poetry.lock

[[package]]
name = "adjusttext"
version = "0.7.3"
description = "Iteratively adjust text position in matplotlib plots to minimize overlaps"
category = "main"
optional = false
python-versions = "*"

[package.dependencies]
matplotlib = "*"
numpy = "*"

[[package]]
name = "alabaster"
version = "0.7.13"
description = "A configurable sidebar-enabled Sphinx theme"
category = "dev"
optional = false
python-versions = ">=3.6"

[[package]]
name = "anndata"
version = "0.8.0"
description = "Annotated data."
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
h5py = ">=3"
natsort = "*"
numpy = ">=1.16.5"
packaging = ">=20"
pandas = ">=1.1.1"
scipy = ">1.4"

[package.extras]
dev = ["black (>=20.8b1)", "docutils", "setuptools_scm"]
doc = ["nbsphinx", "scanpydoc (>=0.7.3)", "sphinx (>=4.1,<4.2)", "sphinx-autodoc-typehints (>=1.11.0)", "sphinx-rtd-theme", "sphinx_issues", "typing_extensions", "zarr"]
test = ["boltons", "dask[array]", "joblib", "loompy (>=3.0.5)", "matplotlib", "openpyxl", "pytest (>=6.0)", "pytest-cov (>=2.10)", "scanpy", "sklearn", "zarr"]

[[package]]
name = "appnope"
version = "0.1.3"
description = "Disable App Nap on macOS >= 10.9"
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "arrow"
version = "1.2.3"
description = "Better dates & times for Python"
category = "main"
optional = false
python-versions = ">=3.6"

[package.dependencies]
python-dateutil = ">=2.7.0"

[[package]]
name = "arviz"
version = "0.14.0"
description = "Exploratory analysis of Bayesian models"
category = "main"
optional = false
python-versions = ">=3.8"

[package.dependencies]
matplotlib = ">=3.5"
netcdf4 = "*"
numpy = ">=1.20.0"
packaging = "*"
pandas = ">=1.4.0"
scipy = ">=1.8.0"
setuptools = ">=60.0.0"
typing-extensions = ">=4.1.0"
xarray = ">=0.21.0"
xarray-einstats = ">=0.3"

[package.extras]
all = ["bokeh (>=1.4.0,<3.0)", "contourpy", "dask[distributed]", "numba", "ujson", "zarr (>=2.5.0)"]

[[package]]
name = "asttokens"
version = "2.2.1"
description = "Annotate AST trees with source code positions"
category = "main"
optional = false
python-versions = "*"

[package.dependencies]
six = "*"

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

[[package]]
name = "attrs"
version = "22.2.0"
description = "Classes Without Boilerplate"
category = "dev"
optional = false
python-versions = ">=3.6"

[package.extras]
cov = ["attrs[tests]", "coverage-enable-subprocess", "coverage[toml] (>=5.3)"]
dev = ["attrs[docs,tests]"]
docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope.interface"]
tests = ["attrs[tests-no-zope]", "zope.interface"]
tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy (>=0.971,<0.990)", "mypy (>=0.971,<0.990)", "pympler", "pympler", "pytest (>=4.3.0)", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-mypy-plugins", "pytest-xdist[psutil]", "pytest-xdist[psutil]"]

[[package]]
name = "babel"
version = "2.11.0"
description = "Internationalization utilities"
category = "dev"
optional = false
python-versions = ">=3.6"

[package.dependencies]
pytz = ">=2015.7"

[[package]]
name = "backcall"
version = "0.2.0"
description = "Specifications for callback functions passed in to an API"
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "backports-zoneinfo"
version = "0.2.1"
description = "Backport of the standard library zoneinfo module"
category = "main"
optional = false
python-versions = ">=3.6"

[package.extras]
tzdata = ["tzdata"]

[[package]]
name = "bandit"
version = "1.7.4"
description = "Security oriented static analyser for python code."
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
colorama = {version = ">=0.3.9", markers = "platform_system == \"Windows\""}
GitPython = ">=1.0.1"
PyYAML = ">=5.3.1"
stevedore = ">=1.20.0"

[package.extras]
test = ["beautifulsoup4 (>=4.8.0)", "coverage (>=4.5.4)", "fixtures (>=3.0.0)", "flake8 (>=4.0.0)", "pylint (==1.9.4)", "stestr (>=2.5.0)", "testscenarios (>=0.5.0)", "testtools (>=2.3.0)", "toml"]
toml = ["toml"]
yaml = ["PyYAML"]

[[package]]
name = "beautifulsoup4"
version = "4.11.1"
description = "Screen-scraping library"
category = "dev"
optional = false
python-versions = ">=3.6.0"

[package.dependencies]
soupsieve = ">1.2"

[package.extras]
html5lib = ["html5lib"]
lxml = ["lxml"]

[[package]]
name = "black"
version = "22.12.0"
description = "The uncompromising code formatter."
category = "dev"
optional = false
python-versions = ">=3.7"

[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 = "bleach"
version = "6.0.0"
description = "An easy safelist-based HTML-sanitizing tool."
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
six = ">=1.9.0"
webencodings = "*"

[package.extras]
css = ["tinycss2 (>=1.1.0,<1.2)"]

[[package]]
name = "certifi"
version = "2022.12.7"
description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
python-versions = ">=3.6"

[[package]]
name = "cffi"
version = "1.15.1"
description = "Foreign Function Interface for Python calling C code."
category = "main"
optional = false
python-versions = "*"

[package.dependencies]
pycparser = "*"

[[package]]
name = "cfgv"
version = "3.3.1"
description = "Validate configuration and produce human readable error messages."
category = "dev"
optional = false
python-versions = ">=3.6.1"

[[package]]
name = "cftime"
version = "1.6.2"
description = "Time-handling functionality from netcdf4-python"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
numpy = ">1.13.3"

[[package]]
name = "charset-normalizer"
version = "3.0.1"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "classify-imports"
version = "4.2.0"
description = "Utilities for refactoring imports in python-like syntax."
category = "dev"
optional = false
python-versions = ">=3.7"

[[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 = "0.4.6"
description = "Cross-platform colored terminal text."
category = "main"
optional = false
python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"

[[package]]
name = "comm"
version = "0.1.2"
description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
category = "main"
optional = false
python-versions = ">=3.6"

[package.dependencies]
traitlets = ">=5.3"

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

[[package]]
name = "contourpy"
version = "1.0.7"
description = "Python library for calculating contours of 2D quadrilateral grids"
category = "main"
optional = false
python-versions = ">=3.8"

[package.dependencies]
numpy = ">=1.16"

[package.extras]
bokeh = ["bokeh", "chromedriver", "selenium"]
docs = ["furo", "sphinx-copybutton"]
mypy = ["contourpy[bokeh]", "docutils-stubs", "mypy (==0.991)", "types-Pillow"]
test = ["Pillow", "matplotlib", "pytest"]
test-no-images = ["pytest"]

[[package]]
name = "coverage"
version = "7.1.0"
description = "Code coverage measurement for Python"
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}

[package.extras]
toml = ["tomli"]

[[package]]
name = "custom-inherit"
version = "2.4.0"
description = "A Python package that provides customized docstring inheritance       schemes between derived classes and their parents."
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "cycler"
version = "0.11.0"
description = "Composable style cycles"
category = "main"
optional = false
python-versions = ">=3.6"

[[package]]
name = "debugpy"
version = "1.6.6"
description = "An implementation of the Debug Adapter Protocol for Python"
category = "main"
optional = false
python-versions = ">=3.7"

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

[[package]]
name = "defusedxml"
version = "0.7.1"
description = "XML bomb protection for Python stdlib modules"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"

[[package]]
name = "distlib"
version = "0.3.6"
description = "Distribution utilities"
category = "dev"
optional = false
python-versions = "*"

[[package]]
name = "docutils"
version = "0.17.1"
description = "Docutils -- Python Documentation Utilities"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"

[[package]]
name = "dparse"
version = "0.6.2"
description = "A parser for Python dependency files"
category = "dev"
optional = false
python-versions = ">=3.5"

[package.dependencies]
packaging = "*"
toml = "*"

[package.extras]
conda = ["pyyaml"]
pipenv = ["pipenv"]

[[package]]
name = "ete3"
version = "3.1.2"
description = "A Python Environment for (phylogenetic) Tree Exploration"
category = "main"
optional = false
python-versions = "*"

[[package]]
name = "exceptiongroup"
version = "1.1.0"
description = "Backport of PEP 654 (exception groups)"
category = "dev"
optional = false
python-versions = ">=3.7"

[package.extras]
test = ["pytest (>=6)"]

[[package]]
name = "executing"
version = "1.2.0"
description = "Get the currently executing AST node of a frame, and other information"
category = "main"
optional = false
python-versions = "*"

[package.extras]
tests = ["asttokens", "littleutils", "pytest", "rich"]

[[package]]
name = "fastjsonschema"
version = "2.16.2"
description = "Fastest Python implementation of JSON schema"
category = "dev"
optional = false
python-versions = "*"

[package.extras]
devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benchmark", "pytest-cache", "validictory"]

[[package]]
name = "filelock"
version = "3.9.0"
description = "A platform independent file lock."
category = "dev"
optional = false
python-versions = ">=3.7"

[package.extras]
docs = ["furo (>=2022.12.7)", "sphinx (>=5.3)", "sphinx-autodoc-typehints (>=1.19.5)"]
testing = ["covdefaults (>=2.2.2)", "coverage (>=7.0.1)", "pytest (>=7.2)", "pytest-cov (>=4)", "pytest-timeout (>=2.1)"]

[[package]]
name = "flake8"
version = "5.0.4"
description = "the modular source code checker: pep8 pyflakes and co"
category = "dev"
optional = false
python-versions = ">=3.6.1"

[package.dependencies]
mccabe = ">=0.7.0,<0.8.0"
pycodestyle = ">=2.9.0,<2.10.0"
pyflakes = ">=2.5.0,<2.6.0"

[[package]]
name = "flake8-bandit"
version = "4.1.1"
description = "Automated security testing with bandit and flake8."
category = "dev"
optional = false
python-versions = ">=3.6"

[package.dependencies]
bandit = ">=1.7.3"
flake8 = ">=5.0.0"

[[package]]
name = "flake8-bugbear"
version = "23.1.20"
description = "A plugin for flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycodestyle."
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
attrs = ">=19.2.0"
flake8 = ">=3.0.0"

[package.extras]
dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit", "pytest", "tox"]

[[package]]
name = "flake8-docstrings"
version = "1.7.0"
description = "Extension for flake8 which uses pydocstyle to check docstrings"
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
flake8 = ">=3"
pydocstyle = ">=2.1"

[[package]]
name = "flake8-rst-docstrings"
version = "0.3.0"
description = "Python docstring reStructuredText (RST) validator for flake8"
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
flake8 = ">=3"
pygments = "*"
restructuredtext-lint = "*"

[package.extras]
develop = ["build", "twine"]

[[package]]
name = "fonttools"
version = "4.38.0"
description = "Tools to manipulate font files"
category = "main"
optional = false
python-versions = ">=3.7"

[package.extras]
all = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "fs (>=2.2.0,<3)", "lxml (>=4.0,<5)", "lz4 (>=1.7.4.2)", "matplotlib", "munkres", "scipy", "skia-pathops (>=0.5.0)", "sympy", "uharfbuzz (>=0.23.0)", "unicodedata2 (>=14.0.0)", "xattr", "zopfli (>=0.1.4)"]
graphite = ["lz4 (>=1.7.4.2)"]
interpolatable = ["munkres", "scipy"]
lxml = ["lxml (>=4.0,<5)"]
pathops = ["skia-pathops (>=0.5.0)"]
plot = ["matplotlib"]
repacker = ["uharfbuzz (>=0.23.0)"]
symfont = ["sympy"]
type1 = ["xattr"]
ufo = ["fs (>=2.2.0,<3)"]
unicode = ["unicodedata2 (>=14.0.0)"]
woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]

[[package]]
name = "furo"
version = "2022.12.7"
description = "A clean customisable Sphinx documentation theme."
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
beautifulsoup4 = "*"
pygments = ">=2.7"
sphinx = ">=5.0,<7.0"
sphinx-basic-ng = "*"

[[package]]
name = "future"
version = "0.18.3"
description = "Clean single-source support for Python 3 and 2"
category = "main"
optional = false
python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"

[[package]]
name = "gitdb"
version = "4.0.10"
description = "Git Object Database"
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
smmap = ">=3.0.1,<6"

[[package]]
name = "gitpython"
version = "3.1.30"
description = "GitPython is a python library used to interact with Git repositories"
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
gitdb = ">=4.0.1,<5"

[[package]]
name = "h5py"
version = "3.8.0"
description = "Read and write HDF5 files from Python"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
numpy = ">=1.14.5"

[[package]]
name = "identify"
version = "2.5.16"
description = "File identification library for Python"
category = "dev"
optional = false
python-versions = ">=3.7"

[package.extras]
license = ["ukkonen"]

[[package]]
name = "idna"
version = "3.4"
description = "Internationalized Domain Names in Applications (IDNA)"
category = "main"
optional = false
python-versions = ">=3.5"

[[package]]
name = "igraph"
version = "0.10.4"
description = "High performance graph data structures and algorithms"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
texttable = ">=1.6.2"

[package.extras]
cairo = ["cairocffi (>=1.2.0)"]
doc = ["Sphinx (>=4.2.0)", "sphinxbootstrap4theme (>=0.6.0)"]
matplotlib = ["matplotlib (>=3.5.0,<3.6.0)"]
plotly = ["plotly (>=5.3.0)"]
plotting = ["cairocffi (>=1.2.0)"]
test = ["Pillow (>=9)", "matplotlib (>=3.6.0)", "networkx (>=2.5)", "numpy (>=1.19.0)", "pandas (>=1.1.0)", "plotly (>=5.3.0)", "pytest (>=7.0.1)", "pytest-timeout (>=2.1.0)", "scipy (>=1.5.0)"]
test-musl = ["networkx (>=2.5)", "pytest (>=7.0.1)", "pytest-timeout (>=2.1.0)"]

[[package]]
name = "imagesize"
version = "1.4.1"
description = "Getting image size from png/jpeg/jpeg2000/gif file"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"

[[package]]
name = "importlib-metadata"
version = "6.0.0"
description = "Read metadata from Python packages"
category = "main"
optional = false
python-versions = ">=3.7"

[package.dependencies]
zipp = ">=0.5"

[package.extras]
docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
perf = ["ipython"]
testing = ["flake8 (<5)", "flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "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 (>=0.9.2)"]

[[package]]
name = "importlib-resources"
version = "5.10.2"
description = "Read resources from Python packages"
category = "dev"
optional = false
python-versions = ">=3.7"

[package.dependencies]
zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}

[package.extras]
docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
testing = ["flake8 (<5)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"]

[[package]]
name = "iniconfig"
version = "2.0.0"
description = "brain-dead simple config-ini parsing"
category = "dev"
optional = false
python-versions = ">=3.7"

[[package]]
name = "ipykernel"
version = "6.21.0"
description = "IPython Kernel for Jupyter"
category = "main"
optional = false
python-versions = ">=3.8"

[package.dependencies]
appnope = {version = "*", markers = "platform_system == \"Darwin\""}
comm = ">=0.1.1"
debugpy = ">=1.6.5"
ipython = ">=7.23.1"
jupyter-client = ">=6.1.12"
jupyter-core = ">=4.12,<5.0.0 || >=5.1.0"
matplotlib-inline = ">=0.1"
packaging = "*"
psutil = "*"
pyzmq = ">=17"
tornado = ">=6.1"
traitlets = ">=5.4.0"

[package.extras]
cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"]
docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
pyqt5 = ["pyqt5"]
pyside6 = ["pyside6"]
test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov", "pytest-timeout"]

[[package]]
name = "ipython"
version = "8.9.0"
description = "IPython: Productive Interactive Computing"
category = "main"
optional = false
python-versions = ">=3.8"

[package.dependencies]
appnope = {version = "*", markers = "sys_platform == \"darwin\""}
backcall = "*"
colorama = {version = "*", markers = "sys_platform == \"win32\""}
decorator = "*"
jedi = ">=0.16"
matplotlib-inline = "*"
pexpect = {version = ">4.3", markers = "sys_platform != \"win32\""}
pickleshare = "*"
prompt-toolkit = ">=3.0.30,<3.1.0"
pygments = ">=2.4.0"
stack-data = "*"
traitlets = ">=5"

[package.extras]
all = ["black", "curio", "docrepr", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.20)", "pandas", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
black = ["black"]
doc = ["docrepr", "ipykernel", "matplotlib", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
kernel = ["ipykernel"]
nbconvert = ["nbconvert"]
nbformat = ["nbformat"]
notebook = ["ipywidgets", "notebook"]
parallel = ["ipyparallel"]
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sphinx = "*"

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

[[package]]
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[[package]]
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[[package]]
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[[package]]
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[[package]]
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