"""Sctoolbox a collection of single cell analysis functions."""

from setuptools import setup

from setuptools import find_namespace_packages

import re

import os

import glob

import sys

import subprocess

# Install these dependencies before everything else

# do this here (not in conda) to make this package buildable without prior steps

pre_deps = [

"cmake>=3.18", # fixes ERROR: Failed to build installable wheels for some pyproject.toml based projects (louvain)

"setuptools_scm>=9.0.3" # due to https://github.com/pypa/setuptools-scm/issues/938

]

# get a clean bash path (not altered by the pip build process)

# pip installs each package using separate build environment. So the pre-dependencies would be only available during sctoolbox installation.

# This is circumvented by installing the pre-dependencies globally. Which is similar to doing "pip install <pre-deps>" before "pip install sctoolbox".

# TODO only works on Linux based systems

clean_path = subprocess.check_output(["echo $PATH"], shell=True).decode("utf-8").strip()

for dep in pre_deps:

subprocess.run([sys.executable, "-m", "pip", "install", dep], env={'PATH': clean_path}, check=True)

# Module requirements

extras_require = {"converter": ['rpy2', 'anndata2ri'],

"atac": ['uropa',

'pybedtools>=0.9.1', # https://github.com/daler/pybedtools/issues/384

'pygenometracks>=3.8',

'peakqc',

'tobias>=0.17.2'], # to avoid installation error

"interactive": ['click'],

"batch_correction": ['bbknn', 'harmonypy', 'scanorama'],

# pycirclize https://github.com/moshi4/pyCirclize/issues/75

"receptor_ligand": ['scikit-learn', 'igraph', 'pycirclize>=1.7.1', 'liana', 'mudata>=0.3.1', 'networkx>=3.5'], # anndata>=10.9 requires mudata>=0.3.1; networkx>=3.5 for numpy 2 support

# "velocity": ['scvelo @ git+https://github.com/rwiegan/scvelo.git'], # install from fork until this is merged: https://github.com/theislab/scvelo/pull/1308

"pseudotime": ["scFates"], # omit scFates due to version conflict https://github.com/LouisFaure/scFates/issues/50

"gsea": ["gseapy"],

"deseq2": ["pydeseq2>=0.5.2"] # https://github.com/owkin/PyDESeq2/issues/242

# "scar": ["scar @ git+https://github.com/Novartis/scar.git"] # PyPI doesn't accept git packages

}

# contains all requirements aka a full installation

extras_require["all"] = list(dict.fromkeys([item for sublist in extras_require.values() for item in sublist if item != "scFates"])) # flatten list of all requirements; omit scFates, see line 39

# contains the requirements needed to run notebooks 1-4 (atac & rna); skipping rarely used dependencies (e.g. scar)

extras_require["core"] = sum([value for key, value in extras_require.items() if key in ["converter", "atac", "interactive", "batch_correction"]], start=[])

# contains dependencies needed for the downstream notebooks (general & notebooks after 4)

extras_require["downstream"] = sum([value for key, value in extras_require.items() if key in ["receptor_ligand", "velocity", "gsea", "deseq2"]], start=[]) # , "pseudotime" ; see line 39 for more info

def find_version(f: str) -> str:

"""

Get package version from version file.

Parameters

----------

f : str

Path to version file.

Returns

-------

str

Version string.

Raises

------

RuntimeError

If version string is missing.

"""

version_file = open(f).read()

version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]", version_file, re.M)

if version_match:

return version_match.group(1)

else:

raise RuntimeError("Unable to find version string.")

# Find all packages in sctoolbox

packages = find_namespace_packages("sctoolbox")

packages = ["sctoolbox." + package for package in packages] # add sctoolbox. prefix to all packages

# Find top level modules in sctoolbox

modules = glob.glob("sctoolbox/*.py")

modules = [m.replace("/", ".")[:-3] for m in modules if not m.endswith("__init__.py")] # omit file ending and adjust path to import format e.g. sctoolbox._modules

# Readme from git

def readme():

"""Collect the readme file content."""

with open('README.md') as f:

return f.read()

setup(

# This is the name of the package important in PyPI, important during installation "pip install SC-Framework".

# The package is imported using "import sctoolbox" defined by the folder name.

name='SC-Framework',

description='Custom modules for single cell analysis',

long_description=readme(),

long_description_content_type='text/markdown',

version=find_version(os.path.join("sctoolbox", "_version.py")),

license='MIT',

packages=packages,

py_modules=modules,

python_requires='>=3.9,<3.13', # dict type hints as we use it require python 3.9; 3.13 not supported by cmake # https://github.com/python-cmake-buildsystem/python-cmake-buildsystem/issues/350

install_requires=[

'pysam',

'matplotlib',

'matplotlib_venn',

'scanpy[louvain,leiden]>=1.11', # 'colorbar_loc' not available before 1.9; fix run_rank_genes error 1.11; also install community detection (louvain & leiden)

'anndata>=0.8', # anndata 0.7 is not upward compatible

'numba>=0.57.0rc1', # minimum version supporting python>=3.10, but 0.57 fails with "cannot import name 'quicksort' from 'numba.misc'" for scrublet

'numpy>=2',

'kneed',

'qnorm',

'plotly',

'scipy>=1.14',

'statsmodels>=0.14.5',

'tqdm',

'pandas>1.5.3', # https://gitlab.gwdg.de/loosolab/software/sc_framework/-/issues/200

'seaborn>0.12',

'ipympl',

'ipywidgets>=8.0.0', # needed to show labels in interactive accordion widgets

'scrublet',

'IPython',

'openpyxl',

'apybiomart',

'requests',

'python-gitlab',

'psutil',

'deprecation',

'pyyaml',

'beartype>=0.18.2', # Version 0.18.0 is not working properly

'packaging',

'throttler',

'upsetplot',

'pptreport>=1.1.4', # to fix placeholder not found error

'boto3',

'Jinja2'

],

include_package_data=True,

extras_require=extras_require

)