style: enable B905 to prevent issues with zip

deepmd/calculator.py

@@ -103,7 +103,7 @@ def __init__(
             self.type_dict = type_dict
         else:
             self.type_dict = dict(
-                zip(self.dp.get_type_map(), range(self.dp.get_ntypes()))
+                zip(self.dp.get_type_map(), range(self.dp.get_ntypes()), strict=False)
             )
 
     def calculate(

deepmd/dpmodel/atomic_model/linear_atomic_model.py

@@ -155,7 +155,7 @@ def get_model_sels(self) -> list[int | list[int]]:
     def _sort_rcuts_sels(self) -> tuple[tuple[Array, Array], list[int]]:
         # sort the pair of rcut and sels in ascending order, first based on sel, then on rcut.
         zipped = sorted(
-            zip(self.get_model_rcuts(), self.get_model_nsels()),
+            zip(self.get_model_rcuts(), self.get_model_nsels(), strict=False),
             key=lambda x: (x[1], x[0]),
         )
         return [p[0] for p in zipped], [p[1] for p in zipped]
@@ -235,12 +235,14 @@ def forward_atomic(
         )
         raw_nlists = [
             nlists[get_multiple_nlist_key(rcut, sel)]
-            for rcut, sel in zip(self.get_model_rcuts(), self.get_model_nsels())
+            for rcut, sel in zip(
+                self.get_model_rcuts(), self.get_model_nsels(), strict=False
+            )
         ]
         nlists_ = [
             nl if mt else nlist_distinguish_types(nl, extended_atype, sel)
             for mt, nl, sel in zip(
-                self.mixed_types_list, raw_nlists, self.get_model_sels()
+                self.mixed_types_list, raw_nlists, self.get_model_sels(), strict=False
             )
         ]
         ener_list = []

deepmd/dpmodel/descriptor/hybrid.py

@@ -101,7 +101,7 @@ def __init__(
             start_idx = np.cumsum(np.pad(hybrid_sel, (1, 0), "constant"))[:-1]
             end_idx = start_idx + np.array(sub_sel)
             cut_idx = np.concatenate(
-                [range(ss, ee) for ss, ee in zip(start_idx, end_idx)]
+                [range(ss, ee) for ss, ee in zip(start_idx, end_idx, strict=False)]
             )
             nlist_cut_idx.append(cut_idx)
         self.nlist_cut_idx = nlist_cut_idx
@@ -310,7 +310,7 @@ def call(
             )
         else:
             nl_distinguish_types = None
-        for descrpt, nci in zip(self.descrpt_list, self.nlist_cut_idx):
+        for descrpt, nci in zip(self.descrpt_list, self.nlist_cut_idx, strict=False):
             # cut the nlist to the correct length
             if self.mixed_types() == descrpt.mixed_types():
                 nl = xp.take(nlist, nci, axis=2)

deepmd/dpmodel/infer/deep_eval.py

@@ -229,6 +229,7 @@ def eval(
             zip(
                 [x.name for x in request_defs],
                 out,
+                strict=False,
             )
         )
 

deepmd/dpmodel/utils/nlist.py

@@ -234,7 +234,7 @@ def build_multiple_neighbor_list(
     rr = xp.where(nlist_mask, xp.full_like(rr, float("inf")), rr)
     nlist0 = nlist
     ret = {}
-    for rc, ns in zip(rcuts[::-1], nsels[::-1]):
+    for rc, ns in zip(rcuts[::-1], nsels[::-1], strict=False):
         tnlist_1 = nlist0[:, :, :ns]
         tnlist_1 = xp.where(rr[:, :, :ns] > rc, xp.full_like(tnlist_1, -1), tnlist_1)
         ret[get_multiple_nlist_key(rc, ns)] = tnlist_1

deepmd/jax/infer/deep_eval.py

@@ -249,6 +249,7 @@ def eval(
             zip(
                 [x.name for x in request_defs],
                 out,
+                strict=False,
             )
         )
 

deepmd/pd/utils/dataset.py

@@ -5,6 +5,9 @@
     Dataset,
 )
 
+from deepmd.pd.utils.env import (
+    NUM_WORKERS,
+)
 from deepmd.utils.data import (
     DataRequirementItem,
     DeepmdData,
@@ -32,7 +35,7 @@ def __len__(self):
 
     def __getitem__(self, index):
         """Get a frame from the selected system."""
-        b_data = self._data_system.get_item_paddle(index)
+        b_data = self._data_system.get_item_paddle(index, max(1, NUM_WORKERS))
         b_data["natoms"] = self._natoms_vec
         return b_data
 

deepmd/tf/descriptor/loc_frame.py

@@ -187,7 +187,7 @@ def compute_input_stats(
             sumn = []
             sumv2 = []
             for cc, bb, tt, nn, mm in zip(
-                data_coord, data_box, data_atype, natoms_vec, mesh
+                data_coord, data_box, data_atype, natoms_vec, mesh, strict=False
             ):
                 sysv, sysv2, sysn = self._compute_dstats_sys_nonsmth(cc, bb, tt, nn, mm)
                 sumv.append(sysv)

deepmd/tf/descriptor/se_a.py

@@ -374,7 +374,7 @@ def compute_input_stats(
             sumr2 = []
             suma2 = []
             for cc, bb, tt, nn, mm in zip(
-                data_coord, data_box, data_atype, natoms_vec, mesh
+                data_coord, data_box, data_atype, natoms_vec, mesh, strict=False
             ):
                 sysr, sysr2, sysa, sysa2, sysn = self._compute_dstats_sys_smth(
                     cc, bb, tt, nn, mm
@@ -1331,7 +1331,7 @@ def init_variables(
                 start_index_old[0] = 0
 
                 for nn, oo, ii, jj in zip(
-                    n_descpt, n_descpt_old, start_index, start_index_old
+                    n_descpt, n_descpt_old, start_index, start_index_old, strict=False
                 ):
                     if nn < oo:
                         # new size is smaller, copy part of std

deepmd/tf/descriptor/se_a_ef.py

@@ -419,7 +419,13 @@ def compute_input_stats(
             sumr2 = []
             suma2 = []
             for cc, bb, tt, nn, mm, ee in zip(
-                data_coord, data_box, data_atype, natoms_vec, mesh, data_efield
+                data_coord,
+                data_box,
+                data_atype,
+                natoms_vec,
+                mesh,
+                data_efield,
+                strict=False,
             ):
                 sysr, sysr2, sysa, sysa2, sysn = self._compute_dstats_sys_smth(
                     cc, bb, tt, nn, mm, ee

deepmd/tf/descriptor/se_atten.py

@@ -379,7 +379,13 @@ def compute_input_stats(
             if mixed_type:
                 sys_num = 0
                 for cc, bb, tt, nn, mm, r_n in zip(
-                    data_coord, data_box, data_atype, natoms_vec, mesh, real_natoms_vec
+                    data_coord,
+                    data_box,
+                    data_atype,
+                    natoms_vec,
+                    mesh,
+                    real_natoms_vec,
+                    strict=False,
                 ):
                     sysr, sysr2, sysa, sysa2, sysn = self._compute_dstats_sys_smth(
                         cc, bb, tt, nn, mm, mixed_type, r_n
@@ -392,7 +398,7 @@ def compute_input_stats(
                     suma2.append(sysa2)
             else:
                 for cc, bb, tt, nn, mm in zip(
-                    data_coord, data_box, data_atype, natoms_vec, mesh
+                    data_coord, data_box, data_atype, natoms_vec, mesh, strict=False
                 ):
                     sysr, sysr2, sysa, sysa2, sysn = self._compute_dstats_sys_smth(
                         cc, bb, tt, nn, mm

deepmd/tf/descriptor/se_r.py

@@ -271,7 +271,7 @@ def compute_input_stats(
         sumn = []
         sumr2 = []
         for cc, bb, tt, nn, mm in zip(
-            data_coord, data_box, data_atype, natoms_vec, mesh
+            data_coord, data_box, data_atype, natoms_vec, mesh, strict=False
         ):
             sysr, sysr2, sysn = self._compute_dstats_sys_se_r(cc, bb, tt, nn, mm)
             sumr.append(sysr)

deepmd/tf/descriptor/se_t.py

@@ -258,7 +258,7 @@ def compute_input_stats(
             sumr2 = []
             suma2 = []
             for cc, bb, tt, nn, mm in zip(
-                data_coord, data_box, data_atype, natoms_vec, mesh
+                data_coord, data_box, data_atype, natoms_vec, mesh, strict=False
             ):
                 sysr, sysr2, sysa, sysa2, sysn = self._compute_dstats_sys_smth(
                     cc, bb, tt, nn, mm

deepmd/tf/infer/deep_eval.py

@@ -760,7 +760,8 @@ def eval(
             output = (output,)
 
         output_dict = {
-            odef.name: oo for oo, odef in zip(output, self.output_def.var_defs.values())
+            odef.name: oo
+            for oo, odef in zip(output, self.output_def.var_defs.values(), strict=False)
         }
         # ugly!!
         if self.modifier_type is not None and issubclass(self.model_type, DeepPot):

deepmd/tf/nvnmd/entrypoints/mapt.py

@@ -439,11 +439,11 @@ def run_u2s(self):
 
         u = N2 * np.reshape(np.arange(0, N + 1) / N, [-1, 1])  # pylint: disable=no-explicit-dtype
         res_lst = run_sess(sess, vals, feed_dict={dic_ph["u"]: u})
-        res_dic = dict(zip(keys, res_lst))
+        res_dic = dict(zip(keys, res_lst, strict=False))
 
         u2 = N2 * np.reshape(np.arange(0, N * 16 + 1) / (N * 16), [-1, 1])  # pylint: disable=no-explicit-dtype
         res_lst2 = run_sess(sess, vals, feed_dict={dic_ph["u"]: u2})
-        res_dic2 = dict(zip(keys, res_lst2))  # reference for compare
+        res_dic2 = dict(zip(keys, res_lst2, strict=False))  # reference for compare
 
         # change value
         for tt in range(ndim):
@@ -536,11 +536,11 @@ def run_s2g(self):
 
         s = N2 * np.reshape(np.arange(0, N + 1) / N, [-1, 1]) + smin_  # pylint: disable=no-explicit-dtype
         res_lst = run_sess(sess, vals, feed_dict={dic_ph["s"]: s})
-        res_dic = dict(zip(keys, res_lst))
+        res_dic = dict(zip(keys, res_lst, strict=False))
 
         s2 = N2 * np.reshape(np.arange(0, N * 16 + 1) / (N * 16), [-1, 1]) + smin_  # pylint: disable=no-explicit-dtype
         res_lst2 = run_sess(sess, vals, feed_dict={dic_ph["s"]: s2})
-        res_dic2 = dict(zip(keys, res_lst2))
+        res_dic2 = dict(zip(keys, res_lst2, strict=False))
 
         sess.close()
         return res_dic, res_dic2
@@ -601,7 +601,7 @@ def run_t2g(self):
         vals = list(dic_ph.values())
         #
         res_lst = run_sess(sess, vals, feed_dict={})
-        res_dic = dict(zip(keys, res_lst))
+        res_dic = dict(zip(keys, res_lst, strict=False))
 
         sess.close()
         return res_dic

deepmd/tf/train/trainer.py

@@ -967,4 +967,4 @@ def get_data_dict(self, batch_list: list[np.ndarray]) -> dict[str, np.ndarray]:
         dict[str, np.ndarray]
             The dict of the loaded data.
         """
-        return dict(zip(self.data_keys, batch_list))
+        return dict(zip(self.data_keys, batch_list, strict=False))

deepmd/utils/batch_size.py

@@ -248,7 +248,7 @@ def concate_result(r: list[Any]) -> Any:
             return ret
 
         if not returned_dict:
-            r_list = [concate_result(r) for r in zip(*results)]
+            r_list = [concate_result(r) for r in zip(*results, strict=False)]
             r = tuple(r_list)
             if len(r) == 1:
                 # avoid returning tuple if callable doesn't return tuple

deepmd/utils/data_system.py

@@ -172,7 +172,9 @@ def __init__(
                 rule = int(words[1])
                 filtered_data_systems = []
                 filtered_system_dirs = []
-                for sys_dir, data_sys in zip(self.system_dirs, self.data_systems):
+                for sys_dir, data_sys in zip(
+                    self.system_dirs, self.data_systems, strict=False
+                ):
                     if data_sys.get_natoms() <= rule:
                         filtered_data_systems.append(data_sys)
                         filtered_system_dirs.append(sys_dir)

deepmd/utils/model_branch_dict.py

@@ -169,7 +169,7 @@ def as_table(self) -> str:
         # Step 3: Determine actual width for each column
         # For the first two columns, we already decided the exact widths above.
         col_widths: list[int] = []
-        for idx, col in enumerate(zip(*wrapped_rows)):
+        for idx, col in enumerate(zip(*wrapped_rows, strict=False)):
             if idx == 0:
                 col_widths.append(branch_col_width)
             elif idx == 1:
@@ -187,7 +187,8 @@ def draw_row_line(cells_parts: list[list[str]]) -> str:
             return (
                 "| "
                 + " | ".join(
-                    part.ljust(width) for part, width in zip(cells_parts, col_widths)
+                    part.ljust(width)
+                    for part, width in zip(cells_parts, col_widths, strict=False)
                 )
                 + " |"
             )

deepmd/utils/update_sel.py

@@ -43,7 +43,7 @@ def update_one_sel(
             sel = [int(self.wrap_up_4(ii * ratio)) for ii in tmp_sel]
         else:
             # sel is set by user
-            for ii, (tt, dd) in enumerate(zip(tmp_sel, sel)):
+            for ii, (tt, dd) in enumerate(zip(tmp_sel, sel, strict=False)):
                 if dd and tt > dd:
                     # we may skip warning for sel=0, where the user is likely
                     # to exclude such type in the descriptor

pyproject.toml

@@ -382,6 +382,7 @@ select = [
     "TCH", # flake8-type-checking
     "PYI", # flake8-pyi
     "ANN", # type annotations
+    "B905", # zip-without-explicit-strict
 ]
 
 ignore = [
@@ -429,9 +430,9 @@ runtime-evaluated-base-classes = ["torch.nn.Module"]
 "backend/**" = ["ANN"]
 "data/**" = ["ANN"]
 "deepmd/tf/**" = ["TID253", "ANN"]
-"deepmd/pt/**" = ["TID253"]
+"deepmd/pt/**" = ["TID253", "B905"]
 "deepmd/jax/**" = ["TID253"]
-"deepmd/pd/**" = ["TID253", "ANN"]
+"deepmd/pd/**" = ["TID253", "ANN", "B905"]
 
 "source/**" = ["ANN"]
 "source/tests/tf/**" = ["TID253", "ANN"]

source/tests/common/dpmodel/test_pairtab_atomic_model.py

@@ -158,6 +158,7 @@ def test_extrapolation_nonzero_rmax(self, mock_loadtxt) -> None:
                 0.035,
                 0.025,
             ],
+            strict=False,
         ):
             extended_coord = np.array(
                 [