apply ruff rules and fix lots of bugs

doc/conf.py

@@ -11,13 +11,10 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
-import subprocess
 import sys
 from datetime import date
 
 # import sys
-import recommonmark
-from recommonmark.transform import AutoStructify
 
 # -- Project information -----------------------------------------------------
 

dpgen/__init__.py

@@ -1,5 +1,3 @@
-from __future__ import print_function, unicode_literals
-
 import logging
 import os
 

dpgen/arginfo.py

@@ -20,7 +20,6 @@ def general_mdata_arginfo(name: str, tasks: Tuple[str]) -> Argument:
     Argument
         arginfo
     """
-
     doc_api_version = "Please set to 1.0"
     doc_deepmd_version = "DeePMD-kit version, e.g. 2.1.3"
     doc_run_mdata = "machine.json file"

dpgen/auto_test/ABACUS.py

@@ -1,6 +1,5 @@
 import os
 
-import numpy as np
 from dpdata import LabeledSystem
 from monty.serialization import dumpfn
 
@@ -22,7 +21,7 @@ def __init__(self, inter_parameter, path_to_poscar):
         self.deepks = inter_parameter.get("deepks_desc", None)
         self.deepks_model = inter_parameter.get("deepks_model", None)
         self.path_to_poscar = path_to_poscar
-        self.if_define_orb_file = False if self.orbfile == None else True
+        self.if_define_orb_file = False if self.orbfile is None else True
 
     def make_potential_files(self, output_dir):
         stru = os.path.abspath(os.path.join(output_dir, "STRU"))
@@ -41,7 +40,7 @@ def make_potential_files(self, output_dir):
         else:
             stru_path = output_dir
 
-        if pp_files == None:
+        if pp_files is None:
             raise RuntimeError("No pseudopotential information in STRU file")
 
         pp_dir = os.path.abspath(self.potcar_prefix)
@@ -101,8 +100,7 @@ def make_potential_files(self, output_dir):
             filename_in_para = os.path.split(file_param)[1]
             if filename_in_stru != filename_in_para:
                 dlog.warning(
-                    "file name in STRU is not match that defined in parameter setting file: '%s', '%s'."
-                    % (filename_in_stru, filename_in_para)
+                    f"file name in STRU is not match that defined in parameter setting file: '{filename_in_stru}', '{filename_in_para}'."
                 )
 
             src_file = os.path.join(pp_dir, file_param)
@@ -119,7 +117,7 @@ def make_potential_files(self, output_dir):
 
     def modify_input(self, incar, x, y):
         if x in incar and incar[x] != y:
-            dlog.info("setting %s to %s" % (x, y))
+            dlog.info(f"setting {x} to {y}")
         incar[x] = y
 
     def make_input_file(self, output_dir, task_type, task_param):

dpgen/auto_test/EOS.py

@@ -76,7 +76,7 @@ def __init__(self, parameter, inter_param=None):
             parameter["init_from_suffix"] = parameter.get("init_from_suffix", "00")
             self.init_from_suffix = parameter["init_from_suffix"]
         self.parameter = parameter
-        self.inter_param = inter_param if inter_param != None else {"type": "vasp"}
+        self.inter_param = inter_param if inter_param is not None else {"type": "vasp"}
 
     def make_confs(self, path_to_work, path_to_equi, refine=False):
         path_to_work = os.path.abspath(path_to_work)
@@ -259,7 +259,7 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                 res_data[vol] = task_result["energies"][-1] / sum(
                     task_result["atom_numbs"]
                 )
-                ptr_data += "%7.3f  %8.4f \n" % (
+                ptr_data += "{:7.3f}  {:8.4f} \n".format(
                     vol,
                     task_result["energies"][-1] / sum(task_result["atom_numbs"]),
                 )

dpgen/auto_test/Elastic.py

@@ -50,7 +50,7 @@ def __init__(self, parameter, inter_param=None):
         # parameter['reproduce'] = False
         # self.reprod = parameter['reproduce']
         self.parameter = parameter
-        self.inter_param = inter_param if inter_param != None else {"type": "vasp"}
+        self.inter_param = inter_param if inter_param is not None else {"type": "vasp"}
 
     def make_confs(self, path_to_work, path_to_equi, refine=False):
         path_to_work = os.path.abspath(path_to_work)

dpgen/auto_test/Gamma.py

@@ -7,10 +7,8 @@
 import numpy as np
 from ase.lattice.cubic import BodyCenteredCubic as bcc
 from ase.lattice.cubic import FaceCenteredCubic as fcc
-from ase.lattice.hexagonal import HexagonalClosedPacked as hcp
 from monty.serialization import dumpfn, loadfn
 from pymatgen.core.structure import Structure
-from pymatgen.core.surface import SlabGenerator
 from pymatgen.io.ase import AseAtomsAdaptor
 
 import dpgen.auto_test.lib.abacus as abacus
@@ -22,9 +20,7 @@
 
 
 class Gamma(Property):
-    """
-    Calculation of common gamma lines for bcc and fcc
-    """
+    """Calculation of common gamma lines for bcc and fcc."""
 
     def __init__(self, parameter, inter_param=None):
         parameter["reproduce"] = parameter.get("reproduce", False)
@@ -95,7 +91,7 @@ def __init__(self, parameter, inter_param=None):
             parameter["init_from_suffix"] = parameter.get("init_from_suffix", "00")
             self.init_from_suffix = parameter["init_from_suffix"]
         self.parameter = parameter
-        self.inter_param = inter_param if inter_param != None else {"type": "vasp"}
+        self.inter_param = inter_param if inter_param is not None else {"type": "vasp"}
 
     def make_confs(self, path_to_work, path_to_equi, refine=False):
         path_to_work = os.path.abspath(path_to_work)
@@ -359,7 +355,7 @@ def __poscar_fix(self, poscar) -> None:
             + fix_dict[self.add_fix[2]]
             + "\n"
         )
-        with open(poscar, "r") as fin1:
+        with open(poscar) as fin1:
             contents = fin1.readlines()
             contents.insert(insert_pos - 1, "Selective dynamics\n")
             for ii in range(insert_pos, 0, 1):
@@ -387,7 +383,7 @@ def __inLammpes_fix(self, inLammps) -> None:
             + fix_dict[self.add_fix[2]]
             + "\n"
         )
-        with open(inLammps, "r") as fin1:
+        with open(inLammps) as fin1:
             contents = fin1.readlines()
             for ii in range(len(contents)):
                 upper = re.search("variable        N equal count\(all\)", contents[ii])

dpgen/auto_test/Interstitial.py

@@ -10,7 +10,6 @@
 
 import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.lammps as lammps
-import dpgen.generator.lib.abacus_scf as abacus_scf
 from dpgen.auto_test.Property import Property
 from dpgen.auto_test.refine import make_refine
 from dpgen.auto_test.reproduce import make_repro, post_repro
@@ -76,7 +75,7 @@ def __init__(self, parameter, inter_param=None):
             parameter["init_from_suffix"] = parameter.get("init_from_suffix", "00")
             self.init_from_suffix = parameter["init_from_suffix"]
         self.parameter = parameter
-        self.inter_param = inter_param if inter_param != None else {"type": "vasp"}
+        self.inter_param = inter_param if inter_param is not None else {"type": "vasp"}
 
     def make_confs(self, path_to_work, path_to_equi, refine=False):
         path_to_work = os.path.abspath(path_to_work)
@@ -248,7 +247,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     num_atom = super_size * 2
                     chl = -num_atom - 2
                     os.chdir(path_to_work)
-                    with open("POSCAR", "r") as fin:
+                    with open("POSCAR") as fin:
                         fin.readline()
                         scale = float(fin.readline().split()[0])
                         latt_param = float(fin.readline().split()[0])
@@ -257,7 +256,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     if not os.path.isfile("task.000000/POSCAR"):
                         raise RuntimeError("need task.000000 structure as reference")
 
-                    with open("task.000000/POSCAR", "r") as fin:
+                    with open("task.000000/POSCAR") as fin:
                         pos_line = fin.read().split("\n")
 
                     super_latt_param = float(pos_line[2].split()[0])
@@ -467,13 +466,13 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
     def post_process(self, task_list):
         if True:
-            fin1 = open(os.path.join(task_list[0], "..", "element.out"), "r")
+            fin1 = open(os.path.join(task_list[0], "..", "element.out"))
             for ii in task_list:
                 conf = os.path.join(ii, "conf.lmp")
                 inter = os.path.join(ii, "inter.json")
                 insert_ele = fin1.readline().split()[0]
                 if os.path.isfile(conf):
-                    with open(conf, "r") as fin2:
+                    with open(conf) as fin2:
                         conf_line = fin2.read().split("\n")
                         insert_line = conf_line[-2]
                     type_map = loadfn(inter)["type_map"]
@@ -505,9 +504,7 @@ def _compute_lower(self, output_file, all_tasks, all_res):
         ptr_data = os.path.dirname(output_file) + "\n"
 
         if not self.reprod:
-            with open(
-                os.path.join(os.path.dirname(output_file), "element.out"), "r"
-            ) as fin:
+            with open(os.path.join(os.path.dirname(output_file), "element.out")) as fin:
                 fc = fin.read().split("\n")
             ptr_data += "Insert_ele-Struct: Inter_E(eV)  E(eV) equi_E(eV)\n"
             idid = -1
@@ -528,7 +525,7 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                 supercell_index = loadfn(os.path.join(ii, "supercell.json"))
                 # insert_ele = loadfn(os.path.join(ii, 'task.json'))['insert_ele'][0]
                 insert_ele = fc[idid]
-                ptr_data += "%s: %7.3f  %7.3f %7.3f \n" % (
+                ptr_data += "{}: {:7.3f}  {:7.3f} {:7.3f} \n".format(
                     insert_ele + "-" + str(supercell_index) + "-" + structure_dir,
                     evac,
                     task_result["energies"][-1],

dpgen/auto_test/Lammps.py

@@ -138,36 +138,40 @@ def make_input_file(self, output_dir, task_type, task_param):
 
         # deal with user input in.lammps for relaxation
         if os.path.isfile(self.in_lammps) and task_type == "relaxation":
-            with open(self.in_lammps, "r") as fin:
+            with open(self.in_lammps) as fin:
                 fc = fin.read()
         # user input in.lammps for property calculation
         if "input_prop" in cal_setting and os.path.isfile(cal_setting["input_prop"]):
-            with open(os.path.abspath(cal_setting["input_prop"]), "r") as fin:
+            with open(os.path.abspath(cal_setting["input_prop"])) as fin:
                 fc = fin.read()
 
         else:
             if "etol" in cal_setting:
                 dlog.info(
-                    "%s setting etol to %s"
-                    % (self.make_input_file.__name__, cal_setting["etol"])
+                    "{} setting etol to {}".format(
+                        self.make_input_file.__name__, cal_setting["etol"]
+                    )
                 )
                 etol = cal_setting["etol"]
             if "ftol" in cal_setting:
                 dlog.info(
-                    "%s setting ftol to %s"
-                    % (self.make_input_file.__name__, cal_setting["ftol"])
+                    "{} setting ftol to {}".format(
+                        self.make_input_file.__name__, cal_setting["ftol"]
+                    )
                 )
                 ftol = cal_setting["ftol"]
             if "maxiter" in cal_setting:
                 dlog.info(
-                    "%s setting maxiter to %s"
-                    % (self.make_input_file.__name__, cal_setting["maxiter"])
+                    "{} setting maxiter to {}".format(
+                        self.make_input_file.__name__, cal_setting["maxiter"]
+                    )
                 )
                 maxiter = cal_setting["maxiter"]
             if "maxeval" in cal_setting:
                 dlog.info(
-                    "%s setting maxeval to %s"
-                    % (self.make_input_file.__name__, cal_setting["maxeval"])
+                    "{} setting maxeval to {}".format(
+                        self.make_input_file.__name__, cal_setting["maxeval"]
+                    )
                 )
                 maxeval = cal_setting["maxeval"]
 
@@ -300,7 +304,7 @@ def compute(self, output_dir):
             force = []
             virial = []
             stress = []
-            with open(dump_lammps, "r") as fin:
+            with open(dump_lammps) as fin:
                 dump = fin.read().split("\n")
             dumptime = []
             for idx, ii in enumerate(dump):
@@ -354,7 +358,7 @@ def compute(self, output_dir):
                         fz = float(dump[idx + 9 + jj].split()[7])
                         force[-1].append([fx, fy, fz])
 
-            with open(log_lammps, "r") as fp:
+            with open(log_lammps) as fp:
                 if "Total wall time:" not in fp.read():
                     warnings.warn("lammps not finished " + log_lammps + " skip")
                     return None

dpgen/auto_test/Property.py

@@ -11,8 +11,7 @@
 class Property(ABC):
     @abstractmethod
     def __init__(self, parameter):
-        """
-        Constructor
+        """Constructor.
 
         Parameters
         ----------
@@ -23,8 +22,7 @@ def __init__(self, parameter):
 
     @abstractmethod
     def make_confs(self, path_to_work, path_to_equi, refine=False):
-        """
-        Make configurations needed to compute the property.
+        """Make configurations needed to compute the property.
         The tasks directory will be named as path_to_work/task.xxxxxx
         IMPORTANT: handel the case when the directory exists.
 
@@ -47,31 +45,24 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
     @abstractmethod
     def post_process(self, task_list):
-        """
-        post_process the KPOINTS file in elastic.
-        """
+        """post_process the KPOINTS file in elastic."""
         pass
 
     @property
     @abstractmethod
     def task_type(self):
-        """
-        Return the type of each computational task, for example, 'relaxation', 'static'....
-        """
+        """Return the type of each computational task, for example, 'relaxation', 'static'...."""
         pass
 
     @property
     @abstractmethod
     def task_param(self):
-        """
-        Return the parameter of each computational task, for example, {'ediffg': 1e-4}
-        """
+        """Return the parameter of each computational task, for example, {'ediffg': 1e-4}."""
         pass
 
     def compute(self, output_file, print_file, path_to_work):
-        """
-        Postprocess the finished tasks to compute the property.
-        Output the result to a json database
+        """Postprocess the finished tasks to compute the property.
+        Output the result to a json database.
 
         Parameters
         ----------
@@ -107,8 +98,7 @@ def compute(self, output_file, print_file, path_to_work):
 
     @abstractmethod
     def _compute_lower(self, output_file, all_tasks, all_res):
-        """
-        Compute the property.
+        """Compute the property.
 
         Parameters
         ----------

dpgen/auto_test/Surface.py

@@ -11,7 +11,6 @@
 
 import dpgen.auto_test.lib.abacus as abacus
 import dpgen.auto_test.lib.vasp as vasp
-import dpgen.generator.lib.abacus_scf as abacus_scf
 from dpgen import dlog
 from dpgen.auto_test.Property import Property
 from dpgen.auto_test.refine import make_refine
@@ -83,7 +82,7 @@ def __init__(self, parameter, inter_param=None):
             parameter["init_from_suffix"] = parameter.get("init_from_suffix", "00")
             self.init_from_suffix = parameter["init_from_suffix"]
         self.parameter = parameter
-        self.inter_param = inter_param if inter_param != None else {"type": "vasp"}
+        self.inter_param = inter_param if inter_param is not None else {"type": "vasp"}
 
     def make_confs(self, path_to_work, path_to_equi, refine=False):
         path_to_work = os.path.abspath(path_to_work)