modernise build system: Add pyproject.toml and migrate to PEP 517

pyproject.toml

@@ -0,0 +1,64 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cellhub"
+dynamic = ["version"]
+description = "cellhub: Python pipelines for large-scale multimodal single-cell data analysis on HPC clusters"
+authors = [
+    {name = "Sansom lab", email = "stephen.sansom@kennedy.ox.ac.uk"}
+]
+license = {text = "MIT"}
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Topic :: Software Development",
+    "Topic :: Scientific/Engineering",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS"
+]
+keywords = ["computational genomics"]
+requires-python = ">=3.0"
+dependencies = [
+    "numpy==1.26.4",
+    "anndata",
+    "argparse",
+    "bbknn",
+    "h5py",
+    "harmonypy",
+    "loompy",
+    "matplotlib",
+    "pandas",
+    "ruffus",
+    "scanorama",
+    "scanpy",
+    "scvelo",
+    "scipy",
+    "scrublet",
+    "pyyaml",
+    "GMM-demux",
+    "hnswlib",
+    "sqlalchemy",
+    "drmaa",
+    "leidenalg",
+    "sphinx",
+    "tables",
+    "cgatcore",
+    "gevent",
+    "apsw",
+    "sphinx_rtd_theme"
+]
+
+[project.scripts]
+cellhub = "cellhub.entry:main"
+
+[tool.setuptools]
+packages = ["cellhub"]
+
+[tool.setuptools.dynamic]
+version = {attr = "cellhub.version.__version__"}

setup.py

@@ -1,76 +1,3 @@
-import sys
-import os
-import re
-import setuptools
-from setuptools import setup, find_packages, Extension
+from setuptools import setup
 
-from distutils.version import LooseVersion
-if LooseVersion(setuptools.__version__) < LooseVersion('1.1'):
-    print("Version detected:", LooseVersion(setuptools.__version__))
-    raise ImportError(
-        "the cellhub requires setuptools 1.1 higher")
-
-########################################################################
-########################################################################
-IS_OSX = sys.platform == 'darwin'
-
-########################################################################
-########################################################################
-# collect version
-print(sys.path.insert(0, "cellhub"))
-import cellhub.version as version
-
-version = version.__version__
-
-###############################################################
-###############################################################
-# Define dependencies
-#
-major, minor1, minor2, s, tmp = sys.version_info
-
-if major < 3:
-    raise SystemExit("""Requires Python 3 or later.""")
-
-cellhub_packages = find_packages()
-cellhub_package_dirs = {'cellhub': 'cellhub'}
-
-##########################################################
-##########################################################
-# Classifiers
-classifiers = """
-Development Status :: 3 - Alpha
-Intended Audience :: Science/Research
-Intended Audience :: Developers
-License :: OSI Approved
-Programming Language :: Python
-Topic :: Software Development
-Topic :: Scientific/Engineering
-Operating System :: POSIX
-Operating System :: Unix
-Operating System :: MacOS
-"""
-
-setup(
-    # package information
-    name='cellhub',
-    version=version,
-    description='cellhub: pipelines for warehousing single-cell data',
-    author='Sansom lab',
-    author_email='stephen.sansom@kennedy.ox.ac.uk',
-    license="MIT",
-    platforms=["any"],
-    keywords="computational genomics",
-    long_description='''cellhub : pipelines for warehouse single-cell data''',
-    classifiers=[_f for _f in classifiers.split("\n") if _f],
-    url="",
-    # package contents
-    packages=cellhub_packages,
-    package_dir=cellhub_package_dirs,
-    include_package_data=True,
-    entry_points={
-        "console_scripts": ["cellhub = cellhub.entry:main"]
-    },
-    # other options
-    zip_safe=False,
-    test_suite="tests",
-)
+setup()