From a2cb323db418806ed54c21f37073d67562cd0703 Mon Sep 17 00:00:00 2001 From: Peter Van Dyken Date: Thu, 21 Sep 2023 12:18:18 -0400 Subject: [PATCH] Remove dependency upper-caps and update Remove cached-property dep since functionality is provided by functools in py38 Remove all upper version limits in main dependency block. Where kept, justification comment is added Upgraded pvandyken-deprecated dependency, which packages proper typing support (thus, remove our own typings file) --- poetry.lock | 1790 +++++++++---------- pyproject.toml | 24 +- snakebids/core/datasets.py | 16 +- typings/cached_property.pyi | 7 - typings/pvandyken/deprecated/__init__.pyi | 19 - typings/pvandyken/deprecated/deprecated.pyi | 112 -- 6 files changed, 906 insertions(+), 1062 deletions(-) delete mode 100644 typings/cached_property.pyi delete mode 100644 typings/pvandyken/deprecated/__init__.pyi delete mode 100644 typings/pvandyken/deprecated/deprecated.pyi diff --git a/poetry.lock b/poetry.lock index 94809e84..c110fce8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,14 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. 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-32,21 +32,24 @@ patterns = [ ] [tool.poetry.dependencies] -python = ">=3.8,<3.12" -pybids = "^0.16.0" +# upper cap imposed by scipy +python = ">=3.8,<3.13" +# core dep with high breakage potential given plans for redesign, so +# keep upper limit +pybids = ">=0.16.0,<0.17" snakemake = [ { version = ">=5.28.0", python = ">=3.8" }, { version = ">=7.18.2", python = ">=3.11" }, ] -PyYAML = "^6" +PyYAML = ">=6" typing-extensions = ">=3.10.0" -attrs = ">=21.2.0,<24" +attrs = ">=21.2.0" boutiques = "^0.5.25" -more-itertools = ">=8,<11" -cached-property = "^1.5.2" -pvandyken-deprecated = "0.0.3" +more-itertools = ">=8" +# package developed in complete tandem with snakebids, so no need for a range +pvandyken-deprecated = "0.0.4" # Need this until py39 -importlib-resources = ">=5.12.0,<7" +importlib-resources = ">=5.12.0" # Below are non-direct dependencies (i.e. dependencies of other depenencies) # specified to ensure a version with a pre-built wheel is installed depending @@ -78,12 +81,9 @@ hypothesis = "^6.34.1" pytest-benchmark = "^4.0.0" pyfakefs = "^5.1.0" pyparsing = "^3.0.9" -# Version 1.1.312-1.1.315 have a false positive handling some nested function -# calls pathvalidate = "^3.0.0" -# As of pyright==1.1.327 only 1.1.324 is bug free pyright = "==1.1.324" -ruff = "^0.0.285" +ruff = "^0.0.290" pytest-xdist = "^3.3.1" pytest-split = "^0.8.1" tomli = "^2.0.1" diff --git a/snakebids/core/datasets.py b/snakebids/core/datasets.py index 928aef62..9d06bc1e 100644 --- a/snakebids/core/datasets.py +++ b/snakebids/core/datasets.py @@ -1,5 +1,6 @@ from __future__ import annotations +import functools as ft import itertools as it import textwrap import warnings @@ -11,7 +12,6 @@ import attr import more_itertools as itx from bids import BIDSLayout -from cached_property import cached_property from pvandyken.deprecated import deprecated from snakemake.io import expand as sn_expand from typing_extensions import Self, TypedDict @@ -654,7 +654,7 @@ def pformat(self, max_width: int | float | None = None, tabstop: int = 4) -> str ] return "\n".join(output) - @cached_property + @ft.cached_property @deprecated( details=""" The behaviour of path will change in an upcoming release, where it will refer @@ -670,7 +670,7 @@ def path(self) -> dict[str, str]: """ return {key: value.path for key, value in self.items()} - @cached_property + @ft.cached_property @deprecated( details=""" The behaviour of zip_lists will change in an upcoming release, where it will @@ -687,7 +687,7 @@ def zip_lists(self) -> dict[str, ZipList]: """ return {key: value.zip_lists for key, value in self.items()} - @cached_property + @ft.cached_property @deprecated( details=""" The behaviour of entities will change in the 1.0 release, where it will refer @@ -704,7 +704,7 @@ def entities(self) -> dict[str, MultiSelectDict[str, list[str]]]: """ return {key: value.entities for key, value in self.items()} - @cached_property + @ft.cached_property @deprecated( details=""" The behaviour of wildcards will change in an upcoming release, where it will @@ -721,7 +721,7 @@ def wildcards(self) -> dict[str, MultiSelectDict[str, str]]: """ return {key: value.input_wildcards for key, value in self.items()} - @cached_property + @ft.cached_property def subjects(self) -> list[str]: """A list of the subjects in the dataset.""" return [ @@ -732,7 +732,7 @@ def subjects(self) -> list[str]: } ] - @cached_property + @ft.cached_property def sessions(self) -> list[str]: """A list of the sessions in the dataset.""" return [ @@ -743,7 +743,7 @@ def sessions(self) -> list[str]: } ] - @cached_property + @ft.cached_property def subj_wildcards(self) -> dict[str, str]: """The subject and session wildcards applicable to this dataset. diff --git a/typings/cached_property.pyi b/typings/cached_property.pyi deleted file mode 100644 index 44b44dbd..00000000 --- a/typings/cached_property.pyi +++ /dev/null @@ -1,7 +0,0 @@ -from typing import TypeVar - -from snakebids.utils.user_property import UserProperty - -T = TypeVar("T") - -class cached_property(UserProperty[T]): ... diff --git a/typings/pvandyken/deprecated/__init__.pyi b/typings/pvandyken/deprecated/__init__.pyi deleted file mode 100644 index dd0cf3bc..00000000 --- a/typings/pvandyken/deprecated/__init__.pyi +++ /dev/null @@ -1,19 +0,0 @@ -""" -This type stub file was generated by pyright. -""" - -from pvandyken.deprecated.deprecated import ( - DeprecatedWarning, - UnsupportedWarning, - deprecated, - fail_if_not_removed, - set_config, -) - -__all__ = [ - "DeprecatedWarning", - "UnsupportedWarning", - "deprecated", - "fail_if_not_removed", - "set_config", -] diff --git a/typings/pvandyken/deprecated/deprecated.pyi b/typings/pvandyken/deprecated/deprecated.pyi deleted file mode 100644 index a0cf6256..00000000 --- a/typings/pvandyken/deprecated/deprecated.pyi +++ /dev/null @@ -1,112 +0,0 @@ -""" -This type stub file was generated by pyright. -""" -from __future__ import annotations - -from datetime import date -from typing import Any, Callable - -from typing_extensions import ParamSpec, TypeAlias, TypedDict, TypeVar - -_P = ParamSpec("_P") -_T = TypeVar("_T") -MessageLocations: TypeAlias = ... - -class Config(TypedDict): - message_location: MessageLocations - ... - -config = ... - -def set_config(message_location: MessageLocations | None = ...): ... - -class DeprecatedWarning(DeprecationWarning): - """A warning class for deprecated methods - - This is a specialization of the built-in :class:`DeprecationWarning`, - adding parameters that allow us to get information into the __str__ - that ends up being sent through the :mod:`warnings` system. - The attributes aren't able to be retrieved after the warning gets - raised and passed through the system as only the class--not the - instance--and message are what gets preserved. - - Args - function: The function being deprecated. deprecated_in: The version that - ``function`` is deprecated in removed_in: The version or - :class:`datetime.date` specifying when ``function`` gets removed. - details: Optional details about the deprecation. Most often this will include - directions on what to use instead of the now deprecated code. - """ - - def __init__(self, function, deprecated_in, removed_in, details=...) -> None: ... - def __str__(self) -> str: ... - -class UnsupportedWarning(DeprecatedWarning): - """A warning class for methods to be removed - - This is a subclass of :class:`~deprecation.DeprecatedWarning` and is used - to output a proper message about a function being unsupported. - Additionally, the :func:`~deprecation.fail_if_not_removed` decorator - will handle this warning and cause any tests to fail if the system - under test uses code that raises this warning. - """ - - def __str__(self) -> str: ... - -_FuncT = TypeVar("_FuncT", bound=Callable[..., Any]) - -def deprecated( - deprecated_in: str | None = ..., - removed_in: str | date | None = ..., - current_version: str | None = ..., - details: str = ..., - admonition: str | None = ..., -) -> Callable[[_FuncT], _FuncT]: - """Decorate a function to signify its deprecation - - This function wraps a method that will soon be removed and does two things: - * The docstring of the method will be modified to include a notice - about deprecation, e.g., "Deprecated since 0.9.11. Use foo instead." - * Raises a :class:`~deprecation.DeprecatedWarning` - via the :mod:`warnings` module, which is a subclass of the built-in - :class:`DeprecationWarning`. Note that built-in - :class:`DeprecationWarning`s are ignored by default, so for users - to be informed of said warnings they will need to enable them--see - the :mod:`warnings` module documentation for more details. - - Args: - deprecated_in: The version at which the decorated method is considered - deprecated. This will usually be the next version to be released when the - decorator is added. The default is **None**, which effectively means - immediate deprecation. If this is not specified, then the `removed_in` and - `current_version` arguments are ignored. - removed_in: The version or :class:`datetime.date` when the decorated method will - be removed. The default is **None**, specifying that the function is not - currently planned to be removed. Note: This parameter cannot be set to a - value if `deprecated_in=None`. - current_version: The source of version information for the currently running - code. This will usually be a `__version__` attribute on your library. The - default is `None`. When `current_version=None` the automation to determine - if the wrapped function is actually in a period of deprecation or time for - removal does not work, causing a :class:`~deprecation.DeprecatedWarning` to - be raised in all cases. - details: Extra details to be added to the method docstring and warning. For - example, the details may point users to a replacement method, such as "Use - the foo_bar method instead". By default there are no details. - """ - ... - -def fail_if_not_removed( - method, -): # -> _Wrapped[(...), Unknown, (*args: Unknown, **kwargs: Unknown), Unknown]: - """Decorate a test method to track removal of deprecated code - - This decorator catches :class:`~deprecation.UnsupportedWarning` - warnings that occur during testing and causes unittests to fail, - making it easier to keep track of when code should be removed. - - Raises: - Assertion Error - is raised while running the test method. - """ - ...