[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
     -   id: check-toml
 # Python
 -   repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.1.0
     hooks:
     -   id: black-jupyter
 -   repo: https://github.com/PyCQA/isort
@@ -26,7 +26,7 @@ repos:
       files: \.py$
 -   repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
-    rev: v0.0.243
+    rev: v0.0.257
     hooks:
     - id: ruff
       args: ["--fix"]

deepmd/calculator.py

@@ -75,7 +75,7 @@ def __init__(
         model: Union[str, "Path"],
         label: str = "DP",
         type_dict: Dict[str, int] = None,
-        **kwargs
+        **kwargs,
     ) -> None:
         Calculator.__init__(self, label=label, **kwargs)
         self.dp = DeepPotential(str(Path(model).resolve()))

deepmd/descriptor/se_a.py

@@ -866,7 +866,7 @@ def _filter_lower(
         trainable=True,
         suffix="",
     ):
-        """input env matrix, returns R.G."""
+        """Input env matrix, returns R.G."""
         outputs_size = [1] + self.filter_neuron
         # cut-out inputs
         # with natom x (nei_type_i x 4)

deepmd/descriptor/se_atten.py

@@ -793,7 +793,7 @@ def _filter_lower(
         name="filter_",
         reuse=None,
     ):
-        """input env matrix, returns R.G."""
+        """Input env matrix, returns R.G."""
         outputs_size = [1] + self.filter_neuron
         # cut-out inputs
         # with natom x (nei_type_i x 4)

deepmd/entrypoints/compress.py

@@ -55,7 +55,7 @@ def compress(
     mpi_log: str,
     log_path: Optional[str],
     log_level: int,
-    **kwargs
+    **kwargs,
 ):
     """Compress model.
 

deepmd/infer/deep_dipole.py

@@ -37,15 +37,14 @@ def __init__(
         load_prefix: str = "load",
         default_tf_graph: bool = False,
     ) -> None:
-
         # use this in favor of dict update to move attribute from class to
         # instance namespace
         self.tensors = dict(
             {
                 # output tensor
                 "t_tensor": "o_dipole:0",
             },
-            **self.tensors
+            **self.tensors,
         )
 
         DeepTensor.__init__(

deepmd/infer/deep_polar.py

@@ -41,15 +41,14 @@ def __init__(
         load_prefix: str = "load",
         default_tf_graph: bool = False,
     ) -> None:
-
         # use this in favor of dict update to move attribute from class to
         # instance namespace
         self.tensors = dict(
             {
                 # output tensor
                 "t_tensor": "o_polar:0",
             },
-            **self.tensors
+            **self.tensors,
         )
 
         DeepTensor.__init__(
@@ -84,7 +83,6 @@ class DeepGlobalPolar(DeepTensor):
     def __init__(
         self, model_file: str, load_prefix: str = "load", default_tf_graph: bool = False
     ) -> None:
-
         self.tensors.update(
             {
                 "t_sel_type": "model_attr/sel_type:0",

deepmd/infer/deep_pot.py

@@ -75,7 +75,6 @@ def __init__(
         default_tf_graph: bool = False,
         auto_batch_size: Union[bool, int, AutoBatchSize] = True,
     ) -> None:
-
         # add these tensors on top of what is defined by DeepTensor Class
         # use this in favor of dict update to move attribute from class to
         # instance namespace

deepmd/infer/deep_wfc.py

@@ -37,15 +37,14 @@ def __init__(
         load_prefix: str = "load",
         default_tf_graph: bool = False,
     ) -> None:
-
         # use this in favor of dict update to move attribute from class to
         # instance namespace
         self.tensors = dict(
             {
                 # output tensor
                 "t_tensor": "o_wfc:0",
             },
-            **self.tensors
+            **self.tensors,
         )
         DeepTensor.__init__(
             self,

deepmd/loggers/loggers.py

@@ -235,7 +235,6 @@ def set_log_handles(
 
     # * add file handler ***************************************************************
     if log_path:
-
         # create directory
         log_path.parent.mkdir(exist_ok=True, parents=True)
 

deepmd/model/ener.py

@@ -151,7 +151,6 @@ def build(
         suffix="",
         reuse=None,
     ):
-
         if input_dict is None:
             input_dict = {}
         with tf.variable_scope("model_attr" + suffix, reuse=reuse):

deepmd/model/multi.py

@@ -183,7 +183,6 @@ def build(
         suffix="",
         reuse=None,
     ):
-
         if input_dict is None:
             input_dict = {}
         with tf.variable_scope("model_attr" + suffix, reuse=reuse):

deepmd/model/tensor.py

@@ -117,7 +117,6 @@ def build(
         suffix="",
         reuse=None,
     ):
-
         if input_dict is None:
             input_dict = {}
         with tf.variable_scope("model_attr" + suffix, reuse=reuse):

deepmd/nvnmd/entrypoints/wrap.py

@@ -459,7 +459,7 @@ def wrap(
     nvnmd_weight: Optional[str] = "nvnmd/weight.npy",
     nvnmd_map: Optional[str] = "nvnmd/map.npy",
     nvnmd_model: Optional[str] = "nvnmd/model.pb",
-    **kwargs
+    **kwargs,
 ):
     wrapObj = Wrap(nvnmd_config, nvnmd_weight, nvnmd_map, nvnmd_model)
     wrapObj.wrap()

deepmd/nvnmd/utils/config.py

@@ -163,7 +163,7 @@ def init_fitn(self, jdata: dict, jdata_parent: dict = {}) -> dict:
         return jdata
 
     def init_dpin(self, jdata: dict, jdata_parent: dict = {}) -> dict:
-        r"""initial members about other deepmd input."""
+        r"""Initial members about other deepmd input."""
         return jdata
 
     def init_size(self, jdata: dict, jdata_parent: dict = {}) -> dict:

deepmd/train/trainer.py

@@ -729,7 +729,6 @@ def _init_session(self):
             run_sess(self.sess, bcast_op)
 
     def train(self, train_data=None, valid_data=None):
-
         # if valid_data is None:  # no validation set specified.
         #     valid_data = train_data  # using training set as validation set.
 
@@ -793,7 +792,6 @@ def train(self, train_data=None, valid_data=None):
         total_train_time = 0.0
 
         while cur_batch < stop_batch:
-
             # first round validation:
             if not self.multi_task_mode:
                 train_batch = train_data.get_batch()

deepmd/utils/compat.py

@@ -287,7 +287,6 @@ def remove_decay_rate(jdata: Dict[str, Any]):
 def convert_input_v1_v2(
     jdata: Dict[str, Any], warning: bool = True, dump: Optional[Union[str, Path]] = None
 ) -> Dict[str, Any]:
-
     tr_cfg = jdata["training"]
     tr_data_keys = {
         "systems",

deepmd/utils/neighbor_stat.py

@@ -89,7 +89,7 @@ def builder():
         self.sub_sess = tf.Session(graph=sub_graph, config=default_tf_session_config)
 
     def get_stat(self, data: DeepmdDataSystem) -> Tuple[float, List[int]]:
-        """get the data statistics of the training data, including nearest nbor distance between atoms, max nbor size of atoms.
+        """Get the data statistics of the training data, including nearest nbor distance between atoms, max nbor size of atoms.
 
         Parameters
         ----------

deepmd/utils/path.py

@@ -106,7 +106,7 @@ def __truediv__(self, key: str) -> "DPPath":
 
     @abstractmethod
     def __lt__(self, other: "DPPath") -> bool:
-        """whether this DPPath is less than other for sorting."""
+        """Whether this DPPath is less than other for sorting."""
 
     @abstractmethod
     def __str__(self) -> str:
@@ -204,7 +204,7 @@ def __truediv__(self, key: str) -> "DPPath":
         return type(self)(self.path / key)
 
     def __lt__(self, other: "DPOSPath") -> bool:
-        """whether this DPPath is less than other for sorting."""
+        """Whether this DPPath is less than other for sorting."""
         return self.path < other.path
 
     def __str__(self) -> str:
@@ -349,11 +349,11 @@ def _connect_path(self, path: str) -> str:
         return f"{self.name}/{path}"
 
     def __lt__(self, other: "DPH5Path") -> bool:
-        """whether this DPPath is less than other for sorting."""
+        """Whether this DPPath is less than other for sorting."""
         if self.root_path == other.root_path:
             return self.name < other.name
         return self.root_path < other.root_path
 
     def __str__(self) -> str:
-        """returns path of self."""
+        """Returns path of self."""
         return f"{self.root_path}#{self.name}"

doc/conf.py

@@ -150,7 +150,6 @@ def run_apidoc(_):
 
 
 def setup(app):
-
     # Add hook for building doxygen xml when needed
     app.connect("builder-inited", run_apidoc)
 

source/install/build_tf.py

@@ -162,7 +162,6 @@ def post_process(self):
             with tarfile.open(self.path) as tar:
 
                 def is_within_directory(directory, target):
-
                     abs_directory = os.path.abspath(directory)
                     abs_target = os.path.abspath(target)
 
@@ -171,7 +170,6 @@ def is_within_directory(directory, target):
                     return prefix == abs_directory
 
                 def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
-
                     for member in tar.getmembers():
                         member_path = os.path.join(path, member.name)
                         if not is_within_directory(path, member_path):

source/tests/common.py

@@ -660,7 +660,7 @@ def stats_energy(self):
             return np.average(eners)
 
     def load_energy(self, set_name, nframes, nvalues, energy_file, atom_energy_file):
-        """return : coeff_ener, ener, coeff_atom_ener, atom_ener."""
+        """Return : coeff_ener, ener, coeff_atom_ener, atom_ener."""
         # load atom_energy
         coeff_atom_ener, atom_ener = self.load_data(
             set_name, atom_energy_file, [nframes, nvalues], False
@@ -765,13 +765,13 @@ def get_set(self, data, idx=None):
         return new_data
 
     def get_test(self):
-        """returned property prefector [4] in order:
+        """Returned property prefector [4] in order:
         energy, force, virial, atom_ener.
         """
         return self.get_set(self.test_set)
 
     def get_batch(self, batch_size):
-        """returned property prefector [4] in order:
+        """Returned property prefector [4] in order:
         energy, force, virial, atom_ener.
         """
         set_size = self.batch_set["energy"].shape[0]

source/tests/test_argument_parser.py

@@ -90,7 +90,6 @@ def attr_and_type_check(
         mapping = {**{"command": dict(type=str, value=command)}, **mapping}
 
         for argument, test_data in mapping.items():
-
             # get expected type
             expected_type = test_data["type"]
 

source/tests/test_compat_input.py

@@ -39,7 +39,6 @@ def assertDictAlmostEqual(self, d1, d2, msg=None, places=7):
                 self.assertAlmostEqual(d1[kk], d2[kk], places=places, msg=msg)
 
     def test_json_yaml_equal(self):
-
         inputs = ("water_v1", "water_se_a_v1")
 
         for i in inputs:

source/tests/test_deepmd_data_sys.py

@@ -403,7 +403,7 @@ def test_sys_prob_floating_point_error(self):
         self.assertEqual(ds.sys_probs.size, len(sys_probs))
 
     def test_get_mixed_batch(self):
-        """test get_batch with mixed system."""
+        """Test get_batch with mixed system."""
         batch_size = "mixed:3"
         test_size = 2
 

source/tests/test_descrpt_sea_ef_rot.py

@@ -66,7 +66,7 @@ def build_efv(self, dcoord, dbox, dtype, tnatoms, name, op, reuse=None):
                     "rcut_smth": 5.5,
                     "seed": 1,
                     "uniform_seed": True,
-                }
+                },
             )
         else:
             descrpt = DescrptSeA(

source/tests/test_get_potential.py

@@ -49,7 +49,6 @@ def tearDown(self):
             f.unlink()
 
     def test_factory(self):
-
         msg = "Returned wrong type of potential. Expected: {}, got: {}"
 
         dp = DeepPotential(self.work_dir / "deep_dipole.pb")