move to pyproject.toml python pkg setup

.bumpversion.cfg

@@ -19,9 +19,9 @@ replace = {new_version}
 search = __version__ = '{current_version}'
 replace = __version__ = '{new_version}'
 
-[bumpversion:file:setup.py]
-search = version='{current_version}'
-replace = version='{new_version}'
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
 
 [bumpversion:file:conda/recipe/pcgrr/meta.yaml]
 search = version: {current_version}

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017 Sigve Nakken
+Copyright (c) 2024 Sigve Nakken
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

pyproject.toml

@@ -0,0 +1,57 @@
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "pcgr"
+version = "1.4.1.9001" # versioned by bump2version
+description = "Personal Cancer Genome Reporter (PCGR) - variant interpretation for precision cancer medicine"
+authors = [
+    {name = "Sigve Nakken", email = "[email protected]"},
+    ]
+maintainers = [
+    {name = "Sigve Nakken", email = "[email protected]"},
+    {name = "Peter Diakumis", email = "[email protected]"},
+    ]
+readme = "README.md"
+license = {file = "LICENSE"}
+keywords = ["cancer", "genomics", "pcgr"]
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: R",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    ]
+
+
+[project.urls]
+Homepage = "https://sigven.github.io/pcgr/"
+Documentation = "https://sigven.github.io/pcgr/"
+Repository = "https://github.com/sigven/pcgr"
+Changelog = "https://sigven.github.io/pcgr/articles/CHANGELOG.html"
+
+
+[project.scripts]
+pcgr = "pcgr.main:cli"
+cpsr = "pcgr.cpsr:main"
+
+
+[tool.setuptools.packages]
+find = {}
+
+
+[tool.setuptools]
+script-files = [
+    "scripts/cpsr_validate_input.py",
+    "scripts/pcgr_summarise.py",
+    "scripts/pcgr_validate_input.py",
+    "scripts/pcgr_vcfanno.py",
+    "scripts/pcgrr.R",
+    "scripts/cpsr.R",
+    ]

setup.py

@@ -1,26 +1,5 @@
+#!/usr/bin/env python
 import setuptools
 
-setuptools.setup(
-    name='pcgr',
-    version='1.4.1.9001', # versioned by bump2version
-    license='MIT',
-    author='Sigve Nakken',
-    author_email='[email protected]',
-    description='Personal Cancer Genome Reporter (PCGR) - variant interpretation for precision cancer medicine',
-    url='https://github.com/sigven/pcgr',
-    packages=setuptools.find_packages(),
-    entry_points={
-        'console_scripts': [
-            'pcgr = pcgr.main:cli',
-            'cpsr = pcgr.cpsr:main'
-        ]
-    },
-    scripts=[
-        'scripts/cpsr_validate_input.py',
-        'scripts/pcgr_summarise.py',
-        'scripts/pcgr_validate_input.py',
-        'scripts/pcgr_vcfanno.py',
-        'scripts/pcgrr.R',
-        'scripts/cpsr.R'
-    ]
-)
+if __name__ == "__main__":
+    setuptools.setup()