[MRG] move setup.cfg into pyproject.toml

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,8 +8,10 @@ Please also be sure to note here if file formats, command-line
 interface, and/or the top-level sourmash API will change because of
 this PR.
 
-If you are a new contributor, please provide
-[your ORCID](https://orcid.org).  If you don't have one, please
+If you are a new contributor, please add your name and
+[your ORCID](https://orcid.org) to the `pyproject.toml` author list
+(maintaining alphabetical order by last name).
+If you don't have an ORCID, please
 [register for one](https://orcid.org/register).
 
 Once the items above are done, and all checks pass, request a review!

pyproject.toml

@@ -1,13 +1,141 @@
 [build-system]
 requires = [
-    "setuptools >= 48, <60",
+    "setuptools >= 61",
     "setuptools_scm[toml] >= 4, <6",
     "setuptools_scm_git_archive",
     "milksnake",
     "wheel >= 0.29.0",
 ]
 build-backend = 'setuptools.build_meta'
 
+[project]
+name = "sourmash"
+description = "tools for comparing DNA sequences with MinHash sketches"
+readme = "README.md"
+
+authors = [
+  { name="Luiz Irber", orcid="0000-0003-4371-9659" },
+  { name="Mohamed Abuelanin", orcid="0000-0002-3419-4785" },
+  { name="Harriet Alexander", orcid="0000-0003-1308-8008" },
+  { name="Abhishek Anant", orcid="0000-0002-5751-2010" },
+  { name="Keya Barve", orcid="0000-0003-3241-2117" },
+  { name="Colton Baumler", orcid="0000-0002-5926-7792" },
+  { name="Olga Botvinnik", orcid="0000-0003-4412-7970" },
+  { name="Phillip Brooks", orcid="0000-0003-3987-244X" },
+  { name="Peter Cock", orcid="0000-0001-9513-9993" },
+  { name="Daniel Dsouza", orcid="0000-0001-7843-8596" },
+  { name="Laurent Gautier", orcid="0000-0003-0638-3391" },
+  { name="Tim Head", orcid="0000-0003-0931-3698" },
+  { name="Mahmudur Rahman Hera", orcid="0000-0002-5992-9012" },
+  { name="Hannah Eve Houts", orcid="0000-0002-7954-4793" },
+  { name="Lisa K. Johnson", orcid="0000-0002-3600-7218" },
+  { name="Fabian Klötzl", orcid="0000-0002-6930-0592" },
+  { name="David Koslicki", orcid="0000-0002-0640-954X" },
+  { name="Katrin Leinweber", orcid="0000-0001-5135-5758" },
+  { name="Marisa Lim", orcid="0000-0003-2097-8818" },
+  { name="Ricky Lim", orcid="0000-0003-1313-7076" },
+  { name="Ivan Ogasawara", orcid="0000-0001-5049-4289" },
+  { name="N. Tessa Pierce", orcid="0000-0002-2942-5331" },
+  { name="Taylor Reiter", orcid="0000-0002-7388-421X" },
+  { name="Camille Scott", orcid="0000-0001-8822-8779" },
+  { name="Andreas Sjödin", orcid="0000-0001-5350-4219" },
+  { name="Connor T. Skennerton", orcid="0000-0003-1320-4873" },
+  { name="Jason Stajich", orcid="0000-0002-7591-0020" },
+  { name="Daniel Standage", orcid="0000-0003-0342-8531" },
+  { name="S. Joshua Swamidass", orcid="0000-0003-2191-0778" },
+  { name="Connor Tiffany", orcid="0000-0001-8188-7720" },
+  { name="Pranathi Vemuri", orcid="0000-0002-5748-9594"},
+  { name="Erik Young", orcid="0000-0002-9195-9801" },
+  { name="Nick H", orcid="0000-0002-1685-302X" },
+  { name="C. Titus Brown", orcid="0000-0001-6001-2677" },
+]
+
+maintainers = [
+  { name="Luiz Irber", email="luiz@sourmash.bio", orcid="0000-0003-4371-9659" },
+  { name="C. Titus Brown", email="titus@idyll.org", orcid="0000-0001-6001-2677" },
+]
+
+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 :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+  "screed>=1.0.5",
+  "cffi>=1.14.0",
+  "numpy",
+  "matplotlib",
+  "scipy",
+  "deprecation>=2.0.6",
+  "cachetools>=4,<6",
+  "bitstring>=3.1.9,<4",
+]
+
+requires-python = ">=3.8"
+license = { file = "LICENSE" }
+dynamic = ["version"]
+
+[project.urls]
+"Documentation" = "https://sourmash.readthedocs.io"
+"CI" = "https://github.com/dib-lab/sourmash/actions"
+"Source" = "https://github.com/dib-lab/sourmash"
+"Tracker" = "https://github.com/dib-lab/sourmash/issues"
+
+[project.scripts]
+"sourmash" = "sourmash.__main__:main"
+
+[project.optional-dependencies]
+test = [
+  "pytest>=6.2.4,<7.2.0",
+  "pytest-cov>=2.12,<4.0",
+  "pyyaml>=6,<7",
+  "recommonmark",
+  "hypothesis",
+]
+demo = [
+  "jupyter",
+  "jupyter_client",
+  "ipython",
+]
+doc = [
+  "sphinx>=4.4.0,<6",
+  "myst-parser==0.18.0",
+  "Jinja2==3.1.2",
+  "alabaster",
+  "sphinxcontrib-napoleon",
+  "nbsphinx",
+  "ipython",
+  "docutils>=0.17.1,<0.19.0",
+]
+storage = [
+  "ipfshttpclient>=0.4.13",
+  "redis",
+]
+# hmm, I think this is a hack, but it works...
+# https://github.com/pypa/pip/issues/10393#issuecomment-941885429
+all = ["sourmash[test,demo,doc,storage]"]
+
+[tool.setuptools]
+zip-safe = false
+platforms = ["any"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+version = {attr = "sourmash.version.version"}
+
 [tool.setuptools_scm]
 write_to = "src/sourmash/version.py"
 git_describe_command = "git describe --dirty --tags --long --match v* --first-parent"
@@ -26,3 +154,18 @@ skip = "*-win32 *-manylinux_i686 *-musllinux_ppc64le *-musllinux_s390x"
 before-build = "source .ci/install_cargo.sh"
 environment = { PATH="$HOME/.cargo/bin:$PATH" }
 build-verbosity = 3
+
+[tool.pytest.ini_options]
+addopts = "--doctest-glob='doc/*.md'"
+norecursedirs = [
+  "utils",
+  "build",
+  "buildenv",
+  ".tox",
+  ".asv",
+  ".eggs",
+]
+testpaths = [
+  "tests",
+  "doc",
+]

tox.ini

@@ -16,7 +16,6 @@ isolated_build = true
 skip_missing_interpreters = true
 
 [testenv]
-setuptools_version = setuptools<60
 description = run the tests with pytest under {basepython}
 setenv =
     PIP_DISABLE_VERSION_CHECK = 1