Blackified code

mala/__init__.py

@@ -6,17 +6,43 @@
 """
 
 from .version import __version__
-from .common import Parameters, printout, check_modules, get_size, get_rank, \
-    finalize
-from .descriptors import Bispectrum, Descriptor, AtomicDensity, \
-    MinterpyDescriptors
-from .datahandling import DataHandler, DataScaler, DataConverter, Snapshot, \
-    DataShuffler
-from .network import Network, Tester, Trainer, HyperOpt, \
-    HyperOptOptuna, HyperOptNASWOT, HyperOptOAT, Predictor, \
-    HyperparameterOAT, HyperparameterNASWOT, HyperparameterOptuna, \
-    HyperparameterACSD, ACSDAnalyzer, Runner
-from .targets import LDOS, DOS, Density, fermi_function, \
-    AtomicForce, Target
+from .common import (
+    Parameters,
+    printout,
+    check_modules,
+    get_size,
+    get_rank,
+    finalize,
+)
+from .descriptors import (
+    Bispectrum,
+    Descriptor,
+    AtomicDensity,
+    MinterpyDescriptors,
+)
+from .datahandling import (
+    DataHandler,
+    DataScaler,
+    DataConverter,
+    Snapshot,
+    DataShuffler,
+)
+from .network import (
+    Network,
+    Tester,
+    Trainer,
+    HyperOpt,
+    HyperOptOptuna,
+    HyperOptNASWOT,
+    HyperOptOAT,
+    Predictor,
+    HyperparameterOAT,
+    HyperparameterNASWOT,
+    HyperparameterOptuna,
+    HyperparameterACSD,
+    ACSDAnalyzer,
+    Runner,
+)
+from .targets import LDOS, DOS, Density, fermi_function, AtomicForce, Target
 from .interfaces import MALA
 from .datageneration import TrajectoryAnalyzer, OFDFTInitializer

mala/common/__init__.py

@@ -1,4 +1,5 @@
 """General functions for MALA, such as parameters."""
+
 from .parameters import Parameters
 from .parallelizer import printout, get_rank, get_size, finalize
 from .check_modules import check_modules

mala/common/check_modules.py

@@ -1,42 +1,65 @@
 """Function to check module availability in MALA."""
+
 import importlib
 
 
 def check_modules():
     """Check whether/which optional modules MALA can access."""
     # The optional libs in MALA.
     optional_libs = {
-        "mpi4py": {"available": False, "description":
-                   "Enables inference parallelization."},
-        "horovod": {"available": False, "description":
-                    "Enables training parallelization."},
-        "lammps": {"available": False, "description":
-                   "Enables descriptor calculation for data preprocessing "
-                   "and inference."},
-        "oapackage": {"available": False, "description":
-                      "Enables usage of OAT method for hyperparameter "
-                      "optimization."},
-        "total_energy": {"available": False, "description":
-                         "Enables calculation of total energy."},
-        "asap3": {"available": False, "description":
-                  "Enables trajectory analysis."},
-        "dftpy": {"available": False, "description":
-                  "Enables OF-DFT-MD initialization."},
-        "minterpy": {"available": False, "description":
-            "Enables minterpy descriptor calculation for data preprocessing."}
+        "mpi4py": {
+            "available": False,
+            "description": "Enables inference parallelization.",
+        },
+        "horovod": {
+            "available": False,
+            "description": "Enables training parallelization.",
+        },
+        "lammps": {
+            "available": False,
+            "description": "Enables descriptor calculation for data preprocessing "
+            "and inference.",
+        },
+        "oapackage": {
+            "available": False,
+            "description": "Enables usage of OAT method for hyperparameter "
+            "optimization.",
+        },
+        "total_energy": {
+            "available": False,
+            "description": "Enables calculation of total energy.",
+        },
+        "asap3": {
+            "available": False,
+            "description": "Enables trajectory analysis.",
+        },
+        "dftpy": {
+            "available": False,
+            "description": "Enables OF-DFT-MD initialization.",
+        },
+        "minterpy": {
+            "available": False,
+            "description": "Enables minterpy descriptor calculation for data preprocessing.",
+        },
     }
 
     # Find out if libs are available.
     for lib in optional_libs:
-        optional_libs[lib]["available"] = importlib.util.find_spec(lib) \
-                                          is not None
+        optional_libs[lib]["available"] = (
+            importlib.util.find_spec(lib) is not None
+        )
 
     # Print info about libs.
     print("The following optional modules are available in MALA:")
     for lib in optional_libs:
-        available_string = "installed" if optional_libs[lib]["available"] \
-            else "not installed"
-        print("{0}: \t {1} \t {2}".format(lib, available_string,
-                                          optional_libs[lib]["description"]))
-        optional_libs[lib]["available"] = \
+        available_string = (
+            "installed" if optional_libs[lib]["available"] else "not installed"
+        )
+        print(
+            "{0}: \t {1} \t {2}".format(
+                lib, available_string, optional_libs[lib]["description"]
+            )
+        )
+        optional_libs[lib]["available"] = (
             importlib.util.find_spec(lib) is not None
+        )

mala/common/json_serializable.py

@@ -48,14 +48,14 @@ def from_json(cls, json_dict):
 
     def _standard_serializer(self):
         data = {}
-        members = inspect.getmembers(self,
-                                     lambda a: not (inspect.isroutine(a)))
+        members = inspect.getmembers(
+            self, lambda a: not (inspect.isroutine(a))
+        )
         for member in members:
             # Filter out all private members, builtins, etc.
             if member[0][0] != "_":
                 data[member[0]] = member[1]
-        json_dict = {"object": type(self).__name__,
-                     "data": data}
+        json_dict = {"object": type(self).__name__, "data": data}
         return json_dict
 
     @classmethod

mala/common/parallelizer.py

@@ -1,4 +1,5 @@
 """Functions for operating MALA in parallel."""
+
 from collections import defaultdict
 import platform
 import warnings
@@ -46,8 +47,10 @@ def set_horovod_status(new_value):
 
     """
     if use_mpi is True and new_value is True:
-        raise Exception("Cannot use horovod and inference-level MPI at "
-                        "the same time yet.")
+        raise Exception(
+            "Cannot use horovod and inference-level MPI at "
+            "the same time yet."
+        )
     global use_horovod
     use_horovod = new_value
 
@@ -66,8 +69,10 @@ def set_mpi_status(new_value):
 
     """
     if use_horovod is True and new_value is True:
-        raise Exception("Cannot use horovod and inference-level MPI at "
-                        "the same time yet.")
+        raise Exception(
+            "Cannot use horovod and inference-level MPI at "
+            "the same time yet."
+        )
     global use_mpi
     use_mpi = new_value
     if use_mpi:
@@ -96,6 +101,7 @@ def set_lammps_instance(new_instance):
 
     """
     import lammps
+
     global lammps_instance
     if isinstance(new_instance, lammps.core.lammps):
         lammps_instance = new_instance
@@ -162,7 +168,7 @@ def get_local_rank():
             ranks_nodes = comm.allgather((comm.Get_rank(), this_node))
             node2rankssofar = defaultdict(int)
             local_rank = None
-            for (rank, node) in ranks_nodes:
+            for rank, node in ranks_nodes:
                 if rank == comm.Get_rank():
                     local_rank = node2rankssofar[node]
                 node2rankssofar[node] += 1
@@ -204,13 +210,13 @@ def get_comm():
 def barrier():
     """General interface for a barrier."""
     if use_horovod:
-        hvd.allreduce(torch.tensor(0), name='barrier')
+        hvd.allreduce(torch.tensor(0), name="barrier")
     if use_mpi:
         comm.Barrier()
     return
 
 
-def printout(*values, sep=' ', min_verbosity=0):
+def printout(*values, sep=" ", min_verbosity=0):
     """
     Interface to built-in "print" for parallel runs. Can be used like print.