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

Author: JaGeo

.pre-commit-config.yaml

@@ -4,17 +4,20 @@ repos:
     hooks:
     - id: autoflake
       args: [--in-place, --remove-all-unused-imports, --remove-unused-variable, --ignore-init-module-imports]
+
   - repo: https://github.com/psf/black
-    rev: 21.4b2
+    rev: 21.11b1
     hooks:
     - id: black
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.4
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 4.0.1
     hooks:
       - id: flake8
         args: [--max-line-length=125]
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.0.1
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer

atomate/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.1"

atomate/common/__init__.py

@@ -1 +1 @@
-__author__ = 'Anubhav Jain <[email protected]>'
+__author__ = "Anubhav Jain <[email protected]>"

atomate/common/firetasks/__init__.py

@@ -1 +1 @@
-__author__ = 'Anubhav Jain <[email protected]>'
+__author__ = "Anubhav Jain <[email protected]>"

atomate/common/firetasks/parse_outputs.py

@@ -1,11 +1,10 @@
 import json
 import os
 
-from fireworks import explicit_serialize, FiretaskBase, FWAction
-from fireworks.utilities.fw_serializers import DATETIME_HANDLER
-
-from atomate.utils.utils import env_chk, get_logger, load_class
 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
 
 __author__ = "Shyam Dwaraknath <[email protected]>, Anubhav Jain <[email protected]>"
 
@@ -53,9 +52,7 @@ def run_task(self, fw_spec):
 
         # parse the calc directory
         logger.info(
-            "PARSING DIRECTORY: {} USING DRONE: {}".format(
-                calc_dir, self["drone"].__class__.__name__
-            )
+            f"PARSING DIRECTORY: {calc_dir} USING DRONE: {self['drone'].__class__.__name__}"
         )
         # get the database connection
         db_file = env_chk(self.get("db_file"), fw_spec)

atomate/common/firetasks/tests/__init__.py

@@ -1 +1 @@
-__author__ = 'Anubhav Jain <[email protected]>'
+__author__ = "Anubhav Jain <[email protected]>"

atomate/common/powerups.py

@@ -5,7 +5,7 @@
 from typing import List
 
 from atomate.utils.utils import get_fws_and_tasks
-from fireworks import Workflow, FileWriteTask
+from fireworks import FileWriteTask, Workflow
 from fireworks.utilities.fw_utilities import get_slug
 
 __author__ = "Janine George, Guido Petretto, Ryan Kingsbury"
@@ -86,21 +86,23 @@ def add_tags(original_wf, tags_list):
     return original_wf
 
 
-def add_namefile(original_wf, use_slug=True):
+def add_namefile(original_wf: Workflow, use_slug: bool = True) -> Workflow:
     """
     Every FireWork begins by writing an empty file with the name
-    "FW--<fw.name>". This makes it easy to figure out what jobs are in what
-    launcher directories, e.g. "ls -l launch*/FW--*" from within a "block" dir.
+    "FW--<fw.name>-<fw.fw_id>". This makes it easy to figure out what jobs are
+    in what launcher directories, e.g. "ls -l launch*/FW--*" from within a
+    "block" dir.
 
     Args:
         original_wf (Workflow)
-        use_slug (bool): whether to replace whitespace-type chars with a slug
+        use_slug (bool): whether to replace whitespace-type chars with a slug.
+            Defaults to True.
 
     Returns:
        Workflow
     """
     for idx, fw in enumerate(original_wf.fws):
-        fname = f"FW--{fw.name}"
+        fname = f"FW--{fw.name}-{fw.fw_id}"
         if use_slug:
             fname = get_slug(fname)
 

atomate/feff/firetasks/__init__.py

@@ -1,4 +1,3 @@
-
 from .glue_tasks import *
 from .parse_outputs import *
 from .run_calc import *

atomate/feff/fireworks/__init__.py

@@ -1,2 +1 @@
-
 from .core import *

atomate/feff/fireworks/core.py

@@ -33,7 +33,7 @@ def __init__(
         db_file=None,
         parents=None,
         metadata=None,
-        **kwargs
+        **kwargs,
     ):
         """
         Write the input set for FEFF-XAS spectroscopy, run FEFF and insert the absorption
@@ -63,7 +63,7 @@ def __init__(
             structure,
             edge=edge,
             radius=radius,
-            **override_default_feff_params
+            **override_default_feff_params,
         )
         spectrum_type = feff_input_set.__class__.__name__[2:-3]
 
@@ -90,8 +90,8 @@ def __init__(
         super().__init__(
             t,
             parents=parents,
-            name="{}-{}".format(structure.composition.reduced_formula, name),
-            **kwargs
+            name=f"{structure.composition.reduced_formula}-{name}",
+            **kwargs,
         )
 
 
@@ -114,7 +114,7 @@ def __init__(
         db_file=None,
         parents=None,
         metadata=None,
-        **kwargs
+        **kwargs,
     ):
         """
         Write the input set for FEFF-EELSS spectroscopy, run feff and insert the core-loss spectrum
@@ -154,7 +154,7 @@ def __init__(
             collection_angle,
             convergence_angle,
             user_eels_settings=user_eels_settings,
-            **override_default_feff_params
+            **override_default_feff_params,
         )
         spectrum_type = feff_input_set.__class__.__name__[2:-3]
 
@@ -181,8 +181,8 @@ def __init__(
         super().__init__(
             t,
             parents=parents,
-            name="{}-{}".format(structure.composition.reduced_formula, name),
-            **kwargs
+            name=f"{structure.composition.reduced_formula}-{name}",
+            **kwargs,
         )
 
 
@@ -203,7 +203,7 @@ def __init__(
         filepad_file=None,
         labels=None,
         metadata=None,
-        **kwargs
+        **kwargs,
     ):
         """
         Write the input set for FEFF-EXAFS spectroscopy with customized scattering paths, run feff,
@@ -237,7 +237,7 @@ def __init__(
             structure,
             edge=edge,
             radius=radius,
-            **override_default_feff_params
+            **override_default_feff_params,
         )
 
         t = [
@@ -260,6 +260,6 @@ def __init__(
         super().__init__(
             t,
             parents=parents,
-            name="{}-{}".format(structure.composition.reduced_formula, name),
-            **kwargs
+            name=f"{structure.composition.reduced_formula}-{name}",
+            **kwargs,
         )