Add pyproject.toml, with pixi as project management tool. add pixi.lock

.flake8

@@ -46,6 +46,3 @@ per-file-ignores =
         libensemble/tests/functionality_tests/test_active_persistent_worker_abort.py:E402
         libensemble/tests/unit_tests/test_persistent_aposmm.py:E402
         libensemble/tests/unit_tests/RENAME_test_persistent_aposmm.py:E402
-
-        # Allow undefined name '__version__'
-        setup.py:F821

.gitignore

@@ -26,3 +26,4 @@ dist/
 .spyproject/
 
 .hypothesis
+.pixi

.pre-commit-config.yaml

@@ -1,32 +1,32 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
     - id: end-of-file-fixer
       exclude: ^(.*\.xml|.*\.svg)$
     - id: trailing-whitespace
       exclude: ^(.*\.xml|.*\.svg)$
 
 - repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
     - id: isort
       args: [--profile=black, --line-length=120]
 
 - repo: https://github.com/psf/black
-  rev: 22.12.0
+  rev: 24.10.0
   hooks:
     - id: black
       args: [--line-length=120]
 
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+  rev: 7.1.1
   hooks:
   -   id: flake8
       args: [--max-line-length=120]
 
 - repo: https://github.com/asottile/blacken-docs
-  rev: v1.12.1
+  rev: 1.19.1
   hooks:
   -   id: blacken-docs
       additional_dependencies: [black==22.12.0]

MANIFEST.in

@@ -1,3 +1,4 @@
+include pyproject.toml
 include setup.py
 include *.cfg
 include *.rst

docs/dev_guide/release_management/release_process.rst

@@ -21,7 +21,7 @@ Before release
 - Year in ``LICENSE`` is checked for correctness.
   (Note: The year generated in docs by ``docs/conf.py`` should be automatic).
 
-- ``setup.py`` and ``libensemble/__init__.py`` are checked to ensure all
+- ``pyproject.toml`` and ``libensemble/__init__.py`` are checked to ensure all
   information is up to date.
 
 - Update ``.wci.yml`` in root directory (version, date and any other

pyproject.toml

@@ -0,0 +1,131 @@
+[project]
+
+authors = [{name = "Jeffrey Larson"}, {name = "Stephen Hudson"},
+            {name = "Stefan M. Wild"}, {name = "David Bindel"},
+            {name = "John-Luke Navarro"}]
+
+dependencies = ["numpy", "psutil", "pydantic", "pyyaml", "tomli"]
+
+description = "A Python toolkit for coordinating asynchronous and dynamic ensembles of calculations."
+name = "libensemble"
+requires-python = ">=3.9"
+license = {file = "LICENSE"}
+readme = "README.rst"
+
+classifiers = [
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Natural Language :: English",
+        "Operating System :: POSIX :: Linux",
+        "Operating System :: Unix",
+        "Operating System :: MacOS",
+        "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
+        "Programming Language :: Python :: Implementation :: CPython",
+        "Topic :: Scientific/Engineering",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+]
+version = "1.4.3+dev"
+
+[project.urls]
+Documentation = "https://libensemble.readthedocs.io/en/main/"
+Repository = "https://github.com/Libensemble/libensemble"
+Issues = "https://github.com/Libensemble/libensemble/issues"
+
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = ["setuptools", "wheel", "pip>=24.3.1,<25", "setuptools>=75.1.0,<76", ]
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["libensemble*"]
+
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["osx-arm64", "linux-64", "osx-64"]
+
+[tool.pixi.pypi-dependencies]
+libensemble = { path = ".", editable = true }
+
+[tool.pixi.environments]
+default = []
+dev = ["dev"]
+
+[tool.pixi.feature.dev.dependencies]
+mpi = ">=1.0.1,<2"
+mpich = ">=4.2.3,<5"
+mpi4py = ">=4.0.1,<5"
+flake8 = ">=7.1.1,<8"
+coverage = ">=7.6.4,<8"
+pytest = ">=8.3.3,<9"
+pytest-cov = ">=5.0.0,<6"
+pytest-timeout = ">=2.3.1,<3"
+mock = ">=5.1.0,<6"
+python-dateutil = ">=2.9.0,<3"
+anyio = ">=4.6.2.post1,<5"
+matplotlib = ">=3.9.2,<4"
+mpmath = ">=1.3.0,<2"
+rich = ">=13.9.3,<14"
+sphinx = ">=8.1.3,<9"
+sphinxcontrib-bibtex = ">=2.6.3,<3"
+sphinxcontrib-spelling = ">=4.3.0,<5"
+sphinx-design = ">=0.6.1,<0.7"
+sphinx_rtd_theme = ">=3.0.1,<4"
+sphinx-copybutton = ">=0.5.2,<0.6"
+pre-commit = ">=4.0.1,<5"
+nlopt = ">=2.8.0,<3"
+scipy = ">=1.9.1,<2"
+
+[tool.pixi.dependencies]
+python = ">=3.9,<3.14"
+pip = ">=24.3.1,<25"
+setuptools = ">=75.1.0,<76"
+numpy = ">=1.21,<3"
+pydantic = ">=1.10,<3"
+pyyaml = ">=6.0,<7"
+tomli = ">=1.2.1,<3"
+psutil = ">=5.9.4,<7"
+
+[tool.pixi.target.osx-arm64.dependencies]
+clang_osx-arm64 = ">=19.1.2,<20"
+
+[tool.black]
+line-length = 120
+target-version = ['py39', 'py310', 'py311', 'py312', 'py313']
+force-exclude = '''
+(
+  /(
+    | \.git
+    | \.github
+  )/
+    | libensemble/files/to/avoid
+)
+'''
+
+[tool.typos.default]
+extend-ignore-identifiers-re = [
+    ".*NDArray.*",
+    "8ba9de56.*"
+]
+
+[tool.typos.default.extend-words]
+als = "als"
+datas = "datas"
+numer = "numer"
+inout = "inout"
+arange = "arange"
+wrk = "wrk"
+EOF = "EOF"
+HPE = "HPE"
+RO = "RO"
+lst = "lst"
+noy = "noy"
+
+[tool.typos.files]
+extend-exclude = ["*.bib", "*.xml", "docs/nitpicky"]

setup.py

@@ -1,115 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# This is for setting up libEnsemble, license and details can be
-# found at https://github.com/Libensemble/libensemble/
-
-"""libEnsemble
-
-libEnsemble is a Python toolkit for coordinating workflows of asynchronous
-and dynamic ensembles of calculations.
-
-libEnsemble can help users take advantage of massively parallel resources to
-solve design, decision, and inference problems and expand the class of
-problems that can benefit from increased parallelism.
-
-"""
-
-from pathlib import Path
-
 from setuptools import setup
-from setuptools.command.test import test as TestCommand
-
-exec(open("libensemble/version.py").read())
-
-
-class Run_TestSuite(TestCommand):
-    def run_tests(self):
-        import os
-        import sys
-
-        py_version = sys.version_info[0]
-        print("Python version from setup.py is", py_version)
-        run_string = "libensemble/tests/run-tests.sh -p " + str(py_version)
-        os.system(run_string)
-
-
-class ToxTest(TestCommand):
-    user_options = []
-
-    def initialize_options(self):
-        TestCommand.initialize_options(self)
-
-    def run_tests(self):
-        import tox
-
-        tox.cmdline()
-
 
-setup(
-    name="libensemble",
-    version=__version__,
-    description="Library to coordinate the concurrent evaluation of dynamic ensembles of calculations",
-    long_description=Path("README.rst").read_text(encoding="utf-8"),
-    url="https://github.com/Libensemble/libensemble",
-    author="Jeffrey Larson, Stephen Hudson, Stefan M. Wild, David Bindel and John-Luke Navarro",
-    author_email="libensemble@lists.mcs.anl.gov",
-    license="BSD 3-clause",
-    packages=[
-        "libensemble",
-        "libensemble.gen_funcs",
-        "libensemble.sim_funcs",
-        "libensemble.sim_funcs.branin",
-        "libensemble.alloc_funcs",
-        "libensemble.tests",
-        "libensemble.comms",
-        "libensemble.utils",
-        "libensemble.tools",
-        "libensemble.tools.live_data",
-        "libensemble.executors",
-        "libensemble.resources",
-        "libensemble.tests.unit_tests",
-        "libensemble.tests.regression_tests",
-    ],
-    install_requires=["numpy>=1.21", "psutil>=5.9.4", "pydantic>=1.10", "tomli>=1.2.1", "pyyaml>=6.0"],
-    # numpy - oldest working version. psutil - oldest working version.
-    # pyyaml - oldest working version.
-    # If run tests through setup.py - downloads these but does not install
-    tests_require=[
-        "pytest>=3.1",
-        "pytest-cov>=2.5",
-        "pytest-pep8>=1.0",
-        "pytest-timeout",
-        "mock",
-    ],
-    extras_require={
-        "docs": [
-            "autodoc_pydantic",
-            "sphinx<9",
-            "sphinx_design",
-            "sphinx_rtd_theme",
-            "sphinxcontrib-bibtex",
-            "sphinxcontrib-spelling",
-            "sphinx-copybutton",
-        ],
-    },
-    classifiers=[
-        "Development Status :: 5 - Production/Stable",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: BSD License",
-        "Natural Language :: English",
-        "Operating System :: POSIX :: Linux",
-        "Operating System :: Unix",
-        "Operating System :: MacOS",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Programming Language :: Python :: 3.12",
-        "Programming Language :: Python :: 3.13",
-        "Programming Language :: Python :: Implementation :: CPython",
-        "Topic :: Scientific/Engineering",
-        "Topic :: Software Development :: Libraries :: Python Modules",
-    ],
-    cmdclass={"test": Run_TestSuite, "tox": ToxTest},
-)
+setup()