formatting

Author: svandenhaute

psiflow/data/dataset.py

@@ -43,6 +43,7 @@ class Dataset:
 
     This class provides methods for manipulating and analyzing collections of atomic structures.
     """
+
     extxyz: psiflow._DataFuture
 
     def __init__(
@@ -415,6 +416,7 @@ def _concatenate_multiple(*args: list[np.ndarray]) -> list[np.ndarray]:
     Note:
         This function is wrapped as a Parsl app and executed using the default_threads executor.
     """
+
     def pad_arrays(
         arrays: list[np.ndarray],
         pad_dimension: int = 1,
@@ -621,6 +623,7 @@ class Computable:
         outputs (ClassVar[tuple[str, ...]]): Names of output quantities.
         batch_size (ClassVar[Optional[int]]): Default batch size for computation.
     """
+
     outputs: ClassVar[tuple[str, ...]] = ()
     batch_size: ClassVar[Optional[int]] = None
 

psiflow/execution.py

@@ -131,8 +131,8 @@ def from_config(
             provider_cls = SlurmProvider
             provider_kwargs = kwargs.pop("slurm")  # do not allow empty dict
             provider_kwargs["init_blocks"] = 0
-            if not 'exclusive' in provider_kwargs:
-                provider_kwargs['exclusive'] = False
+            if "exclusive" not in provider_kwargs:
+                provider_kwargs["exclusive"] = False
         else:
             provider_cls = LocalProvider  # noqa: F405
             provider_kwargs = kwargs.pop("local", {})
@@ -452,7 +452,7 @@ def from_config(
         max_idletime: float = 20,
         internal_tasks_max_threads: int = 10,
         default_threads: int = 4,
-        htex_address: str = '127.0.0.1',
+        htex_address: str = "127.0.0.1",
         zip_staging: Optional[bool] = None,
         container_uri: Optional[str] = None,
         container_engine: str = "apptainer",
@@ -552,11 +552,14 @@ def from_config(
         context = ExecutionContext(config, definitions, path / "context_dir")
 
         if make_symlinks:
-            src, dest = Path.cwd() / f'psiflow_log', path / 'parsl.log'
+            src, dest = Path.cwd() / "psiflow_log", path / "parsl.log"
             _create_symlink(src, dest)
-            src, dest = Path.cwd() / f'psiflow_submit_scripts', path / '000' / 'submit_scripts'
+            src, dest = (
+                Path.cwd() / "psiflow_submit_scripts",
+                path / "000" / "submit_scripts",
+            )
             _create_symlink(src, dest, is_dir=True)
-            src, dest = Path.cwd() / f'psiflow_task_logs', path / '000' / 'task_logs'
+            src, dest = Path.cwd() / "psiflow_task_logs", path / "000" / "task_logs"
             _create_symlink(src, dest, is_dir=True)
 
         return context
@@ -684,5 +687,3 @@ def _create_symlink(src: Path, dest: Path, is_dir: bool = False) -> None:
     else:
         dest.touch(exist_ok=True)
     src.symlink_to(dest, target_is_directory=is_dir)
-
-

psiflow/geometry.py

@@ -274,26 +274,30 @@ def from_string(cls, s: str, natoms: Optional[int] = None) -> Optional[Geometry]
 
         # read and format per_atom data
         column_indices = {}
-        if 'Properties' in comment_dict:
-            properties = comment_dict['Properties'].split(':')
+        if "Properties" in comment_dict:
+            properties = comment_dict["Properties"].split(":")
             count = 0
             for i in range(len(properties) // 3):
                 name = properties[3 * i]
                 ncolumns = int(properties[3 * i + 2])
                 column_indices[name] = count
                 count += ncolumns
-            assert 'pos' in column_indices  # positions need to be there
+            assert "pos" in column_indices  # positions need to be there
 
         per_atom = np.recarray(natoms, dtype=per_atom_dtype)
         per_atom.forces[:] = np.nan
-        POS_INDEX = column_indices.get('pos', 1)
-        FORCES_INDEX = column_indices.get('forces', None)
+        POS_INDEX = column_indices.get("pos", 1)
+        FORCES_INDEX = column_indices.get("forces", None)
         for i in range(natoms):
             values = lines[i + 1].split()
             per_atom.numbers[i] = chemical_symbols.index(values[0])
-            per_atom.positions[i, :] = [float(_) for _ in values[POS_INDEX:POS_INDEX + 3]]
+            per_atom.positions[i, :] = [
+                float(_) for _ in values[POS_INDEX : POS_INDEX + 3]
+            ]
             if FORCES_INDEX is not None:
-                per_atom.forces[i, :] = [float(_) for _ in values[FORCES_INDEX:FORCES_INDEX + 3]]
+                per_atom.forces[i, :] = [
+                    float(_) for _ in values[FORCES_INDEX : FORCES_INDEX + 3]
+                ]
 
         order = {}
         for key, value in comment_dict.items():

psiflow/learning.py

@@ -17,7 +17,7 @@
 from psiflow.models import Model
 from psiflow.reference import Reference, evaluate
 from psiflow.sampling import SimulationOutput, Walker, sample
-from psiflow.utils.apps import boolean_or, setup_logger, unpack_i, isnan
+from psiflow.utils.apps import boolean_or, isnan, setup_logger, unpack_i
 
 logger = setup_logger(__name__)
 

psiflow/reference/_cp2k.py

@@ -68,9 +68,9 @@ def set_global_section(cp2k_input_dict: dict, properties: tuple):
     global_dict = cp2k_input_dict["global"]
 
     # override low/silent print levels
-    level = global_dict.pop('print_level', 'MEDIUM')
-    if level in ['SILENT', 'LOW']:
-        global_dict['print_level'] = 'MEDIUM'
+    level = global_dict.pop("print_level", "MEDIUM")
+    if level in ["SILENT", "LOW"]:
+        global_dict["print_level"] = "MEDIUM"
 
     if properties == ("energy",):
         global_dict["run_type"] = "ENERGY"
@@ -156,11 +156,11 @@ def _prepare_input(
     if "forces" in properties:
         cp2k_input_dict["force_eval"]["print"] = {"FORCES": {}}
     cp2k_input_str = dict_to_str(cp2k_input_dict)
-    with open(outputs[0], 'w') as f:
+    with open(outputs[0], "w") as f:
         f.write(cp2k_input_str)
 
 
-prepare_input = python_app(_prepare_input, executors=['default_threads'])
+prepare_input = python_app(_prepare_input, executors=["default_threads"])
 
 
 # typeguarding for some reason incompatible with WQ
@@ -175,14 +175,9 @@ def cp2k_singlepoint_pre(
     cd_command = "cd $mytmpdir"
     cp_command = "cp {} cp2k.inp".format(inputs[0].filepath)
 
-    command_list = [
-        tmp_command,
-        cd_command,
-        cp_command,
-        cp2k_command
-    ]
+    command_list = [tmp_command, cd_command, cp_command, cp2k_command]
 
-    return ' && '.join(command_list)
+    return " && ".join(command_list)
 
 
 @typeguard.typechecked
@@ -242,7 +237,7 @@ def wrapped_app_pre(geometry, stdout: str, stderr: str):
                 geometry,
                 cp2k_input_dict=self.cp2k_input_dict,
                 properties=tuple(self.outputs),
-                outputs=[psiflow.context().new_file('cp2k_', '.inp')],
+                outputs=[psiflow.context().new_file("cp2k_", ".inp")],
             )
             return app_pre(
                 cp2k_command=cp2k_command,

psiflow/reference/reference.py

@@ -55,7 +55,7 @@ def _nan_if_unsuccessful(
         return result
 
 
-nan_if_unsuccessful = python_app(_nan_if_unsuccessful, executors=['default_threads'])
+nan_if_unsuccessful = python_app(_nan_if_unsuccessful, executors=["default_threads"])
 
 
 @join_app

psiflow/utils/apps.py

@@ -141,4 +141,4 @@ def _isnan(a: Union[float, np.ndarray]) -> bool:
     return bool(np.any(np.isnan(a)))
 
 
-isnan = python_app(_isnan, executors=['default_threads'])
+isnan = python_app(_isnan, executors=["default_threads"])