Merge pull request #732 from janosh/isort

Sort imports

Author: itsduowang

.pre-commit-config.yaml

@@ -28,3 +28,8 @@ repos:
     hooks:
       - id: pyupgrade
         args: [--py37-plus]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort

atomate/common/firetasks/glue_tasks.py

@@ -1,13 +1,13 @@
+import glob
 import os
-import monty
 import shutil
-import glob
 
-from fireworks import explicit_serialize, FiretaskBase, FWAction
+import monty
+from fireworks import FiretaskBase, FWAction, explicit_serialize
+from monty.shutil import copy_r, gzip_dir
 
-from atomate.utils.utils import env_chk, load_class, recursive_get_result
 from atomate.utils.fileio import FileClient
-from monty.shutil import copy_r, gzip_dir
+from atomate.utils.utils import env_chk, load_class, recursive_get_result
 
 __author__ = "Anubhav Jain"
 __email__ = "[email protected]"
@@ -377,7 +377,7 @@ def copy_files(self):
             try:
                 self.fileclient.copy(prev_path_full, dest_path)
             except FileNotFoundError as exc:
-                if continue_on_missing:
+                if self.continue_on_missing:
                     continue
                 else:
                     raise exc

atomate/common/firetasks/parse_outputs.py

@@ -1,11 +1,12 @@
 import json
 import os
 
-from atomate.common.firetasks.glue_tasks import get_calc_loc
-from atomate.utils.utils import env_chk, get_logger, load_class
 from fireworks import FiretaskBase, FWAction, explicit_serialize
 from fireworks.utilities.fw_serializers import DATETIME_HANDLER
 
+from atomate.common.firetasks.glue_tasks import get_calc_loc
+from atomate.utils.utils import env_chk, get_logger, load_class
+
 __author__ = "Shyam Dwaraknath <[email protected]>, Anubhav Jain <[email protected]>"
 
 logger = get_logger(__name__)

atomate/common/firetasks/run_calc.py

@@ -2,8 +2,7 @@
 import subprocess
 
 from custodian import Custodian
-
-from fireworks import explicit_serialize, FiretaskBase
+from fireworks import FiretaskBase, explicit_serialize
 
 from atomate.utils.utils import env_chk, get_logger
 

atomate/common/firetasks/tests/test_parse_outputs.py

@@ -3,7 +3,6 @@
 
 from fireworks import Firework, Workflow
 from fireworks.core.rocket_launcher import rapidfire
-
 from pymatgen.apps.borg.hive import AbstractDrone
 
 from atomate.common.firetasks.parse_outputs import ToDbTask

atomate/common/powerups.py

@@ -4,10 +4,11 @@
 from importlib import import_module
 from typing import List
 
-from atomate.utils.utils import get_fws_and_tasks
 from fireworks import FileWriteTask, Workflow
 from fireworks.utilities.fw_utilities import get_slug
 
+from atomate.utils.utils import get_fws_and_tasks
+
 __author__ = "Janine George, Guido Petretto, Ryan Kingsbury"
 __email__ = (
     "[email protected], [email protected], [email protected]"

atomate/common/tests/test_powerups.py

@@ -1,20 +1,19 @@
 import unittest
 
-from atomate.utils.utils import get_fws_and_tasks
-from atomate.vasp.workflows.base.core import get_wf
-
+from fireworks import Firework, ScriptTask, Workflow
 from pymatgen.io.vasp.sets import MPRelaxSet
 from pymatgen.util.testing import PymatgenTest
 
 from atomate.common.powerups import (
-    set_queue_adapter,
+    add_additional_fields_to_taskdocs,
+    add_metadata,
     add_priority,
     add_tags,
     powerup_by_kwargs,
-    add_additional_fields_to_taskdocs,
-    add_metadata,
+    set_queue_adapter,
 )
-from fireworks import Firework, ScriptTask, Workflow
+from atomate.utils.utils import get_fws_and_tasks
+from atomate.vasp.workflows.base.core import get_wf
 
 __author__ = "Janine George, Guido Petretto"
 __email__ = "[email protected]"

atomate/feff/firetasks/glue_tasks.py

@@ -1,6 +1,6 @@
 from fireworks import explicit_serialize
 
-from atomate.common.firetasks.glue_tasks import get_calc_loc, CopyFiles
+from atomate.common.firetasks.glue_tasks import CopyFiles, get_calc_loc
 
 __author__ = "Kiran Mathew"
 __email__ = "[email protected]"

atomate/feff/firetasks/run_calc.py

@@ -4,7 +4,7 @@
 
 import subprocess
 
-from fireworks import explicit_serialize, FiretaskBase
+from fireworks import FiretaskBase, explicit_serialize
 
 from atomate.utils.utils import env_chk, get_logger
 

atomate/feff/firetasks/tests/test_tasks.py

@@ -3,8 +3,8 @@
 from glob import glob
 
 from pymatgen.core import Structure
-from pymatgen.io.feff.sets import MPEXAFSSet
 from pymatgen.io.feff.inputs import Paths
+from pymatgen.io.feff.sets import MPEXAFSSet
 
 from atomate.feff.firetasks.glue_tasks import CopyFeffOutputs
 from atomate.feff.firetasks.write_inputs import WriteEXAFSPaths