Consolidate package metadata from setup.py/setup.cfg into pyproject.toml

Migrate all metadata, dependencies, and tool configuration into pyproject.toml
using the modern PEP 517/518/621 [project] table, eliminating setup.py and
setup.cfg. Flake8 config moves to a dedicated .flake8 file since flake8 does
not natively support pyproject.toml. Also removes the stale setup.py references
from tox.ini's lint env.

Notable changes:
- setuptools requirement bumped to >=61.0.0 for native [project] table support
- wheel removed from build-system.requires (handled automatically by pip)
- license field uses SPDX expression (Apache-2.0) per PEP 639; redundant
  License classifier removed
- [all] extra uses self-referential syntax dandischema[style,test]
- mypy exclude anchored to ^dandischema/_version\.py$ to match the actual
  path written by versioningit
- pydantic-mypy warn_untypes_fields dropped (was a typo, silently ignored)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: candleindark

.flake8

@@ -0,0 +1,6 @@
+[flake8]
+max-line-length = 100
+ignore = E203,W503
+exclude =
+    */__init__.py
+    .tox/

pyproject.toml

@@ -1,7 +1,66 @@
 [build-system]
-# Setuptools version should match setup.py; wheel because pip will insert it noisily
-requires = ["setuptools >= 42.0.0", "versioningit", "wheel"]
-build-backend = 'setuptools.build_meta'
+requires = ["setuptools >= 61.0.0", "versioningit"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "dandischema"
+description = "Schemata for DANDI archive project"
+readme = {file = "README.md", content-type = "text/markdown"}
+license = "Apache-2.0"
+authors = [
+    {name = "DANDI developers", email = "team@dandiarchive.org"},
+]
+maintainers = [
+    {name = "Yaroslav O. Halchenko", email = "debian@onerussian.com"},
+]
+classifiers = [
+    "Development Status :: 1 - Planning",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering",
+]
+requires-python = ">=3.10"
+dependencies = [
+    "jsonschema[format]",
+    "packaging>=14.0",
+    "pydantic-settings",
+    "pydantic[email]~=2.4",
+    "requests",
+    "zarr_checksum",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "http://dandiarchive.org"
+"Source Code" = "https://github.com/dandi/dandischema"
+
+[project.optional-dependencies]
+style = [
+    "flake8",
+    "pre-commit",
+]
+test = [
+    "anys",
+    "mypy",
+    "pytest",
+    "pytest-cov",
+    "pytest-rerunfailures",
+]
+all = [
+    "dandischema[style]",
+    "dandischema[test]",
+]
+
+[tool.setuptools.packages.find]
+namespaces = true
+include = ["dandischema*"]
 
 [tool.versioningit]
 default-version = "0+unknown"
@@ -19,10 +78,34 @@ distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 file = "dandischema/_version.py"
 
 [tool.black]
-exclude='\.eggs|\.git|\.mypy_cache|\.tox|\.venv|_build|buck-out|build|dist'
+exclude = '\.eggs|\.git|\.mypy_cache|\.tox|\.venv|_build|buck-out|build|dist'
 
 [tool.isort]
 profile = "black"
 force_sort_within_sections = true
 reverse_relative = true
 known_first_party = ["dandischema"]
+
+[tool.mypy]
+allow_incomplete_defs = false
+allow_untyped_defs = false
+ignore_missing_imports = false
+no_implicit_optional = true
+implicit_reexport = false
+local_partial_types = true
+pretty = true
+show_error_codes = true
+show_traceback = true
+strict_equality = true
+warn_redundant_casts = true
+warn_return_any = true
+warn_unreachable = true
+plugins = ["pydantic.mypy"]
+exclude = ['^dandischema/_version\.py$']
+
+[[tool.mypy.overrides]]
+module = "dandischema._version"
+follow_imports = "skip"
+
+[tool.pydantic-mypy]
+init_forbid_extra = true

setup.cfg

@@ -18,8 +18,8 @@ deps =
     codespell~=2.0
     flake8
 commands =
-    codespell dandischema setup.py
-    flake8 --config=setup.cfg {posargs} dandischema setup.py
+    codespell dandischema
+    flake8 {posargs} dandischema
 
 [testenv:typing]
 deps =