[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

sevenn/train/dataload.py

@@ -47,7 +47,7 @@ def _graph_build_matscipy(cutoff: float, pbc, cell, pos):
         cell[2, :] = max_positions * 5 * cutoff * identity[2, :]
     # it does not have self-interaction
     edge_src, edge_dst, edge_vec, shifts = neighbour_list(
-        quantities="ijDS",
+        quantities='ijDS',
         pbc=pbc,
         cell=cell,
         positions=pos,
@@ -63,7 +63,7 @@ def _graph_build_matscipy(cutoff: float, pbc, cell, pos):
 def _graph_build_ase(cutoff: float, pbc, cell, pos):
     # building neighbor list
     edge_src, edge_dst, edge_vec, shifts = primitive_neighbor_list(
-        "ijDS", pbc, cell, pos, cutoff, self_interaction=True
+        'ijDS', pbc, cell, pos, cutoff, self_interaction=True
     )
 
     is_zero_idx = np.all(edge_vec == 0, axis=1)
@@ -155,9 +155,9 @@ def atoms_to_graph(
     Requires grad is handled by 'dataset' not here.
     """
     if not y_from_calc:
-        y_energy = atoms.info["y_energy"]
-        y_force = atoms.arrays["y_force"]
-        y_stress = atoms.info.get("y_stress", np.full((6,), np.nan))
+        y_energy = atoms.info['y_energy']
+        y_force = atoms.arrays['y_force']
+        y_stress = atoms.info.get('y_stress', np.full((6,), np.nan))
         if y_stress.shape == (3, 3):
             y_stress = np.array(
                 [
@@ -182,7 +182,7 @@ def atoms_to_graph(
             y_stress = np.array(y_stress[[0, 1, 2, 5, 3, 4]])
         except RuntimeError:
             y_stress = np.full((6,), np.nan)
-    assert y_stress.shape == (6,), "If you see this, please report to the maintainer"
+    assert y_stress.shape == (6,), 'If you see this, please report to the maintainer'
 
     pos = atoms.get_positions()
     cell = np.array(atoms.get_cell())
@@ -218,12 +218,12 @@ def atoms_to_graph(
         info = copy.deepcopy(atoms.info)
         # save only metadata
         # TODO: is it really necessary?
-        if "y_energy" in info:
-            del info["y_energy"]
-        if "y_force" in info:
-            del info["y_force"]
-        if "y_stress" in info:
-            del info["y_stress"]
+        if 'y_energy' in info:
+            del info['y_energy']
+        if 'y_force' in info:
+            del info['y_force']
+        if 'y_stress' in info:
+            del info['y_stress']
         data[KEY.INFO] = info
 
     else:
@@ -265,7 +265,7 @@ def graph_build(
         pool.join()
     else:
         graph_list = [
-            atoms_to_graph(*input_) for input_ in tqdm(inputs, desc="graph_build (1)")
+            atoms_to_graph(*input_) for input_ in tqdm(inputs, desc='graph_build (1)')
         ]
 
     graph_list = [AtomGraphData.from_numpy_dict(g) for g in graph_list]
@@ -306,25 +306,25 @@ def _set_atoms_y(
     for atoms in atoms_list:
         # access energy
         if energy_key is not None:
-            atoms.info["y_energy"] = atoms.info[energy_key]
+            atoms.info['y_energy'] = atoms.info[energy_key]
             del atoms.info[energy_key]
         else:
             try:
-                atoms.info["y_energy"] = atoms.get_potential_energy(
+                atoms.info['y_energy'] = atoms.get_potential_energy(
                     force_consistent=True
                 )
             except NotImplementedError:
-                atoms.info["y_energy"] = atoms.get_potential_energy()
+                atoms.info['y_energy'] = atoms.get_potential_energy()
         # access force
         if force_key is not None:
-            atoms.arrays["y_force"] = atoms.arrays[force_key]
+            atoms.arrays['y_force'] = atoms.arrays[force_key]
             del atoms.arrays[force_key]
         else:
-            atoms.arrays["y_force"] = atoms.get_forces(apply_constraint=False)
+            atoms.arrays['y_force'] = atoms.get_forces(apply_constraint=False)
         # access stress
         if stress_key is not None:
             y_stress = -1 * atoms.info[stress_key]
-            atoms.info["y_stress"] = np.array(y_stress[[0, 1, 2, 5, 3, 4]])
+            atoms.info['y_stress'] = np.array(y_stress[[0, 1, 2, 5, 3, 4]])
             del atoms.info[stress_key]
         else:
             try:
@@ -333,9 +333,9 @@ def _set_atoms_y(
                 # (ASE automatically converts vasp kB to eV/A^3)
                 # So we restore it
                 y_stress = -1 * atoms.get_stress()
-                atoms.info["y_stress"] = np.array(y_stress[[0, 1, 2, 5, 3, 4]])
+                atoms.info['y_stress'] = np.array(y_stress[[0, 1, 2, 5, 3, 4]])
             except RuntimeError:
-                atoms.info["y_stress"] = np.full((6,), np.nan)
+                atoms.info['y_stress'] = np.full((6,), np.nan)
     return atoms_list
 
 
@@ -344,7 +344,7 @@ def ase_reader(
     energy_key: Optional[str] = None,
     force_key: Optional[str] = None,
     stress_key: Optional[str] = None,
-    index: str = ":",
+    index: str = ':',
     **kwargs,
 ) -> list[ase.Atoms]:
     """
@@ -358,7 +358,7 @@ def ase_reader(
 
 
 # Reader
-def structure_list_reader(filename: str, format_outputs="vasp-out"):
+def structure_list_reader(filename: str, format_outputs='vasp-out'):
     """
     Deprecated
     Read from structure_list using braceexpand and ASE
@@ -377,27 +377,27 @@ def structure_list_reader(filename: str, format_outputs="vasp-out"):
 
     def parse_label(line):
         line = line.strip()
-        if line.startswith("[") is False:
+        if line.startswith('[') is False:
             return False
-        elif line.endswith("]") is False:
-            raise ValueError("wrong structure_list title format")
+        elif line.endswith(']') is False:
+            raise ValueError('wrong structure_list title format')
         return line[1:-1]
 
     def parse_fileline(line):
         line = line.strip().split()
         if len(line) == 1:
-            line.append(":")
+            line.append(':')
         elif len(line) != 2:
-            raise ValueError("wrong structure_list format")
+            raise ValueError('wrong structure_list format')
         return line[0], line[1]
 
-    structure_list_file = open(filename, "r")
+    structure_list_file = open(filename, 'r')
     lines = structure_list_file.readlines()
 
     raw_str_dict = {}
-    label = "Default"
+    label = 'Default'
     for line in lines:
-        if line.strip() == "":
+        if line.strip() == '':
             continue
         tmp_label = parse_label(line)
         if tmp_label:
@@ -408,36 +408,36 @@ def parse_fileline(line):
             files_expr, index_expr = parse_fileline(line)
             raw_str_dict[label].append((files_expr, index_expr))
         else:
-            raise ValueError("wrong structure_list format")
+            raise ValueError('wrong structure_list format')
     structure_list_file.close()
 
     structures_dict = {}
-    info_dct = {"data_from": "user_OUTCAR"}
+    info_dct = {'data_from': 'user_OUTCAR'}
     for title, file_lines in raw_str_dict.items():
         stct_lists = []
         for file_line in file_lines:
             files_expr, index_expr = file_line
             index = string2index(index_expr)
             for expanded_filename in list(braceexpand(files_expr)):
-                f_stream = open(expanded_filename, "r")
+                f_stream = open(expanded_filename, 'r')
                 # generator of all outcar ionic steps
                 gen_all = outcarchunks(f_stream, ocp)
                 try:  # TODO: index may not slice, it can be integer
                     it_atoms = islice(gen_all, index.start, index.stop, index.step)
                 except ValueError:
                     # TODO: support
                     # negative index
-                    raise ValueError("Negative index is not supported yet")
+                    raise ValueError('Negative index is not supported yet')
 
                 info_dct_f = {
                     **info_dct,
-                    "file": os.path.abspath(expanded_filename),
+                    'file': os.path.abspath(expanded_filename),
                 }
                 for idx, o in enumerate(it_atoms):
                     try:
                         istep = index.start + idx * index.step
                         atoms = o.build()
-                        atoms.info = {**info_dct_f, "ionic_step": istep}
+                        atoms.info = {**info_dct_f, 'ionic_step': istep}
                     except TypeError:  # it is not slice of ionic steps
                         atoms = o.build()
                         atoms.info = info_dct_f
@@ -450,12 +450,12 @@ def parse_fileline(line):
 def match_reader(reader_name: str, **kwargs):
     reader = None
     metadata = {}
-    if reader_name == "structure_list":
+    if reader_name == 'structure_list':
         reader = partial(structure_list_reader, **kwargs)
-        metadata.update({"origin": "structure_list"})
+        metadata.update({'origin': 'structure_list'})
     else:
         reader = partial(ase_reader, **kwargs)
-        metadata.update({"origin": "ase_reader"})
+        metadata.update({'origin': 'ase_reader'})
     return reader, metadata
 
 
@@ -486,7 +486,7 @@ def file_to_dataset(
     elif isinstance(atoms, dict):
         atoms_dct = atoms
     else:
-        raise TypeError("The return of reader is not list or dict")
+        raise TypeError('The return of reader is not list or dict')
 
     graph_dct = {}
     for label, atoms_list in atoms_dct.items():