pre-commit run black -a

janosh · janosh · commit 0d1203d0c64c · 2021-12-02T11:11:13.000Z
diff --git a/atomate/__init__.py b/atomate/__init__.py
@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.1"
diff --git a/atomate/common/__init__.py b/atomate/common/__init__.py
@@ -1 +1 @@
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
diff --git a/atomate/common/firetasks/__init__.py b/atomate/common/firetasks/__init__.py
@@ -1 +1 @@
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
diff --git a/atomate/common/firetasks/parse_outputs.py b/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 <shyamd@lbl.gov>, Anubhav Jain <ajain@lbl.gov>"
 
@@ -53,7 +52,7 @@ def run_task(self, fw_spec):
 
         # parse the calc directory
         logger.info(
-            f"PARSING DIRECTORY: {calc_dir} USING DRONE: {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)
diff --git a/atomate/common/firetasks/tests/__init__.py b/atomate/common/firetasks/tests/__init__.py
@@ -1 +1 @@
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
diff --git a/atomate/lammps/__init__.py b/atomate/lammps/__init__.py
@@ -1 +1 @@
-__author__ = 'Kiran Mathew'
+__author__ = "Kiran Mathew"
diff --git a/atomate/qchem/test_files/FF_before_run/orig/test_cust.py b/atomate/qchem/test_files/FF_before_run/orig/test_cust.py
@@ -5,10 +5,17 @@
 my_input = "test.qin"
 my_output = "test.qout"
 
-myjob = QCJob.opt_with_frequency_flattener(qchem_command="qchem -slurm",multimode="openmp",input_file=my_input,output_file=my_output,max_iterations=10,max_molecule_perturb_scale=0.3,max_cores=12)
-myhandler = QChemErrorHandler(input_file=my_input,output_file=my_output)
+myjob = QCJob.opt_with_frequency_flattener(
+    qchem_command="qchem -slurm",
+    multimode="openmp",
+    input_file=my_input,
+    output_file=my_output,
+    max_iterations=10,
+    max_molecule_perturb_scale=0.3,
+    max_cores=12,
+)
+myhandler = QChemErrorHandler(input_file=my_input, output_file=my_output)
 
-c = Custodian([myhandler],myjob,max_errors_per_job=10,max_errors=10)
+c = Custodian([myhandler], myjob, max_errors_per_job=10, max_errors=10)
 
 c.run()
-
diff --git a/atomate/qchem/test_files/FF_before_run/test_cust.py b/atomate/qchem/test_files/FF_before_run/test_cust.py
@@ -5,10 +5,17 @@
 my_input = "test.qin"
 my_output = "test.qout"
 
-myjob = QCJob.opt_with_frequency_flattener(qchem_command="qchem -slurm",multimode="openmp",input_file=my_input,output_file=my_output,max_iterations=10,max_molecule_perturb_scale=0.3,max_cores=12)
-myhandler = QChemErrorHandler(input_file=my_input,output_file=my_output)
+myjob = QCJob.opt_with_frequency_flattener(
+    qchem_command="qchem -slurm",
+    multimode="openmp",
+    input_file=my_input,
+    output_file=my_output,
+    max_iterations=10,
+    max_molecule_perturb_scale=0.3,
+    max_cores=12,
+)
+myhandler = QChemErrorHandler(input_file=my_input, output_file=my_output)
 
-c = Custodian([myhandler],myjob,max_errors_per_job=10,max_errors=10)
+c = Custodian([myhandler], myjob, max_errors_per_job=10, max_errors=10)
 
 c.run()
-
diff --git a/atomate/qchem/test_files/FF_working/test_cust.py b/atomate/qchem/test_files/FF_working/test_cust.py
@@ -5,10 +5,17 @@
 my_input = "test.qin"
 my_output = "test.qout"
 
-myjob = QCJob.opt_with_frequency_flattener(qchem_command="qchem -slurm",multimode="openmp",input_file=my_input,output_file=my_output,max_iterations=10,max_molecule_perturb_scale=0.3,max_cores=12)
-myhandler = QChemErrorHandler(input_file=my_input,output_file=my_output)
+myjob = QCJob.opt_with_frequency_flattener(
+    qchem_command="qchem -slurm",
+    multimode="openmp",
+    input_file=my_input,
+    output_file=my_output,
+    max_iterations=10,
+    max_molecule_perturb_scale=0.3,
+    max_cores=12,
+)
+myhandler = QChemErrorHandler(input_file=my_input, output_file=my_output)
 
-c = Custodian([myhandler],myjob,max_errors_per_job=10,max_errors=10)
+c = Custodian([myhandler], myjob, max_errors_per_job=10, max_errors=10)
 
 c.run()
-
diff --git a/atomate/qchem/test_files/real_run/test_cust.py b/atomate/qchem/test_files/real_run/test_cust.py
@@ -5,10 +5,15 @@
 my_input = "mol.qin"
 my_output = "mol.qout"
 
-myjob = QCJob(qchem_command="qchem -slurm",multimode="openmp",input_file=my_input,output_file=my_output,max_cores=12)
-myhandler = QChemErrorHandler(input_file=my_input,output_file=my_output)
+myjob = QCJob(
+    qchem_command="qchem -slurm",
+    multimode="openmp",
+    input_file=my_input,
+    output_file=my_output,
+    max_cores=12,
+)
+myhandler = QChemErrorHandler(input_file=my_input, output_file=my_output)
 
-c = Custodian([myhandler],[myjob],max_errors_per_job=10,max_errors=10)
+c = Custodian([myhandler], [myjob], max_errors_per_job=10, max_errors=10)
 
 c.run()
-
diff --git a/atomate/utils/__init__.py b/atomate/utils/__init__.py
@@ -1 +1 @@
-__author__ = 'ajain'
+__author__ = "ajain"
diff --git a/atomate/utils/tests/__init__.py b/atomate/utils/tests/__init__.py
@@ -1 +1 @@
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
diff --git a/atomate/vasp/__init__.py b/atomate/vasp/__init__.py
@@ -1 +1 @@
-__author__ = 'ajain'
+__author__ = "ajain"
diff --git a/atomate/vasp/builders/dielectric.py b/atomate/vasp/builders/dielectric.py
@@ -4,11 +4,10 @@
 
 logger = get_logger(__name__)
 
-__author__ = 'Shyue Ping Ong <ongsp@uscd.edu>, Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Shyue Ping Ong <ongsp@uscd.edu>, Anubhav Jain <ajain@lbl.gov>"
 
 
 class DielectricBuilder:
-
     def __init__(self, materials_write):
         """
         Starting with an existing materials collection, adds some averages and
@@ -21,9 +20,14 @@ def __init__(self, materials_write):
 
     def run(self):
         logger.info("EpsilonBuilder starting...")
-        q = {"dielectric": {"$exists": True}, "dielectric.eps_ionic_avg": {"$exists": False}}
-
-        for m in tqdm(self._materials.find(q, projection=["material_id", "dielectric"])):
+        q = {
+            "dielectric": {"$exists": True},
+            "dielectric.eps_ionic_avg": {"$exists": False},
+        }
+
+        for m in tqdm(
+            self._materials.find(q, projection=["material_id", "dielectric"])
+        ):
             try:
                 eps = m["dielectric"]
                 d = {}
@@ -32,25 +36,33 @@ def run(self):
 
                 d["dielectric.epsilon_ionic_avg"] = float(np.average(eig_ionic))
                 d["dielectric.epsilon_static_avg"] = float(np.average(eig_static))
-                d["dielectric.epsilon_avg"] = d["dielectric.epsilon_ionic_avg"] + \
-                                              d["dielectric.epsilon_static_avg"]
-                d["dielectric.has_neg_eps"] = bool(np.any(eig_ionic < -0.1) or
-                                                   np.any(eig_static < -0.1))
-
-                self._materials.update_one({"material_id": m["material_id"]}, {"$set": d})
-
-            except:
+                d["dielectric.epsilon_avg"] = (
+                    d["dielectric.epsilon_ionic_avg"]
+                    + d["dielectric.epsilon_static_avg"]
+                )
+                d["dielectric.has_neg_eps"] = bool(
+                    np.any(eig_ionic < -0.1) or np.any(eig_static < -0.1)
+                )
+
+                self._materials.update_one(
+                    {"material_id": m["material_id"]}, {"$set": d}
+                )
+
+            except Exception:
                 import traceback
+
                 logger.exception(traceback.format_exc())
 
         logger.info("EpsilonBuilder finished processing.")
 
     def reset(self):
         logger.info("Resetting EpsilonBuilder")
-        keys = ["dielectric.epsilon_ionic_avg",
-                "dielectric.epsilon_static_avg",
-                "dielectric.epsilon_avg",
-                "dielectric.has_neg_eps"]
+        keys = [
+            "dielectric.epsilon_ionic_avg",
+            "dielectric.epsilon_static_avg",
+            "dielectric.epsilon_avg",
+            "dielectric.has_neg_eps",
+        ]
 
         self._materials.update_many({}, {"$unset": {k: "" for k in keys}})
         logger.info("Finished resetting EpsilonBuilder")
diff --git a/atomate/vasp/builders/examples/run_builders.py b/atomate/vasp/builders/examples/run_builders.py
@@ -9,21 +9,29 @@
 from atomate.vasp.builders.dielectric import DielectricBuilder
 from atomate.vasp.builders.fix_tasks import FixTasksBuilder
 from atomate.vasp.builders.materials_descriptor import MaterialsDescriptorBuilder
-from atomate.vasp.builders.materials_ehull import MaterialsEhullBuilder
+from atomate.vasp.builders.materials_ehull import MaterialsEhullBuilder  # noqa: F401
 from atomate.vasp.builders.tags import TagsBuilder
 from atomate.vasp.builders.tasks_materials import TasksMaterialsBuilder
 
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
 
 module_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
 
 if __name__ == "__main__":
 
-    dbfile = os.path.join(module_dir, "db.json")  # make sure to modify w/your db details
-
-    build_sequence = [FixTasksBuilder, TasksMaterialsBuilder, TagsBuilder,
-                      MaterialsDescriptorBuilder, BandgapEstimationBuilder, DielectricBuilder,
-                      BoltztrapMaterialsBuilder]
+    dbfile = os.path.join(
+        module_dir, "db.json"
+    )  # make sure to modify w/your db details
+
+    build_sequence = [
+        FixTasksBuilder,
+        TasksMaterialsBuilder,
+        TagsBuilder,
+        MaterialsDescriptorBuilder,
+        BandgapEstimationBuilder,
+        DielectricBuilder,
+        BoltztrapMaterialsBuilder,
+    ]
     for cls in build_sequence:
         b = cls.from_file(dbfile)
         # b.reset()  # uncomment if you want to start a builder from scratch!
@@ -33,4 +41,4 @@
 
     # mapi_key = None  # Replace with your Materials API key!
     # ehull_builder = MaterialsEhullBuilder.from_file(dbfile, mapi_key=mapi_key)
-    # ehull_builder.run()
+    # ehull_builder.run()
diff --git a/atomate/vasp/builders/materials_descriptor.py b/atomate/vasp/builders/materials_descriptor.py
@@ -10,15 +10,15 @@
 
 logger = get_logger(__name__)
 
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
 
 
 class MaterialsDescriptorBuilder(AbstractBuilder):
     def __init__(self, materials_write, update_all=False):
         """
         Starting with an existing materials collection, adds some compositional and structural
         descriptors.
-        
+
         Args:
             materials_write: mongodb collection for materials (write access needed)
             update_all: (bool) - if true, updates all docs. If false, updates incrementally
@@ -38,7 +38,7 @@ def run(self):
 
         pbar = tqdm(mats)
         for m in pbar:
-            pbar.set_description("Processing materials_id: {}".format(m['material_id']))
+            pbar.set_description("Processing materials_id: {}".format(m["material_id"]))
             struct = Structure.from_dict(m["structure"])
             d = {"descriptors": {}}
             d["descriptors"]["dimensionality"] = get_dimensionality(struct)
@@ -55,7 +55,11 @@ def reset(self):
         logger.info("Finished resetting MaterialsDescriptorBuilder")
 
     def _build_indexes(self):
-        for i in ["descriptors.dimensionality", "descriptors.density", "descriptors.nsites"]:
+        for i in [
+            "descriptors.dimensionality",
+            "descriptors.density",
+            "descriptors.nsites",
+        ]:
             self._materials.create_index(i)
 
     @classmethod
@@ -69,4 +73,4 @@ def from_file(cls, db_file, m="materials", **kwargs):
             **kwargs: other parameters to feed into the builder
         """
         db_write = get_database(db_file, admin=True)
-        return cls(db_write[m], **kwargs)
+        return cls(db_write[m], **kwargs)
diff --git a/atomate/vasp/firetasks/exchange.py b/atomate/vasp/firetasks/exchange.py
@@ -5,13 +5,8 @@
 from atomate.utils.utils import get_logger, env_chk
 from atomate.vasp.database import VaspCalcDb
 
-from datetime import datetime
-import numpy as np
 
-from pymatgen.core import Structure
-from pymatgen.command_line.bader_caller import bader_analysis_from_path
 from pymatgen.analysis.magnetism.heisenberg import HeisenbergMapper, HeisenbergModel
-from pymatgen.analysis.magnetism import CollinearMagneticStructureAnalyzer, Ordering
 from pymatgen.command_line.vampire_caller import VampireCaller
 
 __author__ = "Nathan C. Frey"
@@ -26,7 +21,7 @@ class HeisenbergModelMapping(FiretaskBase):
     Map structures and energies to a Heisenberg model and compute exchange
     parameters for a given NN cutoff.
 
-    * heisenberg_settings: 
+    * heisenberg_settings:
         cutoff (float): Starting point for nearest neighbor search.
         tol (float): Tolerance for equivalent NN bonds.
 
@@ -35,7 +30,7 @@ class HeisenbergModelMapping(FiretaskBase):
         energies (list): Energies / atom (eV).
 
     Optional parameters:
-        heisenberg_settings (dict): A config dict for Heisenberg model 
+        heisenberg_settings (dict): A config dict for Heisenberg model
             mapping, detailed above.
 
     """
@@ -122,7 +117,7 @@ class HeisenbergConvergence(FiretaskBase):
     """
     Quick check to see if the Heisenberg model has "converged" for any
     particular nearest neighbor cutoff value in the sense that |J_ij| < |E_0|
-    for all i, j. 
+    for all i, j.
 
     If not, it doesn't make sense to do Monte Carlo and the system is either
     1) not well described by the Heisenberg Model (perhaps the magnetic
diff --git a/atomate/vasp/tests/__init__.py b/atomate/vasp/tests/__init__.py
@@ -1 +1 @@
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
diff --git a/atomate/vasp/vasp_config.py b/atomate/vasp/vasp_config.py
@@ -1,5 +1,6 @@
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
 
 import warnings
+
 warnings.warn("vasp_config renamed to config.")
-from .config import *
+from .config import *  # noqa: F401, F403, E402
diff --git a/atomate/vasp/workflows/base/__init__.py b/atomate/vasp/workflows/base/__init__.py
@@ -1 +1 @@
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
diff --git a/atomate/vasp/workflows/presets/__init__.py b/atomate/vasp/workflows/presets/__init__.py
@@ -1 +1 @@
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
diff --git a/atomate/vasp/workflows/tests/__init__.py b/atomate/vasp/workflows/tests/__init__.py
@@ -1 +1 @@
-__author__ = 'Anubhav Jain <ajain@lbl.gov>'
+__author__ = "Anubhav Jain <ajain@lbl.gov>"
diff --git a/dev_scripts/gibbs.py b/dev_scripts/gibbs.py
diff --git a/docs_rst/conf.py b/docs_rst/conf.py
diff --git a/scripts/atwf b/scripts/atwf
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-__version__ = "1.0.1"`
	`1`	`+__version__ = "1.0.1"`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-__author__ = 'Anubhav Jain <[email protected]>'`
	`1`	`+__author__ = "Anubhav Jain <[email protected]>"`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-__author__ = 'Kiran Mathew'`
	`1`	`+__author__ = "Kiran Mathew"`