batch replace 'except:' with 'except Exception:' (#703)

The latter will not catch `KeyboardInterrupt` and `SystemExit`. See https://stackoverflow.com/a/18982726/9567349.

dpgen/auto_test/Lammps.py

@@ -289,7 +289,7 @@ def compute(self,
                             if len(line) and str(ii) == line[0]:
                                 try:
                                     [float(kk) for kk in line]
-                                except:
+                                except Exception:
                                     continue
                                 stress.append([])
                                 virial.append([])

dpgen/data/gen.py

@@ -571,7 +571,7 @@ def make_scale(jdata):
                 try:
                     pos_src = os.path.join(os.path.join(init_path, ii), 'CONTCAR')
                     assert(os.path.isfile(pos_src))
-                except:
+                except Exception:
                     raise RuntimeError("not file %s, vasp relaxation should be run before scale poscar")
             scale_path = os.path.join(work_path, ii)
             scale_path = os.path.join(scale_path, "scale-%.3f" % jj)
@@ -604,7 +604,7 @@ def make_scale_ABACUS(jdata):
                 try:
                     pos_src = os.path.join(os.path.join(init_path, ii), 'OUT.ABACUS/STRU_ION_D')
                     assert(os.path.isfile(pos_src))
-                except:
+                except Exception:
                     raise RuntimeError("not file %s, vasp relaxation should be run before scale poscar")
             scale_path = os.path.join(work_path, ii)
             scale_path = os.path.join(scale_path, "scale-%.3f" % jj)
@@ -1238,7 +1238,7 @@ def gen_init_bulk(args) :
        jdata=loadfn(args.PARAM)
        if args.MACHINE is not None:
           mdata=loadfn(args.MACHINE)
-    except:
+    except Exception:
        with open (args.PARAM, 'r') as fp :
            jdata = json.load (fp)
        if args.MACHINE is not None:

dpgen/data/reaction.py

@@ -191,7 +191,7 @@ def gen_init_reaction(args):
         jdata = loadfn(args.PARAM)
         if args.MACHINE is not None:
             mdata = loadfn(args.MACHINE)
-    except:
+    except Exception:
         with open(args.PARAM, 'r') as fp:
             jdata = json.load(fp)
         if args.MACHINE is not None:

dpgen/data/surf.py

@@ -447,7 +447,7 @@ def make_scale(jdata):
                 try:
                     pos_src = os.path.join(os.path.join(init_path, ii), 'CONTCAR')
                     assert(os.path.isfile(pos_src))
-                except:
+                except Exception:
                     raise RuntimeError("not file %s, vasp relaxation should be run before scale poscar")
             scale_path = os.path.join(work_path, ii)
             scale_path = os.path.join(scale_path, "scale-%.3f" % jj)
@@ -583,7 +583,7 @@ def gen_init_surf(args):
        jdata=loadfn(args.PARAM)
        if args.MACHINE is not None:
           mdata=loadfn(args.MACHINE)
-    except:
+    except Exception:
         with open (args.PARAM, 'r') as fp :
             jdata = json.load (fp)
         if args.MACHINE is not None:

dpgen/data/tools/cessp2force_lin.py

@@ -290,7 +290,7 @@ def Parser():
                 try:
                     name = str(item.split('=')[0])
                     number = int(item.split('=')[1])
-                except:
+                except Exception:
                     sys.stderr.write("\nERROR: Could not read the -c string\n")
                     sys.exit()
                 if number >= max_types:

dpgen/database/run.py

@@ -83,7 +83,7 @@ def _parsing_vasp(paths,config_info_dict, id_prefix,iters=True):
         iter_record.sort()
         dlog.info("iter_record")
         dlog.info(iter_record)
-      except:
+      except Exception:
         pass
     for path in paths:
       try:

dpgen/database/vasp.py

@@ -27,7 +27,7 @@ def __init__(self,symbols=None,functional="PBE",pp_file=None,pp_lists=None):
         else:
            try:
               self.potcars=Potcar(symbols=symbols, functional=functional)
-           except:
+           except Exception:
               warnings.warn ("""Inproperly configure of POTCAR !""")
               self.potcars=None
 
@@ -80,7 +80,7 @@ def from_file(cls,filename):
         try:
              potcars=Potcar.from_file(filename)
              return cls(pp_lists=potcars)
-        except:
+        except Exception:
              with open(filename,'r') as f:
                   content=f.readlines()
              functional=content[0].strip().split(':')[-1].strip()
@@ -179,7 +179,7 @@ def from_directory(input_dir, optional_files=None):
                                  ("POSCAR", Poscar), ("POTCAR", DPPotcar)]:
                 fullzpath = zpath(os.path.join(input_dir, fname))
                 sub_d[fname.lower()] = ftype.from_file(fullzpath)
-        except:
+        except Exception:
             for fname, ftype in [("INCAR", Incar), 
                                  ("POSCAR", Poscar), ("POTCAR", DPPotcar)]:
                 fullzpath = zpath(os.path.join(input_dir, fname))

dpgen/dispatcher/ALI.py

@@ -352,7 +352,7 @@ def delete_template(self):
                 response = self.client.do_action_with_exception(request)
                 flag = 1
                 break
-            except:
+            except Exception:
                 count += 1
         # count = 10 and still failed, continue
 
@@ -382,7 +382,7 @@ def get_image_id(self, img_name):
                             return img["ImageId"]
                     flag = 1
                     break
-                except:
+                except Exception:
                     count += 1
                     time.sleep(10)
         if not flag:
@@ -441,7 +441,7 @@ def change_apg_capasity(self, capasity):
                 response = self.client.do_action_with_exception(request)
                 flag = 1
                 break
-            except:
+            except Exception:
                 count += 1
                 time.sleep(10)
         if not flag:
@@ -510,5 +510,5 @@ def get_ip(self, instance_list):
                         else:
                             ip_list.append(response["Instances"]["Instance"][0]["VpcAttributes"]["PrivateIpAddress"]['IpAddress'][0])
             return ip_list
-        except: return []
+        except Exception: return []
 

dpgen/dispatcher/Dispatcher.py

@@ -333,7 +333,7 @@ def make_dispatcher(mdata, mdata_resource=None, work_path=None, run_tasks=None,
             context_type = 'local'
         try:
             batch_type = mdata['batch']
-        except:
+        except Exception:
             dlog.info('cannot find key "batch" in machine file, try to use deprecated key "machine_type"')
             batch_type = mdata['machine_type']
         lazy_local = (mdata.get('lazy-local', False)) or (mdata.get('lazy_local', False))

dpgen/dispatcher/DispatcherList.py

@@ -178,7 +178,7 @@ def make_dispatcher(self, ii):
                 self.dispatcher_list[ii]["dispatcher_status"] = "unsubmitted"
                 flag = 1
                 break
-            except:
+            except Exception:
                 count += 1
                 time.sleep(60)
         if not flag:
@@ -201,7 +201,7 @@ def check_dispatcher_status(self, ii, allow_failue=False):
                     finished = self.dispatcher_list[ii]["dispatcher"].all_finished(self.dispatcher_list[ii]["entity"].job_handler, allow_failue, clean)
                     if finished:
                         self.dispatcher_list[ii]["dispatcher_status"] = "finished"
-                except:
+                except Exception:
                     pass                    
             elif status == 1:
                 # self.dispatcher_list[ii]["dispatcher_status"] = "terminated"

dpgen/dispatcher/LSF.py

@@ -11,7 +11,7 @@ class LSF(Batch) :
     def check_status(self):
         try:
             job_id = self._get_job_id()
-        except:
+        except Exception:
             return JobStatus.terminated
         if job_id == "" :
             raise RuntimeError("job %s has not been submitted" % self.context.remote_root)

dpgen/dispatcher/SSHContext.py

@@ -125,7 +125,7 @@ def __init__ (self,
         self.ssh_session.ensure_alive()
         try:
            self.sftp.mkdir(self.remote_root)
-        except: 
+        except Exception: 
            pass
 
     @property

dpgen/dispatcher/Shell.py

@@ -93,9 +93,9 @@ def sub_script_cmd(self,
             fp_max_errors = 3
             try:
                 fp_max_errors = res['fp_max_errors']
-            except:
+            except Exception:
                 pass
-        except:
+        except Exception:
             cvasp=False
 
         _cmd = cmd.split('1>')[0].strip()

dpgen/dispatcher/Slurm.py

@@ -130,9 +130,9 @@ def sub_script_cmd(self,
             fp_max_errors = 3
             try:
                 fp_max_errors = res['fp_max_errors']
-            except:
+            except Exception:
                 pass
-        except:
+        except Exception:
             cvasp=False
 
         _cmd = cmd.split('1>')[0].strip()

dpgen/generator/run.py

@@ -576,7 +576,7 @@ def run_train (iter_index,
 
     try:
         train_group_size = mdata['train_group_size']
-    except:
+    except Exception:
         train_group_size = 1
 
     api_version = mdata.get('api_version', '0.9')
@@ -2530,11 +2530,11 @@ def post_fp_vasp (iter_index,
         for oo in sys_outcars :
             try:
                 _sys = dpdata.LabeledSystem(oo, type_map = jdata['type_map'])
-            except:
+            except Exception:
                 dlog.info('Try to parse from vasprun.xml')
                 try:
                    _sys = dpdata.LabeledSystem(oo.replace('OUTCAR','vasprun.xml'), type_map = jdata['type_map'])
-                except:
+                except Exception:
                    _sys = dpdata.LabeledSystem()
                    dlog.info('Failed fp path: %s'%oo.replace('OUTCAR',''))
             if len(_sys) == 1:
@@ -2914,7 +2914,7 @@ def run_iter (param_file, machine_file) :
        warnings.simplefilter('ignore', ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
        jdata=loadfn(param_file)
        mdata=loadfn(machine_file)
-    except:
+    except Exception:
        with open (param_file, 'r') as fp :
            jdata = json.load (fp)
        with open (machine_file, 'r') as fp:

dpgen/remote/RemoteJob.py

@@ -63,7 +63,7 @@ def download(self,
                 elif os.path.isdir(os.path.join(self.remote_root,job_dir,ii)):
                     try:
                         os.rmdir(os.path.join(self.local_root,job_dir,ii))
-                    except:
+                    except Exception:
                         print('dir is not empty   '+str(os.path.join(self.local_root,job_dir,ii)))
                     else:
                         shutil.copytree(os.path.join(self.remote_root,job_dir,ii),os.path.join(self.local_root,job_dir,ii))
@@ -176,7 +176,7 @@ def __init__ (self,
            sftp = self.ssh.open_sftp()        
            sftp.mkdir(self.remote_root)
            sftp.close()
-        except: 
+        except Exception: 
            pass
         # open('job_uuid', 'w').write(self.job_uuid)
 
@@ -410,7 +410,7 @@ def _submit():
                else:
                   dlog.debug('task is finished')
 
-           except:
+           except Exception:
                dlog.debug('no job_id file')
                dlog.debug('task restart point !!!')
                _submit()
@@ -529,9 +529,9 @@ def _make_script(self,
            cvasp=res['cvasp']
            try:
               fp_max_errors = res['fp_max_errors']
-           except:
+           except Exception:
               fp_max_errors = 3
-        except:
+        except Exception:
            cvasp=False
 
         for ii,jj in zip(job_dirs, args) :
@@ -765,7 +765,7 @@ def submit(self,
                 dlog.debug('task is running')
             else:
                 dlog.debug('task is finished')
-            #except:
+            #except Exception:
                #dlog.debug('no job_id file')
                #dlog.debug('task restart point !!!')
                #self._submit(job_dirs, cmd, args, resources)
@@ -805,7 +805,7 @@ def check_limit(self, task_max):
     def check_status(self) :
         try:
             job_id = self._get_job_id()
-        except:
+        except Exception:
             return JobStatus.terminated
         if job_id == "" :
             raise RuntimeError("job %s is has not been submitted" % self.remote_root)

dpgen/remote/decide_machine.py

@@ -68,7 +68,7 @@ def convert_mdata(mdata, task_types=["train", "model_devi", "fp"]):
 # 						if 'command' in profile:
 # 							mdata['train_command'] = profile["command"]
 # 						continue_flag = True
-# 			except:
+# 			except Exception:
 # 				pass
 # 		if ("hostname" not in mdata["train"][0]["machine"]) or (len(mdata["train"]) == 1):
 # 			mdata["train_machine"] = mdata["train"][0]["machine"]
@@ -180,7 +180,7 @@ def convert_mdata(mdata, task_types=["train", "model_devi", "fp"]):
 # 						mdata['model_devi_command'] = profile['command']
 # 						mdata['model_devi_group_size'] = profile['group_size']
 # 						continue_flag = True
-# 			except:
+# 			except Exception:
 # 				pass
 # 		if ("hostname" not in mdata["model_devi"][0]["machine"]) or (len(mdata["model_devi"]) == 1):
 # 			mdata["model_devi_machine"] = mdata["model_devi"][0]["machine"]
@@ -263,7 +263,7 @@ def convert_mdata(mdata, task_types=["train", "model_devi", "fp"]):
 # 						mdata['fp_group_size'] = profile['group_size']
 #
 # 						continue_flag = True
-# 			except:
+# 			except Exception:
 # 				pass
 # 		if ("hostname" not in mdata["fp"][0]["machine"]) or (len(mdata["fp"]) == 1):
 # 			mdata["fp_machine"] = mdata["fp"][0]["machine"]

dpgen/remote/group_jobs.py

@@ -341,7 +341,7 @@ def group_slurm_jobs(ssh_sess,
             if not job_fin[idx] :
                 try:
                   status = rjob.check_status()
-                except:
+                except Exception:
                   ssh_sess = SSHSession(ssh_sess.remote_profile)
                   for _idx,_rjob in enumerate(job_list):
                     job_list[_idx] = SlurmJob(ssh_sess, work_path, _rjob.job_uuid)
@@ -426,5 +426,5 @@ def delete(self):
       f_path_map=self.f_path_map
       try:
          os.remove(f_path_map)
-      except:
+      except Exception:
          pass

dpgen/simplify/simplify.py

@@ -263,7 +263,7 @@ def run_model_devi(iter_index, jdata, mdata):
     # submit
     try:
         model_devi_group_size = mdata['model_devi_group_size']
-    except:
+    except Exception:
         model_devi_group_size = 1
 
     forward_files = [rest_data_name]
@@ -599,7 +599,7 @@ def run_iter(param_file, machine_file):
             'ignore', ruamel.yaml.error.MantissaNoDotYAML1_1Warning)
         jdata = loadfn(param_file)
         mdata = loadfn(machine_file)
-    except:
+    except Exception:
         with open(param_file, 'r') as fp:
             jdata = json.load(fp)
         with open(machine_file, 'r') as fp:

dpgen/tools/relabel.py

@@ -127,7 +127,7 @@ def create_init_tasks(target_folder, param_file, output, fp_json, verbose = True
                 try:                    
                     fp_params = fp_jdata['user_fp_params']
                     user_input = True
-                except:
+                except Exception:
                     fp_params = fp_jdata['fp_params']
                     user_input = False
                 make_pwscf('.', fp_params, mass_map, fp_pp_files, fp_pp_files, user_input)
@@ -240,7 +240,7 @@ def create_tasks(target_folder, param_file, output, fp_json, verbose = True, num
                 try:                    
                     fp_params = fp_jdata['user_fp_params']
                     user_input = True
-                except:
+                except Exception:
                     fp_params = fp_jdata['fp_params']
                     user_input = False
                 make_pwscf('.', fp_params, mass_map, fp_pp_files, fp_pp_files, user_input)

dpgen/tools/stat_iter.py

@@ -42,10 +42,10 @@ def stat_iter(target_folder,
             pk_id, task_dirname, OUTCAR_filename=path_doc.rsplit('/', 2) # pylint: disable=unused-variable
             try:
                 _sys = dpdata.LabeledSystem(path_doc, type_map = jdata['type_map'] )
-            except:
+            except Exception:
                 try:
                     _sys = dpdata.LabeledSystem(path_doc.replace('OUTCAR','vasprun.xml'), type_map = jdata['type_map'])
-                except:
+                except Exception:
                     _sys = dpdata.LabeledSystem()
             if len(_sys) == 1:
                 pass