Update dependencies and fix resulting bugs

pyproject.toml

@@ -64,23 +64,23 @@ pandas = [
     { version = "<=2.0.3", python = "<3.9" },
     { version = ">=2.1.1", python = ">=3.12" },
 ]
-# minimum 8.2.0 to use post-copy mesages
-copier = ">=8.2.0"
+# minimum 9.2.0 because of breaking dependency changes and changes to validation errors
+copier = ">=9.2.0"
 jinja2-time = ">=0.2.0"
 # minimum 2.31.0 because of security vulnerability
 requests = ">=2.31.0"
 ruamel-yaml = ">=0.17.2"
 lazy-loader = ">=0.3"
 # Docutils is a requirement of snakemake, for snakebids otherwise it is merely a doc
-# dependency. Can't do 0.21 with poetry because of https://github.com/python-poetry/poetry/issues/9293
-docutils = "!=0.21.1"
+# dependency. 0.21.post1 needs to be excluded because of
+# https://github.com/python-poetry/poetry/issues/9293
+docutils = "!=0.21.post1"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.0.0"
 pytest-mock = "^3.7.0"
 poethepoet = "^0.25.1"
 pre-commit = "^3.0.0"
-# need custom fork of mkinit to handle .pyi files. PR to main repo pending
 # 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
 #   still be resolved
@@ -90,7 +90,9 @@ pytest-benchmark = "^4.0.0"
 pyfakefs = "^5.1.0"
 pyparsing = "^3.0.9"
 pathvalidate = "^3.0.0"
-pyright = "^1.1.339"
+# 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"
 pytest-xdist = "^3.3.1"
 pytest-split = "^0.8.1"

snakebids/io/yaml.py

@@ -14,7 +14,7 @@ def path2str(dumper: Dumper, data: Path):
         return dumper.represent_scalar(
             "tag:yaml.org,2002:str",
             str(data),
-        )  # type: ignore
+        )
 
     def to_dict(dumper: Dumper, data: OrderedDict[Any, Any]):
         return dumper.represent_dict(dict(data))

snakebids/tests/test_generate_inputs.py

@@ -1102,7 +1102,9 @@ def test_collects_only_filtered_entities(
             name="foo", path=get_bids_path(result_filtered), zip_lists=result_filtered
         )
 
-    @settings(deadline=400, suppress_health_check=[HealthCheck.function_scoped_fixture])
+    @settings(
+        deadline=None, suppress_health_check=[HealthCheck.function_scoped_fixture]
+    )
     @given(path_entities=path_entities())
     def test_collect_all_but_filters_when_exclusion_filters_used(
         self,

snakebids/tests/test_template.py

@@ -11,7 +11,6 @@
 import copier
 import more_itertools as itx
 import pathvalidate
-import prompt_toolkit.validation
 import pytest
 import requests_mock
 from hypothesis import HealthCheck, assume, given, settings
@@ -98,7 +97,7 @@ def invalid_emails():
 def test_invalid_email_raises_error(email: str, tmp_path: Path):
     data = get_empty_data("testapp", "setuptools")
     data["email"] = email
-    with pytest.raises(prompt_toolkit.validation.ValidationError):
+    with pytest.raises(ValueError, match="Must be a valid email"):
         copier.run_copy(
             str(Path(itx.first(snakebids.__path__), "project_template")),
             tmp_path / data["app_full_name"],
@@ -184,7 +183,7 @@ def test_gets_correct_snakebids_version(
 @allow_function_scoped
 def test_invalid_app_name_raises_error(name: str, tmp_path: Path):
     data = get_empty_data(name, "setuptools")
-    with pytest.raises(prompt_toolkit.validation.ValidationError):
+    with pytest.raises(ValueError, match="Name must be a valid"):
         copier.run_copy(
             str(Path(itx.first(snakebids.__path__), "project_template")),
             tmp_path / data["app_full_name"],

snakebids/utils/containers.py

@@ -62,8 +62,8 @@ def __repr__(self) -> str:
         return f"{self.__class__.__name__}({list(self._data)})"
 
     @override
-    def __contains__(self, item: object, /) -> bool:
-        return item in self._data
+    def __contains__(self, value: object) -> bool:
+        return value in self._data
 
     @override
     def __hash__(self):

typings/ruamel/yaml/__init__.pyi

@@ -0,0 +1,17 @@
+"""
+This type stub file was generated by pyright.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+from ruamel.yaml.main import *
+
+from .cyaml import *
+
+if False: ...
+_package_data: dict[Any, Any] = ...
+version_info = ...
+__version__ = ...
+__with_libyaml__ = ...

typings/ruamel/yaml/anchor.pyi

@@ -0,0 +1,12 @@
+"""
+This type stub file was generated by pyright.
+"""
+
+if False: ...
+anchor_attrib = ...
+
+class Anchor:
+    __slots__ = ...
+    attrib = ...
+    def __init__(self) -> None: ...
+    def __repr__(self) -> Any: ...