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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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|
@@ -28,12 +28,12 @@ | |
| 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: | ||
| 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: | ||
|
|
@@ -54,13 +54,6 @@ | |
| import warnings | ||
| import platform | ||
|
|
||
| # Make sure I have the right Python version. | ||
| if sys.version_info[:2] < (3, 9): | ||
| print('MDAnalysis requires Python 3.9+. Python {0:d}.{1:d} detected'.format(* | ||
| sys.version_info[:2])) | ||
| print('Please upgrade your version of Python.') | ||
| sys.exit(-1) | ||
|
|
||
| import configparser | ||
| from subprocess import getoutput | ||
|
|
||
|
|
@@ -567,112 +560,20 @@ def long_description(readme): | |
| # (LONG_DESCRIPTION is not really needed) | ||
| LONG_DESCRIPTION = "MDAnalysis -- https://www.mdanalysis.org/" | ||
|
|
||
| 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', | ||
| ] | ||
| config = Config() | ||
| exts, cythonfiles = extensions(config) | ||
|
|
||
| install_requires = [ | ||
| 'numpy>=1.23.2', | ||
| 'GridDataFormats>=0.4.0', | ||
| 'mmtf-python>=1.0.0', | ||
| 'joblib>=0.12', | ||
| 'scipy>=1.5.0', | ||
| 'matplotlib>=1.5.1', | ||
| 'tqdm>=4.43.0', | ||
| 'threadpoolctl', | ||
| 'packaging', | ||
| 'fasteners', | ||
| 'mda-xdrlib', | ||
| 'waterdynamics', | ||
| 'pathsimanalysis', | ||
| ] | ||
|
|
||
| setup(name='MDAnalysis', | ||
| version=RELEASE, | ||
| description='An object-oriented toolkit to analyze molecular dynamics trajectories.', | ||
| 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://docs.mdanalysis.org/', | ||
| 'User Guide': 'https://userguide.mdanalysis.org/', | ||
| 'Issue Tracker': 'https://github.com/mdanalysis/mdanalysis/issues', | ||
| 'User Group': 'https://groups.google.com/g/mdnalysis-discussion/', | ||
| 'Discord': 'https://discord.com/channels/807348386012987462/', | ||
| 'Blog': 'https://www.mdanalysis.org/blog/', | ||
| 'Twitter': 'https://twitter.com/mdanalysis', | ||
| 'Source': 'https://github.com/mdanalysis/mdanalysis', | ||
| }, | ||
| license='GPL-3.0-or-later', | ||
| classifiers=CLASSIFIERS, | ||
| # currently unused & may become obsolte see setuptools #1569 | ||
| provides=['MDAnalysis'], | ||
| packages=find_packages(), | ||
| package_data={'MDAnalysis': | ||
| ['analysis/data/*.npy', | ||
| ], | ||
| }, | ||
| ext_modules=exts, | ||
| python_requires='>=3.9', | ||
| # all standard requirements are available through PyPi and | ||
| # typically can be installed without difficulties through setuptools | ||
| setup_requires=[ | ||
| 'numpy>=1.23.2', | ||
| 'packaging', | ||
| ], | ||
| install_requires=install_requires, | ||
| # extras can be difficult to install through setuptools and/or | ||
| # you might prefer to use the version available through your | ||
| # packaging system | ||
| extras_require={ | ||
| 'extra_formats': [ # additional file formats | ||
| 'netCDF4>=1.0', # for fast AMBER writing, also needs HDF5 | ||
| 'h5py>=2.10', # H5MD | ||
| 'pytng>=0.2.3', # TNG | ||
| 'chemfiles>=0.10', # multiple formats supported by chemfiles | ||
| 'pyedr>=0.7.0', # EDR files for the EDR AuxReader | ||
| 'gsd>3.0.0', # GSD | ||
| 'rdkit>=2020.03.1', # RDKit converter | ||
| 'parmed', # ParmEd converter | ||
| ], | ||
| 'analysis': [ | ||
| 'biopython>=1.80', # sequence generation & alignment | ||
| 'seaborn', # for annotated heat map and nearest neighbor | ||
| # plotting in PSA | ||
| 'scikit-learn', # For clustering and dimensionality | ||
| # reduction functionality in encore | ||
| 'tidynamics>=1.0.0', # For MSD analysis method | ||
| 'networkx>=2.0', # For LeafletFinder | ||
| ], | ||
| }, | ||
| test_suite="MDAnalysisTests", | ||
| tests_require=[ | ||
| 'MDAnalysisTests=={0!s}'.format(RELEASE), # same as this release! | ||
| ], | ||
| zip_safe=False, # as a zipped egg the *.so files are not found (at | ||
| # least in Ubuntu/Linux) | ||
| ) | ||
|
|
||
| # Releases keep their cythonized stuff for shipping. | ||
|
|
||
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