biotope 0.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- biotope-0.1.0/LICENSE +21 -0
- biotope-0.1.0/PKG-INFO +40 -0
- biotope-0.1.0/README.md +14 -0
- biotope-0.1.0/pyproject.toml +106 -0
- biotope-0.1.0/src/biotope/__init__.py +24 -0
biotope-0.1.0/LICENSE
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MIT License
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Copyright (c) 2025 Sebastian Lobentanzer
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Permission is hereby granted, free of charge, to any person obtaining a copy of
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this software and associated documentation files (the "Software"), to deal in
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the Software without restriction, including without limitation the rights to
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use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
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the Software, and to permit persons to whom the Software is furnished to do so,
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subject to the following conditions:
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The above copyright notice and this permission notice (including the next
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paragraph) shall be included in all copies or substantial portions of the
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Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
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FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
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COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
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IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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biotope-0.1.0/PKG-INFO
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Metadata-Version: 2.1
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Name: biotope
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Version: 0.1.0
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Summary: CLI integration for BioCypher ecosystem packages
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License: MIT
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Author: Sebastian Lobentanzer
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Author-email: sebastian.lobentanzer@gmail.com
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Requires-Python: >=3.10,<4.0
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Classifier: Development Status :: 2 - Pre-Alpha
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3 :: Only
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Requires-Dist: click (>=8.1.8,<9.0.0)
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Project-URL: Bug Tracker, https://github.com/biocypher/cli/issues
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Project-URL: Documentation, https://biocypher.org
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Project-URL: Download, https://pypi.org/project/biotope/#files
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Project-URL: Homepage, https://github.com/biocypher/cli
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Project-URL: Source Code, https://github.com/biocypher/cli
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Description-Content-Type: text/markdown
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# biotope
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| | |
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|---|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| Package | [](https://pypi.org/project/biotope/) [](https://pypi.org/project/biotope/) [](https://biotope.readthedocs.io/en/latest/?badge=latest) |
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| Meta | [](LICENSE) [](.github/CODE_OF_CONDUCT.md) [](https://mypy-lang.org/) [](https://github.com/ambv/black) [](https://github.com/astral-sh/ruff) |
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| Automation | |
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_CLI integration for BioCypher ecosystem packages_
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## Copyright
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- Copyright © 2025 Sebastian Lobentanzer.
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- Free software distributed under the [MIT License](./LICENSE).
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biotope-0.1.0/README.md
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# biotope
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|---|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| Package | [](https://pypi.org/project/biotope/) [](https://pypi.org/project/biotope/) [](https://biotope.readthedocs.io/en/latest/?badge=latest) |
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| Meta | [](LICENSE) [](.github/CODE_OF_CONDUCT.md) [](https://mypy-lang.org/) [](https://github.com/ambv/black) [](https://github.com/astral-sh/ruff) |
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| Automation | |
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_CLI integration for BioCypher ecosystem packages_
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## Copyright
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- Copyright © 2025 Sebastian Lobentanzer.
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- Free software distributed under the [MIT License](./LICENSE).
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################################################################################
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# Build Configuration
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################################################################################
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[build-system]
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requires = ["poetry-core>=1.0.0"]
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build-backend = "poetry.core.masonry.api"
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################################################################################
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# Project Configuration
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################################################################################
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[project]
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# This section will be replaced with Poetry's format
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[tool.poetry]
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name = "biotope"
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version = "0.1.0"
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description = "CLI integration for BioCypher ecosystem packages"
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authors = ["Sebastian Lobentanzer <sebastian.lobentanzer@gmail.com>"]
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license = "MIT"
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readme = "README.md"
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classifiers = [
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"Development Status :: 2 - Pre-Alpha",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Operating System :: OS Independent",
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"Programming Language :: Python :: 3 :: Only",
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]
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keywords = []
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[tool.poetry.urls]
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Homepage = "https://github.com/biocypher/cli"
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"Source Code" = "https://github.com/biocypher/cli"
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"Bug Tracker" = "https://github.com/biocypher/cli/issues"
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Documentation = "https://biocypher.org"
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Download = "https://pypi.org/project/biotope/#files"
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[tool.poetry.dependencies]
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python = "^3.10"
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click = "^8.1.8"
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[tool.poetry.group.dev.dependencies]
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pre-commit = "*"
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################################################################################
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# Tool Configuration
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################################################################################
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[tool.pytest.ini_options]
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testpaths = ["tests"]
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markers = ["raises"]
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[tool.coverage.paths]
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source = [
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"src/biotope",
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"*/site-packages/biotope",
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]
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[tool.coverage.run]
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branch = true
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parallel = true
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[tool.coverage.report]
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exclude_lines = ["pragma: no cover"]
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precision = 2
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[tool.ruff]
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line-length = 88
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[tool.ruff.lint]
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select = ["ALL"]
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ignore = [
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"D107", # 'Missing docstring in __init__' ignored because pydoclint wants us to document the class instead.
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"D203", # '1 blank line required before class docstring' ignored because we want no blank line.
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"D212", # 'Multi-line docstring summary should start at the first line' ignored because we want the summary to start on the second line.
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"D407", # 'Missing dashed underline after section' ignored because Google style docstrings don't underline.
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"ANN002", # 'Missing type annotation for {*args} in method'.
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"ANN003", # 'Missing type annotation for {*kwargs} in method'.
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"ANN101", # 'Missing type annotation for {self} in method'.
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"ANN102", # 'Missing type annotation for {cls} in classmethod'.
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]
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exclude = [
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]
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[tool.ruff.lint.extend-per-file-ignores]
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"__init__.py" = [
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"E401", # 'Multiple imports on one line'
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"E402", # 'Module level import not at top of file'
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"F401", # 'Imported but unused'
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"I001", # 'Import block is un-sorted or un-formatted' ignored because we may have to import in a particular, not-alphabetical order.
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]
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"tests/**/*.py" = [
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"S101", # 'Use of assert detected' ignored because we are using pytest.
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"INP001", # 'Insecure input' ignored because we are testing.
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"ANN201", # 'Missing type annotation for {return}' ignored because all tests return `None`.
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]
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[tool.ruff.lint.isort]
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case-sensitive = true
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known-first-party = ["src", "biotope"]
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lines-after-imports = 1
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[tool.pydoclint]
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style = "google" # TODO: Other styles are possible here, like 'numpy'
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arg-type-hints-in-docstring = false
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check-return-types = false
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check-yield-types = false
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# MIT License
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#
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# Copyright (c) 2025 Sebastian Lobentanzer
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy
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# of this software and associated documentation files (the "Software"), to deal
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# in the Software without restriction, including without limitation the rights
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# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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# copies of the Software, and to permit persons to whom the Software is
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# furnished to do so, subject to the following conditions:
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#
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# The above copyright notice and this permission notice (including the next
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# paragraph) shall be included in all copies or substantial portions of the
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# Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# SOFTWARE.
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"""Provide top level symbols."""
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