python_packaging/src/setup.py

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  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
  53 from skbuild import setup
  54
  55 usage = """
  56 The `gmxapi` package requires an existing GROMACS installation, version 2020 or higher.
  57 To specify the GROMACS installation to use, provide a GMXTOOLCHAINDIR
  58 environment variable when running setup.py or `pip`.
  59
  60 Example:
  61     GMXTOOLCHAINDIR=/path/to/gromacs/share/cmake/gromacs pip install gmxapi
  62
  63 If you have multiple builds of GROMACS, distinguished by a suffix `$SUFFIX`, the
  64 tool chain directory will use that suffix.
  65
  66 Example:
  67     GMXTOOLCHAINDIR=/path/to/gromacs/share/cmake/gromacs$SUFFIX pip install gmxapi
  68
  69 In the example, `gmxapi` is downloaded automatically from pypi.org. You can
  70 replace `gmxapi` with a local directory or archive file to build from a source
  71 distribution.
  72
  73 setup.py will use the location of GMXTOOLCHAINDIR to locate the
  74 gmxapi library configured during GROMACS installation. Alternatively, if
  75 gmxapi_DIR is provided, or if GMXRC has been "sourced", the toolchain file
  76 location may be deduced. Note, though, that if multiple GROMACS installations
  77 exist in the same location (with different suffixes) only the first one will be
  78 used when guessing a toolchain, because setup.py does not know which corresponds
  79 to the gmxapi support library.
  80
  81 If specifying GMXTOOLCHAINDIR and gmxapi_DIR, the tool chain directory must be
  82 located within a subdirectory of gmxapi_DIR.
  83
  84 Refer to project web site for complete documentation.
  85
  86 """
  87
  88
  89 class GmxapiInstallError(Exception):
  90     """Error processing setup.py for gmxapi Python package."""
  91
  92
  93 gmx_toolchain_dir = os.getenv('GMXTOOLCHAINDIR')
  94 gmxapi_DIR = os.getenv('gmxapi_DIR')
  95 if gmxapi_DIR is None:
  96     # Infer from GMXRC exports, if available.
  97     gmxapi_DIR = os.getenv('GROMACS_DIR')
  98
  99 def _find_first_gromacs_suffix(directory):
 100     dir_contents = os.listdir(directory)
 101     for entry in dir_contents:
 102         if entry.startswith('gromacs'):
 103             return entry.strip('gromacs')
 104
 105 if gmx_toolchain_dir is None:
 106     # Try to guess from standard GMXRC environment variables.
 107     if gmxapi_DIR is not None:
 108         if os.path.exists(gmxapi_DIR) and os.path.isdir(gmxapi_DIR):
 109             share_cmake = os.path.join(gmxapi_DIR, 'share', 'cmake')
 110             suffix = _find_first_gromacs_suffix(share_cmake)
 111             if suffix is not None:
 112                 gmx_toolchain_dir = os.path.join(share_cmake, 'gromacs' + suffix)
 113
 114 if gmx_toolchain_dir is None:
 115     print(usage)
 116     raise GmxapiInstallError('Could not configure for GROMACS installation. Provide GMXTOOLCHAINDIR.')
 117
 118 suffix = os.path.basename(gmx_toolchain_dir).strip('gromacs')
 119 gmx_toolchain = os.path.abspath(os.path.join(gmx_toolchain_dir, 'gromacs-toolchain' + suffix + '.cmake'))
 120
 121 if gmxapi_DIR is None:
 122     # Example: given /usr/local/gromacs/share/cmake/gromacs/gromacs-toolchain.cmake,
 123     # we would want /usr/local/gromacs.
 124     # Note that we could point more directly to the gmxapi-config.cmake but,
 125     # so far, we have relied on CMake automatically looking into
 126     # <package>_DIR/share/cmake/<package>/ for such a file.
 127     # We would need a slightly different behavior for packages that link against
 128     # libgromacs directly, as sample_restraint currently does.
 129     gmxapi_DIR = os.path.join(os.path.dirname(gmx_toolchain), '..', '..', '..')
 130
 131 gmxapi_DIR = os.path.abspath(gmxapi_DIR)
 132
 133 if not os.path.exists(gmxapi_DIR) or not os.path.isdir(gmxapi_DIR):
 134     print(usage)
 135     raise GmxapiInstallError('Please set a valid gmxapi_DIR.')
 136
 137 if gmxapi_DIR != os.path.commonpath([gmxapi_DIR, gmx_toolchain]):
 138     raise GmxapiInstallError('GROMACS toolchain file {} is not in gmxapi_DIR {}'.format(
 139         gmx_toolchain,
 140         gmxapi_DIR
 141     ))
 142
 143 cmake_platform_hints = '-DCMAKE_TOOLCHAIN_FILE={}'.format(gmx_toolchain)
 144 # Note that <package>_ROOT is not standard until CMake 3.12
 145 # Reference https://cmake.org/cmake/help/latest/policy/CMP0074.html#policy:CMP0074
 146 cmake_gmxapi_hint = '-Dgmxapi_ROOT={}'.format(gmxapi_DIR)
 147 cmake_args = [cmake_platform_hints, cmake_gmxapi_hint]
 148
 149 setup(
 150     name='gmxapi',
 151
 152     # TODO: (pending infrastructure and further discussion) Replace with CMake variables from GMXAPI version.
 153     version='0.1.0.1',
 154     python_requires='>=3.5, <3.9',
 155     setup_requires=['cmake>=3.12',
 156                     'setuptools>=28',
 157                     'scikit-build>=0.7'],
 158
 159     packages=['gmxapi', 'gmxapi.simulation'],
 160
 161     cmake_args=cmake_args,
 162
 163     author='M. Eric Irrgang',
 164     author_email='info@gmxapi.org',
 165     description='gmxapi Python interface for GROMACS',
 166     license='LGPL',
 167     url='http://gmxapi.org/',
 168
 169     # The installed package will contain compiled C++ extensions that cannot be loaded
 170     # directly from a zip file.
 171     zip_safe=False
 172 )