[pre-commit.ci] pre-commit autoupdate (#1171)

<!--pre-commit.ci start-->
updates:
- [github.com/psf/black: 22.12.0 →
23.1.0](psf/black@22.12.0...23.1.0)
- [github.com/charliermarsh/ruff-pre-commit: v0.0.253 →
v0.0.259](astral-sh/ruff-pre-commit@v0.0.253...v0.0.259)
<!--pre-commit.ci end-->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -20,11 +20,11 @@ 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/charliermarsh/ruff-pre-commit
-    rev: v0.0.253
+    rev: v0.0.259
     hooks:
     - id: ruff
       args: ["--fix"]

dpgen/auto_test/Lammps.py

@@ -31,7 +31,6 @@ def __init__(self, inter_parameter, path_to_poscar):
         self.set_inter_type_func()
 
     def set_inter_type_func(self):
-
         if self.inter_type == "deepmd":
             self.inter_func = inter_deepmd
 
@@ -45,7 +44,6 @@ def set_inter_type_func(self):
             self.inter_func = inter_eam_alloy
 
     def set_model_param(self):
-
         if self.inter_type == "deepmd":
             model_name = os.path.basename(self.model)
             deepmd_version = self.inter.get("deepmd_version", "1.2.0")

dpgen/auto_test/common_equi.py

@@ -183,7 +183,6 @@ def run_equi(confs, inter_param, mdata):
             "API version %s has been removed. Please upgrade to 1.0." % api_version
         )
     elif Version(api_version) >= Version("1.0"):
-
         submission = make_submission(
             mdata_machine=machine,
             mdata_resources=resources,

dpgen/auto_test/gen_confs.py

@@ -93,7 +93,6 @@ def gen_element_std(ele_name):
 
 
 def gen_alloy(eles, key):
-
     mpr = MPRester(key)
 
     data = mpr.query(

dpgen/auto_test/lib/util.py

@@ -37,7 +37,6 @@ def insert_data(task, task_type, username, file_name):
 
 
 def make_work_path(jdata, task, reprod_opt, static, user):
-
     task_type = jdata["task_type"]
     conf_dir = jdata["conf_dir"]
     conf_path = os.path.abspath(conf_dir)
@@ -94,7 +93,6 @@ def get_machine_info(mdata, task_type):
 
 
 def collect_task(all_task, task_type):
-
     if task_type == "vasp":
         output_file = "OUTCAR"
         check_finished = vasp.check_finished

dpgen/data/surf.py

@@ -228,7 +228,6 @@ def poscar_elong(poscar_in, poscar_out, elong, shift_center=True):
 
 
 def make_unit_cell(jdata):
-
     from_poscar = jdata.get("from_poscar", False)
     if not from_poscar:
         latt = jdata["latt"]
@@ -249,7 +248,6 @@ def make_unit_cell(jdata):
 
 
 def make_super_cell_pymatgen(jdata):
-
     make_unit_cell(jdata)
     out_dir = jdata["out_dir"]
     path_uc = os.path.join(out_dir, global_dirname_02)

dpgen/database/run.py

@@ -55,7 +55,6 @@ def _main(param):
 
 
 def parsing_vasp(path, config_info_dict, skip_init, output=OUTPUT, id_prefix=None):
-
     fp_iters = os.path.join(path, ITERS_PAT)
     dlog.debug(fp_iters)
     f_fp_iters = glob(fp_iters)
@@ -114,7 +113,7 @@ def _parsing_vasp(paths, config_info_dict, id_prefix, iters=True):
                 iter_info = tmp_iter.split(".")[-1]
                 sys_info = path.split("/")[-4]
                 config_info_int = int(tmp_.split(".")[1])
-                for (key, value) in config_info_dict.items():
+                for key, value in config_info_dict.items():
                     if config_info_int in value:
                         config_info = key
                 attrib["config_info"] = config_info

dpgen/dispatcher/Dispatcher.py

@@ -20,7 +20,6 @@ def make_submission(
     outlog,
     errlog,
 ):
-
     if mdata_machine["local_root"] != "./":
         raise RuntimeError(f"local_root must be './' in dpgen's machine.json.")
 

dpgen/generator/lib/calypso_check_outcar.py

@@ -90,7 +90,6 @@ def Write_Outcar(element, ele, volume, lat, pos, ene, force, stress, pstress):
 
 
 def check():
-
     from ase.io import read
     from deepmd.calculator import DP
 

dpgen/generator/lib/calypso_run_model_devi.py

@@ -34,7 +34,6 @@ def write_model_devi_out(devi, fname):
 
 
 def Modd(all_models, type_map):
-
     # Model Devi
 
     cwd = os.getcwd()
@@ -44,7 +43,6 @@ def Modd(all_models, type_map):
     pcount = 0
     strus_lists = glob.glob(os.path.join(cwd, "*.structures"))
     for num, strus_path in enumerate(strus_lists):
-
         structures_data = dpdata.System(strus_path, "deepmd/npy", type_map=type_map)
 
         # every 500 confs in one task dir
@@ -115,7 +113,6 @@ def Modd(all_models, type_map):
 
 
 if __name__ == "__main__":
-
     cwd = os.getcwd()
     model_path = os.path.join(
         os.path.abspath(os.path.join(cwd, os.pardir)), "gen_stru_analy"

dpgen/generator/lib/lammps.py

@@ -213,7 +213,6 @@ def get_all_dumped_forces(file_name):
     exist_atoms = False
 
     for idx, ii in enumerate(lines):
-
         if "ITEM: NUMBER OF ATOMS" in ii:
             natoms = int(lines[idx + 1])
             exist_natoms = True

dpgen/generator/lib/make_calypso.py

@@ -129,7 +129,6 @@ def make_calypso_input(
 
 
 def _make_model_devi_buffet(jdata, calypso_run_opt_path):
-
     calypso_input_path = jdata.get("calypso_input_path")
     if jdata.get("vsc", False):
         # [input.dat.Li.250, input.dat.Li.300]
@@ -164,7 +163,6 @@ def _make_model_devi_buffet(jdata, calypso_run_opt_path):
 
 
 def _make_model_devi_native_calypso(iter_index, model_devi_jobs, calypso_run_opt_path):
-
     for iiidx, jobbs in enumerate(model_devi_jobs):
         if iter_index in jobbs.get("times"):
             cur_job = model_devi_jobs[iiidx]

dpgen/generator/lib/parse_calypso.py

@@ -4,7 +4,6 @@
 
 
 def _parse_calypso_input(var, input_path):
-
     if os.path.basename(input_path) != "input.dat":
         input_path = os.path.join(input_path, "input.dat")
     if not os.path.exists(input_path):

dpgen/generator/lib/run_calypso.py

@@ -37,7 +37,6 @@
 def gen_structures(
     iter_index, jdata, mdata, caly_run_path, current_idx, length_of_caly_runopt_list
 ):
-
     # run calypso
     # vsc means generate elemental, binary and ternary at the same time
     vsc = jdata.get("vsc", False)  # take CALYPSO as confs generator
@@ -343,7 +342,6 @@ def gen_structures(
 
 
 def gen_main(iter_index, jdata, mdata, caly_run_opt_list, gen_idx):
-
     iter_name = make_iter_name(iter_index)
     work_path = os.path.join(iter_name, model_devi_name)
 
@@ -456,7 +454,6 @@ def analysis(iter_index, jdata, calypso_model_devi_path):
 
 
 def run_calypso_model_devi(iter_index, jdata, mdata):
-
     dlog.info("start running CALYPSO")
 
     iter_name = make_iter_name(iter_index)

dpgen/generator/run.py

@@ -662,7 +662,6 @@ def run_train(iter_index, jdata, mdata):
     if Version(mdata["deepmd_version"]) >= Version("1") and Version(
         mdata["deepmd_version"]
     ) < Version("3"):
-
         # 1.x
         ## Commands are like `dp train` and `dp freeze`
         ## train_command should not be None
@@ -1783,7 +1782,6 @@ def _make_model_devi_amber(
 
 
 def run_md_model_devi(iter_index, jdata, mdata):
-
     # rmdlog.info("This module has been run !")
     model_devi_exec = mdata["model_devi_command"]
 
@@ -1842,7 +1840,6 @@ def run_md_model_devi(iter_index, jdata, mdata):
             if use_plm_path:
                 forward_files += ["plmpath.pdb"]
     elif model_devi_engine == "gromacs":
-
         gromacs_settings = jdata.get("gromacs_settings", {})
         mdp_filename = gromacs_settings.get("mdp_filename", "md.mdp")
         topol_filename = gromacs_settings.get("topol_filename", "processed.top")
@@ -1956,7 +1953,6 @@ def run_md_model_devi(iter_index, jdata, mdata):
 
 
 def run_model_devi(iter_index, jdata, mdata):
-
     model_devi_engine = jdata.get("model_devi_engine", "lammps")
     if model_devi_engine != "calypso":
         run_md_model_devi(iter_index, jdata, mdata)
@@ -3851,7 +3847,6 @@ def run_fp(iter_index, jdata, mdata):
 
 
 def post_fp_check_fail(iter_index, jdata, rfailed=None):
-
     ratio_failed = rfailed if rfailed else jdata.get("ratio_failed", 0.05)
     iter_name = make_iter_name(iter_index)
     work_path = os.path.join(iter_name, fp_name)
@@ -3880,7 +3875,6 @@ def post_fp_check_fail(iter_index, jdata, rfailed=None):
 
 
 def post_fp_vasp(iter_index, jdata, rfailed=None):
-
     ratio_failed = rfailed if rfailed else jdata.get("ratio_failed", 0.05)
     model_devi_engine = jdata.get("model_devi_engine", "lammps")
     if model_devi_engine != "calypso":
@@ -4169,7 +4163,6 @@ def post_fp_gaussian(iter_index, jdata):
 
 
 def post_fp_cp2k(iter_index, jdata, rfailed=None):
-
     ratio_failed = rfailed if rfailed else jdata.get("ratio_failed", 0.10)
     model_devi_jobs = jdata["model_devi_jobs"]
     assert iter_index < len(model_devi_jobs)
@@ -4230,7 +4223,6 @@ def post_fp_cp2k(iter_index, jdata, rfailed=None):
 
 
 def post_fp_pwmat(iter_index, jdata, rfailed=None):
-
     ratio_failed = rfailed if rfailed else jdata.get("ratio_failed", 0.05)
     model_devi_jobs = jdata["model_devi_jobs"]
     assert iter_index < len(model_devi_jobs)
@@ -4355,7 +4347,6 @@ def post_fp(iter_index, jdata):
 
 
 def set_version(mdata):
-
     deepmd_version = "1"
     mdata["deepmd_version"] = deepmd_version
     return mdata

dpgen/tools/auto_gen_param.py

@@ -1,4 +1,4 @@
-#%%
+# %%
 import argparse
 import json
 import os
@@ -212,7 +212,6 @@ def get_model_devi_jobs(
     temps_intervel=0.1,
     num_temps=5,
 ):
-
     if temps_iterator is None:
         temps_iterator = default_temps_generator(
             melt_point=melt_point, temps_intervel=temps_intervel, num_temps=num_temps
@@ -243,7 +242,6 @@ def get_sys_configs(system_list):
 
 
 def get_init_data_sys(scan_dir="./", init_file_name="type.raw"):
-
     init_data_sys = []
     for t in os.walk(scan_dir):
         if init_file_name in t[2]:
@@ -272,7 +270,6 @@ def get_basic_param_json(
     temps_intervel=0.1,
     num_temps=5,
 ):
-
     init_data_sys = get_init_data_sys(scan_dir=scan_dir, init_file_name=init_file_name)
     print(f"length of init_data_sys: {len(init_data_sys)} {init_data_sys}")
     system_dict = scan_files(scan_dir, file_name, min_allow_files_num)
@@ -336,4 +333,4 @@ def auto_gen_param(args):
         raise RuntimeError("must provide melt point or PARAM")
 
 
-#%%
+# %%

tests/auto_test/test_elastic.py

@@ -67,7 +67,6 @@ def test_task_param(self):
         self.assertEqual(self.prop_param[0], self.elastic.task_param())
 
     def test_make_confs(self):
-
         shutil.copy(
             os.path.join(self.source_path, "Al-fcc.json"),
             os.path.join(self.equi_path, "result.json"),

tests/auto_test/test_eos.py

@@ -74,7 +74,6 @@ def test_task_param(self):
         self.assertEqual(self.prop_param[0], self.eos.task_param())
 
     def test_make_confs_0(self):
-
         if not os.path.exists(os.path.join(self.equi_path, "CONTCAR")):
             with self.assertRaises(RuntimeError):
                 self.eos.make_confs(self.target_path, self.equi_path)

tests/auto_test/test_refine.py

@@ -59,7 +59,6 @@ def tearDown(self):
             shutil.rmtree("confs/std-fcc/relaxation")
 
     def test_make_eos(self):
-
         pwd = os.getcwd()
         confs = self.jdata["structures"]
         inter_param = self.jdata["interaction"]

tests/data/test_coll_abacus.py

@@ -40,7 +40,6 @@ def tearDown(self):
         shutil.rmtree(self.odir)
 
     def test_coll(self):
-
         with open(abacus_param_file, "r") as fp:
             jdata = json.load(fp)
         jdata["out_dir"] = self.odir

tests/data/test_coll_vasp.py

@@ -49,7 +49,6 @@ def tearDown(self):
         shutil.rmtree(self.odir)
 
     def test_coll(self):
-
         with open(param_file, "r") as fp:
             jdata = json.load(fp)
         jdata["out_dir"] = self.odir

tests/database/test_db_vasp.py

@@ -51,7 +51,6 @@ def setUp(self):
         self.output = jdata["output"]
 
     def testDPPotcar(self):
-
         refd = {
             "@module": "dpgen.database.vasp",
             "@class": "DPPotcar",

tests/generator/test_post_fp.py

@@ -76,7 +76,6 @@ def tearDown(self):
         shutil.rmtree("iter.000000")
 
     def test_post_fp_vasp_0(self):
-
         with open(param_file, "r") as fp:
             jdata = json.load(fp)
         jdata["use_ele_temp"] = 2
@@ -127,7 +126,6 @@ def test_post_fp_vasp_0(self):
         self.assertEqual(list(list(aparam)[1]), [1, 1])
 
     def test_post_fp_vasp_1(self):
-
         with open(param_file, "r") as fp:
             jdata = json.load(fp)
         jdata["use_ele_temp"] = 1