<commit_before>import os
import sys
import errno
import argparse
from subprocess import call, PIPE, Popen

HOME_DIR = os.environ.get('HOME')


def install_pysimm(prefix):
    os.chdir(prefix)
    call('git clone https://github.com/polysimtools/pysimm', shell=True)
    call("echo export PYTHONPATH='$PYTHONPATH':{} >> {}".format(prefix,
                                                                os.path.join(HOME_DIR, '.bashrc')),
         shell=True)
    call("export PYTHONPATH='$PYTHONPATH':{}".format(prefix),
         shell=True)
    call("echo export PATH='$PATH':{} >> {}".format(os.path.join(prefix, 'bin'),
                                                    os.path.join(HOME_DIR, '.bashrc')),
         shell=True)
    call("export PATH='$PATH':{}".format(os.path.join(prefix, 'bin')),
         shell=True)


def apt_update():
    call('sudo apt-get update', shell=True)


def apt_install(*packages):
    call('sudo apt-get -y install {}'.format(' '.join(packages)),
         shell=True)


def install_lammps(prefix, *packages):
    os.chdir(prefix)
    call('git clone git://git.lammps.org/lammps-ro.git lammps', shell=True)
    os.chdir(os.path.join(prefix,'lammps','src'))
    for package in packages:
        call('make yes-{}'.format(package), shell=True)
    call('make mpi', shell=True)
    call("echo export PATH='$PATH':{} >> {}".format(os.path.join(prefix, 'lammps', 'src'),
                                                    os.path.join(HOME_DIR,'.bashrc')),
         shell=True)
    call("export PATH='$PATH':{}".format(os.path.join(prefix, 'lammps', 'src')),
         shell=True)
    call("echo export LAMMPS_EXEC={} >> {}".format(os.path.join(prefix, 'lammps', 'src', 'lmp_mpi'),
                                                   os.path.join(HOME_DIR,'.bashrc')),
         shell=True)
    call("export LAMMPS_EXEC={}".format(os.path.join(prefix, 'lammps', 'src', 'lmp_mpi')),
         shell=True)
         
def install_ambertools(dir_):
    os.chdir(dir_)
    call("echo export AMBERHOME={} >> {}".format(dir_, os.path.join(HOME_DIR,'.bashrc')),
         shell=True)
    call('./configure gnu', shell=True)
    call('make install', shell=True)
    call("echo export ANTECHAMBER_EXEC={} >> {}".format(os.path.join(dir_, 'bin', 'antechamber'),
                                                   os.path.join(HOME_DIR,'.bashrc')),
         shell=True)
    
    call("export ANTECHAMBER_EXEC={}".format(os.path.join(dir_, 'bin', 'antechamber')),
         shell=True)


def parse_args():<commit_msg>removed explicit export, didnt work<commit_after>import os
import sys
import errno
import argparse
from subprocess import call, PIPE, Popen

HOME_DIR = os.environ.get('HOME')


def install_pysimm(prefix):
    os.chdir(prefix)
    call('git clone https://github.com/polysimtools/pysimm', shell=True)
    call("echo export PYTHONPATH='$PYTHONPATH':{} >> {}".format(prefix,
                                                                os.path.join(HOME_DIR, '.bashrc')),
         shell=True)
    call("echo export PATH='$PATH':{} >> {}".format(os.path.join(prefix, 'bin'),
                                                    os.path.join(HOME_DIR, '.bashrc')),
         shell=True)


def apt_update():
    call('sudo apt-get update', shell=True)


def apt_install(*packages):
    call('sudo apt-get -y install {}'.format(' '.join(packages)),
         shell=True)


def install_lammps(prefix, *packages):
    os.chdir(prefix)
    call('git clone git://git.lammps.org/lammps-ro.git lammps', shell=True)
    os.chdir(os.path.join(prefix,'lammps','src'))
    for package in packages:
        call('make yes-{}'.format(package), shell=True)
    call('make mpi', shell=True)
    call("echo export PATH='$PATH':{} >> {}".format(os.path.join(prefix, 'lammps', 'src'),
                                                    os.path.join(HOME_DIR,'.bashrc')),
         shell=True)
    call("echo export LAMMPS_EXEC={} >> {}".format(os.path.join(prefix, 'lammps', 'src', 'lmp_mpi'),
                                                   os.path.join(HOME_DIR,'.bashrc')),
         shell=True)
         
def install_ambertools(dir_):
    os.chdir(dir_)
    call("echo export AMBERHOME={} >> {}".format(dir_, os.path.join(HOME_DIR,'.bashrc')),
         shell=True)
    call('./configure gnu', shell=True)
    call('make install', shell=True)
    call("echo export ANTECHAMBER_EXEC={} >> {}".format(os.path.join(dir_, 'bin', 'antechamber'),
                                                   os.path.join(HOME_DIR,'.bashrc')),
         shell=True)


def parse_args():
{'fraction_non_alphanumeric': 0.1737704918032787, 'fraction_numerical': 0.0, 'mean_word_length': 2.4072970960536115, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 27, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 20, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7015093', 'n_tokens_mistral': 1473, 'n_tokens_neox': 1437, 'n_words': 256}