content: ##
  # Copyright 2015-2015 Ghent University
  #
  # This file is part of EasyBuild,
  # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
  # with support of Ghent University (http://ugent.be/hpc),
  # the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
  # the Hercules foundation (http://www.herculesstichting.be/in_English)
  # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
  #
  # http://github.com/hpcugent/easybuild
  #
  # EasyBuild is free software: you can redistribute it and/or modify
  # it under the terms of the GNU General Public License as published by
  # the Free Software Foundation v2.
  #
  # EasyBuild is distributed in the hope that it will be useful,
  # but WITHOUT ANY WARRANTY; without even the implied warranty of
  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  # GNU General Public License for more details.
  #
  # You should have received a copy of the GNU General Public License
  # along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
  ##
  """
  EasyBuild support for building and installing Xmipp, implemented as an easyblock
  
  @author: Jens Timmerman (Ghent University)
  @author: Pablo Escobar (sciCORE, SIB, University of Basel)
  @author: Kenneth Hoste (Ghent University)
  """
  import fileinput
  import os
  import re
  import stat
  import sys
  
  import easybuild.tools.environment as env
  import easybuild.tools.toolchain as toolchain
  from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
  from easybuild.framework.easyblock import EasyBlock
  from easybuild.framework.easyconfig import CUSTOM
  from easybuild.tools.build_log import EasyBuildError
  from easybuild.tools.filetools import adjust_permissions, mkdir, write_file
  from easybuild.tools.modules import get_software_root, get_software_version
  from easybuild.tools.run import run_cmd
  
  
  class EB_Xmipp(EasyBlock):
      """
      easyblock to install Xmipp
      """
  
      def __init__(self, *args, **kwargs):
          """Easyblock constructor, enable building in installation directory."""
          super(EB_Xmipp, self).__init__(*args, **kwargs)
          self.build_in_installdir = True
          self.xmipp_pythonpaths = []
  
      def extract_step(self):
          """Extract Xmipp sources."""
          # strip off 'xmipp' part to avoid having everything in a 'xmipp' subdirectory
          self.cfg.update('unpack_options', '--strip-components=1')
          super(EB_Xmipp, self).extract_step()
  
      def configure_step(self):
          """Set configure options."""
          if self.toolchain.mpi_family() == toolchain.INTELMPI:
              mpi_bindir = os.path.join(get_software_root('impi'), 'intel64', 'bin')
          else:
              mpi_bindir = os.path.join(get_software_root(self.toolchain.MPI_MODULE_NAME[0]), 'bin')
  
          root_java = get_software_root("Java")
          if not get_software_root("Java"):
              raise EasyBuildError("Module for dependency Java not loaded.")
  
          configure_args = ' '.join([
              'profile=no fast=yes warn=no release=yes gtest=yes static=no cuda=no debug=no matlab=no',
              'LINKERFORPROGRAMS=%s' % os.getenv('CXX'),
              'MPI_BINDIR=%s' % mpi_bindir,
              'MPI_LIB=mpi',
              'JAVA_HOME=%s' % os.getenv('JAVA_HOME'),
              'JAVAC=javac',
              'CC=%s' % os.getenv('CC'),
              # pass $CXXFLAGS in Python list syntax and avoid spaces, e.g.: ['-O2','-march=native']
              'CXXFLAGS=%s' % str(os.getenv('CXXFLAGS').split(' ')).replace(' ', ''),
              'CXX=%s' % os.getenv('CXX'),
              'MPI_CC=%s' % os.getenv('MPICC'),
              # pass $CFLAGS in Python list syntax and avoid spaces, e.g.: ['-O2','-march=native']
              'CCFLAGS=%s' % str(os.getenv('CFLAGS').split(' ')).replace(' ', ''),
              'MPI_CXX=%s' % os.getenv('MPICXX'),
              'MPI_INCLUDE=%s' % os.getenv('MPI_INC_DIR'),
              'MPI_LIBDIR=%s' % os.getenv('MPI_LIB_DIR'),
              'MPI_LINKERFORPROGRAMS=%s' % os.getenv('MPICXX'),
              'LIBPATH=%s' % os.getenv('LD_LIBRARY_PATH'),
          ])
  
          # define list of configure options, which will be passed to Xmipp's install.sh script via --configure-args
          self.cfg['configopts'] = configure_args
          self.log.info("Configure arguments for Xmipp install.sh script: %s", self.cfg['configopts'])
  
      def build_step(self):
          """No custom build step (see install step)."""
          pass
  
      def install_step(self):
          """Build/install Xmipp using provided install.sh script."""
          pylibdir = det_pylibdir()
  
          self.xmipp_pythonpaths = [
              # location where Python packages will be installed by Xmipp installer
              pylibdir,
              'protocols',
              os.path.join('libraries', 'bindings', 'python'),
          ]
  
          python_root = get_software_root('Python')
          if python_root:
              # extend $PYTHONPATH
              all_pythonpaths = [os.path.join(self.installdir, p) for p in self.xmipp_pythonpaths]
              # required so packages installed as extensions in Pythpn dep are picked up
              all_pythonpaths.append(os.path.join(python_root, pylibdir))
              all_pythonpaths.append(os.environ.get('PYTHONPATH', ''))
  
              env.setvar('PYTHONPATH', os.pathsep.join(all_pythonpaths))
  
              # location where Python packages will be installed by Xmipp installer must exist already (setuptools)
              mkdir(os.path.join(self.installdir, pylibdir), parents=True)
  
              # put dummy xmipp_python script in place if Python is used as a dependency
              bindir = os.path.join(self.installdir, 'bin')
              mkdir(bindir)
  
              xmipp_python = os.path.join(bindir, 'xmipp_python')
              xmipp_python_script_body = '\n'.join([
                  '#!/bin/sh',
                  '%s/bin/python "$@"' % python_root,
              ])
              write_file(xmipp_python, xmipp_python_script_body)
              adjust_permissions(xmipp_python, stat.S_IXUSR|stat.S_IXGRP|stat.S_IXOTH)
  
              pyshortver = '.'.join(get_software_version('Python').split('.')[:2])
  
              # make sure Python.h and numpy header are found
              env.setvar('CPATH', os.pathsep.join([
                  os.path.join(python_root, 'include', 'python%s' % pyshortver),
                  os.path.join(python_root, pylibdir, 'numpy', 'core', 'include'),
                  os.environ.get('CPATH', ''),
              ]))
  
          cmd_opts = []
  
          # disable (re)building of supplied dependencies
          dep_names = [dep['name'] for dep in self.cfg['dependencies']]
          for dep in ['FFTW', 'HDF5', ('libjpeg-turbo', 'jpeg'), ('LibTIFF', 'tiff'), 'matplotlib', 'Python', 'SQLite',
                      'Tcl', 'Tk']:
              if isinstance(dep, tuple):
                  dep, opt = dep
              else:
                  opt = dep.lower()
              # don't check via get_software_root, check listed dependencies directly (relevant for FFTW)
              if dep in dep_names:
                  cmd_opts.append('--%s=false' % opt)
                  # Python should also provide numpy/mpi4py
                  if dep == 'Python':
                      cmd_opts.extend(['--numpy=false', '--mpi4py=false'])
  
          if '--tcl=false' in cmd_opts and '--tk=false' in cmd_opts:
              cmd_opts.append('--tcl-tk=false')
  
          # patch install.sh script to inject configure options
          # setting $CONFIGURE_ARGS or using --configure-args doesn't work...
          for line in fileinput.input('install.sh', inplace=1, backup='.orig.eb'):
              line = re.sub(r"^CONFIGURE_ARGS.*$", 'CONFIGURE_ARGS="%s"' % self.cfg['configopts'], line)
              sys.stdout.write(line)
  
          cmd = './install.sh -j %s --unattended=true %s' % (self.cfg['parallel'], ' '.join(cmd_opts))
          out, _ = run_cmd(cmd, log_all=True, simple=False)
  
          if not re.search("Xmipp has been successfully compiled", out):
              raise EasyBuildError("Xmipp installation did not complete successfully?")
  
      def sanity_check_step(self):
          """Custom sanity check for Xmipp."""
          custom_paths = {
              # incomplete list, random picks, cfr. http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/ListOfProgramsv3
              'files': ['bin/xmipp_%s' % x for x in ['compile', 'imagej', 'mpi_run', 'phantom_create',
                                                     'transform_filter', 'tomo_project', 'volume_align']],
              'dirs': ['lib'],
          }
          super(EB_Xmipp, self).sanity_check_step(custom_paths=custom_paths)
  
      def make_module_extra(self):
          """Define Xmipp specific variables in generated module file, i.e. XMIPP_HOME."""
          txt = super(EB_Xmipp, self).make_module_extra()
          txt += self.module_generator.set_environment('XMIPP_HOME', self.installdir)
          txt += self.module_generator.prepend_paths('PYTHONPATH', self.xmipp_pythonpaths)
          return txt
  