poetry.lock

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curies = "*"
more-click = "*"
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pystow = ">=0.1.13"
requests = "*"
tqdm = "*"

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charts = ["matplotlib", "matplotlib-venn", "pandas", "seaborn"]
docs = ["autodoc-pydantic", "sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
export = ["ndex2", "pyyaml", "rdflib", "rdflib-jsonld"]
gha = ["more-itertools"]
health = ["click-default-group", "pandas", "tabulate"]
tests = ["coverage", "more-itertools", "pytest"]
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description = "Python package for providing Mozilla's CA Bundle."
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description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
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docdata = ["docdata"]
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optuna = ["optuna"]
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torch = ["torch"]

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pytrie = "*"
requests = "*"

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packaging = "*"

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

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description = "A list-like structure which implements collections.abc.MutableSequence"
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python-versions = ">=3.7"

[[package]]
name = "fsspec"
version = "2022.8.2"
description = "File-system specification"
category = "main"
optional = false
python-versions = ">=3.7"

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aiohttp = {version = "<4.0.0a0 || >4.0.0a0,<4.0.0a1 || >4.0.0a1", optional = true, markers = "extra == \"http\""}
requests = {version = "*", optional = true, markers = "extra == \"http\""}

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adl = ["adlfs"]
arrow = ["pyarrow (>=1)"]
dask = ["dask", "distributed"]
dropbox = ["dropbox", "dropboxdrivefs", "requests"]
entrypoints = ["importlib-metadata"]
fuse = ["fusepy"]
gcs = ["gcsfs"]
git = ["pygit2"]
github = ["requests"]
gs = ["gcsfs"]
gui = ["panel"]
hdfs = ["pyarrow (>=1)"]
http = ["aiohttp (!=4.0.0a0,!=4.0.0a1)", "requests"]
libarchive = ["libarchive-c"]
oci = ["ocifs"]
s3 = ["s3fs"]
sftp = ["paramiko"]
smb = ["smbprotocol"]
ssh = ["paramiko"]
tqdm = ["tqdm"]

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description = "Python rendering of the OWL Functional syntax"
category = "main"
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python-versions = ">=3.7"

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description = "Internationalized Domain Names in Applications (IDNA)"
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six = "*"

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pyyaml = "*"

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decorator = "*"
ply = "*"
six = "*"

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nearley = ["js2py"]
regex = ["regex"]

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docs = ["sphinx", "sphinx-rtd-theme"]

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python-versions = ">=3.7"

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jinja2 = "*"
jsonpatch = "*"
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linkml-runtime = ">=1.1.6"
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[[package]]
name = "linkml-runtime"
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category = "main"
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python-versions = ">=3.7.1,<4.0.0"

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rdflib = ">=6.0.0"
requests = "*"

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description = "Python port of markdown-it. Markdown parsing, done right!"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
mdurl = ">=0.1,<1.0"

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profiling = ["gprof2dot"]
rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]

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name = "markupsafe"
version = "2.1.1"
description = "Safely add untrusted strings to HTML/XML markup."
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name = "mdit-py-plugins"
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description = "Collection of plugins for markdown-it-py"
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click = "*"

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category = "main"
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[[package]]
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fsspec = {version = "*", extras = ["http"]}
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pronto = ">=2.4.0"

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

[[package]]
name = "oaklib"
version = "0.1.43"
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"

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bioregistry = ">=0.5.64,<0.6.0"
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ols-client = ">=0.1.1,<0.2.0"
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pystow = ">=0.4.4,<0.5.0"
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semsql = ">=0.1.6,<0.2.0"
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sssom = ">=0.3.16,<0.4.0"
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gilda = ["gilda (>=0.10.1,<0.11.0)"]

[[package]]
name = "ols-client"
version = "0.1.2"
description = "A client to the EBI Ontology Lookup Service"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
class-resolver = "*"
click = "*"
more-click = "*"
pystow = "*"
requests = "*"

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

[[package]]
name = "ontoportal-client"
version = "0.0.3"
description = "A client to BioPortal and other OntoPortal instances."
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
pystow = "*"
typing-extensions = "*"

[package.extras]
docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-rtd-theme"]
tests = ["coverage", "pytest", "unittest-templates"]

[[package]]
name = "openpyxl"
version = "3.0.10"
description = "A Python library to read/write Excel 2010 xlsx/xlsm files"
category = "main"
optional = false
python-versions = ">=3.6"

[package.dependencies]
et-xmlfile = "*"

[[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 = "1.4.2"
description = "Powerful data structures for data analysis, time series, and statistics"
category = "main"
optional = false
python-versions = ">=3.8"

[package.dependencies]
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python-dateutil = ">=2.8.1"
pytz = ">=2020.1"

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test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]

[[package]]
name = "pandasql"
version = "0.7.3"
description = "sqldf for pandas"
category = "main"
optional = false
python-versions = "*"

[package.dependencies]
numpy = "*"
pandas = "*"
sqlalchemy = "*"

[[package]]
name = "parse"
version = "1.19.0"
description = "parse() is the opposite of format()"
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "pluggy"
version = "0.13.1"
description = "plugin and hook calling mechanisms for python"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"

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dev = ["pre-commit", "tox"]

[[package]]
name = "ply"
version = "3.11"
description = "Python Lex & Yacc"
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "prefixcommons"
version = "0.1.9"
description = "Library for working prefixcommons.org CURIEs"
category = "main"
optional = false
python-versions = "*"

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

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

[[package]]
name = "prefixmaps"
version = "0.1.3"
description = ""
category = "main"
optional = false
python-versions = ">=3.7.6,<4.0.0"

[package.dependencies]
importlib-metadata = ">=4.12.0,<5.0.0"
PyYAML = ">=6.0,<7.0"

[[package]]
name = "pronto"
version = "2.5.0"
description = "Python frontend to ontologies."
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
chardet = ">=3.0,<5.0"
fastobo = ">=0.12.1,<0.13.0"
networkx = ">=2.3,<3.0"
python-dateutil = ">=2.8,<3.0"

[[package]]
name = "py"
version = "1.11.0"
description = "library with cross-python path, ini-parsing, io, code, log facilities"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"

[[package]]
name = "py4j"
version = "0.10.9.5"
description = "Enables Python programs to dynamically access arbitrary Java objects"
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "pydantic"
version = "1.9.0"
description = "Data validation and settings management using python 3.6 type hinting"
category = "main"
optional = false
python-versions = ">=3.6.1"

[package.dependencies]
typing-extensions = ">=3.7.4.3"

[package.extras]
dotenv = ["python-dotenv (>=0.10.4)"]
email = ["email-validator (>=1.0.3)"]

[[package]]
name = "pygments"
version = "2.12.0"
description = "Pygments is a syntax highlighting package written in Python."
category = "main"
optional = false
python-versions = ">=3.6"

[[package]]
name = "pyjsg"
version = "0.11.10"
description = "Python JSON Schema Grammar interpreter"
category = "main"
optional = false
python-versions = "*"

[package.dependencies]
antlr4-python3-runtime = ">=4.9.3,<4.10.0"
jsonasobj = ">=1.2.1"

[[package]]
name = "pyparsing"
version = "2.4.7"
description = "Python parsing module"
category = "main"
optional = false
python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"

[[package]]
name = "pyrsistent"
version = "0.18.1"
description = "Persistent/Functional/Immutable data structures"
category = "main"
optional = false
python-versions = ">=3.7"

[[package]]
name = "PyShEx"
version = "0.8.1"
description = "Python ShEx Implementation"
category = "main"
optional = false
python-versions = ">=3.6"

[package.dependencies]
cfgraph = ">=0.2.1"
chardet = "*"
pyshexc = "0.9.1"
rdflib-shim = "*"
requests = ">=2.22.0"
shexjsg = ">=0.8.2"
sparqlslurper = ">=0.5.1"
sparqlwrapper = ">=1.8.5"
urllib3 = "*"

[[package]]
name = "PyShExC"
version = "0.9.1"
description = "PyShExC - Python ShEx compiler"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
antlr4-python3-runtime = ">=4.9.3,<4.10.0"
chardet = "*"
jsonasobj = ">=1.2.1"
pyjsg = ">=0.11.10"
rdflib-shim = "*"
shexjsg = ">=0.8.1"

[[package]]
name = "pystow"
version = "0.4.6"
description = "Easily pick a place to store data for your python package."
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
click = "*"
requests = "*"
tqdm = "*"

[package.extras]
aws = ["boto3"]
docs = ["sphinx", "sphinx-autodoc-typehints", "sphinx-automodapi", "sphinx-click", "sphinx-rtd-theme"]
pandas = ["pandas"]
rdf = ["rdflib"]
tests = ["coverage", "pytest", "requests-file"]
xml = ["lxml"]

[[package]]
name = "pytest"
version = "5.4.3"
description = "pytest: simple powerful testing with Python"
category = "dev"
optional = false
python-versions = ">=3.5"

[package.dependencies]
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 = "*"

[package.extras]
checkqa-mypy = ["mypy (==v0.761)"]
testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]

[[package]]
name = "python-dateutil"
version = "2.8.2"
description = "Extensions to the standard Python datetime module"
category = "main"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"

[package.dependencies]
six = ">=1.5"

[[package]]
name = "pytrie"
version = "0.4.0"
description = "A pure Python implementation of the trie data structure."
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python-versions = "*"

[package.dependencies]
sortedcontainers = "*"

[[package]]
name = "pytz"
version = "2022.1"
description = "World timezone definitions, modern and historical"
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "pyyaml"
version = "6.0"
description = "YAML parser and emitter for Python"
category = "main"
optional = false
python-versions = ">=3.6"

[[package]]
name = "ratelimit"
version = "2.2.1"
description = "API rate limit decorator"
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "rdflib"
version = "6.1.1"
description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
category = "main"
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[package.dependencies]
isodate = "*"
pyparsing = "*"
setuptools = "*"

[package.extras]
docs = ["sphinx (<5)", "sphinxcontrib-apidoc"]
html = ["html5lib"]
tests = ["berkeleydb", "html5lib", "networkx", "pytest", "pytest-cov", "pytest-subtests"]

[[package]]
name = "rdflib-jsonld"
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description = "rdflib extension adding JSON-LD parser and serializer"
category = "main"
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python-versions = "*"

[package.dependencies]
rdflib = ">=5.0.0"

[[package]]
name = "rdflib-shim"
version = "1.0.3"
description = "Shim for rdflib 5 and 6 incompatibilities"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
rdflib = ">=5.0.0"
rdflib-jsonld = "0.6.1"

[[package]]
name = "requests"
version = "2.27.1"
description = "Python HTTP for Humans."
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"

[package.dependencies]
certifi = ">=2017.4.17"
charset-normalizer = {version = ">=2.0.0,<2.1.0", markers = "python_version >= \"3\""}
idna = {version = ">=2.5,<4", markers = "python_version >= \"3\""}
urllib3 = ">=1.21.1,<1.27"

[package.extras]
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use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"]

[[package]]
name = "rfc3987"
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description = "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)"
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optional = false
python-versions = "*"

[[package]]
name = "ruamel.yaml"
version = "0.17.21"
description = "ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order"
category = "main"
optional = false
python-versions = ">=3"

[package.dependencies]
"ruamel.yaml.clib" = {version = ">=0.2.6", markers = "platform_python_implementation == \"CPython\" and python_version < \"3.11\""}

[package.extras]
docs = ["ryd"]
jinja2 = ["ruamel.yaml.jinja2 (>=0.2)"]

[[package]]
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optional = false
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[[package]]
name = "scipy"
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category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
numpy = ">=1.16.5"

[[package]]
name = "semsql"
version = "0.1.7"
description = ""
category = "main"
optional = false
python-versions = ">=3.8,<4.0"

[package.dependencies]
click = ">=8.1.3,<9.0.0"
linkml-runtime = ">=1.2.15,<2.0.0"
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[[package]]
name = "setuptools"
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description = "Easily download, build, install, upgrade, and uninstall Python packages"
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optional = false
python-versions = ">=3.7"

[package.extras]
docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8 (<5)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mock", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]

[[package]]
name = "ShExJSG"
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optional = false
python-versions = "*"

[package.dependencies]
pyjsg = ">=0.11.10"

[[package]]
name = "six"
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description = "Python 2 and 3 compatibility utilities"
category = "main"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"

[[package]]
name = "snowballstemmer"
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category = "main"
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python-versions = "*"

[[package]]
name = "sortedcontainers"
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[[package]]
name = "sparqlslurper"
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rdflib-shim = "*"
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[[package]]
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python-versions = ">=3.7"

[package.dependencies]
rdflib = ">=6.1.1"

[package.extras]
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docs = ["sphinx (<5)", "sphinx-rtd-theme"]
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pandas = ["pandas (>=1.3.5)"]

[[package]]
name = "sphinx"
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category = "main"
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python-versions = ">=3.6"

[package.dependencies]
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babel = ">=1.3"
colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
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importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
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requests = ">=2.5.0"
snowballstemmer = ">=1.1"
sphinxcontrib-applehelp = "*"
sphinxcontrib-devhelp = "*"
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sphinxcontrib-qthelp = "*"
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lint = ["docutils-stubs", "flake8 (>=3.5.0)", "isort", "mypy (>=0.931)", "types-requests", "types-typed-ast"]
test = ["cython", "html5lib", "pytest", "pytest-cov", "typed-ast"]

[[package]]
name = "sphinx-click"
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python-versions = ">=3.7"

[package.dependencies]
click = ">=7.0"
docutils = "*"
sphinx = ">=2.0"

[[package]]
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python-versions = ">=3.5"

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

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

[[package]]
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[package.extras]
lint = ["docutils-stubs", "flake8", "mypy"]
test = ["html5lib", "pytest"]

[[package]]
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[package.extras]
test = ["flake8", "mypy", "pytest"]

[[package]]
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python-versions = ">=3.5"

[package.extras]
lint = ["docutils-stubs", "flake8", "mypy"]
test = ["pytest"]

[[package]]
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python-versions = ">=3.5"

[package.extras]
lint = ["docutils-stubs", "flake8", "mypy"]
test = ["pytest"]

[[package]]
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python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"

[package.dependencies]
greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}

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aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
asyncio = ["greenlet (!=0.4.17)"]
asyncmy = ["asyncmy (>=0.2.3,!=0.2.4)", "greenlet (!=0.4.17)"]
mariadb_connector = ["mariadb (>=1.0.1)"]
mssql = ["pyodbc"]
mssql_pymssql = ["pymssql"]
mssql_pyodbc = ["pyodbc"]
mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"]
mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"]
mysql_connector = ["mysql-connector-python"]
oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"]
postgresql = ["psycopg2 (>=2.7)"]
postgresql_asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
postgresql_pg8000 = ["pg8000 (>=1.16.6)"]
postgresql_psycopg2binary = ["psycopg2-binary"]
postgresql_psycopg2cffi = ["psycopg2cffi"]
pymysql = ["pymysql", "pymysql (<1)"]
sqlcipher = ["sqlcipher3_binary"]

[[package]]
name = "sqlalchemy-utils"
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category = "main"
optional = false
python-versions = "~=3.4"

[package.dependencies]
six = "*"
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babel = ["Babel (>=1.3)"]
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intervals = ["intervals (>=0.7.1)"]
password = ["passlib (>=1.6,<2.0)"]
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