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pdm.lock
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# This file is @generated by PDM.
# It is not intended for manual editing.
[[package]]
name = "adjusttext"
version = "0.8"
summary = "Iteratively adjust text position in matplotlib plots to minimize overlaps"
dependencies = [
"matplotlib",
"numpy",
]
[[package]]
name = "anndata"
version = "0.9.1"
requires_python = ">=3.8"
summary = "Annotated data."
dependencies = [
"h5py>=3",
"natsort",
"numpy>=1.16.5",
"packaging>=20",
"pandas>=1.1.1",
"scipy>1.4",
]
[[package]]
name = "annoy"
version = "1.17.3"
summary = "Approximate Nearest Neighbors in C++/Python optimized for memory usage and loading/saving to disk."
[[package]]
name = "backports-zoneinfo"
version = "0.2.1"
requires_python = ">=3.6"
summary = "Backport of the standard library zoneinfo module"
[[package]]
name = "biothings-client"
version = "0.3.0"
requires_python = ">=2.7"
summary = "Python Client for BioThings API services."
dependencies = [
"requests>=2.3.0",
]
[[package]]
name = "bleach"
version = "6.0.0"
requires_python = ">=3.7"
summary = "An easy safelist-based HTML-sanitizing tool."
dependencies = [
"six>=1.9.0",
"webencodings",
]
[[package]]
name = "bokeh"
version = "3.1.1"
requires_python = ">=3.8"
summary = "Interactive plots and applications in the browser from Python"
dependencies = [
"Jinja2>=2.9",
"PyYAML>=3.10",
"contourpy>=1",
"numpy>=1.16",
"packaging>=16.8",
"pandas>=1.2",
"pillow>=7.1.0",
"tornado>=5.1",
"xyzservices>=2021.09.1",
]
[[package]]
name = "certifi"
version = "2023.5.7"
requires_python = ">=3.6"
summary = "Python package for providing Mozilla's CA Bundle."
[[package]]
name = "charset-normalizer"
version = "3.1.0"
requires_python = ">=3.7.0"
summary = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
[[package]]
name = "click"
version = "8.1.3"
requires_python = ">=3.7"
summary = "Composable command line interface toolkit"
dependencies = [
"colorama; platform_system == \"Windows\"",
]
[[package]]
name = "cloudpickle"
version = "2.2.1"
requires_python = ">=3.6"
summary = "Extended pickling support for Python objects"
[[package]]
name = "colorama"
version = "0.4.6"
requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
summary = "Cross-platform colored terminal text."
[[package]]
name = "colorcet"
version = "3.0.1"
requires_python = ">=2.7"
summary = "Collection of perceptually uniform colormaps"
dependencies = [
"pyct>=0.4.4",
]
[[package]]
name = "contourpy"
version = "1.1.0"
requires_python = ">=3.8"
summary = "Python library for calculating contours of 2D quadrilateral grids"
dependencies = [
"numpy>=1.16",
]
[[package]]
name = "cycler"
version = "0.11.0"
requires_python = ">=3.6"
summary = "Composable style cycles"
[[package]]
name = "dask"
version = "2023.5.0"
requires_python = ">=3.8"
summary = "Parallel PyData with Task Scheduling"
dependencies = [
"click>=8.0",
"cloudpickle>=1.5.0",
"fsspec>=2021.09.0",
"importlib-metadata>=4.13.0",
"packaging>=20.0",
"partd>=1.2.0",
"pyyaml>=5.3.1",
"toolz>=0.10.0",
]
[[package]]
name = "datashader"
version = "0.15.0"
requires_python = ">=3.8"
summary = "Data visualization toolchain based on aggregating into a grid"
dependencies = [
"colorcet",
"dask",
"datashape",
"numba",
"numpy",
"pandas",
"param",
"pillow",
"pyct",
"requests",
"scipy",
"toolz",
"xarray",
]
[[package]]
name = "datashape"
version = "0.5.2"
summary = "A data description language."
dependencies = [
"multipledispatch>=0.4.7",
"numpy>=1.7",
"python-dateutil",
]
[[package]]
name = "docopt"
version = "0.6.2"
summary = "Pythonic argument parser, that will make you smile"
[[package]]
name = "et-xmlfile"
version = "1.1.0"
requires_python = ">=3.6"
summary = "An implementation of lxml.xmlfile for the standard library"
[[package]]
name = "fonttools"
version = "4.40.0"
requires_python = ">=3.8"
summary = "Tools to manipulate font files"
[[package]]
name = "fsspec"
version = "2023.6.0"
requires_python = ">=3.8"
summary = "File-system specification"
[[package]]
name = "goatools"
version = "1.3.1"
summary = "Python scripts to find enrichment of GO terms"
dependencies = [
"docopt",
"numpy",
"openpyxl",
"pandas",
"pydot",
"requests",
"scipy",
"statsmodels",
"xlsxwriter",
]
[[package]]
name = "h5py"
version = "3.9.0"
requires_python = ">=3.8"
summary = "Read and write HDF5 files from Python"
dependencies = [
"numpy>=1.17.3",
]
[[package]]
name = "h5sparse"
version = "0.1.0"
summary = "Scipy sparse matrix in HDF5."
dependencies = [
"h5py",
"numpy",
"scipy",
"six",
]
[[package]]
name = "holoviews"
version = "1.16.2"
requires_python = ">=3.7"
summary = "Stop plotting your data - annotate your data and let it visualize itself."
dependencies = [
"colorcet",
"numpy>=1.0",
"packaging",
"pandas>=0.20.0",
"panel>=0.13.1",
"param<3.0,>=1.12.0",
"pyviz-comms>=0.7.4",
]
[[package]]
name = "idna"
version = "3.4"
requires_python = ">=3.5"
summary = "Internationalized Domain Names in Applications (IDNA)"
[[package]]
name = "igraph"
version = "0.10.4"
requires_python = ">=3.7"
summary = "High performance graph data structures and algorithms"
dependencies = [
"texttable>=1.6.2",
]
[[package]]
name = "importlib-metadata"
version = "6.7.0"
requires_python = ">=3.7"
summary = "Read metadata from Python packages"
dependencies = [
"zipp>=0.5",
]
[[package]]
name = "importlib-resources"
version = "5.12.0"
requires_python = ">=3.7"
summary = "Read resources from Python packages"
dependencies = [
"zipp>=3.1.0; python_version < \"3.10\"",
]
[[package]]
name = "jinja2"
version = "3.1.2"
requires_python = ">=3.7"
summary = "A very fast and expressive template engine."
dependencies = [
"MarkupSafe>=2.0",
]
[[package]]
name = "joblib"
version = "1.2.0"
requires_python = ">=3.7"
summary = "Lightweight pipelining with Python functions"
[[package]]
name = "kiwisolver"
version = "1.4.4"
requires_python = ">=3.7"
summary = "A fast implementation of the Cassowary constraint solver"
[[package]]
name = "leidenalg"
version = "0.9.1"
requires_python = ">=3.7"
summary = "Leiden is a general algorithm for methods of community detection in large networks."
dependencies = [
"igraph<0.11,>=0.10.0",
]
[[package]]
name = "linkify-it-py"
version = "2.0.2"
requires_python = ">=3.7"
summary = "Links recognition library with FULL unicode support."
dependencies = [
"uc-micro-py",
]
[[package]]
name = "llvmlite"
version = "0.40.1rc1"
requires_python = ">=3.8"
summary = "lightweight wrapper around basic LLVM functionality"
[[package]]
name = "locket"
version = "1.0.0"
requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
summary = "File-based locks for Python on Linux and Windows"
[[package]]
name = "louvain"
version = "0.8.0"
requires_python = ">=3.7"
summary = "louvain is a general algorithm for methods of community detection in large networks."
dependencies = [
"igraph<0.11,>=0.10.0",
]
[[package]]
name = "markdown"
version = "3.4.3"
requires_python = ">=3.7"
summary = "Python implementation of John Gruber's Markdown."
dependencies = [
"importlib-metadata>=4.4; python_version < \"3.10\"",
]
[[package]]
name = "markdown-it-py"
version = "2.2.0"
requires_python = ">=3.7"
summary = "Python port of markdown-it. Markdown parsing, done right!"
dependencies = [
"mdurl~=0.1",
]
[[package]]
name = "markupsafe"
version = "2.1.3"
requires_python = ">=3.7"
summary = "Safely add untrusted strings to HTML/XML markup."
[[package]]
name = "matplotlib"
version = "3.7.1"
requires_python = ">=3.8"
summary = "Python plotting package"
dependencies = [
"contourpy>=1.0.1",
"cycler>=0.10",
"fonttools>=4.22.0",
"importlib-resources>=3.2.0; python_version < \"3.10\"",
"kiwisolver>=1.0.1",
"numpy>=1.20",
"packaging>=20.0",
"pillow>=6.2.0",
"pyparsing>=2.3.1",
"python-dateutil>=2.7",
]
[[package]]
name = "mdit-py-plugins"
version = "0.4.0"
requires_python = ">=3.8"
summary = "Collection of plugins for markdown-it-py"
dependencies = [
"markdown-it-py<4.0.0,>=1.0.0",
]
[[package]]
name = "mdurl"
version = "0.1.2"
requires_python = ">=3.7"
summary = "Markdown URL utilities"
[[package]]
name = "mizani"
version = "0.9.2"
requires_python = ">=3.8"
summary = "Scales for Python"
dependencies = [
"backports-zoneinfo; python_version < \"3.9\"",
"matplotlib>=3.5.0",
"numpy>=1.19.0",
"pandas>=1.3.5",
"scipy>=1.5.0",
"tzdata; platform_system == \"Windows\" or platform_system == \"Emscripten\"",
]
[[package]]
name = "multipledispatch"
version = "0.6.0"
summary = "Multiple dispatch"
dependencies = [
"six",
]
[[package]]
name = "mygene"
version = "3.2.2"
summary = "Python Client for MyGene.Info services."
dependencies = [
"biothings-client>=0.2.6",
]
[[package]]
name = "natsort"
version = "8.4.0"
requires_python = ">=3.7"
summary = "Simple yet flexible natural sorting in Python."
[[package]]
name = "numba"
version = "0.57.1rc1"
requires_python = ">=3.8"
summary = "compiling Python code using LLVM"
dependencies = [
"importlib-metadata; python_version < \"3.9\"",
"llvmlite<0.41,>=0.40.0dev0",
"numpy<1.25,>=1.21",
]
[[package]]
name = "numexpr"
version = "2.8.4"
requires_python = ">=3.7"
summary = "Fast numerical expression evaluator for NumPy"
dependencies = [
"numpy>=1.13.3",
]
[[package]]
name = "numpy"
version = "1.24.3"
requires_python = ">=3.8"
summary = "Fundamental package for array computing in Python"
[[package]]
name = "openpyxl"
version = "3.1.2"
requires_python = ">=3.6"
summary = "A Python library to read/write Excel 2010 xlsx/xlsm files"
dependencies = [
"et-xmlfile",
]
[[package]]
name = "packaging"
version = "23.1"
requires_python = ">=3.7"
summary = "Core utilities for Python packages"
[[package]]
name = "pandas"
version = "2.0.2"
requires_python = ">=3.8"
summary = "Powerful data structures for data analysis, time series, and statistics"
dependencies = [
"numpy>=1.20.3; python_version < \"3.10\"",
"numpy>=1.21.0; python_version >= \"3.10\"",
"numpy>=1.23.2; python_version >= \"3.11\"",
"python-dateutil>=2.8.2",
"pytz>=2020.1",
"tzdata>=2022.1",
]
[[package]]
name = "panel"
version = "1.1.1"
requires_python = ">=3.8"
summary = "The powerful data exploration & web app framework for Python."
dependencies = [
"bleach",
"bokeh<3.2.0,>=3.1.1",
"linkify-it-py",
"markdown",
"markdown-it-py<3",
"mdit-py-plugins",
"pandas>=1.2",
"param>=1.12.0",
"pyviz-comms>=0.7.4",
"requests",
"tqdm>=4.48.0",
"typing-extensions",
"xyzservices>=2021.09.1",
]
[[package]]
name = "param"
version = "1.13.0"
requires_python = ">=2.7"
summary = "Make your Python code clearer and more reliable by declaring Parameters."
[[package]]
name = "partd"
version = "1.4.0"
requires_python = ">=3.7"
summary = "Appendable key-value storage"
dependencies = [
"locket",
"toolz",
]
[[package]]
name = "patsy"
version = "0.5.3"
summary = "A Python package for describing statistical models and for building design matrices."
dependencies = [
"numpy>=1.4",
"six",
]
[[package]]
name = "pillow"
version = "9.5.0"
requires_python = ">=3.7"
summary = "Python Imaging Library (Fork)"
[[package]]
name = "plotnine"
version = "0.12.1"
requires_python = ">=3.8"
summary = "A Grammar of Graphics for Python"
dependencies = [
"matplotlib>=3.6.0",
"mizani>=0.9.0",
"numpy>=1.23.0",
"pandas>=1.5.0",
"patsy>=0.5.1",
"scipy>=1.5.0",
"statsmodels>=0.14.0",
]
[[package]]
name = "pyct"
version = "0.5.0"
requires_python = ">=3.7"
summary = "Python package common tasks for users (e.g. copy examples, fetch data, ...)"
dependencies = [
"param>=1.7.0",
]
[[package]]
name = "pydot"
version = "1.4.2"
requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
summary = "Python interface to Graphviz's Dot"
dependencies = [
"pyparsing>=2.1.4",
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