From f1f89196852ce4ad220c8e608e3e79e9308e24a9 Mon Sep 17 00:00:00 2001
From: Ellen Zhong <ellen.zhong@virginia.edu>
Date: Fri, 20 Jun 2014 09:04:17 -0400
Subject: [PATCH] added verbosity flag to convert

---
 testing/UnitTest.py       |  6 +++---
 testing/convert.py        | 10 ++++++----
 testing/gromacs_driver.py |  2 +-
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/testing/UnitTest.py b/testing/UnitTest.py
index c7637f71..dfb3456f 100644
--- a/testing/UnitTest.py
+++ b/testing/UnitTest.py
@@ -108,7 +108,7 @@ def test_desmond(args):
         h1, h2 = add_handler(odir)
         flags = ['--des_in', f, '--desmond', '--gromacs', '--lammps', '--odir', odir]
         flags = add_flags(args, flags)
-        logger.info('Converting %s with command:\n    python convert.py %s' % (f,' '.join(flags)))
+        logger.info('Converting %s with command:\n    python convert.py %s\n' % (f,' '.join(flags)))
         try:
             diff = convert.main(flags) # reuses code from convert.py
             assert(len(diff) == N_FORMATS)
@@ -138,7 +138,7 @@ def test_gromacs(args):
         h1, h2 = add_handler(odir)
         flags = ['--gro_in', g, t, '--desmond', '--gromacs', '--lammps', '--odir', odir]
         flags = add_flags(args, flags)
-        logger.info('Converting %s, %s with command:\n    python convert.py %s' 
+        logger.info('Converting %s, %s with command:\n    python convert.py %s\n' 
                     % (g, t,' '.join(flags)))
         try:
             diff = convert.main(flags) # reuses code from convert.py
@@ -167,7 +167,7 @@ def test_lammps(args):
         h1, h2 = add_handler(odir)
         flags = ['--lmp_in', f, '--desmond', '--gromacs', '--lammps', '--odir', odir]
         flags = add_flags(args, flags)
-        logger.info('Converting %s with command:\n    python convert.py %s' % (f,' '.join(flags)))
+        logger.info('Converting %s with command:\n    python convert.py %s\n' % (f,' '.join(flags)))
         try:
             diff = convert.main(flags) # reuses code from convert.py
             assert(len(diff) == N_FORMATS)
diff --git a/testing/convert.py b/testing/convert.py
index bfda17ae..79d02c52 100644
--- a/testing/convert.py
+++ b/testing/convert.py
@@ -21,9 +21,9 @@
 # Make a global logging object.
 if __name__ == '__main__':
     logger = logging.getLogger('InterMolLog')
-    logger.setLevel(logging.INFO) # specifies lowest severity log messages to handle (DEBUG will be ignored)
+    logger.setLevel(logging.DEBUG) # specifies lowest severity log messages to handle
     h = logging.StreamHandler()
-    #f = logging.Formatter("%(levelname)s %(asctime)s %(funcName)s %(lineno)d %(message)s")
+    h.setLevel(logging.INFO) # ignores DEBUG level for now
     f = logging.Formatter("%(levelname)s %(asctime)s %(message)s", "%Y-%m-%d %H:%M:%S")
     h.setFormatter(f)
     logger.addHandler(h)
@@ -71,7 +71,7 @@ def get_parser():
             metavar='path', default='lmp_openmpi',
             help='path for LAMMPS binary, needed for energy evaluation')
     group_misc.add_argument('-v', '--verbose', dest='verbose', action='store_true',
-            help='verbosity')
+            help='high verbosity, includes DEBUG level output')
 
     # prints help if no arguments given
     if len(sys.argv)==1:
@@ -88,6 +88,8 @@ def main(args=''):
         args = parser.parse_args(args)
 
     logger = logging.getLogger('InterMolLog')
+    if args.verbose:
+        h.setLevel(logging.DEBUG)
     System._sys = System('InterMol')
 
     # --------------- PROCESS INPUTS ----------------- #
@@ -210,7 +212,7 @@ def main(args=''):
                 e_outfile.append(-1)
 
         # display energy comparison results
-        out = ['']
+        out = ['InterMol Conversion Energy Comparison Results','']
         out.append('{0} input energy file: {1}'.format(input_type, e_infile))
         for type, file in zip(output_type, e_outfile):
             out.append('{0} output energy file: {1}'.format(type, file))
diff --git a/testing/gromacs_driver.py b/testing/gromacs_driver.py
index c731a27f..d7a3328b 100644
--- a/testing/gromacs_driver.py
+++ b/testing/gromacs_driver.py
@@ -83,7 +83,7 @@ def gromacs_energies(top=None, gro=None, mdp=None, gropath='',grosuff='', grompp
     select = " ".join(map(str, range(1, 20))) + " 0 "
     cmd = 'echo {select} | {genergy_bin} -f {ener} -o {ener_xvg} -dp'.format(
             select=select, genergy_bin=genergy_bin, ener=ener, ener_xvg=ener_xvg)
-    logger.debug('Running GROMACS with command:\n    %s' % ' '.join(cmd))
+    logger.debug('Running GROMACS with command:\n    %s' % cmd)
     with open(stdout, 'wa') as out, open(stderr, 'wa') as err:
         exit = subprocess.call(cmd, stdout=out, stderr=err, shell=True)
     if exit: