Build changes for 2.16

1. setup.py -> pyproject.toml new standard, PEP 621.
2. all source code now under `src`.

This is a start for the new standard. Main issue is build isolation
forces CMake caching to break, so I have disabled the caching for now.

pyproject.toml

@@ -1,3 +1,56 @@
 [build-system]
 build-backend = "setuptools.build_meta"
-requires = ["setuptools","numpy>=1.20.3","swig>=4.0.0","cmake>=0.29.24", "ninja"]
+requires = [
+  "setuptools",
+  "numpy<2.0",       # as per petsc
+  "swig>=4.0.0",
+  "cmake>=0.29.24", 
+  "ninja"
+]
+
+[project]
+name    = "underworld"
+version = "2.16.0"
+authors = [
+  {name = "Louis Moresi", email="louis.moresi@anu.edu.au"},
+  {name = "Julian Giordani", email="julian.giordnai@sydney.edu.au"},
+  {name = "John Mansour", email="john.mansour@gmail.com"},
+  {name = "Romain Beaucher", email="romain.beucher@anu.edu.au"},
+]
+maintainers = [
+  {name = "Underworld Team", email="help@underworldcode.org"},
+]
+dependencies = [
+  "numpy>=1.20.3",
+  "mpi4py>=1.2.2",
+  "h5py",
+  "pint",
+  "scipy",
+]
+description = "Underworld2 is a python-friendly, parallel, scalable, easy-to-use toolkit for solving problems in solid and fluid mechanics."
+readme = "README.md"
+license = {file = "./LICENSE.md"}
+keywords = ["Underworld", "MPI", "Geodynamics"]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Science/Research",
+  "Operating System :: POSIX",
+  "Programming Language :: C",
+  "Programming Language :: C++",
+  "Programming Language :: Python",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Software Development :: Libraries",
+]
+[project.optional-dependencies]
+full = [
+  "badlands",
+  "lavavu",
+  "matplotlib",
+  "nbmake",
+]
+
+[project.urls]
+homepage      = "https://www.underworldcode.org"
+repository    = "https://github.com/underworldcode/underworld2"
+documentation = "https://underworld2.readthedocs.io/en/latest/"

setup.py

@@ -44,7 +44,7 @@
 
 from typing import List
 from pathlib import Path
-from setuptools import setup, Extension, find_packages
+from setuptools import setup, Extension, find_namespace_packages
 from setuptools.command.build_ext import build_ext
 
 
@@ -259,23 +259,12 @@ def extend_cmake_prefix_path(path: str) -> None:
 metadata = {
     'provides': ['underworld'],
     'zip_safe': False,
-    'install_requires': ['numpy>=1.20.3', 'mpi4py>=1.2.2', 'h5py', 'pint', 'scipy'],
-    'extras_require': {
-        'full': ["badlands","lavavu","matplotlib","nbmake"],  # for all 3rd party packages
-    },
+#    'install_requires': ['numpy>=1.20.3', 'mpi4py>=1.2.2', 'h5py', 'pint', 'scipy'],
+#    'extras_require': {
+#        'full': ["badlands","lavavu","matplotlib","nbmake"],  # for all 3rd party packages
+#    },
 }
 
-classifiers = """
-Development Status :: 5 - Production/Stable
-Intended Audience :: Developers
-Intended Audience :: Science/Research
-Operating System :: POSIX
-Programming Language :: C
-Programming Language :: C++
-Programming Language :: Python
-Topic :: Scientific/Engineering
-Topic :: Software Development :: Libraries
-"""
 
 version = {}
 with open("src/underworld/_version.py") as fp:
@@ -298,31 +287,26 @@ def extend_cmake_prefix_path(path: str) -> None:
 functionality of the code running in a parallel HPC environment.",
     long_description=long_description,
     long_description_content_type="text/markdown",
-    classifiers=classifiers.split('\n')[1:-1],
-    keywords=['Underworld', 'MPI', 'Geodynamics'],
     platforms=['POSIX'],
     license='LGPL-3',
-
     url='https://github.com/underworldcode/underworld2',
     download_url="",
-
-    author='Underworld Team',
-    author_email='help@underworldcode.org',
-    maintainer='Underworld Team',
     maintainer_email='help@underworldcode.org',
     include_package_data=True, # use the file './MANIFEST.in' for package data files
     package_dir={"":"src"}, # directory containing underworld package
-    packages=find_packages(
+    packages=find_namespace_packages(
       where='src',
-      include = ['underworld', 'UWGeodynamics'],),
+      include = ['underworld*', 'UWGeodynamics*'],),
     ext_modules=[
         CMakeExtension(name='libUnderworld',
                        install_prefix="underworld",
                        source_dir=str(Path("src/underworld/libUnderworld").absolute()),
                        cmake_configure_options=[
                            f"-DPython3_ROOT_DIR={Path(sys.prefix)}",
-                           "-DCALL_FROM_SETUP_PY:BOOL=ON"]
-                       #, cmake_build_type="Debug" ## Uncomment for debug
+                           "-DCALL_FROM_SETUP_PY:BOOL=ON",
+                           "--fresh",  # force no cache, important for python isolation builds as build tools will change location
+                           #"cmake_build_type="Debug" ## Uncomment for debug
+                       ],
                        ),
     ],
     cmdclass=dict(build_ext=BuildExtension),