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Refactor: Consolidate all metadata into pyproject.toml
Migrate all package metadata from setup.cfg to pyproject.toml following modern Python packaging standards (PEP 517/518/621). Changes: pyproject.toml: - Add complete [project] section with all package metadata - Package name, description, readme, license - Authors and maintainers information - Python version requirement (>=3.9) - All dependencies (runtime requirements) - All optional-dependencies (extensions, extras, style, test, tools, all) - Entry points for CLI and pytest plugin - Project URLs (Homepage, Source Code, Documentation) - Add [tool.setuptools] configuration for package discovery - Consolidate tool configurations: - [tool.versioneer] for version management - [tool.flake8] for linting - [tool.codespell] for spell checking (fixed regex escaping, excluded pyproject.toml) - [tool.mypy] with grouped module overrides per mypy documentation - [tool.pydantic-mypy] for pydantic plugin - Preserve existing [tool.black] and [tool.isort] configurations setup.cfg: - Reduce to minimal configuration - Keep only [flake8] section (doesn't support pyproject.toml) - Keep [versioneer] section (versioneer checks both files) - Remove all [metadata], [options], and mypy sections .pre-commit-config.yaml: - Exclude pyproject.toml from codespell checks (it contains codespell config comments that would trigger false positives) setup.py: - No changes (still required for versioneer integration) Verification: - Build succeeds with python -m build - Package metadata correctly preserved in wheel - All dependencies and entry points maintained - Versioneer continues to work properly 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com> Conflicts: setup.cfg -- master meanwhile boosted min version of dandischema to 0.11.1 - I did the same
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‎.pre-commit-config.yaml‎

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@@ -22,7 +22,7 @@ repos:
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rev: v2.0.0
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hooks:
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- id: codespell
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exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py)$
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exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py|pyproject\.toml)$
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- repo: https://github.com/PyCQA/flake8
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rev: 7.0.0
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hooks:

‎pyproject.toml‎

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@@ -3,6 +3,132 @@
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requires = ["setuptools >= 38.3.0", "wheel"]
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build-backend = 'setuptools.build_meta'
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[project]
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name = "dandi"
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description = "Command line client for interaction with DANDI instances"
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readme = "README.md"
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requires-python = ">=3.9"
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license = {text = "Apache 2.0"}
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authors = [
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{name = "DANDI developers", email = "team@dandiarchive.org"},
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]
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maintainers = [
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{name = "Yaroslav O. Halchenko", email = "debian@onerussian.com"},
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]
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keywords = []
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classifiers = [
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"Development Status :: 1 - Planning",
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"Environment :: Console",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: Apache Software License",
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"Operating System :: OS Independent",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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"Topic :: Scientific/Engineering",
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]
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dependencies = [
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"bidsschematools ~= 1.0",
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"bids-validator-deno >= 2.0.5",
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# >=8.2.0: https://github.com/pallets/click/issues/2911
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"click >= 7.1, <8.2.0",
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"click-didyoumean",
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"dandischema >= 0.11.1, < 0.12.0",
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"etelemetry >= 0.2.2",
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# For pydantic to be able to use type annotations like `X | None`
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"eval_type_backport; python_version < '3.10'",
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"fasteners",
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"fscacher >= 0.3.0",
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# 3.14.4: https://github.com/hdmf-dev/hdmf/issues/1186
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"hdmf != 3.5.0,!=3.14.4",
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"humanize",
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"interleave ~= 0.3",
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"joblib",
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"keyring != 23.9.0",
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"keyrings.alt",
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"packaging",
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"platformdirs",
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"pycryptodomex", # for EncryptedKeyring backend in keyrings.alt
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"pydantic ~= 2.0",
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"pynwb >= 1.0.3,!=1.1.0,!=2.3.0",
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"numcodecs < 0.16",
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"nwbinspector >= 0.4.28,!=0.4.32",
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"pyout >=0.5, !=0.6.0",
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"python-dateutil",
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"requests ~= 2.20",
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"ruamel.yaml >=0.15, <1",
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"semantic-version",
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"tenacity",
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"tensorstore",
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# possibly silently incomplete downloads: https://github.com/dandi/dandi-cli/issues/1500
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"urllib3 >= 2.0.0",
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"yarl ~= 1.9",
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"zarr >= 2.10, <= 3.0.8",
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"zarr_checksum ~= 0.4.0",
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]
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dynamic = ["version"]
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[project.optional-dependencies]
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# PyNWB extensions we know and somewhat care about
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# e.g. import whenever pynwb fails without them
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extensions = [
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"allensdk",
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"ndx-hed",
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"ndx-events",
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]
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extras = [
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"duecredit >= 0.6.0",
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"fsspec[http]",
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]
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style = [
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"flake8",
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"pre-commit",
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]
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test = [
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"anys ~= 0.2",
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"coverage",
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"opencv-python",
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"pytest",
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"pytest-cov",
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"pytest-mock",
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"pytest-rerunfailures",
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"pytest-timeout",
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"responses != 0.24.0, != 0.25.5",
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"vcrpy",
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]
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tools = [
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"boto3",
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]
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all = [
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"dandi[extensions]",
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"dandi[extras]",
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"dandi[style]",
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"dandi[test]",
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"dandi[tools]",
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]
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[project.urls]
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Homepage = "http://dandiarchive.org"
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"Source Code" = "https://github.com/dandi/dandi-cli"
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Documentation = "https://dandi.readthedocs.io"
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[project.scripts]
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dandi = "dandi.cli.command:main"
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[project.entry-points.pytest11]
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dandi = "dandi.pytest_plugin"
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[tool.setuptools]
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zip-safe = false
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include-package-data = true
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[tool.setuptools.packages.find]
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include = ["dandi*"]
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namespaces = true
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[tool.black]
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exclude='\.eggs|\.git|\.mypy_cache|\.tox|\.venv|_build|buck-out|build|dist|_version\.py|versioneer\.py'
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reverse_relative = true
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sort_relative_in_force_sorted_sections = true
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known_first_party = ["dandi"]
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[tool.versioneer]
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VCS = "git"
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style = "pep440"
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versionfile_source = "dandi/_version.py"
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versionfile_build = "dandi/_version.py"
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tag_prefix = ""
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parentdir_prefix = ""
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[tool.flake8]
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max-line-length = 100
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ignore = ["E203", "W503"]
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extend-exclude = [
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"_version.py",
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"versioneer.py",
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]
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[tool.codespell]
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skip = "_version.py,due.py,versioneer.py,*.vcr.yaml,venv,venvs,pyproject.toml"
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# Don't warn about "[l]ist" in the abbrev_prompt() docstring:
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# TE is present in the BIDS schema
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ignore-regex = "(\\[\\w\\]\\w+|TE|ignore \"bu\" strings)"
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ignore-words-list = "ba,bu,fo"
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[tool.mypy]
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# TODO: Eventually uncomment these:
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#allow_untyped_defs = False
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implicit_reexport = false
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allow_incomplete_defs = false
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ignore_missing_imports = false
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no_implicit_optional = true
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local_partial_types = true
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pretty = true
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show_error_codes = true
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show_traceback = true
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strict_equality = true
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warn_redundant_casts = true
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warn_return_any = true
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warn_unreachable = true
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plugins = ["pydantic.mypy"]
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exclude = "_version\\.py|due\\.py"
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[[tool.mypy.overrides]]
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module = "dandi.*"
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ignore_missing_imports = true
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[[tool.mypy.overrides]]
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module = [
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"dandi._version",
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"dandi.due",
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]
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follow_imports = "skip"
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[[tool.mypy.overrides]]
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module = [
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"bidsschematools.*",
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"click_didyoumean.*",
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"etelemetry.*",
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"fasteners.*",
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"fscacher.*",
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"fsspec.*",
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"h5py.*",
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"hdmf.*",
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"joblib.*",
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"keyrings.alt.*",
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"nwbinspector.*",
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"pynwb.*",
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"pyout.*",
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"semantic_version.*",
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"vcr.*",
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"zarr.*",
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]
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ignore_missing_imports = true
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[tool.pydantic-mypy]
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init_forbid_extra = true

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