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Docs and bugfix (#1)
* docs * anndata as dependency * generalize multiplex leiden * readthedocs config * add shashwat * omics instead of transcriptomics * fix leidenalg to 0.10
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‎.readthedocs.yaml

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version: 2
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build:
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os: ubuntu-22.04
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tools:
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python: "3.10"
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sphinx:
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configuration: docs/source/conf.py
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python:
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install:
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- method: pip
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path: .
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extra_requirements:
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- docs

‎LICENSE

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MIT License
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Copyright (c) 2024 Niklas Müller-Bötticher, Naveed Ishaque, Roland Eils, Berlin Institute of Health @ Charité
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Copyright (c) 2024 Niklas Müller-Bötticher, Shashwat Sahay, Naveed Ishaque, Roland Eils, Berlin Institute of Health @ Charité
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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

‎README.md

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# SpatialLeiden
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[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
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[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
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[![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
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[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
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[![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
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[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
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``SpatialLeiden`` is an implementation of
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[Multiplex Leiden clustering](https://leidenalg.readthedocs.io/en/stable/multiplex.html)
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that can be used to cluster spatially resolved omics data.
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``SpatialLeiden`` integrates with the [scverse](https://scverse.org/) by leveraging
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[scanpy](https://scanpy.readthedocs.io/) and [anndata](https://anndata.readthedocs.io/)
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but can also be used independently.
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## Installation
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`spatialleiden` will be made available on [PyPI](https://pypi.org/) and
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[bioconda](https://bioconda.github.io/). For detailed installation instructions
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please refer to the [documentation](https://spatialleiden.readthedocs.io/en/stable/installation.html).
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## Documentation
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For documentation of the package please refer to the [ReadTheDocs page](https://spatialleiden.readthedocs.io/)
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## Versioning
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This project follows the [SemVer](https://semver.org/) guidelines for versioning.
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## License
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This project is licensed under the MIT License - for details please refer to the
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[LICENSE](./LICENSE) file.

‎docs/source/api.rst

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API
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===
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.. currentmodule:: spatialleiden
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Multiplex Leiden
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----------------
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.. autosummary::
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:nosignatures:
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:toctree: ./generated/
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spatialleiden
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multiplex_leiden
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Resolution search
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-----------------
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.. autosummary::
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:nosignatures:
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:toctree: ./generated/
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search_resolution
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search_resolution_latent
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search_resolution_spatial
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Utility functions
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-----------------
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.. autosummary::
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:nosignatures:
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:toctree: ./generated/
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distance2connectivity

‎docs/source/conf.py

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import importlib.metadata
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import os
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import sys
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from datetime import datetime
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sys.path.insert(0, os.path.abspath("../.."))
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# -- Project information -----------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
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project = "SpatialLeiden"
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copyright = f"""
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{datetime.now():%Y}, Niklas Müller-Bötticher, Shashwat Sahay, Naveed Ishaque, Roland Eils,
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Berlin Institute of Health @ Charité"""
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author = "Niklas Müller-Bötticher & Shashwat Sahay"
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version = importlib.metadata.version("spatialleiden")
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release = version
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# -- General configuration ---------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
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extensions = [
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"sphinx_copybutton",
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"sphinx.ext.autodoc",
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"sphinx.ext.intersphinx",
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"sphinx.ext.napoleon",
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"sphinx.ext.autosummary",
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"sphinx.ext.mathjax",
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]
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autodoc_typehints = "none"
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autodoc_typehints_format = "short"
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python_use_unqualified_type_names = True # still experimental
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autosummary_generate = True
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autosummary_imported_members = True
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nitpicky = True
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nitpick_ignore = [("py:class", "optional")]
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exclude_patterns: list[str] = []
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intersphinx_mapping = dict(
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anndata=("https://anndata.readthedocs.io/en/stable/", None),
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matplotlib=("https://matplotlib.org/stable/", None),
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numpy=("https://numpy.org/doc/stable/", None),
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python=("https://docs.python.org/3", None),
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scanpy=("https://scanpy.readthedocs.io/en/stable/", None),
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scipy=("https://docs.scipy.org/doc/scipy/", None),
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)
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# -- Options for HTML output -------------------------------------------------
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# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
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html_theme = "sphinx_rtd_theme"
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html_static_path: list[str] = []

‎docs/source/index.rst

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What is ``SpatialLeiden``?
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==========================
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SpatialLeiden is an implementation of
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`Multiplex Leiden clustering <https://leidenalg.readthedocs.io/en/stable/multiplex.html>`_
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that can be used to cluster spatially resolved omics data.
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SpatialLeiden integrates with the `scverse <https://scverse.org/>`_ by leveraging
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`scanpy <https://scanpy.readthedocs.io/>`_ and `anndata <https://anndata.readthedocs.io/>`_
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but can also be used independently.
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.. toctree::
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:maxdepth: 1
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:caption: Contents:
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self
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installation
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api
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Indices and tables
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==================
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- :ref:`genindex`
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- :ref:`search`

‎docs/source/installation.rst

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Installation
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============
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PyPi and ``pip``
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----------------
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To install ``spatialleiden`` from `PyPI <https://pypi.org/>`_ using ``pip`` just run
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.. code-block:: bash
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pip install spatialleiden
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bioconda and ``conda``
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----------------------
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``spatialleiden`` is not yet available for
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`Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ installations. But we are
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planning to add it to `bioconda <https://bioconda.github.io/>`_ soon.
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.. .. code-block:: bash
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.. conda install -c conda-forge spatialleiden
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.. .. note::
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.. Of course, it is also possible to use ``mamba`` instead of ``conda``
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.. to speed up the installation.
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From GitHub
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-----------
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You can install the latest versions directly from
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`GitHub <https://github.com/HiDiHlabs/SpatialLeiden>`_. To do so clone the repository
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using the ``git clone`` command. Navigate into the downloaded directory and install
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using
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.. code-block:: bash
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pip install -e .
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If you want to install the development version you can install the additional optional
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dependencies with
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.. code-block:: bash
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pip install -e '.[dev]'

‎pyproject.toml

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[project]
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name = "spatialleiden"
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description = "Implementation of multiplex Leiden for analysis of spatial tnanscriptomics data."
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description = "Implementation of multiplex Leiden for analysis of spatial omics data."
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readme = { file = "README.md", content-type = "text/markdown" }
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license = { file = "LICENSE" }
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requires-python = ">=3.10"
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dynamic = ["version"]
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authors = [
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{ name = "Niklas Müller-Bötticher", email = "[email protected]" },
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{ name = "Shashwat Sahay", email = "[email protected]" },
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]
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dependencies = [
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"anndata",
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"igraph",
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"leidenalg~=0.10.2",
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"numpy>=1.21",
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"scanpy",
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"scipy>=1.9",
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]
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dependencies = ["igraph", "leidenalg>=0.10", "numpy>=1.21", "scanpy", "scipy>=1.9"]
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classifiers = [
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",

‎spatialleiden/__init__.py

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from importlib.metadata import PackageNotFoundError, version
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from ._multiplex_leiden import leiden_multiplex, spatialleiden
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from ._multiplex_leiden import multiplex_leiden, spatialleiden
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from ._resolution_search import (
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search_resolution,
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search_resolution_latent,
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__all__ = [
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"leiden_multiplex",
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"multiplex_leiden",
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"spatialleiden",
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"search_resolution",
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"search_resolution_latent",

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