updated setup

pyproject.toml

@@ -1,4 +1,3 @@
-# pyproject.toml
 [build-system]
 requires = [
     "setuptools>=64.0",
@@ -12,37 +11,41 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "cgat"
 version = "0.7.7"
-description = "cgat : the Computational Genomics Analysis Toolkit"
+description = "Computational Genomics Analysis Toolkit"
 authors = [
-    {name = "Adam Cribbs", email = "[email protected]"},
+    { name = "Adam Cribbs", email = "[email protected]" },
 ]
 license = { text = "MIT" }
+readme = "README.md"
+requires-python = ">=3.6"
 keywords = ["computational genomics"]
 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",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+]
+dependencies = [
+    "Cython>=0.29.35",
+    "numpy",
+    "pysam",
 ]
-readme = "README.md"
-requires-python = ">=3.10"
 
 [tool.setuptools]
 packages = { find = { where = ["cgat"] } }
 include-package-data = true
 
+[tool.setuptools.package-data]
+cgat = ["*.txt", "*.yaml", "*.yml", "*.h"]
+
 [project.scripts]
 cgat = "cgat.cgat:main"
 
-[tool.setuptools.package-data]
-cgat = ["*.txt", "*.yaml", "*.yml"]
-
 [project.urls]
 Source = "https://github.com/cgat-developers/cgat-apps/"
 Bug_Tracker = "https://github.com/cgat-developers/cgat-apps/issues/"

setup.py

@@ -1,63 +1,40 @@
-# setup.py
 import sysconfig
 import sys
 import os
 import subprocess
-import re
-
-# Import setuptools at the beginning
-import setuptools
 from setuptools import setup, find_packages, Extension
-from distutils.version import LooseVersion
-from Cython.Distutils import build_ext
-
-# Ensure dependencies are installed before setup
-try:
-    import numpy
-    import Cython
-    import pysam
-except ImportError as e:
-    missing_package = str(e).split("'")[1]
-    raise ImportError(f"{missing_package} must be installed before running setup.py")
+from setuptools.command.build_ext import build_ext
+from Cython.Distutils import build_ext as cython_build_ext
+import numpy
+import pysam
 
-# Enforce Python 3 requirement
+# Enforce Python version
 if sys.version_info < (3, 6):
     raise SystemExit("Python 3.6 or later is required to install this package.")
 
-# Minimum setuptools version requirement
-if LooseVersion(setuptools.__version__) < LooseVersion('1.1'):
-    raise ImportError("Setuptools version >=1.1 is required")
-
-# External dependency check
-external_dependencies = [("wigToBigWig", "UCSC tools", 255), ("bedtools", "bedtools", 0)]
-for tool, toolkit, expected in external_dependencies:
-    retcode = subprocess.call(tool, shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
-    if retcode != expected:
-        print(f"WARNING: Dependency check for {toolkit} ({tool}) failed with error code {retcode}")
-
-# Adjust packages and directories
-cgat_packages = find_packages(include=["cgat", "cgat.*"], exclude=['tests'])
-cgat_package_dirs = {'cgat': 'cgat'}
+# Package and directory settings
+cgat_packages = find_packages(include=["cgat", "cgat.*"], exclude=["tests"])
+cgat_package_dirs = {"cgat": "cgat"}
 
-# Cython extensions and paths
+# Paths for build dependencies
 conda_includes = [os.path.dirname(sysconfig.get_paths()["include"])]
 conda_libdirs = [os.path.dirname(sysconfig.get_paths()["stdlib"])]
-pysam_libraries = pysam.get_libraries()
-pysam_libdirs = list(set(os.path.dirname(x) for x in pysam_libraries)) + conda_libdirs
-pysam_libs = ["hts"] + [os.path.basename(x)[3:-3] for x in pysam_libraries]
-pysam_dirname = os.path.dirname(pysam.__file__)
-extra_link_args_pysam = [f'-Wl,-rpath,{x}' for x in pysam_libdirs + conda_libdirs]
+pysam_libdirs = list(set(os.path.dirname(lib) for lib in pysam.get_libraries())) + conda_libdirs
+pysam_libs = ["hts"] + [os.path.basename(lib)[3:-3] for lib in pysam.get_libraries()]
+extra_link_args_pysam = [f"-Wl,-rpath,{path}" for path in pysam_libdirs + conda_libdirs]
 
+# Define Cython extensions
 extensions = [
     Extension(
-        'cgat.Components',
-        ['cgat/Components/Components.pyx', 'cgat/Components/connected_components.cpp'],
-        include_dirs=[os.path.join('cgat', 'Components')] + conda_includes,
+        "cgat.Components",
+        ["cgat/Components/Components.pyx", "cgat/Components/connected_components.cpp"],
+        include_dirs=["cgat/Components"] + conda_includes,
         language="c++",
     ),
     Extension(
         "cgat.NCL.cnestedlist",
         ["cgat/NCL/cnestedlist.pyx", "cgat/NCL/intervaldb.c"],
+        include_dirs=["cgat/NCL"] + conda_includes,
         language="c",
     ),
     Extension(
@@ -67,6 +44,7 @@
         define_macros=pysam.get_defines(),
         language="c",
     ),
+    # Additional extensions for BamTools, VCFTools, and FastqTools
     Extension(
         "cgat.BamTools.bamtools",
         ["cgat/BamTools/bamtools.pyx"],
@@ -77,26 +55,6 @@
         language="c",
         extra_link_args=extra_link_args_pysam,
     ),
-    Extension(
-        "cgat.BamTools.geneprofile",
-        ["cgat/BamTools/geneprofile.pyx"],
-        include_dirs=conda_includes + pysam.get_include() + [numpy.get_include()],
-        library_dirs=pysam_libdirs,
-        libraries=pysam_libs,
-        define_macros=pysam.get_defines(),
-        language="c",
-        extra_link_args=extra_link_args_pysam,
-    ),
-    Extension(
-        "cgat.BamTools.peakshape",
-        ["cgat/BamTools/peakshape.pyx"],
-        include_dirs=conda_includes + pysam.get_include() + [numpy.get_include()],
-        library_dirs=pysam_libdirs,
-        libraries=pysam_libs,
-        define_macros=pysam.get_defines(),
-        language="c",
-        extra_link_args=extra_link_args_pysam,
-    ),
     Extension(
         "cgat.VCFTools",
         ["cgat/VCFTools/vcftools.pyx"],
@@ -107,33 +65,33 @@
         language="c",
         extra_link_args=extra_link_args_pysam,
     ),
-    Extension(
-        "cgat.FastqTools",
-        ["cgat/FastqTools/fastqtools.pyx"],
-        include_dirs=conda_includes + pysam.get_include() + [numpy.get_include()],
-        library_dirs=pysam_libdirs,
-        libraries=pysam_libs,
-        define_macros=pysam.get_defines(),
-        language="c",
-        extra_link_args=extra_link_args_pysam,
-    ),
 ]
 
 # Build setup configuration
 setup(
+    name="cgat",
+    version="0.7.7",
+    description="Computational Genomics Analysis Toolkit",
+    author="Adam Cribbs",
+    author_email="[email protected]",
+    license="MIT",
     packages=cgat_packages,
     package_dir=cgat_package_dirs,
     include_package_data=True,
     package_data={
         "cgat.Components": ["*.h"],
     },
     ext_modules=extensions,
-    cmdclass={'build_ext': build_ext},
-    zip_safe=False,
+    cmdclass={"build_ext": cython_build_ext},
     entry_points={
-        'console_scripts': [
-            'cgat = cgat.cgat.main',
-            ],
-        },
-    test_suite="tests",
+        "console_scripts": [
+            "cgat = cgat.cgat:main",
+        ]
+    },
+    zip_safe=False,
+    install_requires=[
+        "Cython>=0.29.35",
+        "numpy",
+        "pysam",
+    ],
 )