configure ruff

.github/workflows/test.yml

@@ -23,7 +23,7 @@ jobs:
         pip install -e .[test]
         pip install mock coverage pytest
     - name: Test
-      run: SKIP_UT_WITH_DFLOW=0 DFLOW_DEBUG=1 coverage run --source=./dpgen2 -m unittest -v -f && coverage report
+      run: SKIP_UT_WITH_DFLOW=0 DFLOW_DEBUG=1 coverage run --source=./dpgen2 -m unittest -v && coverage report
     - uses: codecov/codecov-action@v4
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -17,11 +17,13 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.3
+    rev: v0.6.3
     hooks:
+    - id: ruff
+      args: ["--fix"]
     - id: ruff-format
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
     - id: isort
     files: \.py$

docs/conf.py

@@ -6,20 +6,21 @@
 
 # -- Path setup --------------------------------------------------------------
 
+import datetime
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
 import sys
-from datetime import (
-    date,
-)
 
 # -- Project information -----------------------------------------------------
 
 project = "DPGEN2"
-copyright = "2022-%d, DeepModeling" % date.today().year
+copyright = (
+    "2022-%d, DeepModeling" % datetime.datetime.now(tz=datetime.timezone.utc).year
+)
 author = "DeepModeling"
 
 

docs/input.md

@@ -70,11 +70,11 @@ This section defines how the configuration space is explored.
 		"command": "lmp -var restart 0"
 	},
 	"convergence": {
-	    "type" :	"fixed-levels",
-	    "conv_accuracy" :	0.9,
-	    "level_f_lo":	0.05,
-	    "level_f_hi":	0.50,
-	    "_comment" : "all"
+        "type" :	"fixed-levels",
+        "conv_accuracy" :	0.9,
+        "level_f_lo":	0.05,
+        "level_f_hi":	0.50,
+        "_comment" : "all"
 	},
 	"max_numb_iter" :	5,
 	"fatal_at_max" :	false,
@@ -94,29 +94,29 @@ This section defines how the configuration space is explored.
 		}
 	],
 	"stages":	[
-	    [
+        [
 		{
-		    "_comment" : "stage 0, task group 0",
-		    "type" : "lmp-md",
-		    "ensemble": "nvt", "nsteps":  50, "temps": [50, 100], "trj_freq": 10,
-		    "conf_idx": [0], "n_sample" : 3
+            "_comment" : "stage 0, task group 0",
+            "type" : "lmp-md",
+            "ensemble": "nvt", "nsteps":  50, "temps": [50, 100], "trj_freq": 10,
+            "conf_idx": [0], "n_sample" : 3
 		},
 		{
-		    "_comment" : "stage 0, task group 1",
-		    "type" : "lmp-template",
-		    "lmp" : "template.lammps", "plm" : "template.plumed",
-		    "trj_freq" : 10, "revisions" : {"V_NSTEPS" : [40], "V_TEMP" : [150, 200]},
-		    "conf_idx": [0], "n_sample" : 3
+            "_comment" : "stage 0, task group 1",
+            "type" : "lmp-template",
+            "lmp" : "template.lammps", "plm" : "template.plumed",
+            "trj_freq" : 10, "revisions" : {"V_NSTEPS" : [40], "V_TEMP" : [150, 200]},
+            "conf_idx": [0], "n_sample" : 3
 		}
-	    ],
-	    [
+        ],
+        [
 		{
-		    "_comment" : "stage 1, task group 0",
-		    "type" : "lmp-md",
-		    "ensemble": "npt", "nsteps":  50, "press": [1e0], "temps": [50, 100, 200], "trj_freq": 10,
-		    "conf_idx": [1], "n_sample" : 3
+            "_comment" : "stage 1, task group 0",
+            "type" : "lmp-md",
+            "ensemble": "npt", "nsteps":  50, "press": [1e0], "temps": [50, 100, 200], "trj_freq": 10,
+            "conf_idx": [1], "n_sample" : 3
 		}
-	    ]
+        ]
 	]
 }
 ```
@@ -197,7 +197,7 @@ Any of the config in the {dargs:argument}`"step_configs"<step_configs>` can be o
 ```json
 "default_step_config" : {
 	"template_config" : {
-	    "image" : "dpgen2:x.x.x"
+        "image" : "dpgen2:x.x.x"
 	}
 },
 ```

dpgen2/__init__.py

@@ -4,3 +4,6 @@
     from .__about__ import (
         __version__,
     )
+
+
+__all__ = ["__version__"]

dpgen2/conf/__init__.py

@@ -12,3 +12,11 @@
     "alloy": AlloyConfGenerator,
     "file": FileConfGenerator,
 }
+
+
+__all__ = [
+    "AlloyConfGenerator",
+    "ConfGenerator",
+    "FileConfGenerator",
+    "conf_styles",
+]

dpgen2/conf/alloy_conf.py

@@ -5,7 +5,6 @@
 )
 from typing import (
     List,
-    Optional,
     Tuple,
     Union,
 )
@@ -14,7 +13,6 @@
 import numpy as np
 from dargs import (
     Argument,
-    Variant,
 )
 
 from .conf_generator import (
@@ -184,7 +182,7 @@ def __init__(
         sys.data["atom_numbs"] = [0] * self.ntypes
         sys.data["atom_numbs"][0] = self.natoms
         sys.data["atom_types"] = np.array([0] * self.natoms, dtype=int)
-        self.type_population = [ii for ii in range(self.ntypes)]
+        self.type_population = list(range(self.ntypes))
         # record sys
         self.sys = sys
 

dpgen2/conf/conf_generator.py

@@ -41,7 +41,7 @@ def get_file_content(
         type_map,
         fmt="lammps/lmp",
     ) -> List[str]:
-        r"""Get the file content of configurations
+        r"""Get the file content of configurations.
 
         Parameters
         ----------

dpgen2/conf/file_conf.py

@@ -1,19 +1,16 @@
 import glob
-import os
 from pathlib import (
     Path,
 )
 from typing import (
     List,
     Optional,
-    Tuple,
     Union,
 )
 
 import dpdata
 from dargs import (
     Argument,
-    Variant,
 )
 
 from .conf_generator import (

dpgen2/conf/unit_cells.py

@@ -40,16 +40,16 @@ def gen_box(self):
     def poscar_unit(self, latt):
         box = self.gen_box()
         ret = ""
-        ret += "BCC : a = %f \n" % latt
-        ret += "%.16f\n" % (latt)
-        ret += "%.16f %.16f %.16f\n" % (box[0][0], box[0][1], box[0][2])
-        ret += "%.16f %.16f %.16f\n" % (box[1][0], box[1][1], box[1][2])
-        ret += "%.16f %.16f %.16f\n" % (box[2][0], box[2][1], box[2][2])
+        ret += f"BCC : a = {latt:f} \n"
+        ret += f"{latt:.16f}\n"
+        ret += f"{box[0][0]:.16f} {box[0][1]:.16f} {box[0][2]:.16f}\n"
+        ret += f"{box[1][0]:.16f} {box[1][1]:.16f} {box[1][2]:.16f}\n"
+        ret += f"{box[2][0]:.16f} {box[2][1]:.16f} {box[2][2]:.16f}\n"
         ret += "Type\n"
         ret += "%d\n" % self.numb_atoms()
         ret += "Direct\n"
-        ret += "%.16f %.16f %.16f\n" % (0.0, 0.0, 0.0)
-        ret += "%.16f %.16f %.16f\n" % (0.5, 0.5, 0.5)
+        ret += f"{0.0:.16f} {0.0:.16f} {0.0:.16f}\n"
+        ret += f"{0.5:.16f} {0.5:.16f} {0.5:.16f}\n"
         return ret
 
 
@@ -63,18 +63,18 @@ def gen_box(self):
     def poscar_unit(self, latt):
         box = self.gen_box()
         ret = ""
-        ret += "FCC : a = %f \n" % latt
-        ret += "%.16f\n" % (latt)
-        ret += "%.16f %.16f %.16f\n" % (box[0][0], box[0][1], box[0][2])
-        ret += "%.16f %.16f %.16f\n" % (box[1][0], box[1][1], box[1][2])
-        ret += "%.16f %.16f %.16f\n" % (box[2][0], box[2][1], box[2][2])
+        ret += f"FCC : a = {latt:f} \n"
+        ret += f"{latt:.16f}\n"
+        ret += f"{box[0][0]:.16f} {box[0][1]:.16f} {box[0][2]:.16f}\n"
+        ret += f"{box[1][0]:.16f} {box[1][1]:.16f} {box[1][2]:.16f}\n"
+        ret += f"{box[2][0]:.16f} {box[2][1]:.16f} {box[2][2]:.16f}\n"
         ret += "Type\n"
         ret += "%d\n" % self.numb_atoms()
         ret += "Direct\n"
-        ret += "%.16f %.16f %.16f\n" % (0.0, 0.0, 0.0)
-        ret += "%.16f %.16f %.16f\n" % (0.5, 0.5, 0.0)
-        ret += "%.16f %.16f %.16f\n" % (0.5, 0.0, 0.5)
-        ret += "%.16f %.16f %.16f\n" % (0.0, 0.5, 0.5)
+        ret += f"{0.0:.16f} {0.0:.16f} {0.0:.16f}\n"
+        ret += f"{0.5:.16f} {0.5:.16f} {0.0:.16f}\n"
+        ret += f"{0.5:.16f} {0.0:.16f} {0.5:.16f}\n"
+        ret += f"{0.0:.16f} {0.5:.16f} {0.5:.16f}\n"
         return ret
 
 
@@ -91,16 +91,16 @@ def gen_box(self):
     def poscar_unit(self, latt):
         box = self.gen_box()
         ret = ""
-        ret += "HCP : a = %f / sqrt(2)\n" % latt
+        ret += f"HCP : a = {latt:f} / sqrt(2)\n"
         ret += "%.16f\n" % (latt / np.sqrt(2))
-        ret += "%.16f %.16f %.16f\n" % (box[0][0], box[0][1], box[0][2])
-        ret += "%.16f %.16f %.16f\n" % (box[1][0], box[1][1], box[1][2])
-        ret += "%.16f %.16f %.16f\n" % (box[2][0], box[2][1], box[2][2])
+        ret += f"{box[0][0]:.16f} {box[0][1]:.16f} {box[0][2]:.16f}\n"
+        ret += f"{box[1][0]:.16f} {box[1][1]:.16f} {box[1][2]:.16f}\n"
+        ret += f"{box[2][0]:.16f} {box[2][1]:.16f} {box[2][2]:.16f}\n"
         ret += "Type\n"
         ret += "%d\n" % self.numb_atoms()
         ret += "Direct\n"
-        ret += "%.16f %.16f %.16f\n" % (0, 0, 0)
-        ret += "%.16f %.16f %.16f\n" % (1.0 / 3, 1.0 / 3, 1.0 / 2)
+        ret += f"{0:.16f} {0:.16f} {0:.16f}\n"
+        ret += f"{1.0 / 3:.16f} {1.0 / 3:.16f} {1.0 / 2:.16f}\n"
         return ret
 
 
@@ -114,15 +114,15 @@ def gen_box(self):
     def poscar_unit(self, latt):
         box = self.gen_box()
         ret = ""
-        ret += "SC : a = %f \n" % latt
-        ret += "%.16f\n" % (latt)
-        ret += "%.16f %.16f %.16f\n" % (box[0][0], box[0][1], box[0][2])
-        ret += "%.16f %.16f %.16f\n" % (box[1][0], box[1][1], box[1][2])
-        ret += "%.16f %.16f %.16f\n" % (box[2][0], box[2][1], box[2][2])
+        ret += f"SC : a = {latt:f} \n"
+        ret += f"{latt:.16f}\n"
+        ret += f"{box[0][0]:.16f} {box[0][1]:.16f} {box[0][2]:.16f}\n"
+        ret += f"{box[1][0]:.16f} {box[1][1]:.16f} {box[1][2]:.16f}\n"
+        ret += f"{box[2][0]:.16f} {box[2][1]:.16f} {box[2][2]:.16f}\n"
         ret += "Type\n"
         ret += "%d\n" % self.numb_atoms()
         ret += "Direct\n"
-        ret += "%.16f %.16f %.16f\n" % (0.0, 0.0, 0.0)
+        ret += f"{0.0:.16f} {0.0:.16f} {0.0:.16f}\n"
         return ret
 
 
@@ -142,21 +142,17 @@ def poscar_unit(self, latt):
         box = self.gen_box()
         ret = ""
         ret += "DIAMOND\n"
-        ret += "%.16f\n" % (latt)
-        ret += "%.16f %.16f %.16f\n" % (box[0][0], box[0][1], box[0][2])
-        ret += "%.16f %.16f %.16f\n" % (box[1][0], box[1][1], box[1][2])
-        ret += "%.16f %.16f %.16f\n" % (box[2][0], box[2][1], box[2][2])
+        ret += f"{latt:.16f}\n"
+        ret += f"{box[0][0]:.16f} {box[0][1]:.16f} {box[0][2]:.16f}\n"
+        ret += f"{box[1][0]:.16f} {box[1][1]:.16f} {box[1][2]:.16f}\n"
+        ret += f"{box[2][0]:.16f} {box[2][1]:.16f} {box[2][2]:.16f}\n"
         ret += "Type\n"
         ret += "%d\n" % self.numb_atoms()
         ret += "Direct\n"
-        ret += "%.16f %.16f %.16f\n" % (
-            0.12500000000000,
-            0.12500000000000,
-            0.12500000000000,
+        ret += (
+            f"{0.12500000000000:.16f} {0.12500000000000:.16f} {0.12500000000000:.16f}\n"
         )
-        ret += "%.16f %.16f %.16f\n" % (
-            0.87500000000000,
-            0.87500000000000,
-            0.87500000000000,
+        ret += (
+            f"{0.87500000000000:.16f} {0.87500000000000:.16f} {0.87500000000000:.16f}\n"
         )
         return ret

dpgen2/entrypoint/args.py

@@ -9,13 +9,9 @@
     Variant,
 )
 
-import dpgen2
 from dpgen2.conf import (
     conf_styles,
 )
-from dpgen2.constants import (
-    default_image,
-)
 from dpgen2.exploration.report import (
     conv_styles,
 )
@@ -186,7 +182,7 @@ def variant_filter():
                 kk,
                 dict,
                 conf_filter_styles[kk].args(),
-                doc="Configuration filter of type %s" % kk,
+                doc=f"Configuration filter of type {kk}",
             )
         )
     return Variant(

dpgen2/entrypoint/common.py

@@ -3,24 +3,16 @@
     Path,
 )
 from typing import (
-    Dict,
     List,
-    Optional,
     Union,
 )
 
 import dflow
 
 from dpgen2.utils import (
     bohrium_config_from_dict,
-    dump_object_to_file,
-    load_object_from_file,
-    matched_step_key,
-    print_keys_in_nice_format,
-    sort_slice_ops,
     workflow_config_from_dict,
 )
-from dpgen2.utils.step_config import normalize as normalize_step_dict
 
 
 def global_config_workflow(
@@ -64,5 +56,5 @@ def expand_idx(in_list) -> List[int]:
                 ret += [int(range_str[0])]
             else:
                 raise RuntimeError("not expected range string", step_str[0])
-    ret = sorted(list(set(ret)))
+    ret = sorted(set(ret))
     return ret

dpgen2/entrypoint/download.py

@@ -3,7 +3,6 @@
     Dict,
     List,
     Optional,
-    Union,
 )
 
 from dflow import (
@@ -14,9 +13,6 @@
 from dpgen2.entrypoint.common import (
     global_config_workflow,
 )
-from dpgen2.utils.dflow_query import (
-    matched_step_key,
-)
 from dpgen2.utils.download_dpgen2_artifacts import (
     download_dpgen2_artifacts,
     download_dpgen2_artifacts_by_def,