Clean up of setup.py, Moving more to pyproject.toml (westpa#519)

* moved most things over to pyproject.toml

* move a little back

* healthy medium

* move requires-python down above dependencies

* lint changes to black

Author: jeremyleung521

pyproject.toml

@@ -8,13 +8,59 @@ requires = [
     "Cython >=0.29.16",  # Note: sync with setup.py
     "numpy >=2.0.0, <3",  # Force numpy>=2 during build time so it works on both 1.XX and 2.XX
     "scipy >=0.19.1",
-    "versioneer-518"
+    "versioneer-518",
 ]
 # Uncommenting this requires adding the top level of the repo to sys.path in the setup.py
 # so that it can find the vendorized copy of versioneer. I see that other projects don't
 # always include this (pandas, numpy, etc), so leaving this off for now
 # build-backend = "setuptools.build_meta"
 
+
+[project]
+name = "westpa"
+dynamic = ["version", "scripts"]
+license = "MIT"
+license-files = ["LICEN[CS]E.*"]
+readme = {file = "README.rst", content-type = "text/x-rst"}
+keywords = []
+description = 'WESTPA is a package for constructing and running stochastic simulations using the "weighted ensemble" approach of Huber and Kim (1996).'
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "Operating System :: POSIX",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Cython",
+]
+requires-python = ">=3.10"
+dependencies = [
+  "numpy >= 1.25.0,<3",
+  "scipy >= 0.19.1",
+  "h5py >= 2.10",
+  "mdtraj >= 1.9.5",
+  "pyyaml",
+  "pyzmq",
+  "matplotlib",
+  "blessings",
+  "ipykernel",
+  "tqdm",
+  "pandas",
+  "tables",
+]
+
+[project.optional-dependencies]
+tests = ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout"]
+mpi = ["mpi4py"]
+dev = ["westpa[tests]", "pre-commit"]
+
+[project.urls]
+Homepage = "https://westpa.github.io"
+Repository = "https://github.com/westpa/westpa"
+Documentation = "https://github.readthedocs.io"
+Issues = "https://github.com/westpa/westpa/issues"
+
+
 [tool.black]
 line-length = 132
 skip-string-normalization = true
@@ -44,6 +90,9 @@ exclude = '''
 )
 '''
 
+[tool.setuptools.packages.find]
+where = ["src"]
+
 # See the docstring in versioneer.py for instructions. Note that you must
 # re-run 'versioneer.py setup' after changing this section, and commit the
 # resulting files.

setup.py

@@ -1,6 +1,6 @@
 import sys
 
-from setuptools import setup, Extension, find_packages
+from setuptools import setup, Extension
 
 import versioneer
 
@@ -98,58 +98,12 @@ def extensions():
 
 console_scripts = console_scripts_core + console_scripts_tools
 
-CLASSIFIERS = [
-    "Development Status :: 5 - Production/Stable",
-    "Intended Audience :: Developers",
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: MIT License",
-    "Operating System :: POSIX",
-    "Programming Language :: Python",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Cython",
-]
-
-INSTALL_REQUIRES = [
-    "numpy >= 1.25.0, <3",
-    "scipy >= 0.19.1",
-    "h5py >= 2.10",
-    "mdtraj >= 1.9.5",
-    "pyyaml",
-    "pyzmq",
-    "matplotlib",
-    "blessings",
-    "ipykernel",
-    "tqdm",
-    "pandas",
-    "tables",
-]
-
-EXTRAS_REQUIRE = {
-    "tests": ["pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout"],
-    "mpi": ["mpi4py"],
-}
-
-EXTRAS_REQUIRE["dev"] = EXTRAS_REQUIRE["tests"] + ["pre-commit"]
-
 
 metadata = dict(
-    name='westpa',
-    url='http://github.com/westpa/westpa',
-    license='MIT',
-    long_description=open('README.rst', encoding='utf8').read(),
     version=versioneer.get_version(),
-    keywords='',
     cmdclass=versioneer.get_cmdclass(),
-    python_requires=">=3.10",
     zip_safe=False,
-    classifiers=CLASSIFIERS,
     entry_points={'console_scripts': console_scripts},
-    install_requires=INSTALL_REQUIRES,
-    extras_require=EXTRAS_REQUIRE,
-    package_data={},
-    packages=find_packages(where='src'),
-    package_dir={"": "src"},
-    description='WESTPA is a package for constructing and running stochastic simulations using the "weighted ensemble" approach of Huber and Kim (1996).',
 )
 
 

src/westpa/cli/tools/w_reweight.py

@@ -92,7 +92,7 @@ def _pop_eval_block(
     do_correl,
     mcbs_enable,
     estimator_kwargs,
-    **kwargs
+    **kwargs,
 ):
     # As our reweighting estimator is a weird function, we can't use the general mclib block.
     # A little hack to make our estimator play nice, as jstate must be there.
@@ -680,7 +680,7 @@ def w_postanalysis_stateprobs(self):
                     name='Bin Population Evolution',
                     mcbs_enable=self.mcbs_enable,
                     data_input={},
-                    **submit_kwargs
+                    **submit_kwargs,
                 )
                 # print(future_kwargs)
                 futures.append(generate_future(self.work_manager, 'Bin Pop Evolution', _pop_eval_block, future_kwargs))

src/westpa/mclib/__init__.py

@@ -204,7 +204,7 @@ def _1D_simple_eval_block(
     do_correl,
     mcbs_enable,
     subsample=np.mean,
-    **extra
+    **extra,
 ):
     # This is actually appropriate for anything with a directly measured, 1D dataset, i.e.,
     # Fluxes, color populations, and state populations.
@@ -242,7 +242,7 @@ def _2D_simple_eval_block(
     do_correl,
     mcbs_enable,
     subsample=np.mean,
-    **extra
+    **extra,
 ):
     # This is really just a simple 2D block for less complex datasets, but there it is.
     # It's probably limited in this use case to conditional_fluxes, but anything that's an i to j process that is directly measured

src/westpa/tools/kinetics_tool.py

@@ -302,7 +302,7 @@ def run_calculation(
                     name=name,
                     mcbs_enable=self.mcbs_enable,
                     data_input={},
-                    **extra
+                    **extra,
                 )
 
                 # Slice up the datasets for this iteration slice.

src/westpa/westext/stringmethod/string_method.py

@@ -87,7 +87,7 @@ def __init__(
         fourier_P=2,
         fourier_maxiters=100,
         fourier_tol=1.0e-6,
-        **kwargs
+        **kwargs,
     ):
         super().__init__(centers, **kwargs)