From f942e555a8da1c949b64218ee563310e5c248efe Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Thu, 27 Sep 2018 15:48:42 -0500
Subject: [PATCH] Added --debug option to mrdna script
---
bin/mrdna | 45 +++++++++++++++++++++++++++++++++++++++++++--
1 file changed, 43 insertions(+), 2 deletions(-)
diff --git a/bin/mrdna b/bin/mrdna
index b16ac40..8c1fc07 100755
--- a/bin/mrdna
+++ b/bin/mrdna
@@ -23,6 +23,8 @@ parser.add_argument('--fine-steps', type=float, default=1e7,
help='Simulation steps for fine model (50 fs/step)')
parser.add_argument('--backbone-scale', type=float, default=1.0,
help='Factor to scale DNA backbone in atomic model; try 0.25 to avoid clashes for atomistic simulations')
+parser.add_argument('--debug', action='store_true',
+ help='Run through the python debugger?')
parser.add_argument('--draw-cylinders', action='store_true',
help='Whether or not to draw the cylinders')
@@ -37,8 +39,7 @@ parser.add_argument('input_file', type=str,
args = parser.parse_args()
-if __name__ == '__main__':
-
+def main():
infile = pathlib.Path(args.input_file)
try:
prefix = infile.stem
@@ -100,3 +101,43 @@ if __name__ == '__main__':
simulate( **run_args )
+
+if __name__ == '__main__':
+ if args.debug:
+
+ class Restart(Exception):
+ """Causes a debugger to be restarted for the debugged python program."""
+ pass
+
+ import traceback
+ import sys
+ from pdb import Pdb
+ pdb = Pdb()
+
+ while True:
+ try:
+ # pdb._runscript(mainpyfile)
+ pdb.runcall(main)
+ if pdb._user_requested_quit:
+ break
+ print("The program finished and will be restarted")
+ except Restart:
+ print("Restarting...")
+ print("\t" + " ".join(args))
+ except SystemExit:
+ # In most cases SystemExit does not warrant a post-mortem session.
+ print("The program exited via sys.exit(). Exit status:", end=' ')
+ print(sys.exc_info()[1])
+ except SyntaxError:
+ traceback.print_exc()
+ sys.exit(1)
+ except:
+ traceback.print_exc()
+ print("Uncaught exception. Entering post mortem debugging")
+ print("Running 'cont' or 'step' will restart the program")
+ t = sys.exc_info()[2]
+ pdb.interaction(None, t)
+ print("Post mortem debugger finished. mrdna will be restarted")
+
+ else:
+ main()
--
GitLab