Avamb new

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018 Technical University of Denmark
+Copyright (c) 2023 University of Copenhagen
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -0,0 +1 @@
+include vamb/kernel.npz

pyproject.toml

@@ -0,0 +1,26 @@
+[project]
+name = "vamb"
+dynamic = ["version"]
+dependencies = [
+    "numpy ~= 1.20",
+    "torch ~= 1.13",
+    "pycoverm ~= 0.6"
+]
+# Currently pycoverm does not have binaries for Python > 3.11.
+# The dependency resolver, will not error on Python 3.11, but attempt
+# to build pycoverm from source, but will not get the deps required for that.
+requires-python = "<3.12.*,>=3.9.0"
+scripts = {vamb = "vamb.__main__:main"}
+
+[metadata]
+author = "Pau Piera and Jakob Nybo Nissen"
+author_email = "[email protected]"
+url = "https://github.com/RasmussenLab/vamb"
+description = "Variational and Adversarial autoencoders for Metagenomic Binning"
+license = "MIT"
+[tool.setuptools.dynamic]
+version = {attr = "vamb.__version__"}
+
+[build-system]
+requires = ["setuptools ~= 63.0", "Cython ~= 0.29"]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -1,2 +1,3 @@
-[metadata]
-description-file = README.md
+[options]
+packages = find:
+include_package_data = True

setup.py

@@ -1,35 +1,3 @@
-import sys
-from setuptools import setup, find_packages
-from setuptools import Extension
-import os
+from setuptools import Extension, setup
 
-SETUP_METADATA = \
-               {
-    "name": "vamb",
-    "description": "Variational autoencoder for metagenomic binning",
-    "url": "https://github.com/RasmussenLab/vamb",
-    "author": "Jakob Nybo Nissen and Simon Rasmussen",
-    "author_email": "[email protected]",
-    "version": "3.0.9",
-    "license": "MIT",
-    "packages": find_packages(),
-    "package_data": {"vamb": ["kernel.npz"]},
-    "entry_points": {'console_scripts': [
-        'vamb = vamb.__main__:main'
-        ]
-    },
-    "scripts": ['src/concatenate.py'],
-    "ext_modules": [Extension("vamb._vambtools",
-                               sources=["src/_vambtools.pyx"],
-                               language="c")],
-    "install_requires": ["numpy>=1.20", "torch>=1.13", "pysam>=0.14"],
-    "setup_requires": ['Cython>=0.29', "setuptools>=58.0"],
-    "python_requires": ">=3.5",
-    "classifiers":[
-        "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: MIT License",
-        "Operating System :: OS Independent",
-    ],
-    }
-
-setup(**SETUP_METADATA)
+setup(ext_modules=[Extension(name="vamb._vambtools", sources=["src/_vambtools.pyx"])])