poetry.lock

[[package]]
name = "aiohttp"
version = "3.8.1"
description = "Async http client/server framework (asyncio)"
category = "main"
optional = false
python-versions = ">=3.6"

[package.dependencies]
aiosignal = ">=1.1.2"
async-timeout = ">=4.0.0a3,<5.0"
attrs = ">=17.3.0"
charset-normalizer = ">=2.0,<3.0"
frozenlist = ">=1.1.1"
multidict = ">=4.5,<7.0"
yarl = ">=1.0,<2.0"

[package.extras]
speedups = ["aiodns", "brotli", "cchardet"]

[[package]]
name = "aiosignal"
version = "1.2.0"
description = "aiosignal: a list of registered asynchronous callbacks"
category = "main"
optional = false
python-versions = ">=3.6"

[package.dependencies]
frozenlist = ">=1.1.0"

[[package]]
name = "antlr4-python3-runtime"
version = "4.9.3"
description = "ANTLR 4.9.3 runtime for Python 3.7"
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "anyio"
version = "3.6.1"
description = "High level compatibility layer for multiple asynchronous event loop implementations"
category = "main"
optional = false
python-versions = ">=3.6.2"

[package.dependencies]
idna = ">=2.8"
sniffio = ">=1.1"

[package.extras]
doc = ["packaging", "sphinx-rtd-theme", "sphinx-autodoc-typehints (>=1.2.0)"]
test = ["coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "contextlib2", "uvloop (<0.15)", "mock (>=4)", "uvloop (>=0.15)"]
trio = ["trio (>=0.16)"]

[[package]]
name = "appdirs"
version = "1.4.4"
description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "async-timeout"
version = "4.0.2"
description = "Timeout context manager for asyncio programs"
category = "main"
optional = false
python-versions = ">=3.6"

[[package]]
name = "atomicwrites"
version = "1.4.0"
description = "Atomic file writes."
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"

[[package]]
name = "attrs"
version = "21.4.0"
description = "Classes Without Boilerplate"
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"

[package.extras]
dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"]
docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"]
tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"]
tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"]

[[package]]
name = "bcp47"
version = "0.0.4"
description = "Language tags made easy"
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "bioregistry"
version = "0.5.39"
description = "Integrated registry of biological databases and nomenclatures"
category = "main"
optional = false
python-versions = ">=3.6"

[package.dependencies]
click = "*"
more-click = "*"
pydantic = "*"
pystow = ">=0.1.13"
requests = "*"
tqdm = "*"

[package.extras]
align = ["pyyaml", "beautifulsoup4", "tabulate", "defusedxml", "class-resolver"]
charts = ["matplotlib", "matplotlib-venn", "seaborn", "pandas"]
docs = ["sphinx", "sphinx-rtd-theme", "sphinx-click", "sphinx-autodoc-typehints", "sphinx-automodapi", "autodoc-pydantic"]
export = ["pyyaml", "rdflib", "rdflib-jsonld", "ndex2"]
gha = ["more-itertools"]
health = ["click-default-group", "pandas"]
tests = ["coverage", "pytest", "more-itertools"]
web = ["pyyaml", "rdflib", "rdflib-jsonld", "flask", "flasgger", "bootstrap-flask (<=2.0.0)", "markdown"]

[[package]]
name = "black"
version = "22.6.0"
description = "The uncompromising code formatter."
category = "dev"
optional = false
python-versions = ">=3.6.2"

[package.dependencies]
click = ">=8.0.0"
mypy-extensions = ">=0.4.3"
pathspec = ">=0.9.0"
platformdirs = ">=2"
tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""}
typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}

[package.extras]
colorama = ["colorama (>=0.4.3)"]
d = ["aiohttp (>=3.7.4)"]
jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
uvloop = ["uvloop (>=0.15.2)"]

[[package]]
name = "certifi"
version = "2022.6.15"
description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
python-versions = ">=3.6"

[[package]]
name = "chardet"
version = "4.0.0"
description = "Universal encoding detector for Python 2 and 3"
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"

[[package]]
name = "charset-normalizer"
version = "2.1.0"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
category = "main"
optional = false
python-versions = ">=3.6.0"

[package.extras]
unicode_backport = ["unicodedata2"]

[[package]]
name = "class-resolver"
version = "0.3.10"
description = "Lookup and instantiate classes with style."
category = "main"
optional = false
python-versions = ">=3.7"

[package.extras]
click = ["click"]
docdata = ["docdata"]
docs = ["sphinx", "sphinx-rtd-theme", "sphinx-autodoc-typehints", "sphinx-automodapi"]
numpy = ["numpy"]
optuna = ["optuna"]
ray = ["ray"]
tests = ["coverage", "pytest"]
torch = ["torch"]

[[package]]
name = "click"
version = "8.1.3"
description = "Composable command line interface toolkit"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
colorama = {version = "*", markers = "platform_system == \"Windows\""}

[[package]]
name = "colorama"
version = "0.4.5"
description = "Cross-platform colored terminal text."
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"

[[package]]
name = "decorator"
version = "5.1.1"
description = "Decorators for Humans"
category = "main"
optional = false
python-versions = ">=3.5"

[[package]]
name = "deprecated"
version = "1.2.13"
description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"

[package.dependencies]
wrapt = ">=1.10,<2"

[package.extras]
dev = ["tox", "bump2version (<1)", "sphinx (<2)", "importlib-metadata (<3)", "importlib-resources (<4)", "configparser (<5)", "sphinxcontrib-websupport (<2)", "zipp (<2)", "PyTest (<5)", "PyTest-Cov (<2.6)", "pytest", "pytest-cov"]

[[package]]
name = "deprecation"
version = "2.1.0"
description = "A library to handle automated deprecations"
category = "main"
optional = false
python-versions = "*"

[package.dependencies]
packaging = "*"

[[package]]
name = "fastapi"
version = "0.78.0"
description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production"
category = "main"
optional = false
python-versions = ">=3.6.1"

[package.dependencies]
pydantic = ">=1.6.2,<1.7 || >1.7,<1.7.1 || >1.7.1,<1.7.2 || >1.7.2,<1.7.3 || >1.7.3,<1.8 || >1.8,<1.8.1 || >1.8.1,<2.0.0"
starlette = "0.19.1"

[package.extras]
all = ["requests (>=2.24.0,<3.0.0)", "jinja2 (>=2.11.2,<4.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "itsdangerous (>=1.1.0,<3.0.0)", "pyyaml (>=5.3.1,<7.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "orjson (>=3.2.1,<4.0.0)", "email_validator (>=1.1.1,<2.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)"]
dev = ["python-jose[cryptography] (>=3.3.0,<4.0.0)", "passlib[bcrypt] (>=1.7.2,<2.0.0)", "autoflake (>=1.4.0,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "uvicorn[standard] (>=0.12.0,<0.18.0)", "pre-commit (>=2.17.0,<3.0.0)"]
doc = ["mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs-markdownextradata-plugin (>=0.1.7,<0.3.0)", "typer (>=0.4.1,<0.5.0)", "pyyaml (>=5.3.1,<7.0.0)"]
test = ["pytest (>=6.2.4,<7.0.0)", "pytest-cov (>=2.12.0,<4.0.0)", "mypy (==0.910)", "flake8 (>=3.8.3,<4.0.0)", "black (==22.3.0)", "isort (>=5.0.6,<6.0.0)", "requests (>=2.24.0,<3.0.0)", "httpx (>=0.14.0,<0.19.0)", "email_validator (>=1.1.1,<2.0.0)", "sqlalchemy (>=1.3.18,<1.5.0)", "peewee (>=3.13.3,<4.0.0)", "databases[sqlite] (>=0.3.2,<0.6.0)", "orjson (>=3.2.1,<4.0.0)", "ujson (>=4.0.1,!=4.0.2,!=4.1.0,!=4.2.0,!=4.3.0,!=5.0.0,!=5.1.0,<6.0.0)", "python-multipart (>=0.0.5,<0.0.6)", "flask (>=1.1.2,<3.0.0)", "anyio[trio] (>=3.2.1,<4.0.0)", "types-ujson (==4.2.1)", "types-orjson (==3.6.2)", "types-dataclasses (==0.6.5)"]

[[package]]
name = "fastobo"
version = "0.12.1"
description = "Faultless AST for Open Biomedical Ontologies in Python."
category = "main"
optional = false
python-versions = ">=3.7"

[[package]]
name = "flake8"
version = "4.0.1"
description = "the modular source code checker: pep8 pyflakes and co"
category = "dev"
optional = false
python-versions = ">=3.6"

[package.dependencies]
mccabe = ">=0.6.0,<0.7.0"
pycodestyle = ">=2.8.0,<2.9.0"
pyflakes = ">=2.4.0,<2.5.0"

[[package]]
name = "flake8-black"
version = "0.3.3"
description = "flake8 plugin to call black as a code style validator"
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
black = ">=22.1.0"
flake8 = ">=3.0.0"
tomli = "*"

[[package]]
name = "flake8-isort"
version = "4.1.2.post0"
description = "flake8 plugin that integrates isort ."
category = "dev"
optional = false
python-versions = "*"

[package.dependencies]
flake8 = ">=3.2.1,<5"
isort = ">=4.3.5,<6"

[package.extras]
test = ["pytest-cov"]

[[package]]
name = "frozenlist"
version = "1.3.0"
description = "A list-like structure which implements collections.abc.MutableSequence"
category = "main"
optional = false
python-versions = ">=3.7"

[[package]]
name = "fsspec"
version = "2022.5.0"
description = "File-system specification"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
aiohttp = {version = "*", optional = true, markers = "extra == \"http\""}
requests = {version = "*", optional = true, markers = "extra == \"http\""}

[package.extras]
abfs = ["adlfs"]
adl = ["adlfs"]
arrow = ["pyarrow (>=1)"]
dask = ["dask", "distributed"]
dropbox = ["dropboxdrivefs", "requests", "dropbox"]
entrypoints = ["importlib-metadata"]
fuse = ["fusepy"]
gcs = ["gcsfs"]
git = ["pygit2"]
github = ["requests"]
gs = ["gcsfs"]
gui = ["panel"]
hdfs = ["pyarrow (>=1)"]
http = ["requests", "aiohttp"]
libarchive = ["libarchive-c"]
oci = ["ocifs"]
s3 = ["s3fs"]
sftp = ["paramiko"]
smb = ["smbprotocol"]
ssh = ["paramiko"]
tqdm = ["tqdm"]

[[package]]
name = "funowl"
version = "0.1.12"
description = "Python rendering of the OWL Functional syntax"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
bcp47 = "*"
pyjsg = ">=0.11.6"
rdflib = ">=5.0.0"
rdflib-shim = "*"
rfc3987 = "*"

[[package]]
name = "greenlet"
version = "1.1.2"
description = "Lightweight in-process concurrent programming"
category = "main"
optional = false
python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"

[package.extras]
docs = ["sphinx"]

[[package]]
name = "h11"
version = "0.13.0"
description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
category = "main"
optional = false
python-versions = ">=3.6"

[[package]]
name = "hbreader"
version = "0.9.1"
description = "Honey Badger reader - a generic file/url/string open and read tool"
category = "main"
optional = false
python-versions = ">=3.7"

[[package]]
name = "httptools"
version = "0.4.0"
description = "A collection of framework independent HTTP protocol utils."
category = "main"
optional = false
python-versions = ">=3.5.0"

[package.extras]
test = ["Cython (>=0.29.24,<0.30.0)"]

[[package]]
name = "idna"
version = "3.3"
description = "Internationalized Domain Names in Applications (IDNA)"
category = "main"
optional = false
python-versions = ">=3.5"

[[package]]
name = "isodate"
version = "0.6.1"
description = "An ISO 8601 date/time/duration parser and formatter"
category = "main"
optional = false
python-versions = "*"

[package.dependencies]
six = "*"

[[package]]
name = "isort"
version = "5.10.1"
description = "A Python utility / library to sort Python imports."
category = "dev"
optional = false
python-versions = ">=3.6.1,<4.0"

[package.extras]
pipfile_deprecated_finder = ["pipreqs", "requirementslib"]
requirements_deprecated_finder = ["pipreqs", "pip-api"]
colors = ["colorama (>=0.4.3,<0.5.0)"]
plugins = ["setuptools"]

[[package]]
name = "json-flattener"
version = "0.1.9"
description = "Python library for denormalizing nested dicts or json objects to tables and back"
category = "main"
optional = false
python-versions = ">=3.7.0"

[package.dependencies]
click = "*"
pyyaml = "*"

[[package]]
name = "jsonasobj"
version = "2.0.1"
description = "JSON as python objects"
category = "main"
optional = false
python-versions = ">=3.6"

[package.dependencies]
hbreader = "*"

[[package]]
name = "jsonasobj2"
version = "1.0.4"
description = "JSON as python objects - version 2"
category = "main"
optional = false
python-versions = ">=3.6"

[package.dependencies]
hbreader = "*"

[[package]]
name = "jsonschema"
version = "4.7.2"
description = "An implementation of JSON Schema validation for Python"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
attrs = ">=17.4.0"
pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2"

[package.extras]
format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]

[[package]]
name = "kgcl-rdflib"
version = "0.2.0"
description = "Schema fro the KGCL project."
category = "main"
optional = false
python-versions = ">=3.8,<4.0"

[package.dependencies]
kgcl-schema = ">=0.2.0,<0.3.0"
lark = ">=1.1.2,<2.0.0"
linkml-runtime = ">=1.1.24,<2.0.0"

[[package]]
name = "kgcl-schema"
version = "0.2.0"
description = "Schema for the KGCL project."
category = "main"
optional = false
python-versions = ">=3.8,<4.0"

[package.dependencies]
lark = ">=1.1.2,<2.0.0"
linkml-runtime = ">=1.1.24,<2.0.0"

[[package]]
name = "lark"
version = "1.1.2"
description = "a modern parsing library"
category = "main"
optional = false
python-versions = "*"

[package.extras]
atomic_cache = ["atomicwrites"]
nearley = ["js2py"]
regex = ["regex"]

[[package]]
name = "linkml-runtime"
version = "1.2.21"
description = "Runtime environment for LinkML, the Linked open data modeling language"
category = "main"
optional = false
python-versions = ">=3.7.1,<4.0.0"

[package.dependencies]
click = "*"
deprecated = "*"
hbreader = "*"
json-flattener = ">=0.1.9"
jsonasobj2 = ">=1.0.4,<2.0.0"
jsonschema = ">=3.2.0"
prefixcommons = "0.1.11"
pyyaml = "*"
rdflib = ">=6.0.0"
requests = "*"

[[package]]
name = "mccabe"
version = "0.6.1"
description = "McCabe checker, plugin for flake8"
category = "dev"
optional = false
python-versions = "*"

[[package]]
name = "more-click"
version = "0.1.1"
description = "More click."
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
click = "*"

[[package]]
name = "more-itertools"
version = "8.13.0"
description = "More routines for operating on iterables, beyond itertools"
category = "dev"
optional = false
python-versions = ">=3.5"

[[package]]
name = "multidict"
version = "6.0.2"
description = "multidict implementation"
category = "main"
optional = false
python-versions = ">=3.7"

[[package]]
name = "mypy-extensions"
version = "0.4.3"
description = "Experimental type system extensions for programs checked with the mypy typechecker."
category = "dev"
optional = false
python-versions = "*"

[[package]]
name = "networkx"
version = "2.8.4"
description = "Python package for creating and manipulating graphs and networks"
category = "main"
optional = false
python-versions = ">=3.8"

[package.extras]
default = ["numpy (>=1.19)", "scipy (>=1.8)", "matplotlib (>=3.4)", "pandas (>=1.3)"]
developer = ["pre-commit (>=2.19)", "mypy (>=0.960)"]
doc = ["sphinx (>=5)", "pydata-sphinx-theme (>=0.9)", "sphinx-gallery (>=0.10)", "numpydoc (>=1.4)", "pillow (>=9.1)", "nb2plots (>=0.6)", "texext (>=0.6.6)"]
extra = ["lxml (>=4.6)", "pygraphviz (>=1.9)", "pydot (>=1.4.2)", "sympy (>=1.10)"]
test = ["pytest (>=7.1)", "pytest-cov (>=3.0)", "codecov (>=2.1)"]

[[package]]
name = "numpy"
version = "1.23.1"
description = "NumPy is the fundamental package for array computing with Python."
category = "main"
optional = false
python-versions = ">=3.8"

[[package]]
name = "nxontology"
version = "0.4.1"
description = "NetworkX for ontologies"
category = "main"
optional = false
python-versions = ">=3.8"

[package.dependencies]
fsspec = {version = "*", extras = ["http"]}
networkx = ">=2"
pronto = ">=2.4.0"

[package.extras]
dev = ["fire", "pandas", "pre-commit", "pytest"]
viz = ["pygraphviz"]

[[package]]
name = "oaklib"
version = "0.1.33"
description = "Ontology Access Kit: Python library for common ontology operations over a variety of backends"
category = "main"
optional = false
python-versions = ">=3.9,<4.0"

[package.dependencies]
appdirs = ">=1.4.4,<2.0.0"
class-resolver = ">=0.3.10,<0.4.0"
funowl = ">=0.1.12,<0.2.0"
kgcl-rdflib = ">=0.2.0,<0.3.0"
kgcl-schema = ">=0.2.0,<0.3.0"
lark = ">=1.1.2,<2.0.0"
linkml-runtime = ">=1.2.15,<2.0.0"
networkx = ">=2.7.1,<3.0.0"
nxontology = ">=0.4.0,<0.5.0"
pronto = ">=2.5.0,<3.0.0"
pystow = ">=0.4.4,<0.5.0"
ratelimit = ">=2.2.1,<3.0.0"
semsql = ">=0.1.6,<0.2.0"
SPARQLWrapper = "*"
SQLAlchemy = ">=1.4.32,<2.0.0"
sssom = ">=0.3.11,<0.4.0"
sssom-schema = ">=0.9.3,<0.10.0"

[package.extras]
gilda = ["gilda (>=0.10.1,<0.11.0)"]

[[package]]
name = "packaging"
version = "21.3"
description = "Core utilities for Python packages"
category = "main"
optional = false
python-versions = ">=3.6"

[package.dependencies]
pyparsing = ">=2.0.2,<3.0.5 || >3.0.5"

[[package]]
name = "pandas"
version = "1.4.3"
description = "Powerful data structures for data analysis, time series, and statistics"
category = "main"
optional = false
python-versions = ">=3.8"

[package.dependencies]
numpy = [
    {version = ">=1.18.5", markers = "platform_machine != \"aarch64\" and platform_machine != \"arm64\" and python_version < \"3.10\""},
    {version = ">=1.19.2", markers = "platform_machine == \"aarch64\" and python_version < \"3.10\""},
    {version = ">=1.20.0", markers = "platform_machine == \"arm64\" and python_version < \"3.10\""},
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fastobo = ">=0.12.1,<0.13.0"
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python-dateutil = ">=2.8,<3.0"

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python-versions = ">=3.6.1"

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requests = "*"
tqdm = "*"

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docs = ["sphinx", "sphinx-rtd-theme", "sphinx-click", "sphinx-autodoc-typehints", "sphinx-automodapi"]
pandas = ["pandas"]
rdf = ["rdflib"]
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xml = ["lxml"]

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atomicwrites = {version = ">=1.0", markers = "sys_platform == \"win32\""}
attrs = ">=17.4.0"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
more-itertools = ">=4.0.0"
packaging = "*"
pluggy = ">=0.12,<1.0"
py = ">=1.5.0"
wcwidth = "*"

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testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]

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python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"

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six = ">=1.5"

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python-versions = ">=3.5"

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cli = ["click (>=5.0)"]

[[package]]
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description = "World timezone definitions, modern and historical"
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python-versions = "*"

[[package]]
name = "pyyaml"
version = "6.0"
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python-versions = ">=3.6"

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isodate = "*"
pyparsing = "*"

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html = ["html5lib"]
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python-versions = "*"

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rdflib = ">=5.0.0"

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rdflib = ">=5.0.0"
rdflib-jsonld = "0.6.1"

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python-versions = ">=3.7, <4"

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charset-normalizer = ">=2,<3"
idna = ">=2.5,<4"
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asyncmy = ["greenlet (!=0.4.17)", "asyncmy (>=0.2.3,!=0.2.4)"]
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