move most of setup.py to pyproject.toml and setup.cfg

fixing setuptools_scm

use isolated build for package creation

MANIFEST.in

@@ -12,5 +12,5 @@ global-exclude *.rlib
 global-exclude *.orig
 global-exclude *.pyc
 global-exclude *.so
-prune tests/test-data/
-global-exclude *.git/
+prune tests/test-data
+global-exclude *.git

pyproject.toml

@@ -1,9 +1,13 @@
 [build-system]
 requires = [
-    "setuptools >= 40.0.4",
-    "setuptools_scm >= 2.0.0, <4",
+    "setuptools >= 42",
+    "setuptools_scm[toml] >= 3.4.0, <4",
     "setuptools_scm_git_archive",
+    "milksnake",
     "wheel >= 0.29.0",
-    "Cython >= 0.25.2",
 ]
 build-backend = 'setuptools.build_meta'
+
+[tool.setuptools_scm]
+write_to = "sourmash/version.py"
+git_describe_command = "git describe --dirty --tags --long --match v* --first-parent"    

setup.cfg

@@ -1,3 +1,86 @@
 [metadata]
-description-file = README.md
-long-description-content-type = text/markdown
+name = sourmash
+description = tools for comparing DNA sequences with MinHash sketches
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/dib-lab/sourmash
+author = C. Titus Brown
+author_email = [email protected]
+license = BSD 3-clause
+classifiers =
+    Development Status :: 5 - Production/Stable
+    Environment :: Console
+    Environment :: MacOS X
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: BSD License
+    Natural Language :: English
+    Operating System :: POSIX :: Linux
+    Operating System :: MacOS :: MacOS X
+    Programming Language :: Rust
+    Programming Language :: Python :: 3.5
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Topic :: Scientific/Engineering :: Bio-Informatics
+project_urls = 
+    Documentation = https://sourmash.readthedocs.io
+    CI = https://travis-ci.com/dib-lab/sourmash
+
+[options]
+zip_safe = False
+platforms = any
+#packages = find: exclude=["tests", "benchmarks"]
+packages = find:
+include_package_data = True
+install_requires =
+    screed>=0.9
+    cffi>=1.14.0
+    numpy
+    enum34; python_version < "3.4"
+    matplotlib
+    scipy
+    deprecation>=2.0.6
+
+[options.packages.find]
+exclude =
+    tests
+    benchmarks
+
+[bdist_wheel]
+universal = 1
+
+# for explanation of %(extra)s syntax see:
+# https://github.com/pypa/setuptools/issues/1260#issuecomment-438187625
+# this syntax may change in the future
+[options.extras_require]
+test =
+    pytest
+    pytest-cov
+    recommonmark
+    hypothesis
+demo =
+    jupyter
+    jupyter_client
+    ipython
+doc =
+    sphinx
+    myst-parser[sphinx]
+    alabaster
+    sphinxcontrib-napoleon
+    nbsphinx
+    ipython
+10x =
+    bam2fasta==1.0.4
+storage =
+    ipfshttpclient>=0.4.13
+    redis
+all = 
+    %(test)s
+    %(demo)s
+    %(doc)s
+    %(10x)s
+    %(storage)s
+
+[options.entry_points]
+console_scripts =
+    sourmash = sourmash.__main__:main

setup.py

@@ -1,8 +1,8 @@
-from __future__ import print_function
 import os
-from setuptools import setup, find_packages
 import sys
 
+from setuptools import setup
+
 
 DEBUG_BUILD = os.environ.get("SOURMASH_DEBUG") == "1"
 
@@ -28,65 +28,6 @@ def build_native(spec):
     )
 
 
-CLASSIFIERS = [
-    "Environment :: Console",
-    "Environment :: MacOS X",
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: BSD License",
-    "Natural Language :: English",
-    "Operating System :: POSIX :: Linux",
-    "Operating System :: MacOS :: MacOS X",
-    "Programming Language :: Rust",
-    "Programming Language :: Python :: 2.7",
-    "Programming Language :: Python :: 3.5",
-    "Programming Language :: Python :: 3.6",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-]
-
-CLASSIFIERS.append("Development Status :: 5 - Production/Stable")
-
-with open("README.md", "r") as readme:
-    LONG_DESCRIPTION = readme.read()
-
-SETUP_METADATA = {
-    "name": "sourmash",
-    "description": "tools for comparing DNA sequences with MinHash sketches",
-    "url": "https://github.com/dib-lab/sourmash",
-    "author": "C. Titus Brown",
-    "author_email": "[email protected]",
-    "license": "BSD 3-clause",
-    "packages": find_packages(exclude=["tests", "benchmarks"]),
-    "entry_points": {'console_scripts': [
-        'sourmash = sourmash.__main__:main'
-        ]
-    },
-    "install_requires": ['screed>=0.9', 'cffi>=1.14.0', 'numpy',
-                         'enum34; python_version < "3.4"',
-                         'matplotlib', 'scipy', 'deprecation>=2.0.6'],
-    "setup_requires": [
-        "setuptools>=38.6.0",
-        "milksnake",
-        "setuptools_scm>=3.2.0",
-        "setuptools_scm_git_archive",
-    ],
-    "use_scm_version": {
-        "write_to": "sourmash/version.py",
-        "git_describe_command": "git describe --dirty --tags --long --match v* --first-parent"
-    },
-    "zip_safe": False,
-    "platforms": "any",
-    "extras_require": {
-        'test' : ['pytest', 'pytest-cov', 'recommonmark', 'hypothesis'],
-        'demo' : ['jupyter', 'jupyter_client', 'ipython'],
-        'doc' : ['sphinx', 'myst-parser[sphinx]', 'alabaster',
-                 "sphinxcontrib-napoleon", "nbsphinx",
-                 "ipython"],
-        '10x': ['bam2fasta==1.0.4'],
-        'storage': ["ipfshttpclient>=0.4.13", "redis"]
-    },
-    "include_package_data": True,
-    "classifiers": CLASSIFIERS,
-    "milksnake_tasks": [build_native],
-}
-
-setup(**SETUP_METADATA)
+setup(
+  milksnake_tasks=[build_native],
+)