Enable Ruff E, W, F, RUF, NPY, and DTZ rules with comprehensive error fixes

.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@v5
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -49,6 +49,7 @@ tests/caly-*
 tests/coll-*
 tests/dpgen-*
 tests/upload
+upload/
 tests/init_data/
 tests/incar
 tests/potcar

.pre-commit-config.yaml

@@ -17,8 +17,10 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.1.3
+    rev: v0.12.12
     hooks:
+    - id: ruff
+      args: [--fix]
     - id: ruff-format
 -   repo: https://github.com/PyCQA/isort
     rev: 5.12.0

docs/conf.py

@@ -13,13 +13,14 @@
 import os
 import sys
 from datetime import (
-    date,
+    datetime,
+    timezone,
 )
 
 # -- Project information -----------------------------------------------------
 
 project = "DPGEN2"
-copyright = "2022-%d, DeepModeling" % date.today().year
+copyright = "2022-%d, DeepModeling" % datetime.now(timezone.utc).year
 author = "DeepModeling"
 
 

dpgen2/__init__.py

@@ -1,6 +1,4 @@
 try:
     from ._version import version as __version__
 except ImportError:
-    from .__about__ import (
-        __version__,
-    )
+    from .__about__ import __version__ as __version__

dpgen2/conf/__init__.py

@@ -12,3 +12,10 @@
     "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 (

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/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,
 )
@@ -83,7 +79,6 @@ def dp_dist_train_args():
 
 def dp_train_args():
     doc_numb_models = "Number of models trained for evaluating the model deviation"
-    doc_config = "Configuration of training"
     doc_template_script = "File names of the template training script. It can be a `List[str]`, the length of which is the same as `numb_models`. Each template script in the list is used to train a model. Can be a `str`, the models share the same template training script. "
     doc_init_models_paths = "the paths to initial models"
     doc_init_models_uri = "The URI of initial models"

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(

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,

dpgen2/entrypoint/main.py

@@ -1,22 +1,12 @@
 import argparse
 import json
 import logging
-import os
 import textwrap
 from typing import (
     List,
     Optional,
 )
 
-import dflow
-from dflow import (
-    Step,
-    Steps,
-    Workflow,
-    download_artifact,
-    upload_artifact,
-)
-
 from dpgen2 import (
     __version__,
 )
@@ -41,11 +31,8 @@
     status,
 )
 from .submit import (
-    make_concurrent_learning_op,
-    make_naive_exploration_scheduler,
     resubmit_concurrent_learning,
     submit_concurrent_learning,
-    workflow_concurrent_learning,
 )
 from .watch import (
     default_watching_keys,
@@ -327,7 +314,7 @@ def main():
     logging.basicConfig(level=logging.INFO)
 
     args = parse_args()
-    dict_args = vars(args)
+    vars(args)
 
     if args.command == "submit":
         with open(args.CONFIG) as fp:

dpgen2/entrypoint/showkey.py

@@ -1,11 +1,6 @@
-import glob
-import os
-import pickle
-from pathlib import (
-    Path,
-)
+import functools
+import operator
 
-import dpdata
 from dflow import (
     Workflow,
 )
@@ -32,7 +27,7 @@ def showkey(
 
     wf = Workflow(id=wf_id)
     folded_keys = get_resubmit_keys(wf)
-    all_step_keys = sum(folded_keys.values(), [])
+    all_step_keys = functools.reduce(operator.iadd, folded_keys.values(), [])
     prt_str = print_keys_in_nice_format(
         all_step_keys,
         ["run-train", "run-lmp", "run-fp", "diffcsp-gen", "run-relax"],

dpgen2/entrypoint/status.py

@@ -1,9 +1,7 @@
 import logging
 from typing import (
     Dict,
-    List,
     Optional,
-    Union,
 )
 
 from dflow import (
@@ -15,7 +13,6 @@
     global_config_workflow,
 )
 from dpgen2.utils.dflow_query import (
-    get_all_schedulers,
     get_last_scheduler,
 )