Code smells removed

simbad/command_line/simbad_contaminant.py

@@ -52,7 +52,7 @@ def main():
     args = p.parse_args()
 
     if args.work_dir:
-        logging.info('Making a named work directory: {0}'.format(args.work_dir))
+        logging.info('Making a named work directory: %s' % args.work_dir)
         try:
             os.mkdir(args.work_dir)
         except:

simbad/lattice/search.py

@@ -40,13 +40,14 @@ def __repr__(self):
     def _as_dict(self):
         """Convert the :obj:`_LatticeParameterScore <simbad.lattice.search._LatticeParameterScore>`
         object to a dictionary"""
-        dict = {}
+        dictionary = {}
         for k in self.__slots__:
             if k == 'unit_cell':
-                dict['a'], dict['b'], dict['c'], dict['alpha'], dict['beta'], dict['gamma'] = self.unit_cell
+                dictionary['a'], dictionary['b'], dictionary['c'], dictionary['alpha'], dictionary['beta'], \
+                dictionary['gamma'] = self.unit_cell
             else:
-                dict[k] = getattr(self, k)
-        return dict
+                dictionary[k] = getattr(self, k)
+        return dictionary
 
 
 class LatticeSearch(object):
@@ -75,6 +76,7 @@ class LatticeSearch(object):
     and write the same information to a comma-separated file called ``lattice.csv``.
 
     """
+
     def __init__(self, unit_cell, space_group, lattice_db_fname, max_to_keep=20):
         """Initialize a new Lattice Search class
 
@@ -159,7 +161,7 @@ def space_group(self, space_group):
         elif space_group == "C4212":
             space_group = "P422"
         self._space_group = space_group
-        self._search_results = None 
+        self._search_results = None
 
     @property
     def total_db_files(self):
@@ -182,16 +184,16 @@ def unit_cell(self, unit_cell):
             msg = "Unit cell parameters need to be of type str, list or tuple"
             raise TypeError(msg)
         self._unit_cell = unit_cell
-        self._search_results = None 
+        self._search_results = None
 
-    def copy_results(self, pdb_db, dir=os.getcwd()):
+    def copy_results(self, pdb_db, directory=os.getcwd()):
         """Copy the results from a local copy of the PDB
 
         Parameters
         ----------
         pdb_db : str
            The path to the local copy of the PDB
-        dir : str
+        directory : str
            The path to save results to [default: .]
 
         Raises
@@ -207,7 +209,7 @@ def copy_results(self, pdb_db, dir=os.getcwd()):
             msg = "No search results found/available"
             raise ValueError(msg)
 
-        out_dir = os.path.join(dir, 'lattice_input_models')
+        out_dir = os.path.join(directory, 'lattice_input_models')
         if not os.path.isdir(out_dir):
             os.mkdir(out_dir)
         else:
@@ -222,12 +224,12 @@ def copy_results(self, pdb_db, dir=os.getcwd()):
                     with open(f_name_out, 'w') as f_out:
                         f_out.write(f_in.read())
 
-    def download_results(self, dir=os.getcwd()):
+    def download_results(self, directory=os.getcwd()):
         """Download the results directly from the PDB
 
         Parameters
         ----------
-        dir : str
+        directory : str
            The path to save results to [default: .]
 
         Raises
@@ -243,7 +245,7 @@ def download_results(self, dir=os.getcwd()):
             msg = "No search results found/available"
             raise ValueError(msg)
 
-        out_dir = os.path.join(dir, 'lattice_input_models')
+        out_dir = os.path.join(directory, 'lattice_input_models')
         if not os.path.isdir(out_dir):
             os.mkdir(out_dir)
         else:
@@ -261,7 +263,6 @@ def download_results(self, dir=os.getcwd()):
                     os.path.join(out_dir, '{0}.pdb'.format(result.pdb_code))
                 )
 
-
     def search(self, tolerance=0.05):
         """Search for similar Niggli cells
 
@@ -361,6 +362,7 @@ def calculate_penalty(query, reference):
         -------
 
         """
+
         def penalty(q, r):
             delta = abs(numpy.asarray(q, dtype=numpy.float64) - numpy.asarray(r, dtype=numpy.float64))
             return delta[:3].sum().item(), delta[3:].sum().item()

simbad/util/config_util.py

@@ -122,7 +122,7 @@ def _process_options(self):
 
     def _preset_options(self, mode):
         assert hasattr(self, mode), "Unknown mode: {0}".format(mode)
-        logger.info("Using preset mode: {0}".format(mode))
+        logger.info("Using preset mode: %s" % mode)
         for k, v in getattr(self, mode).iteritems():
             if 'cmdline_flags' in self.d and k in self.d['cmdline_flags']:
                 if self.d[k] == v:
@@ -131,10 +131,10 @@ def _preset_options(self, mode):
                     msg = 'WARNING! Overridng {0} setting: {1} => {2} with {3}'.format(mode, k, v, self.d[k])
                 logger.critical(msg)
             elif k in self.d:
-                logger.debug("{0} overriding default setting: {1} => {2} with {3}".format(mode, k, v, self.d[k]))
+                logger.debug("%s overriding default setting: %s => %s with %s" % mode, k, v, self.d[k])
                 self.d[k] = v
             else:
-                logger.debug("{0} setting: {1} => {2}".format(mode, k, v))
+                logger.debug("%s setting: %s => %s" % mode, k, v)
                 self.d[k] = v
         return
 
@@ -146,7 +146,7 @@ def _read_config_file(self, config_file):
 
         for section in config.sections():
 
-            if not section in _SECTIONS_REFERENCE:
+            if section not in _SECTIONS_REFERENCE:
                 _SECTIONS_REFERENCE[section] = []
 
             # Basic switch statement to determine the type of variable
@@ -178,12 +178,11 @@ def _read_config_file(self, config_file):
                 else:
                     self.d[k] = v
 
-            _SECTIONS_REFERENCE[section].append(k)
+                _SECTIONS_REFERENCE[section].append(k)
 
         return
 
     def _read_cmdline_opts(self, cmdline_opts):
-        tmpv = None
         cmdline_flags = []
 
         for k, v in cmdline_opts.iteritems():
@@ -198,8 +197,8 @@ def _read_cmdline_opts(self, cmdline_opts):
 
             if k not in self.d:
                 self.d[k] = v
-            elif v != None:
-                logger.debug("Cmdline setting {0}: {1} => {2}".format(k, self.d[k], v))
+            elif v is not None:
+                logger.debug("Cmdline setting %s: %s => %s" % k, self.d[k], v)
                 self.d[k] = v
 
         self.d['cmdline_flags'] = cmdline_flags
@@ -209,7 +208,7 @@ def _isfloat(self, value):
         try:
             float(value)
             return True
-        except:
+        except ValueError:
             return False
 
     def prettify_parameters(self):
@@ -230,7 +229,7 @@ def write_config_file(self, config_file=None):
             config_file = os.path.join(self.d['work_dir'], self.d['name'] + ".ini")
         # Write config to job specific directory
         self.d["out_config_file"] = config_file
-        logger.info("SIMBAD configuration written to: {0}".format(config_file))
+        logger.info("SIMBAD configuration written to: %s" % config_file)
         with open(config_file, "w") as out: config.write(out)
         return
 

simbad/util/mr_util.py

@@ -82,10 +82,10 @@ def __repr__(self):
     def _as_dict(self):
         """Convert the :obj:`_MrScore <simbad.util.mr_util._MrScore>`
         object to a dictionary"""
-        dict = {}
+        dictionary = {}
         for k in self.__slots__:
-            dict[k] = getattr(self, k)
-        return dict
+            dictionary[k] = getattr(self, k)
+        return dictionary
 
 
 class MrSubmit(object):
@@ -268,7 +268,7 @@ def suppress_stdout(self):
 
     def _run_job(self, model):
         """Function to run MR on each model"""
-        logger.info("Running MR and refinement on {0}".format(model.pdb_code))
+        logger.info("Running MR and refinement on %s" % model.pdb_code)
 
         # Generate MR input file
         self.MR_setup(model)
@@ -495,7 +495,7 @@ def run(job_queue):
                     print "MR with {0} was successful so removing remaining jobs from inqueue".format(model.pdb_code)
                     while not job_queue.empty():
                         job = job_queue.get()
-                        logger.debug("Removed job [{0}] from inqueue".format(job.pdb_code))
+                        logger.debug("Removed job [%s] from inqueue" %s job.pdb_code)
 
         # Create job queue
         job_queue = multiprocessing.Queue()
@@ -530,7 +530,7 @@ def run(job_queue):
                         final_r_free = RP.finalRfree
                         final_r_fact = RP.finalRfact
 
-                        if self._dano != None:
+                        if self._dano is not None:
                             AS = anomalous_util.AnomSearch(self.mtz, self.output_dir, self.mr_program)
                             AS.run(result)
                             a = AS.search_results()
@@ -589,7 +589,7 @@ def run(job_queue):
                         final_r_free = RP.finalRfree
                         final_r_fact = RP.finalRfact
 
-                        if self._dano != None:
+                        if self._dano is not None:
                             AS = anomalous_util.AnomSearch(self.mtz, self.output_dir, self.mr_program)
                             AS.run(result)
                             a = AS.search_results()