[PEP518] Improve testsuite packaging (#4463)

* Adds pyproject.toml to testsuite
* Clears up ambigous packaging
* Keeps setup.py for dynamic things only
* Update license file
* Update links info
* Update some setup.py docstring text
* Adds various missing init files

Author: IAlibay

package/CHANGELOG

@@ -34,6 +34,7 @@ Enhancements
    `n_initial_contacts` attribute, with documentation. (Issue #2604, PR #4415)
 
 Changes
+ * Testsuite packaging now uses a pyproject.toml file (PR #4463)
  * Improvement of setuptools packaging, including deduplication of
    dependency lists (PR #4424)
  * As per NEP29, the minimum version of numpy has been raised to 1.23.

testsuite/LICENSE

@@ -0,0 +1,169 @@
+[build-system]
+requires = [
+  "setuptools >= 40.9.0",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "MDAnalysisTests"
+description = "MDAnalysis testsuite"
+license = {file = "LICENSE" }
+authors = [
+    {name = "MDAnalysis", email = "[email protected]"},
+]
+maintainers = [
+    {name = "MDAnalysis", email = "[email protected]"},
+]
+classifiers = [
+    "Development Status :: 6 - Mature",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+    "Operating System :: POSIX",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows ",
+    "Programming Language :: Python",
+    "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 :: C",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+readme = {file = "README", content-type = "text/x-rst"}
+requires-python = ">=3.9"
+dynamic = ["version", "dependencies"]
+
+[project.urls]
+Homepage = "https://www.mdanalysis.org"
+Download = "https://github.com/MDAnalysis/mdanalysis/releases"
+Documentation = "https://docs.mdanalysis.org/"
+"User Guide" = "https://userguide.mdanalysis.org/"
+"Issue Tracker" = "https://github.com/mdanalysis/mdanalysis/issues"
+"Github Discussions" = "https://github.com/MDAnalysis/mdanalysis/discussions"
+Discord = "https://discord.com/channels/807348386012987462/"
+Blog = "https://www.mdanalysis.org/blog/"
+Source = "https://github.com/mdanalysis/mdanalysis"
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+
+[tool.setuptools.packages.find]
+namespaces = false
+include=[
+    "MDAnalysisTests",
+    "MDAnalysisTests.data",
+    "MDAnalysisTests.data.Amber",
+    "MDAnalysisTests.data.capping",
+    "MDAnalysisTests.data.coordinates",
+    "MDAnalysisTests.data.gms",
+    "MDAnalysisTests.data.gromos11",
+    "MDAnalysisTests.data.merge",
+    "MDAnalysisTests.data.tprs",
+    "MDAnalysisTests.data.tprs.all_bonded",
+    "MDAnalysisTests.data.tprs.virtual_sites",
+    "MDAnalysisTests.data.analysis",
+    "MDAnalysisTests.data.contacts",
+    "MDAnalysisTests.data.dlpoly",
+    "MDAnalysisTests.data.gromacs",
+    "MDAnalysisTests.data.lammps",
+    "MDAnalysisTests.data.mol2",
+    "MDAnalysisTests.data.windows",
+]
+
+[tool.setuptools.package-data]
+MDAnalysisTests = [
+    "data/*.psf",
+    "data/*.dcd",
+    "data/*.pdb",
+    "data/tprs/*.tpr",
+    "data/tprs/all_bonded/*.gro",
+    "data/tprs/all_bonded/*.top",
+    "data/tprs/all_bonded/*.mdp",
+    "data/*.tpr",
+    "data/tprs/*/*.tpr",
+    "data/*.gro",
+    "data/*.xtc",
+    "data/*.trr",
+    "data/*npy",
+    "data/*.crd",
+    "data/*.xyz",
+    "data/Amber/*.bz2",
+    "data/Amber/*.prmtop",
+    "data/Amber/*.top",
+    "data/Amber/*.parm7",
+    "data/Amber/*.rst7",
+    "data/Amber/*.trj",
+    "data/Amber/*.mdcrd",
+    "data/Amber/*.ncdf",
+    "data/Amber/*.nc",
+    "data/Amber/*.inpcrd",
+    "data/gromos11/*.gz",
+    "data/gromos11/*.trc",
+    "data/*.pqr",
+    "data/*.pdbqt",
+    "data/*.bz2",
+    "data/*.gz",
+    "data/*.ent",
+    "data/*.fasta",
+    "data/*.dat",
+    "data/*.dms",
+    "data/merge/2zmm/*.pdb",
+    "data/*.trz",
+    "data/mol2/*.mol2",
+    "data/contacts/*.gro.bz2",
+    "data/contacts/*.dat",
+    "data/capping/*.gro",
+    "data/capping/*.pdb",
+    "data/lammps/*",
+    "data/gms/*.xyz",
+    "data/gms/*.gms",
+    "data/gms/*.gms.gz",
+    "data/*.inpcrd",
+    "data/dlpoly/CONFIG*",
+    "data/dlpoly/HISTORY*",
+    "data/*.xml",
+    "data/coordinates/*",
+    "data/*xvg",
+    "data/*.mmtf",
+    "data/*.mmtf.gz",
+    "data/analysis/*",
+    "data/*.gsd",
+    "data/windows/*",
+    "data/*.itp",
+    "data/gromacs/gromos54a7_edited.ff/*",
+    "data/*.coor",
+    "data/*.h5md",
+    "data/*.in",
+    "data/*.top",
+    "data/*.sdf",
+    "data/*.edr",
+    "data/*.tng",
+    "data/*.pdbx",
+    "data/*.txt",
+]
+
+[tool.pytest.ini_options]
+filterwarnings = [
+    "always",
+    "error:`np.*` is a deprecated alias for the builtin:DeprecationWarning",
+    # don't enforce for third party packages though:
+    "ignore:`np.*` is a deprecated alias for the builtin:DeprecationWarning:networkx.*:",
+    "error:Creating an ndarray from ragged nested sequences",
+    "error:invalid escape sequence \\\\:DeprecationWarning",
+    # Ignore frequent errors popping up in our tests
+    # Elements
+    "ignore:Element information:UserWarning",
+    # Mass
+    "ignore:Failed to guess the mass:UserWarning",
+    # Coordinates
+    "ignore:No coordinate reader found:UserWarning",
+    "ignore:Reader has no dt information, set to 1.0 ps",
+    # NamedStream warnings
+    "ignore:Constructed NamedStream:RuntimeWarning",
+]

testsuite/MDAnalysisTests/data/Amber/__init__.py

@@ -23,32 +23,27 @@
 #
 """Setuptools-based setup script for tests of MDAnalysis.
 
-A working installation of NumPy <http://numpy.scipy.org> is required.
+A working installation of MDAnalysis of the same version is required.
 
 For a basic installation just type the command::
 
-  python setup.py install
+  pip install .
 
-For more in-depth instructions, see the installation section at the
-MDAnalysis Wiki:
+For more in-depth instructions, see the installation section in the
+MDAnalysis User Guide:
 
-  https://github.com/MDAnalysis/mdanalysis/wiki/INSTALL
+  https://userguide.mdanalysis.org/stable/installation.html
 
 Also free to ask on GitHub Discussions for help:
 
   https://github.com/MDAnalysis/mdanalysis/discussions
 
-(Note that the group really is called `mdnalysis-discussion' because
-Google groups forbids any name that contains the string `anal'.)
 """
-from setuptools import setup, find_packages
+from setuptools import setup
 from setuptools.command import sdist
 
 import os
 import shutil
-import codecs
-import sys
-import warnings
 
 
 class MDA_SDist(sdist.sdist):
@@ -77,122 +72,16 @@ def run(self):
                 os.remove(os.path.join(here, 'AUTHORS'))
 
 
-# Make sure I have the right Python version.
-if sys.version_info[:2] < (3, 9):
-    print("MDAnalysis requires Python 3.9 or better. "
-          "Python {0:d}.{1:d} detected".format(*sys.version_info[:2]))
-    print("Please upgrade your version of Python.")
-    sys.exit(-1)
-
-
 if __name__ == '__main__':
     # this must be in-sync with MDAnalysis
     RELEASE = "2.8.0-dev0"
-    with open("README") as summary:
-        LONG_DESCRIPTION = summary.read()
-
-    CLASSIFIERS = [
-        'Development Status :: 6 - Mature',
-        'Environment :: Console',
-        'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)',
-        'Operating System :: POSIX',
-        'Operating System :: MacOS :: MacOS X',
-        'Operating System :: Microsoft :: Windows ',
-        'Programming Language :: Python',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.9',
-        'Programming Language :: Python :: 3.10',
-        'Programming Language :: Python :: 3.11',
-        'Programming Language :: C',
-        'Topic :: Scientific/Engineering',
-        'Topic :: Scientific/Engineering :: Bio-Informatics',
-        'Topic :: Scientific/Engineering :: Chemistry',
-        'Topic :: Software Development :: Libraries :: Python Modules',
-    ]
 
-    setup(name='MDAnalysisTests',
-          version=RELEASE,
-          description='MDAnalysis testsuite',
-          long_description=LONG_DESCRIPTION,
-          long_description_content_type='text/x-rst',
-          author='MDAnalysis Development Team',
-          author_email='[email protected]',
-          maintainer='MDAnalysis Core Developers',
-          maintainer_email='[email protected]',
-          url='https://www.mdanalysis.org',
-          download_url='https://github.com/MDAnalysis/mdanalysis/releases',
-          project_urls={'Documentation': 'https://userguide.mdanalysis.org/stable/testing.html',
-                        'CI Coverage': 'https://codecov.io/gh/MDAnalysis/mdanalysis',
-                        'Developer Group': 'https://groups.google.com/g/mdnalysis-devel',
-                        'Issue Tracker': 'https://github.com/mdanalysis/mdanalysis/issues',
-                        'Source': 'https://github.com/mdanalysis/mdanalysis',
-                        },
-          license='GPL-3.0-or-later',
-          classifiers=CLASSIFIERS,
-          packages=find_packages(),
-          package_dir={'MDAnalysisTests': 'MDAnalysisTests',
-                       'MDAnalysisTests.plugins': 'MDAnalysisTests/plugins'},
-          package_data={'MDAnalysisTests':
-                        ['data/*.psf', 'data/*.dcd', 'data/*.pdb',
-                         'data/tprs/*.tpr',
-                         'data/tprs/all_bonded/*.gro',
-                         'data/tprs/all_bonded/*.top',
-                         'data/tprs/all_bonded/*.mdp', 'data/*.tpr',
-                         'data/tprs/*/*.tpr',
-                         'data/*.gro', 'data/*.xtc', 'data/*.trr', 'data/*npy',
-                         'data/*.crd', 'data/*.xyz',
-                         'data/Amber/*.bz2',
-                         'data/Amber/*.prmtop', 'data/Amber/*.top',
-                         'data/Amber/*.parm7',
-                         'data/Amber/*.rst7',
-                         'data/Amber/*.trj', 'data/Amber/*.mdcrd',
-                         'data/Amber/*.ncdf', 'data/Amber/*.nc',
-                         'data/Amber/*.inpcrd',
-                         'data/gromos11/*.gz', 'data/gromos11/*.trc',
-                         'data/*.pqr', 'data/*.pdbqt', 'data/*.bz2', 'data/*.gz',
-                         'data/*.ent',
-                         'data/*.fasta',
-                         'data/*.dat',
-                         'data/*.dms',
-                         'data/merge/2zmm/*.pdb',
-                         'data/*.trz',
-                         'data/mol2/*.mol2',
-                         'data/contacts/*.gro.bz2', 'data/contacts/*.dat',
-                         'data/capping/*.gro', 'data/capping/*.pdb',
-                         'data/lammps/*',
-                         'data/gms/*.xyz', 'data/gms/*.gms',
-                         'data/gms/*.gms.gz',
-                         'data/*.inpcrd',
-                         'data/dlpoly/CONFIG*',
-                         'data/dlpoly/HISTORY*',
-                         'data/*.xml',
-                         'data/coordinates/*',
-                         'data/*xvg',
-                         'data/*.mmtf', 'data/*.mmtf.gz',
-                         'data/analysis/*',
-                         'data/*.gsd',
-                         'data/windows/*',
-                         'data/*.itp', "data/gromacs/gromos54a7_edited.ff/*",
-                         'data/*.coor',
-                         'data/*.h5md',
-                         'data/*.in',
-                         'data/*.top',
-                         'data/*.sdf',
-                         'data/*.edr',
-                         'data/*.tng',
-                         'data/*.pdbx',
-                         'data/*.txt',
-                        ],
-          },
-          python_requires='>=3.9',
-          install_requires=[
-              'MDAnalysis=={0!s}'.format(RELEASE),  # same as this release!
-              'pytest>=3.3.0', # Raised to 3.3.0 due to Issue 2329
-              'hypothesis',
-          ],
-          # had 'KeyError' as zipped egg (2MB savings are not worth the
-          # trouble)
-          zip_safe=False,
-          cmdclass={'sdist': MDA_SDist},
-          )
+    setup(
+        version=RELEASE,
+        install_requires=[
+            'MDAnalysis=={0!s}'.format(RELEASE),  # same as this release!
+            'pytest>=3.3.0', # Raised to 3.3.0 due to Issue 2329
+            'hypothesis',
+        ],
+        cmdclass={'sdist': MDA_SDist},
+    )