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35 # Python setuptools script to build and install the gmxapi Python interface
36 # from a GROMACS installation directory.
38 # Usage note: things go smoothly when we stick to the setup.py convention of
39 # having a package source directory with the same name as the package at the
40 # same level as the setup.py script and only expect `pip install .` in the
41 # setup.py directory. If we play with the layout more, it is hard to keep all
42 # of the `pip` and `setup.py` cases working as expected. This is annoying
43 # because running the Python interpreter immediately from the same directory
44 # can find the uninstalled source instead of the installed package. We can
45 # ease this pain by building an sdist in the enclosing CMake build scope
46 # and encouraging users to `pip install the_sdist.archive`. Otherwise, we
47 # just have to document that we only support full build-install of the Python
48 # package from the directory containing setup.py, which may clutter that
49 # directory with some artifacts.
53 # Allow setup.py to be run when scikit-build is not installed, such as to
54 # produce source distribution archives with `python setup.py sdist`
56 from skbuild import setup
58 from distutils.core import setup
61 The `gmxapi` package requires an existing GROMACS installation, version 2020 or higher.
62 To specify the GROMACS installation to use, provide a GMXTOOLCHAINDIR
63 environment variable when running setup.py or `pip`.
66 GMXTOOLCHAINDIR=/path/to/gromacs/share/cmake/gromacs pip install gmxapi
68 If you have multiple builds of GROMACS, distinguished by a suffix `$SUFFIX`, the
69 tool chain directory will use that suffix.
72 GMXTOOLCHAINDIR=/path/to/gromacs/share/cmake/gromacs$SUFFIX pip install gmxapi
74 In the example, `gmxapi` is downloaded automatically from pypi.org. You can
75 replace `gmxapi` with a local directory or archive file to build from a source
78 setup.py will use the location of GMXTOOLCHAINDIR to locate the
79 gmxapi library configured during GROMACS installation. Alternatively, if
80 gmxapi_DIR is provided, or if GMXRC has been "sourced", the toolchain file
81 location may be deduced. Note, though, that if multiple GROMACS installations
82 exist in the same location (with different suffixes) only the first one will be
83 used when guessing a toolchain, because setup.py does not know which corresponds
84 to the gmxapi support library.
86 If specifying GMXTOOLCHAINDIR and gmxapi_DIR, the tool chain directory must be
87 located within a subdirectory of gmxapi_DIR.
89 Refer to project web site for complete documentation.
94 class GmxapiInstallError(Exception):
95 """Error processing setup.py for gmxapi Python package."""
98 gmx_toolchain_dir = os.getenv('GMXTOOLCHAINDIR')
99 gmxapi_DIR = os.getenv('gmxapi_DIR')
100 if gmxapi_DIR is None:
101 # Infer from GMXRC exports, if available.
102 gmxapi_DIR = os.getenv('GROMACS_DIR')
104 def _find_first_gromacs_suffix(directory):
105 dir_contents = os.listdir(directory)
106 for entry in dir_contents:
107 if entry.startswith('gromacs'):
108 return entry.strip('gromacs')
110 if gmx_toolchain_dir is None:
111 # Try to guess from standard GMXRC environment variables.
112 if gmxapi_DIR is not None:
113 if os.path.exists(gmxapi_DIR) and os.path.isdir(gmxapi_DIR):
114 share_cmake = os.path.join(gmxapi_DIR, 'share', 'cmake')
115 suffix = _find_first_gromacs_suffix(share_cmake)
116 if suffix is not None:
117 gmx_toolchain_dir = os.path.join(share_cmake, 'gromacs' + suffix)
119 if gmx_toolchain_dir is None:
121 raise GmxapiInstallError('Could not configure for GROMACS installation. Provide GMXTOOLCHAINDIR.')
123 suffix = os.path.basename(gmx_toolchain_dir).strip('gromacs')
124 gmx_toolchain = os.path.abspath(os.path.join(gmx_toolchain_dir, 'gromacs-toolchain' + suffix + '.cmake'))
126 if gmxapi_DIR is None:
127 # Example: given /usr/local/gromacs/share/cmake/gromacs/gromacs-toolchain.cmake,
128 # we would want /usr/local/gromacs.
129 # Note that we could point more directly to the gmxapi-config.cmake but,
130 # so far, we have relied on CMake automatically looking into
131 # <package>_DIR/share/cmake/<package>/ for such a file.
132 # We would need a slightly different behavior for packages that link against
133 # libgromacs directly, as sample_restraint currently does.
134 gmxapi_DIR = os.path.join(os.path.dirname(gmx_toolchain), '..', '..', '..')
136 gmxapi_DIR = os.path.abspath(gmxapi_DIR)
138 if not os.path.exists(gmxapi_DIR) or not os.path.isdir(gmxapi_DIR):
140 raise GmxapiInstallError('Please set a valid gmxapi_DIR.')
142 if gmxapi_DIR != os.path.commonpath([gmxapi_DIR, gmx_toolchain]):
143 raise GmxapiInstallError('GROMACS toolchain file {} is not in gmxapi_DIR {}'.format(
148 cmake_platform_hints = '-DCMAKE_TOOLCHAIN_FILE={}'.format(gmx_toolchain)
149 # Note that <package>_ROOT is not standard until CMake 3.12
150 # Reference https://cmake.org/cmake/help/latest/policy/CMP0074.html#policy:CMP0074
151 cmake_gmxapi_hint = '-Dgmxapi_ROOT={}'.format(gmxapi_DIR)
152 cmake_args = [cmake_platform_hints, cmake_gmxapi_hint]
157 # TODO: single-source version information (currently repeated in gmxapi/version.py)
159 python_requires='>=3.6',
160 install_requires=['networkx>=2.0',
163 packages=['gmxapi', 'gmxapi.simulation'],
164 package_data={'gmxapi': ['gmxconfig.json']},
166 cmake_args=cmake_args,
168 author='M. Eric Irrgang',
169 author_email='info@gmxapi.org',
170 description='gmxapi Python interface for GROMACS',
172 url='http://gmxapi.org/',
174 # The installed package will contain compiled C++ extensions that cannot be loaded
175 # directly from a zip file.