Merge branch 'main' of github.com:hackingmaterials/atomate

Author: JaGeo

.circleci/config.yml

@@ -4,7 +4,7 @@ jobs:
     working_directory: ~/atomate
     docker:
       - image: materialsvirtuallab/circle-ci-pmg-py3:3.7.3
-      - image: circleci/mongo:3.4.15
+      - image: circleci/mongo:latest
     steps:
       - checkout
       - restore_cache:
@@ -37,7 +37,7 @@ jobs:
     working_directory: ~/atomate
     docker:
       - image: materialsvirtuallab/circle-ci-pmg-py3:3.7.3
-      - image: circleci/mongo:3.4.15
+      - image: circleci/mongo:latest
     steps:
       - checkout
       - restore_cache:
@@ -56,9 +56,6 @@ jobs:
             tar -zxvf vampire-5.0-linux.tar.gz
             export PATH=/root/atomate/linux/:$PATH
             pip install --quiet -r requirements.txt -r requirements-ci.txt
-            pip install git+https://github.com/materialsproject/pymatgen.git --upgrade
-            pip install git+https://github.com/materialsproject/custodian.git --upgrade
-            pip install git+https://github.com/materialsproject/fireworks.git --upgrade
             # Add executables and path.
             for EXEPATH in `pwd`/cmd_line/*/Linux_64bit; do export PATH=$PATH:$EXEPATH; done
             pip install --quiet -e .
@@ -80,5 +77,3 @@ workflows:
               branches:
                   ignore:
                       main
-
-

.pre-commit-config.yaml

@@ -2,13 +2,13 @@ repos:
   - repo: https://github.com/myint/autoflake
     rev: v1.4
     hooks:
-    - id: autoflake
-      args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
+      - id: autoflake
+        args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
 
   - repo: https://github.com/psf/black
     rev: 21.11b1
     hooks:
-    - id: black
+      - id: black
 
   - repo: https://github.com/pycqa/flake8
     rev: 4.0.1
@@ -22,3 +22,9 @@ repos:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.0
+    hooks:
+      - id: pyupgrade
+        args: [--py37-plus]

atomate/common/firetasks/tests/test_glue_tasks.py

@@ -1,19 +1,20 @@
 import os
 import unittest
 
+from fireworks import Firework, Workflow
+from fireworks.core.rocket_launcher import rapidfire
+from monty.tempfile import ScratchDir
+
 from atomate.common.firetasks.glue_tasks import (
-    PassCalcLocs,
-    get_calc_loc,
     CopyFilesFromCalcLoc,
     CreateFolder,
     DeleteFiles,
     DeleteFilesPrevFolder,
+    PassCalcLocs,
+    get_calc_loc,
 )
 from atomate.utils.testing import AtomateTest
 from atomate.vasp.firetasks.glue_tasks import CopyVaspOutputs
-from fireworks.core.firework import Firework, Workflow
-from fireworks.core.rocket_launcher import rapidfire
-from monty.tempfile import ScratchDir
 
 __author__ = "Anubhav Jain <[email protected]>"
 
@@ -194,7 +195,7 @@ def test_cleanupfiles_calc_loc(self):
 
     def test_cleanupfiles_calc_dir(self):
         # will test deleting from some folder specified by calc_dir
-        with ScratchDir(".", copy_from_current_on_enter=True) as d:
+        with ScratchDir(".", copy_from_current_on_enter=True):
             current_path = os.getcwd()
             os.mkdir("to_remove.relax0")
             os.mkdir("to_remove.relax1")

atomate/feff/firetasks/__init__.py

@@ -1,4 +1,4 @@
-from .glue_tasks import *
-from .parse_outputs import *
-from .run_calc import *
-from .write_inputs import *
+from .glue_tasks import CopyFeffOutputs
+from .parse_outputs import AddPathsToFilepadTask, SpectrumToDbTask
+from .run_calc import RunFeffDirect
+from .write_inputs import WriteEXAFSPaths, WriteFeffFromIOSet, get_feff_input_set_obj

atomate/feff/firetasks/parse_outputs.py

@@ -4,17 +4,14 @@
 from glob import glob
 
 import numpy as np
-
-from pymatgen.io.feff.inputs import Tags, Atoms
-
 from fireworks import FiretaskBase, FWAction, explicit_serialize
-from fireworks.utilities.fw_serializers import DATETIME_HANDLER
 from fireworks.user_objects.firetasks.filepad_tasks import get_fpad
+from fireworks.utilities.fw_serializers import DATETIME_HANDLER
+from pymatgen.io.feff.inputs import Atoms, Tags
 
-from atomate.utils.utils import env_chk
 from atomate.common.firetasks.glue_tasks import get_calc_loc
-from atomate.utils.utils import get_logger
 from atomate.feff.database import FeffCalcDb
+from atomate.utils.utils import env_chk, get_logger
 
 __author__ = "Kiran Mathew"
 __email__ = "[email protected]"
@@ -117,10 +114,10 @@ def run_task(self, fw_spec):
         fpad = get_fpad(self.get("filepad_file", None))
         labels = self.get("labels", None)
         for i, p in enumerate(paths):
-            l = labels[i] if labels is not None else None
+            label = labels[i] if labels is not None else None
             fpad.add_file(
                 p,
-                label=l,
+                label=label,
                 metadata=self.get("metadata", None),
                 compress=self.get("compress", True),
             )

atomate/feff/fireworks/__init__.py

@@ -1 +1 @@
-from .core import *
+from .core import EELSFW, XASFW, EXAFSPathsFW

atomate/feff/workflows/__init__.py

@@ -1,2 +1,8 @@
-from .core import *
-from .presets import *
+from .core import (
+    get_absorbing_atom_indices,
+    get_unique_site_indices,
+    get_wf_eels,
+    get_wf_exafs_paths,
+    get_wf_xas,
+)
+from .presets import wf_Xanes_K_edge

atomate/lammps/drones.py

@@ -6,13 +6,13 @@
 from datetime import datetime
 
 from pymatgen.apps.borg.hive import AbstractDrone
+from pymatgen.io.lammps.inputs import LammpsRun
+from pymatgen.io.lammps.outputs import LammpsDump
 
-# from pymatgen.io.lammps.output import LammpsLog, LammpsDump, LammpsRun
-# from pymatgen.io.lammps.sets import LammpsInputSet
+from atomate.utils.utils import get_logger, get_uri
 
-from atomate.utils.utils import get_uri
+# from pymatgen.io.lammps.output import LammpsLog, LammpsDump
 
-from atomate.utils.utils import get_logger
 
 __author__ = "Brandon Wood, Kiran Mathew"
 __email__ = "[email protected]"
@@ -154,7 +154,7 @@ def generate_doc(self, dir_name, lmps_input, log, dumps):
             }
             return d
 
-        except:
+        except Exception:
             import traceback
 
             logger.error(traceback.format_exc())

atomate/lammps/firetasks/__init__.py

@@ -1,4 +1,4 @@
-# from .write_inputs import *
-# from .run_calc import *
-# from .parse_outputs import *
-# from .glue_tasks import *
+# from .glue_tasks import CopyPackmolOutputs
+# from .parse_outputs import LammpsToDB
+# from .run_calc import RunLammpsDirect, RunLammpsFake, RunPackmol
+# from .write_inputs import WriteInputFromForceFieldAndTopology, WriteInputFromIOSet

atomate/lammps/firetasks/run_calc.py

@@ -5,9 +5,8 @@
 import os
 import shutil
 
-# from pymatgen.io.lammps.utils import PackmolRunner, LammpsRunner
-
-from fireworks import explicit_serialize, FiretaskBase, FWAction
+from fireworks import FiretaskBase, FWAction, explicit_serialize
+from pymatgen.io.lammps.utils import LammpsRunner, PackmolRunner
 
 from atomate.utils.utils import get_logger