setup.py

import os
import sys
import subprocess
import argparse

def change_localsettings_path(fname, repo_path):
    """
    Requires the sys.path.insert to be all on one line
    Requires "from local_settings import local_settings as settings_loc"
        to immediately follow sys.path.insert
    overwrites existing file!
    """

    with open(fname, 'r') as f:
        lines = f.readlines()
    for i, line in enumerate(lines):
        if line.startswith('sys.path.insert'):
            if 'from local_settings import local_settings as settings_loc' in lines[i+1]:
                break
    if i+1 == len(lines):
        raise RuntimeError('Could not find the line to replace in %s!' % (fname))
    lines[i] = "sys.path.insert(0, '%s')\n" % (repo_path)
    with open(fname, 'w') as f:
        f.write(''.join(lines))
    print('Successfully adjusted %s' % (fname))

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('-f', help='full setup', action='store_true')
    parser.add_argument('-d', help='database only', action='store_true', default=False)
    args = parser.parse_args()

    repo_path = os.getcwd()

    if args.d:
        args.f = False
    else:
        args.f = True

    if args.f:
        message = 'USER INPUT: Settings Name (leave blank for default): '
        if sys.version_info.major == 2:
            fname = raw_input(message)
        elif sys.version_info.major == 3:
            fname = input(message)
        else:
            raise EnvironmentError("Something wrong with your python version?")

    if args.f or args.d:
        # step one: extract the db tarball
        print('Extracting database files...')
        db_dir = os.path.join(repo_path, 'workflow', 'database')
        # wipe out existing db directory
        if os.path.isdir(db_dir):
            subprocess.call(['rm', '-r', db_dir])
        os.makedirs(db_dir)
        for zipfile in ['blastdb.zip', 'pickle_files.zip']:
            cmd = ['unzip', '../%s' %(zipfile)]
            subprocess.call(
                cmd,
                cwd = os.path.join(repo_path, 'workflow','database')
                )
            subprocess.call(["cp", os.path.join(repo_path, "workflow","magi_cpd_similarity.graphml"), 
            os.path.join(repo_path, 'workflow','database','magi_cpd_similarity.graphml')])
        print('Done')

    if args.f:
        # step two: make local_settings.py file

        if fname == '':
            fname = 'user_settings'

        lines = ["import os\n\n"]
        lines.append("repo_location = r'%s'\n\n" % (repo_path))
        lines.append("blastbin =          os.path.join(repo_location, 'workflow','blastbin')\n")
        lines.append("\n")
        lines.append("refseq_path =       os.path.join(repo_location, 'workflow','database','mrs_reaction_filtered_refseq_db_newrxns_actinofixed.pkl')\n")
        lines.append("refseq_db =         os.path.join(repo_location, 'workflow','database','mrs_reaction_filtered_refseq_db_fasta_blastdb_actinofix')\n")
        lines.append("mrs_reaction_path = os.path.join(repo_location, 'workflow','database','mrs_reaction_newrxns_added_actinofix.pkl')\n")
        lines.append("compounds_df =      os.path.join(repo_location, 'workflow','database','unique_compounds_groups_magi.pkl')\n")
        lines.append("mst_path =          os.path.join(repo_location, 'workflow','database','magi_cpd_similarity.graphml')\n")
        lines.append("chemnet_pickle =    os.path.join(repo_location, 'workflow','database','compound_groups.pkl')\n")
        lines.append("c2r =               os.path.join(repo_location, 'workflow','database','c2r.pkl')\n")
        lines.append("\n")
        lines.append("magi_task_path = ''\n")
        lines.append("magiweburl = 'https://magi.nersc.gov'\n")
        lines.append("magiwebsuperuser = ''\n")
        lines.append("magiwebsuperuserpass = ''\n")
        lines.append("admin_email = ''\n")

        with open('local_settings/%s.py' %(fname), 'w') as f:
            for line in lines:
                f.write(line)
        with open('local_settings/local_settings.py', 'a') as f:
            f.write("SETTINGS_FILE= '%s'\n" % (fname))
        print('Successfully wrote local settings files')

    print('Setup Done!')

if __name__ == '__main__':
    main()