Update dependencies

pyproject.toml

@@ -79,9 +79,9 @@ docutils = "!=0.21.post1"
 pluggy = ">=1.3"
 
 [tool.poetry.group.dev.dependencies]
-pytest = "^7.0.0"
+pytest = "^8"
 pytest-mock = "^3.7.0"
-poethepoet = "^0.25.1"
+poethepoet = "^0.26"
 pre-commit = "^3.0.0"
 # a mkinit dep has the 'platform_system == "Windows"' as a marker on an incompatible dependeny
 #   (pydantic<2.0 cf copier), so set the inverse as a marker here so mkinit can
@@ -95,7 +95,7 @@ pathvalidate = "^3.0.0"
 # Bug in .358 preventing the types from the converter arguments of attrs classes to
 # propogate properly
 pyright = "^1.1.339,<1.1.358"
-ruff = "^0.1.7"
+ruff = "^0.4"
 pytest-xdist = "^3.3.1"
 pytest-split = "^0.8.1"
 tomli = "^2.0.1"
@@ -107,9 +107,9 @@ docstring-parser = "^0.16"
 [tool.poetry.group.docs.dependencies]
 sphinx = "^7"
 sphinx-argparse = "^0.4.0"
-sphinxcontrib-asciinema = "^0.3.8"
-myst-parser = "^2.0.0"
-furo = "^2023.9.10"
+sphinxcontrib-asciinema = "^0.4"
+myst-parser = "^3"
+furo = "^2024.4.27"
 sphinx-copybutton = "^0.5.2"
 sphinx-reredirects = "^0.1.3"
 sphinx-design = "^0.5.0"
@@ -152,15 +152,11 @@ docs = "sphinx-autobuild docs build/docs --watch snakebids -W"
 script = "scripts.update_bids:main"
 [[tool.poe.tasks.update-bids.sequence]]
 ref = "mkinit"
-[[tool.poe.tasks.update-bids.sequence]]
-ref = "fmt"
 
 [[tool.poe.tasks.mkinit.sequence]]
 cmd = "mkinit --recursive --nomods --lazy_loader_typed --relative -i snakebids"
 [[tool.poe.tasks.mkinit.sequence]]
-ref = "sort snakebids/**/__init__.py*"
-[[tool.poe.tasks.mkinit.sequence]]
-ref = "fmt snakebids/**/__init__.py*"
+ref = "fix"
 
 [tool.poe.tasks._get_version]
 imports = ["platform"]
@@ -178,6 +174,7 @@ cmd = """
 [tool.pytest.ini_options]
 markers = [
     "docker: marks tests as requiring docker (deselect with '-m \"not docker\"')",
+    "disable_fakefs: disable the fake filesystem in a hypothesis test"
 ]
 
 [tool.coverage.run]
@@ -204,6 +201,9 @@ reportPrivateUsage = false
 reportImportCycles = false
 
 [tool.ruff]
+target-version = "py38"
+
+[tool.ruff.lint]
 select = [
     "E",   # pycodestyle error
     "W",   # pycodestyle warning
@@ -267,11 +267,7 @@ ignore = [
     "ISC002",
 ]
 
-
-target-version = "py38"
-
-
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "snakebids/project_template/**" = ["N999"]
 "snakebids/tests/**" = [
     "D",
@@ -280,14 +276,14 @@ target-version = "py38"
     "SLF",
 ]
 
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
 convention = "numpy"
 ignore-decorators = ["snakebids.utils.utils.property_alias"]
 
-[tool.ruff.flake8-builtins]
+[tool.ruff.lint.flake8-builtins]
 builtins-ignorelist = ["filter"]
 
-[tool.ruff.flake8-import-conventions.extend-aliases]
+[tool.ruff.lint.flake8-import-conventions.extend-aliases]
 itertools = "it"
 functools = "ft"
 operator = "op"
@@ -300,5 +296,5 @@ more_itertools = "itx"
 "snakebids.tests.strategies" = "sb_st"
 "snakebids.utils.sb_itertools" = "sb_it"
 
-[tool.ruff.flake8-pytest-style]
+[tool.ruff.lint.flake8-pytest-style]
 fixture-parentheses = false

scripts/update_bids.py

@@ -1,4 +1,5 @@
 """Recompile the bids function stub file based on latest specs."""
+
 from __future__ import annotations
 
 import inspect

snakebids/app.py

@@ -12,6 +12,7 @@
     bidsapp.app([plugins.SnakemakeBidsApp(...)])
 
 """
+
 from __future__ import annotations
 
 import logging

snakebids/core/datasets.py

@@ -223,12 +223,10 @@ def __repr__(self) -> str:
         return self.pformat()
 
     @overload
-    def __getitem__(self, key: str, /) -> BidsComponentRow:
-        ...
+    def __getitem__(self, key: str, /) -> BidsComponentRow: ...
 
     @overload
-    def __getitem__(self, key: tuple[str, ...], /) -> BidsPartialComponent:
-        ...
+    def __getitem__(self, key: tuple[str, ...], /) -> BidsPartialComponent: ...
 
     def __getitem__(
         self, key: str | tuple[str, ...], /

snakebids/core/filtering.py

@@ -17,8 +17,7 @@ def filter_list(
     filters: Mapping[str, Iterable[str] | str],
     return_indices_only: Literal[False] = ...,
     regex_search: bool = ...,
-) -> ZipList:
-    ...
+) -> ZipList: ...
 
 
 @overload
@@ -27,8 +26,7 @@ def filter_list(
     filters: Mapping[str, Iterable[str] | str],
     return_indices_only: Literal[True],
     regex_search: bool = ...,
-) -> list[int]:
-    ...
+) -> list[int]: ...
 
 
 def filter_list(

snakebids/core/input_generation.py

@@ -1,4 +1,5 @@
 """Utilities for converting Snakemake apps to BIDS apps."""
+
 from __future__ import annotations
 
 import json
@@ -60,8 +61,7 @@ def generate_inputs(
     validate: bool = ...,
     pybids_database_dir: Path | str | None = ...,
     pybids_reset_database: bool = ...,
-) -> BidsDataset:
-    ...
+) -> BidsDataset: ...
 
 
 @overload
@@ -80,8 +80,7 @@ def generate_inputs(
     validate: bool = ...,
     pybids_database_dir: Path | str | None = ...,
     pybids_reset_database: bool = ...,
-) -> BidsDatasetDict:
-    ...
+) -> BidsDatasetDict: ...
 
 
 def generate_inputs(

snakebids/io/console.py

@@ -39,6 +39,7 @@
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 """
+
 from __future__ import annotations
 
 import functools as ft

snakebids/jinja2_ext/toml_encode.py

@@ -10,7 +10,7 @@ def toml_string(item: str):
     Technically encodes as json, a (mostly) strict subset of toml, with some encoding
     fixes
     """
-    return json.dumps(item, ensure_ascii=False).replace("\x7F", "\\u007f")
+    return json.dumps(item, ensure_ascii=False).replace("\x7f", "\\u007f")
 
 
 def toml_encode(item: str):

snakebids/paths/_factory.py

@@ -29,8 +29,7 @@ def __call__(
         suffix: str | None = None,
         extension: str | None = None,
         **entities: str | bool,
-    ) -> str:
-        ...
+    ) -> str: ...
 
 
 def _handle_subses_dir(

snakebids/paths/specs.pyi

@@ -33,7 +33,6 @@ def v0_0_0(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
         If False, downstream path generator will not include the session dir
         `*/ses-{session}/*`
     """
-    ...
 
 def v0_11_0(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
     """Spec corresponding to `BIDS v1.9.0`_.
@@ -67,7 +66,6 @@ def v0_11_0(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
         If False, downstream path generator will not include the session dir
         `*/ses-{session}/*`
     """
-    ...
 
 def latest(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
     """Spec corresponding to `BIDS v1.9.0`_.
@@ -101,4 +99,3 @@ def latest(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSpec:
         If False, downstream path generator will not include the session dir
         `*/ses-{session}/*`
     """
-    ...

snakebids/plugins/base.py

@@ -66,12 +66,10 @@ class PluginBase:
     PREFIX = ""
 
     @overload
-    def pop(self, mapping: dict[str, Any], key: str, default: Any, /) -> Any:
-        ...
+    def pop(self, mapping: dict[str, Any], key: str, default: Any, /) -> Any: ...
 
     @overload
-    def pop(self, mapping: dict[str, Any], key: str, /) -> Any:
-        ...
+    def pop(self, mapping: dict[str, Any], key: str, /) -> Any: ...
 
     def pop(self, mapping: dict[str, Any], *args: Any):
         """Remove specified key from mapping, prepending the plugin prefix."""

snakebids/plugins/pybidsdb.py

@@ -117,6 +117,6 @@ def update_cli_namespace(self, namespace: dict[str, Any], config: dict[str, Any]
             if config["pybidsdb_dir"] is not None
             else None
         )
-        config[
-            "pybids_db_reset"
-        ] = f"{DEPRECATION_FLAG}{int(config['pybidsdb_reset'])}{DEPRECATION_FLAG}"
+        config["pybids_db_reset"] = (
+            f"{DEPRECATION_FLAG}{int(config['pybidsdb_reset'])}{DEPRECATION_FLAG}"
+        )

snakebids/plugins/snakemake.py

@@ -87,13 +87,11 @@ def wrapper(self: SnakemakeBidsApp):
 
 
 @overload
-def _resolve_path(path_candidate: Sequence[Any]) -> list[Any]:
-    ...
+def _resolve_path(path_candidate: Sequence[Any]) -> list[Any]: ...
 
 
 @overload
-def _resolve_path(path_candidate: _T) -> _T:
-    ...
+def _resolve_path(path_candidate: _T) -> _T: ...
 
 
 def _resolve_path(path_candidate: Any) -> Any:

snakebids/snakemake_compat.pyi

@@ -28,7 +28,6 @@ def expand(
         with their values as lists. If allow_missing=True is included
         wildcards in filepattern without values will stay unformatted.
     """
-    ...
 
 class Namedlist[T](list[T | Iterable[T]]): ...
 

snakebids/tests/helpers.py

@@ -1,4 +1,5 @@
 """Helper functions and classes for tests"""
+
 from __future__ import annotations
 
 import functools as ft
@@ -24,9 +25,10 @@
 from hypothesis import HealthCheck, example, settings
 from typing_extensions import ParamSpec
 
-from snakebids import bids
+from snakebids import bids_factory
 from snakebids.core.datasets import BidsDataset
 from snakebids.core.input_generation import generate_inputs
+from snakebids.paths import specs
 from snakebids.types import InputsConfig, ZipList, ZipListLike
 from snakebids.utils.containers import MultiSelectDict, UserDictPy38
 from snakebids.utils.utils import BidsEntity
@@ -102,6 +104,7 @@ def get_bids_path(entities: Iterable[str | BidsEntity], **extras: str) -> str:
     def get_tag(entity: BidsEntity) -> tuple[str, str]:
         return entity.wildcard, f"{{{entity.wildcard}}}"
 
+    bids = bids_factory(specs.latest())
     return bids(
         **dict(get_tag(BidsEntity(entity)) for entity in sorted(entities)),
         **{BidsEntity(entity).wildcard: value for entity, value in extras.items()},
@@ -339,16 +342,14 @@ def inner(func: Callable[_P, _T]) -> Callable[_P, _T]:
 class Benchmark(Protocol):
     def __call__(
         self, func: Callable[_P, _T], *args: _P.args, **kwargs: _P.kwargs
-    ) -> _T:
-        ...
+    ) -> _T: ...
 
 
 """Comparison Dunders copied from typeshed"""
 
 
 class SupportsDunderLT(Protocol[_T_contra]):
-    def __lt__(self, __other: _T_contra) -> bool:
-        ...
+    def __lt__(self, __other: _T_contra) -> bool: ...
 
 
 def is_strictly_increasing(items: Iterable[SupportsDunderLT[Any]]) -> bool:

snakebids/tests/strategies.py

@@ -606,11 +606,9 @@ def multiselect_dicts(
 
 if TYPE_CHECKING:
 
-    def everything() -> st.SearchStrategy[Any]:
-        ...
+    def everything() -> st.SearchStrategy[Any]: ...
 
-    def everything_except(*excluded_types: type[Any]) -> st.SearchStrategy[Any]:
-        ...
+    def everything_except(*excluded_types: type[Any]) -> st.SearchStrategy[Any]: ...
 
 else:
 

snakebids/tests/test_generate_inputs.py

@@ -130,15 +130,23 @@ def test_second_return_never_none(
         pybidsdb_reset: bool | None,
         pybids_database_reset: bool | None,
     ):
-        assert (
-            _normalize_database_args(
-                None,
-                pybidsdb_reset,
-                None,
-                pybids_database_reset,
-            )[1]
-            is not None
-        )
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "ignore",
+                message=r"The parameter `pybids_reset_database` in generate_inputs\(\) "
+                "is deprecated and will be removed in the next release. To reset the "
+                "pybids database, use the `pybidsdb_reset` parameter instead",
+                category=UserWarning,
+            )
+            assert (
+                _normalize_database_args(
+                    None,
+                    pybidsdb_reset,
+                    None,
+                    pybids_database_reset,
+                )[1]
+                is not None
+            )
 
     @given(pybidsdb_dir=st.text().filter(_not_deprecated))
     def test_deprecated_dir_raises_warning(self, pybidsdb_dir: str):

snakebids/tests/test_snakemake_io.py

@@ -1,4 +1,5 @@
 """Tests for snakemake_io"""
+
 from snakebids.utils import snakemake_io