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
@@ -1707,8 +1730,8 @@ def __str__(self):  # __fspath__ calls __str__ by default
     ],
 )
 @given(dataset=sb_st.datasets(unique=True))
-def test_generate_inputs(dataset: BidsDataset, bids_fs: Path, fakefs_tmpdir: Path):
-    root = tempfile.mkdtemp(dir=fakefs_tmpdir)
+def test_generate_inputs(dataset: BidsDataset, tmpdir: Path):
+    root = tempfile.mkdtemp(dir=tmpdir)
     rooted = BidsDataset.from_iterable(
         attrs.evolve(comp, path=os.path.join(root, comp.path))
         for comp in dataset.values()
@@ -1741,8 +1764,8 @@ class TestParticipantFiltering:
     MODE = Literal["include", "exclude"]
 
     @pytest.fixture
-    def tmpdir(self, bids_fs: Path, fakefs_tmpdir: Path):
-        return fakefs_tmpdir
+    def tmpdir(self, bids_fs: Path, tmpdir: Path):
+        return tmpdir
 
     def get_filter_params(self, mode: MODE, filters: list[str] | str):
         class FiltParams(TypedDict, total=False):
@@ -1920,12 +1943,12 @@ def test_exclude_participant_does_not_make_all_other_filters_regex(
 @settings(max_examples=1, suppress_health_check=[HealthCheck.function_scoped_fixture])
 @given(dataset=sb_st.datasets_one_comp(blacklist_entities=["extension"], unique=True))
 def test_when_all_custom_paths_no_layout_indexed(
-    dataset: BidsDataset, bids_fs: Path, fakefs_tmpdir: Path, mocker: MockerFixture
+    dataset: BidsDataset, bids_fs: Path, tmpdir: Path, mocker: MockerFixture
 ):
     # Need to reset mocker at beginning because hypothesis may call this function
     # multiple times
     mocker.stopall()
-    root = tempfile.mkdtemp(dir=fakefs_tmpdir)
+    root = tempfile.mkdtemp(dir=tmpdir)
     rooted = BidsDataset.from_iterable(
         attrs.evolve(comp, path=os.path.join(root, comp.path))
         for comp in dataset.values()