Fix: ignore UP031 (#762)

Author: wanghan-iapcm

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.4
+    rev: v0.8.1
     hooks:
     - id: ruff
       args: ["--fix"]

docs/conf.py

@@ -24,7 +24,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "dpdata"
-copyright = "2019-%d, DeepModeling " % date.today().year
+copyright = "2019-%d, DeepModeling " % date.today().year  # noqa: UP031
 author = "Han Wang"
 
 # The short X.Y version

dpdata/abacus/md.py

@@ -68,7 +68,7 @@ def get_coords_from_dump(dumplines, natoms):
     else:
         nframes_dump = int(nlines / (total_natoms + 9))
     assert nframes_dump > 0, (
-        "Number of lines in MD_dump file = %d. Number of atoms = %d. The MD_dump file is incomplete."
+        "Number of lines in MD_dump file = %d. Number of atoms = %d. The MD_dump file is incomplete."  # noqa: UP031
         % (nlines, total_natoms)
     )
     cells = np.zeros([nframes_dump, 3, 3])
@@ -125,7 +125,7 @@ def get_coords_from_dump(dumplines, natoms):
                     )
             iframe += 1
     assert iframe == nframes_dump, (
-        "iframe=%d, nframe_dump=%d. Number of frames does not match number of lines in MD_dump."
+        "iframe=%d, nframe_dump=%d. Number of frames does not match number of lines in MD_dump."  # noqa: UP031
         % (iframe, nframes_dump)
     )
     stresses *= kbar2evperang3
@@ -145,7 +145,7 @@ def get_energy(outlines, ndump, dump_freq):
                 energy.append(np.nan)
             nenergy += 1
     assert ndump == len(energy), (
-        "Number of total energies in running_md.log = %d. Number of frames in MD_dump = %d. Please check."
+        "Number of total energies in running_md.log = %d. Number of frames in MD_dump = %d. Please check."  # noqa: UP031
         % (len(energy), ndump)
     )
     energy = np.array(energy)
@@ -191,7 +191,7 @@ def get_frame(fname):
             force = np.delete(force, i - ndump, axis=0)
             stress = np.delete(stress, i - ndump, axis=0)
             energy = np.delete(energy, i - ndump, axis=0)
-            unconv_stru += "%d " % i
+            unconv_stru += "%d " % i  # noqa: UP031
     ndump = len(energy)
     if unconv_stru != "":
         warnings.warn(f"Structure {unconv_stru} are unconverged and not collected!")

dpdata/abacus/relax.py

@@ -47,7 +47,7 @@ def get_coords_from_log(loglines, natoms):
             natoms_log += int(line.split()[-1])
 
     assert natoms_log > 0 and natoms_log == natoms, (
-        "ERROR: detected atom number in log file is %d" % natoms
+        "ERROR: detected atom number in log file is %d" % natoms  # noqa: UP031
     )
 
     energy = []
@@ -76,7 +76,7 @@ def get_coords_from_log(loglines, natoms):
                         list(map(lambda x: float(x) * a0, loglines[i + k].split()[1:4]))
                     )
             else:
-                assert False, "Unrecongnized coordinate type, %s, line:%d" % (
+                assert False, "Unrecongnized coordinate type, %s, line:%d" % (  # noqa: UP031
                     loglines[i].split()[0],
                     i,
                 )

dpdata/data_type.py

@@ -122,7 +122,7 @@ def check(self, system: System):
                 elif isinstance(data, list):
                     if len(shape) and shape[0] != len(data):
                         raise DataError(
-                            "Length of %s is %d, but expected %d"
+                            "Length of %s is %d, but expected %d"  # noqa: UP031
                             % (self.name, len(data), shape[0])
                         )
                 else:

dpdata/deepmd/comp.py

@@ -119,7 +119,7 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
     for ii in range(nsets):
         set_stt = ii * set_size
         set_end = (ii + 1) * set_size
-        set_folder = os.path.join(folder, "set.%03d" % ii)
+        set_folder = os.path.join(folder, "set.%03d" % ii)  # noqa: UP031
         os.makedirs(set_folder)
     try:
         os.remove(os.path.join(folder, "nopbc"))
@@ -158,5 +158,5 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
         for ii in range(nsets):
             set_stt = ii * set_size
             set_end = (ii + 1) * set_size
-            set_folder = os.path.join(folder, "set.%03d" % ii)
+            set_folder = os.path.join(folder, "set.%03d" % ii)  # noqa: UP031
             np.save(os.path.join(set_folder, dtype.deepmd_name), ddata[set_stt:set_end])

dpdata/deepmd/hdf5.py

@@ -59,7 +59,7 @@ def to_system_data(
     else:
         my_type_map = []
         for ii in range(ntypes):
-            my_type_map.append("Type_%d" % ii)
+            my_type_map.append("Type_%d" % ii)  # noqa: UP031
     assert len(my_type_map) >= len(data["atom_numbs"])
     for ii in range(len(data["atom_numbs"])):
         data["atom_names"].append(my_type_map[ii])
@@ -217,7 +217,7 @@ def dump(
     for ii in range(nsets):
         set_stt = ii * set_size
         set_end = (ii + 1) * set_size
-        set_folder = g.create_group("set.%03d" % ii)
+        set_folder = g.create_group("set.%03d" % ii)  # noqa: UP031
         for dt, prop in data_types.items():
             if dt in reshaped_data:
                 set_folder.create_dataset(

dpdata/deepmd/raw.py

@@ -27,7 +27,7 @@ def load_type(folder, type_map=None):
     else:
         my_type_map = []
         for ii in range(ntypes):
-            my_type_map.append("Type_%d" % ii)
+            my_type_map.append("Type_%d" % ii)  # noqa: UP031
     data["atom_names"] = my_type_map
     data["atom_numbs"] = []
     for ii, _ in enumerate(data["atom_names"]):

dpdata/gaussian/gjf.py

@@ -186,8 +186,8 @@ def make_gaussian_input(
             mult_frags.append(detect_multiplicity(np.array(symbols)[idx]))
         if use_fragment_guesses:
             multiplicity = sum(mult_frags) - frag_numb + 1 - charge % 2
-            chargekeywords_frag = "%d %d" % (charge, multiplicity) + "".join(
-                [" %d %d" % (charge, mult_frag) for mult_frag in mult_frags]
+            chargekeywords_frag = "%d %d" % (charge, multiplicity) + "".join(  # noqa: UP031
+                [" %d %d" % (charge, mult_frag) for mult_frag in mult_frags]  # noqa: UP031
             )
         else:
             multi_frags = np.array(mult_frags)
@@ -239,10 +239,10 @@ def make_gaussian_input(
     for ii, (symbol, coordinate) in enumerate(zip(symbols, coordinates)):
         if use_fragment_guesses:
             buff.append(
-                "%s(Fragment=%d) %f %f %f" % (symbol, frag_index[ii] + 1, *coordinate)
+                "%s(Fragment=%d) %f %f %f" % (symbol, frag_index[ii] + 1, *coordinate)  # noqa: UP031
             )
         else:
-            buff.append("{} {:f} {:f} {:f}".format(symbol, *coordinate))
+            buff.append("{} {:f} {:f} {:f}".format(symbol, *coordinate))  # noqa: UP031
     if not sys_data.get("nopbc", False):
         # PBC condition
         cell = sys_data["cells"][0]

dpdata/lammps/dump.py

@@ -289,7 +289,7 @@ def system_data(
     system["atom_names"] = []
     if type_map is None:
         for ii in range(len(system["atom_numbs"])):
-            system["atom_names"].append("TYPE_%d" % ii)
+            system["atom_names"].append("TYPE_%d" % ii)  # noqa: UP031
     else:
         assert len(type_map) >= len(system["atom_numbs"])
         for ii in range(len(system["atom_numbs"])):