<commit_before>"""

  This module contains functions for building and loading NMODL mechanisms

  Author: <NAME> (<EMAIL>)
  Copyright: 2012-2014 <NAME>.
  License: This file is part of the "NineLine" package, which is released under
           the MIT Licence, see LICENSE for details.
"""
from __future__ import absolute_import
import os.path
import shutil
import time
import platform
import subprocess as sp

from .__init__ import (path_to_exec, get_build_paths,
                       load_component_translations)

BUILD_ARCHS = [platform.machine(), 'i686', 'x86_64', 'powerpc', 'umac']
_SIMULATOR_BUILD_NAME = 'neuron'
_MODIFICATION_TIME_FILE = 'modification_time'

if 'NRNHOME' in os.environ:
    os.environ['PATH'] += os.pathsep + \
        os.path.join(os.environ['NRNHOME'], platform.machine(), 'bin')
else:
    try:
        if os.environ['HOME'] == '/home/tclose':
            # I apologise for this little hack (this is the path on my machine,
            # to save me having to set the environment variable in eclipse)
            os.environ['PATH'] += os.pathsep + '/opt/NEURON-7.2/x86_64/bin'
    except KeyError:
        pass


def build_celltype_files(biophysics_name, nineml_path, install_dir=None,
                         build_parent_dir=None, method='derivimplicit',
                         build_mode='lazy', silent_build=False, kinetics=[]):
    """
    Generates and builds the required NMODL files for a given NCML cell class

    @param biophysics_name [str]: Name of the celltype to be built
    @param nineml_path [str]: Path to the NCML file from which the NMODL files
                              will be compiled and built
    @param install_dir [str]: Path to the directory where the NMODL files will
                              be generated and compiled
    @param build_parent_dir [str]: Used to set the default 'install_dir' path
    @param method [str]: The method option to be passed to the NeMo interpreter
                              command
    @param kinetics [list(str)]: A list of ionic components to be generated
                              using the kinetics option
    """
    (default_install_dir, params_dir,
     _, _) = get_build_paths(nineml_path, biophysics_name,
                             _SIMULATOR_BUILD_NAME,
                             build_parent_dir=build_parent_dir)
    if not install_dir:
        install_dir = default_install_dir
    if build_mode in ('force', 'build_only'):
        shutil.rmtree(install_dir, ignore_errors=True)
        shutil.rmtree(params_dir, ignore_errors=True)
    elif build_mode in ('compile_only', 'require'):
        if not os.path.exists(install_dir) or not os.path.exists(params_dir):
            raise Exception("Prebuilt installation directory '{install}'"
                            "and/or python parameters directory '{params}'"
                            "are not present, which are required for 'require'"
                            "or 'compile_only' build options"
                            .format(install=install_dir, params=params_dir))
    try:
        if not os.path.exists(install_dir):
            os.makedirs(install_dir)
        if not os.path.exists(params_dir):
            os.makedirs(params_dir)
    except IOError as e:
        raise Exception("Could not create a required neuron build directory,"
                        "check the required permissions or specify a different"
                        " parent build directory -> {}".format(e))
    # Get the stored modification time of the previous build if it exists
    install_mtime_path = os.path.join(install_dir, _MODIFICATION_TIME_FILE)
    params_mtime_path = os.path.join(params_dir, _MODIFICATION_TIME_FILE)
    if os.path.exists(install_mtime_path):
        with open(install_mtime_path) as f:
            prev_install_mtime = f.readline()
    else:
        prev_install_mtime = ''
    if os.path.exists(params_mtime_path):
        with open(params_mtime_path) as f:
            prev_params_mtime = f.readline()
    else:
        prev_params_mtime = ''
    # Get the modification time of the source NCML file for comparison with
    # the build directory
    ncml_mtime = time.ctime(os.path.getmtime(nineml_path))
    rebuilt = False
    if ((ncml_mtime != prev_install_mtime
         or ncml_mtime != prev_params_mtime) and
        build_mode != 'compile_only'):
        nemo_cmd = ("{nemo_path} {nineml_path} -p --pyparams={params}"
                    "--nmodl={output} --nmodl-method={method}"
                    "--nmodl-kinetic={kinetics}"
                    .format(nemo_path=path_to_exec('nemo'),
                            nineml_path=os.path.normpath(nineml_path),
                            output=os.path.normpath(install_dir),
                            params=params_dir, kinetics=','.join(kinetics),
                            method=method))
        try:
            sp.check_call(nemo_cmd, shell=True)
        except sp.CalledProcessError as e:
            raise Exception("Error while compiling NCML description into NMODL"
                            "code -> {}".format(e))
        # Build mode is set to 'force' because the mod files have been
        # regenerated
        with open(install_mtime_path, 'w') as f:
            f.write(ncml_mtime)
        with open(params_mtime_path, 'w') as f:
            f.write(ncml_mtime)
        rebuilt = True
    if rebuilt or build_mode == 'compile_only':
        compile_nmodl(install_dir, build_mode='force', silent=silent_build)
    # Load the parameter name translations from the params dir
    component_translations = load_component_translations(
        biophysics_name, params_dir)
    return install_dir, component_translations


def compile_nmodl(model_dir, build_mode='lazy', silent=False):
    """
    Builds all NMODL files in a directory<commit_msg>added missing whitespaces to nemo command<commit_after>"""

  This module contains functions for building and loading NMODL mechanisms

  Author: <NAME> (tclose<EMAIL>)
  Copyright: 2012-2014 <NAME>.
  License: This file is part of the "NineLine" package, which is released under
           the MIT Licence, see LICENSE for details.
"""
from __future__ import absolute_import
import os.path
import shutil
import time
import platform
import subprocess as sp

from .__init__ import (path_to_exec, get_build_paths,
                       load_component_translations)

BUILD_ARCHS = [platform.machine(), 'i686', 'x86_64', 'powerpc', 'umac']
_SIMULATOR_BUILD_NAME = 'neuron'
_MODIFICATION_TIME_FILE = 'modification_time'

if 'NRNHOME' in os.environ:
    os.environ['PATH'] += os.pathsep + \
        os.path.join(os.environ['NRNHOME'], platform.machine(), 'bin')
else:
    try:
        if os.environ['HOME'] == '/home/tclose':
            # I apologise for this little hack (this is the path on my machine,
            # to save me having to set the environment variable in eclipse)
            os.environ['PATH'] += os.pathsep + '/opt/NEURON-7.2/x86_64/bin'
    except KeyError:
        pass


def build_celltype_files(biophysics_name, nineml_path, install_dir=None,
                         build_parent_dir=None, method='derivimplicit',
                         build_mode='lazy', silent_build=False, kinetics=[]):
    """
    Generates and builds the required NMODL files for a given NCML cell class

    @param biophysics_name [str]: Name of the celltype to be built
    @param nineml_path [str]: Path to the NCML file from which the NMODL files
                              will be compiled and built
    @param install_dir [str]: Path to the directory where the NMODL files will
                              be generated and compiled
    @param build_parent_dir [str]: Used to set the default 'install_dir' path
    @param method [str]: The method option to be passed to the NeMo interpreter
                              command
    @param kinetics [list(str)]: A list of ionic components to be generated
                              using the kinetics option
    """
    (default_install_dir, params_dir,
     _, _) = get_build_paths(nineml_path, biophysics_name,
                             _SIMULATOR_BUILD_NAME,
                             build_parent_dir=build_parent_dir)
    if not install_dir:
        install_dir = default_install_dir
    if build_mode in ('force', 'build_only'):
        shutil.rmtree(install_dir, ignore_errors=True)
        shutil.rmtree(params_dir, ignore_errors=True)
    elif build_mode in ('compile_only', 'require'):
        if not os.path.exists(install_dir) or not os.path.exists(params_dir):
            raise Exception("Prebuilt installation directory '{install}'"
                            "and/or python parameters directory '{params}'"
                            "are not present, which are required for 'require'"
                            "or 'compile_only' build options"
                            .format(install=install_dir, params=params_dir))
    try:
        if not os.path.exists(install_dir):
            os.makedirs(install_dir)
        if not os.path.exists(params_dir):
            os.makedirs(params_dir)
    except IOError as e:
        raise Exception("Could not create a required neuron build directory,"
                        "check the required permissions or specify a different"
                        " parent build directory -> {}".format(e))
    # Get the stored modification time of the previous build if it exists
    install_mtime_path = os.path.join(install_dir, _MODIFICATION_TIME_FILE)
    params_mtime_path = os.path.join(params_dir, _MODIFICATION_TIME_FILE)
    if os.path.exists(install_mtime_path):
        with open(install_mtime_path) as f:
            prev_install_mtime = f.readline()
    else:
        prev_install_mtime = ''
    if os.path.exists(params_mtime_path):
        with open(params_mtime_path) as f:
            prev_params_mtime = f.readline()
    else:
        prev_params_mtime = ''
    # Get the modification time of the source NCML file for comparison with
    # the build directory
    ncml_mtime = time.ctime(os.path.getmtime(nineml_path))
    rebuilt = False
    if ((ncml_mtime != prev_install_mtime
         or ncml_mtime != prev_params_mtime) and
        build_mode != 'compile_only'):
        nemo_cmd = ("{nemo_path} {nineml_path} -p --pyparams={params} "
                    "--nmodl={output} --nmodl-method={method} "
                    "--nmodl-kinetic={kinetics}"
                    .format(nemo_path=path_to_exec('nemo'),
                            nineml_path=os.path.normpath(nineml_path),
                            output=os.path.normpath(install_dir),
                            params=params_dir, kinetics=','.join(kinetics),
                            method=method))
        try:
            sp.check_call(nemo_cmd, shell=True)
        except sp.CalledProcessError as e:
            raise Exception("Error while compiling NCML description into NMODL"
                            "code -> {}".format(e))
        # Build mode is set to 'force' because the mod files have been
        # regenerated
        with open(install_mtime_path, 'w') as f:
            f.write(ncml_mtime)
        with open(params_mtime_path, 'w') as f:
            f.write(ncml_mtime)
        rebuilt = True
    if rebuilt or build_mode == 'compile_only':
        compile_nmodl(install_dir, build_mode='force', silent=silent_build)
    # Load the parameter name translations from the params dir
    component_translations = load_component_translations(
        biophysics_name, params_dir)
    return install_dir, component_translations


def compile_nmodl(model_dir, build_mode='lazy', silent=False):
    """
    Builds all NMODL files in a directory
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