Merge branch '58-get-rid-of-argparse' into 'master'

Resolve "get rid of argparse"

Closes #58

See merge request dbis/software/dbispipeline!40

src/dbispipeline/__main__.py

 """Declaring the main method of this package."""
-import argparse
-
 from dbispipeline.cli.main import main
 
 if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='executes dbis config files')
-    # TODO: configurationfile is required but it is i.e. not needed for restore
-    parser.add_argument('plan', help='file that holds config')
-    parser.add_argument('-f',
-                        '--force',
-                        action='store_true',
-                        help='Run with dirty git')
-    parser.add_argument('--dryrun',
-                        action='store_true',
-                        help='run without sending results to database.')
-    parser.add_argument(
-        '-m',
-        '--mail',
-        choices=[None, 'run', 'total'],
-        default=None,
-        help='Mail notification level. Choose one of [None, \'run\', \'total\''
-        ']. If set no None, no mails will be sent. if set to \'run\', one info'
-        ' mail will be sent for each run. If set to \'total\', one mail will '
-        'be sent after the entire pipeline is complete.')
-    parser.add_argument(
-        '--restore',
-        default=None,
-        type=str,
-        help='Restores the backup contained in the given file.')
-    parser.add_argument(
-        '--slurm',
-        action='store_true',
-        help='send this job to the slurm job queue instead of running it local'
-    )
-    parser.add_argument('-v',
-                        '--verbose',
-                        action='store_true',
-                        help='increase logging')
-    args = parser.parse_args()
-    main(args.dryrun, args.force, args.verbose, args.slurm, args.restore,
-         args.mail, args.plan)
+    main()

src/dbispipeline/cli/main.py

@@ -30,12 +30,6 @@ from dbispipeline.utils import restore_backup
     ' mail will be sent for each run. If set to \'total\', one mail will '
     'be sent after the entire pipeline is complete.')
 @click.argument('plan', type=click.Path(exists=True))
-def _main(dryrun, force, verbose, slurm, restore, mail, plan):
-    main(dryrun, force, verbose, slurm, restore, mail, plan)
-
-
-# this method is split to allow the legacy method of invoking via the modules'
-# __main__.py file to re-use this code.
 def main(dryrun, force, verbose, slurm, restore, mail, plan):
     """Entry point that executes the pipeline given a configuration."""
     if verbose: