moltemplate bugfix update

tools/moltemplate/moltemplate/nbody_reorder_atoms.py

@@ -23,7 +23,15 @@ def main():
     section_name = ''
     if len(sys.argv) == 3:
         section_name = sys.argv[1]
-        module_name = sys.argv[2].rstrip('.py')
+        bond_pattern_module_name = sys.argv[2]
+        # If the file name ends in ".py", then strip off this suffix.
+        # The next line does not work. Too lazy do care why.
+        # bond_pattern_module_name=bond_pattern_module_name.rstrip('.py')
+        # Do this instead
+        pc = bond_pattern_module_name.rfind('.py')
+        if pc != -1:
+            bond_pattern_module_name = bond_pattern_module_name[0:pc]
+
     else:
         sys.stderr.write('Usage Example:\n\n'
                          '      ' + g_program_name + ' Angles nbody_angles.py < angles.txt > new_angles.txt\n\n'
@@ -41,8 +49,9 @@ def main():
     # Load that now.
 
     # search locations
-    package_opts = [[module_name, __package__],
-                    ['nbody_alt_symmetry.'+module_name, __package__]]
+    package_opts = [[bond_pattern_module_name, __package__],
+                    ['nbody_alt_symmetry.'+bond_pattern_module_name,
+                     __package__]]
 
     if __package__:
         for i, _ in enumerate(package_opts):
@@ -59,7 +68,7 @@ def main():
 
     if g is None:
         sys.stderr.write('Error: Unable to locate file \"' +
-                         module_name + '\"\n'
+                         bond_pattern_module_name + '\"\n'
                          '       (Did you mispell the file name?\n'
                          '        Check the \"nbody_alternate_symmetry/\" directory.)\n')
         sys.exit(-1)

tools/moltemplate/setup.py

@@ -14,9 +14,13 @@ setup(
 
   url='https://github.com/jewettaij/moltemplate',
 
-  download_url='https://github.com/jewettaij/moltemplate/tarball/v2.2.1',
+  download_url='https://github.com/jewettaij/moltemplate/archive/v2.3.7.zip',
 
-  keywords=['simulation', 'LAMMPS', 'molecule', 'builder', 'ESPResSo'],
+  version='2.3.7',
+
+  keywords=['simulation', 'LAMMPS', 'molecule editor', 'molecule builder',
+            'ESPResSo'],
+            
 
   # BSD 3-Clause License:
   # - http://choosealicense.com/licenses/bsd-3-clause
@@ -28,8 +32,7 @@ setup(
                'License :: OSI Approved :: BSD License',
                'Operating System :: MacOS :: MacOS X',
                'Operating System :: POSIX :: Linux',
-               'Operating System :: Microsoft :: Windows'
-  ],
+               'Operating System :: Microsoft :: Windows'],
 
   scripts=['moltemplate/scripts/moltemplate.sh',
            'moltemplate/scripts/cleanup_moltemplate.sh',
@@ -58,13 +61,12 @@ setup(
         'raw2data.py=moltemplate.raw2data:main',
         'remove_duplicate_atoms.py=moltemplate.remove_duplicate_atoms:main',
         'remove_duplicates_nbody.py=moltemplate.remove_duplicates_nbody:main',
-        'renumber_DATA_first_column.py=moltemplate.renumber_DATA_first_column:main',
-        'tinkerparm2lt.py=moltemplate.tinkerparm2lt.py']},
+        'renumber_DATA_first_column.py=moltemplate.renumber_DATA_first_column:main']},
 
   package_data={'moltemplate': ['force_fields/*.lt']},
   # install_requires=['numpy', 'scipy', 'biopython'],
   setup_requires=['pytest-runner'],
-  tests_require=['pytest', 'pandas'],
+  tests_require=['pytest'],
   zip_safe=True,
   include_package_data=True
 )