Merge pull request #142 from Lnaden/yapf

Yapf, isort, some LGTM

.yapfignore

@@ -0,0 +1,2 @@
+# Generated files
+*/_version.py

qcengine/cli.py

@@ -6,10 +6,10 @@
 import os.path
 import sys
 
-from . import compute, compute_procedure  # run and run-procedure
 from qcelemental.models import ResultInput  # run and run-procedure
-from . import __version__, list_all_procedures, list_all_programs, list_available_procedures, \
-    list_available_programs, get_procedure, get_program  # info
+
+from . import (__version__, compute, compute_procedure, get_procedure, get_program,  # run and run-procedure; info
+               list_all_procedures, list_all_programs, list_available_procedures, list_available_programs)
 from .config import global_repr  # info
 
 __all__ = ["main"]
@@ -22,24 +22,31 @@ def parse_args():
     subparsers = parser.add_subparsers(dest="command")
 
     info = subparsers.add_parser('info', help="Print information about QCEngine setup, version, and environment.")
-    info.add_argument("category", nargs="*", default="all",
+    info.add_argument("category",
+                      nargs="*",
+                      default="all",
                       choices=["version", "programs", "procedures", "config", "all"],
                       help="The information categories to show.")
 
     run = subparsers.add_parser('run', help="Run a program on a given task. Output is printed as a JSON blob.")
     run.add_argument('program', type=str, help="The program to run.")
-    run.add_argument('data', type=str, help="Data describing the task to run. "
-                                            "One of: (i) A JSON blob, "
-                                            "(ii) A file name, "
-                                            "(iii) '-', indicating data will be read from STDIN.")
-
-    run_procedure = subparsers.add_parser('run-procedure', help="Run a procedure on a given task. "
-                                                                "Output is printed as a JSON blob.")
+    run.add_argument('data',
+                     type=str,
+                     help="Data describing the task to run. "
+                     "One of: (i) A JSON blob, "
+                     "(ii) A file name, "
+                     "(iii) '-', indicating data will be read from STDIN.")
+
+    run_procedure = subparsers.add_parser('run-procedure',
+                                          help="Run a procedure on a given task. "
+                                          "Output is printed as a JSON blob.")
     run_procedure.add_argument('procedure', type=str, help="The procedure to run.")
-    run_procedure.add_argument('data', type=str, help="Data describing the task to run. "
-                                                      "One of: (i) A JSON blob, "
-                                                      "(ii) A file name, "
-                                                      "(iii) '-', indicating data will be read from STDIN.")
+    run_procedure.add_argument('data',
+                               type=str,
+                               help="Data describing the task to run. "
+                               "One of: (i) A JSON blob, "
+                               "(ii) A file name, "
+                               "(iii) '-', indicating data will be read from STDIN.")
 
     args = vars(parser.parse_args())
     if args["command"] is None:
@@ -50,15 +57,14 @@ def parse_args():
 
 
 def info_cli(args):
-
     def info_version():
         import qcelemental
         print(">>> Version information")
         print(f"QCEngine version:    {__version__}")
         print(f"QCElemental version: {qcelemental.__version__}")
         print()
 
-    def info_programs():
+    def info_programs():  # lgtm: [py/similar-function]
         print(">>> Program information")
         all_progs = list_all_programs()
         avail_progs = list_available_programs()
@@ -74,7 +80,7 @@ def info_programs():
         print(" ".join(sorted(all_progs - avail_progs)))
         print()
 
-    def info_procedures():
+    def info_procedures():  # lgtm: [py/similar-function]
         print(">>> Procedure information")
         all_procs = list_all_procedures()
         avail_procs = list_available_procedures()

qcengine/compute.py

@@ -92,7 +92,6 @@ def compute(input_data: Union[Dict[str, Any], 'ResultInput'],
                 except:
                     raise
 
-
     return handle_output_metadata(output_data, metadata, raise_error=raise_error, return_dict=return_dict)
 
 

qcengine/config.py

@@ -85,7 +85,7 @@ class JobConfig(pydantic.BaseModel):
     ncores: int  # Number of ncores per job
     memory: float  # Amount of memory in GiB per node
     scratch_directory: Optional[str]  # What location to use as scratch
-    retries: int # Number of retries on random failures
+    retries: int  # Number of retries on random failures
 
     class Config:
         extra = "forbid"

qcengine/procedures/base.py

@@ -3,8 +3,8 @@
 """
 
 from typing import Set
-from ..exceptions import InputError, ResourceError
 
+from ..exceptions import InputError, ResourceError
 from .geometric import GeometricProcedure
 
 __all__ = ["register_procedure", "get_procedure", "list_all_procedures", "list_available_procedures"]

qcengine/procedures/geometric.py

@@ -13,8 +13,11 @@ class GeometricProcedure(ProcedureHarness):
     class Config(ProcedureHarness.Config):
         pass
 
-    def found(self, raise_error: bool=False) -> bool:
-        return which_import('geometric', return_bool=True, raise_error=raise_error, raise_msg='Please install via `conda install geometric -c conda-forge`.')
+    def found(self, raise_error: bool = False) -> bool:
+        return which_import('geometric',
+                            return_bool=True,
+                            raise_error=raise_error,
+                            raise_msg='Please install via `conda install geometric -c conda-forge`.')
 
     def build_input_model(self, data: Union[Dict[str, Any], 'OptimizationInput']) -> 'OptimizationInput':
         return self._build_model(data, OptimizationInput)

qcengine/procedures/model.py

@@ -19,7 +19,7 @@ def __init__(self, **kwargs):
         super().__init__(**{**self._defaults, **kwargs})
 
     @abc.abstractmethod
-    def build_input_model(self, data: Union[Dict[str, Any], 'BaseModel'], raise_error: bool=True) -> 'BaseModel':
+    def build_input_model(self, data: Union[Dict[str, Any], 'BaseModel'], raise_error: bool = True) -> 'BaseModel':
         """
         Build and validate the input model, passes if the data was a normal BaseModel input.
 
@@ -35,13 +35,12 @@ def build_input_model(self, data: Union[Dict[str, Any], 'BaseModel'], raise_erro
         BaseModel
             The input model for the procedure.
         """
-
     @abc.abstractmethod
     def compute(self, input_data: 'BaseModel', config: 'JobConfig') -> 'BaseModel':
         pass
 
     @abc.abstractmethod
-    def found(self, raise_error: bool=False) -> bool:
+    def found(self, raise_error: bool = False) -> bool:
         """
         Checks if the program can be found.
 
@@ -66,4 +65,4 @@ def get_version(self) -> str:
         str
             Return a valid, safe python version string.
         """
-        pass
+        pass

qcengine/programs/base.py

@@ -3,16 +3,16 @@
 """
 
 from typing import Set
-from ..exceptions import InputError, ResourceError
 
+from ..exceptions import InputError, ResourceError
 from .cfour import CFOURHarness
 from .dftd3 import DFTD3Harness
 from .entos import EntosHarness
 from .gamess import GAMESSHarness
-from .nwchem import NWChemHarness
 from .molpro import MolproHarness
 from .mopac import MopacHarness
 from .mp2d import MP2DHarness
+from .nwchem import NWChemHarness
 from .psi4 import Psi4Harness
 from .rdkit import RDKitHarness
 from .terachem import TeraChemHarness