python_packaging/src/setup.py

   1 #
   2 # This file is part of the GROMACS molecular simulation package.
   3 #
   4 # Copyright (c) 2019, by the GROMACS development team, led by
   5 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6 # and including many others, as listed in the AUTHORS file in the
   7 # top-level source directory and at http://www.gromacs.org.
   8 #
   9 # GROMACS is free software; you can redistribute it and/or
  10 # modify it under the terms of the GNU Lesser General Public License
  11 # as published by the Free Software Foundation; either version 2.1
  12 # of the License, or (at your option) any later version.
  13 #
  14 # GROMACS is distributed in the hope that it will be useful,
  15 # but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17 # Lesser General Public License for more details.
  18 #
  19 # You should have received a copy of the GNU Lesser General Public
  20 # License along with GROMACS; if not, see
  21 # http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23 #
  24 # If you want to redistribute modifications to GROMACS, please
  25 # consider that scientific software is very special. Version
  26 # control is crucial - bugs must be traceable. We will be happy to
  27 # consider code for inclusion in the official distribution, but
  28 # derived work must not be called official GROMACS. Details are found
  29 # in the README & COPYING files - if they are missing, get the
  30 # official version at http://www.gromacs.org.
  31 #
  32 # To help us fund GROMACS development, we humbly ask that you cite
  33 # the research papers on the package. Check out http://www.gromacs.org.
  34
  35 # Python setuptools script to build and install the gmxapi Python interface
  36 # from a GROMACS installation directory.
  37
  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.
  50
  51 import os
  52 import sys
  53
  54 from skbuild import setup
  55 import cmake
  56
  57 usage = """
  58 The `gmxapi` package requires an existing GROMACS installation, version 2020 or higher.
  59 To specify the GROMACS installation to use, provide a GMXTOOLCHAINDIR
  60 environment variable when running setup.py or `pip`.
  61
  62 Example:
  63     GMXTOOLCHAINDIR=/path/to/gromacs/share/cmake/gromacs pip install gmxapi
  64
  65 If you have multiple builds of GROMACS, distinguished by a suffix `$SUFFIX`, the
  66 tool chain directory will use that suffix.
  67
  68 Example:
  69     GMXTOOLCHAINDIR=/path/to/gromacs/share/cmake/gromacs$SUFFIX pip install gmxapi
  70
  71 In the example, `gmxapi` is downloaded automatically from pypi.org. You can
  72 replace `gmxapi` with a local directory or archive file to build from a source
  73 distribution.
  74
  75 setup.py will use the location of GMXTOOLCHAINDIR to locate the
  76 gmxapi library configured during GROMACS installation. Alternatively, if
  77 gmxapi_DIR is provided, or if GMXRC has been "sourced", the toolchain file
  78 location may be deduced. Note, though, that if multiple GROMACS installations
  79 exist in the same location (with different suffixes) only the first one will be
  80 used when guessing a toolchain, because setup.py does not know which corresponds
  81 to the gmxapi support library.
  82
  83 If specifying GMXTOOLCHAINDIR and gmxapi_DIR, the tool chain directory must be
  84 located within a subdirectory of gmxapi_DIR.
  85
  86 Refer to project web site for complete documentation.
  87
  88 """
  89
  90
  91 class GmxapiInstallError(Exception):
  92     """Error processing setup.py for gmxapi Python package."""
  93
  94
  95 gmx_toolchain_dir = os.getenv('GMXTOOLCHAINDIR')
  96 gmxapi_DIR = os.getenv('gmxapi_DIR')
  97 if gmxapi_DIR is None:
  98     # Infer from GMXRC exports, if available.
  99     gmxapi_DIR = os.getenv('GROMACS_DIR')
 100
 101 def _find_first_gromacs_suffix(directory):
 102     dir_contents = os.listdir(directory)
 103     for entry in dir_contents:
 104         if entry.startswith('gromacs'):
 105             return entry.strip('gromacs')
 106
 107 if gmx_toolchain_dir is None:
 108     # Try to guess from standard GMXRC environment variables.
 109     if gmxapi_DIR is not None:
 110         if os.path.exists(gmxapi_DIR) and os.path.isdir(gmxapi_DIR):
 111             share_cmake = os.path.join(gmxapi_DIR, 'share', 'cmake')
 112             suffix = _find_first_gromacs_suffix(share_cmake)
 113             if suffix is not None:
 114                 gmx_toolchain_dir = os.path.join(share_cmake, 'gromacs' + suffix)
 115
 116 if gmx_toolchain_dir is None:
 117     print(usage)
 118     raise GmxapiInstallError('Could not configure for GROMACS installation. Provide GMXTOOLCHAINDIR.')
 119
 120 suffix = os.path.basename(gmx_toolchain_dir).strip('gromacs')
 121 gmx_toolchain = os.path.abspath(os.path.join(gmx_toolchain_dir, 'gromacs-toolchain' + suffix + '.cmake'))
 122
 123 if gmxapi_DIR is None:
 124     # Example: given /usr/local/gromacs/share/cmake/gromacs/gromacs-toolchain.cmake,
 125     # we would want /usr/local/gromacs.
 126     # Note that we could point more directly to the gmxapi-config.cmake but,
 127     # so far, we have relied on CMake automatically looking into
 128     # <package>_DIR/share/cmake/<package>/ for such a file.
 129     # We would need a slightly different behavior for packages that link against
 130     # libgromacs directly, as sample_restraint currently does.
 131     gmxapi_DIR = os.path.join(os.path.dirname(gmx_toolchain), '..', '..', '..')
 132
 133 gmxapi_DIR = os.path.abspath(gmxapi_DIR)
 134
 135 if not os.path.exists(gmxapi_DIR) or not os.path.isdir(gmxapi_DIR):
 136     print(usage)
 137     raise GmxapiInstallError('Please set a valid gmxapi_DIR.')
 138
 139 if gmxapi_DIR != os.path.commonpath([gmxapi_DIR, gmx_toolchain]):
 140     raise GmxapiInstallError('GROMACS toolchain file {} is not in gmxapi_DIR {}'.format(
 141         gmx_toolchain,
 142         gmxapi_DIR
 143     ))
 144
 145 cmake_platform_hints = ['-DCMAKE_TOOLCHAIN_FILE={}'.format(gmx_toolchain)]
 146
 147 # TODO: Use package-specific hinting variable.
 148 # We want to be sure that we find a <package>-config.cmake associated with the
 149 # toolchains file, but we want to preempt most of the normal CMake
 150 # [search procedure](https://cmake.org/cmake/help/latest/command/find_package.html#id5),
 151 # which could lead to hard-to-diagnose build problems.
 152 # Note that <package>_ROOT is not standard until CMake 3.12
 153 # Reference https://cmake.org/cmake/help/latest/policy/CMP0074.html#policy:CMP0074
 154 _cmake_major, _cmake_minor = cmake.__version__.split('.')[0:2]
 155 if int(_cmake_major) >= 3 and int(_cmake_minor) >= 12:
 156     cmake_gmxapi_hint = '-Dgmxapi_ROOT={}'
 157 else:
 158     cmake_gmxapi_hint = '-DCMAKE_PREFIX_PATH={}'
 159 cmake_gmxapi_hint = cmake_gmxapi_hint.format(gmxapi_DIR)
 160
 161 cmake_args = list(cmake_platform_hints)
 162 cmake_args.append(cmake_gmxapi_hint)
 163
 164 setup(
 165     name='gmxapi',
 166
 167     # TODO: (pending infrastructure and further discussion) Replace with CMake variables from GMXAPI version.
 168     version='0.1.0b2',
 169     python_requires='>=3.5, <3.9',
 170     setup_requires=['cmake>=3.9.6',
 171                     'setuptools>=28',
 172                     'scikit-build>=0.7'],
 173
 174     packages=['gmxapi', 'gmxapi.simulation'],
 175
 176     cmake_args=cmake_args,
 177
 178     author='M. Eric Irrgang',
 179     author_email='info@gmxapi.org',
 180     description='gmxapi Python interface for GROMACS',
 181     license='LGPL',
 182     url='http://gmxapi.org/',
 183
 184     # The installed package will contain compiled C++ extensions that cannot be loaded
 185     # directly from a zip file.
 186     zip_safe=False
 187 )