Fix E101 mixed-spaces-and-tabs errors and add __all__ to remaining modules

Co-authored-by: njzjz <[email protected]>

Author: Copilot

dpgen2/conf/__init__.py

@@ -15,7 +15,7 @@
 
 __all__ = [
     "AlloyConfGenerator",
-    "ConfGenerator", 
+    "ConfGenerator",
     "FileConfGenerator",
     "conf_styles",
 ]

dpgen2/exploration/selector/__init__.py

@@ -21,12 +21,12 @@
 }
 
 __all__ = [
+    "BoxLengthFilter",
+    "BoxSkewnessConfFilter",
     "ConfFilter",
     "ConfFilters",
     "ConfSelector",
     "ConfSelectorFrames",
-    "BoxLengthFilter",
-    "BoxSkewnessConfFilter",
     "DistanceConfFilter",
     "conf_filter_styles",
 ]

dpgen2/exploration/task/__init__.py

@@ -43,23 +43,23 @@
 )
 
 __all__ = [
+    "BaseExplorationTaskGroup",
     "CalyTaskGroup",
     "ConfSamplingTaskGroup",
     "CustomizedLmpTemplateTaskGroup",
     "DiffCSPTaskGroup",
+    "ExplorationStage",
+    "ExplorationTask",
+    "ExplorationTaskGroup",
     "LmpTemplateTaskGroup",
+    "NPTTaskGroup",
     "caly_normalize",
     "caly_task_group_args",
     "diffcsp_normalize",
-    "normalize_lmp_task_group_config",
     "lmp_task_group_args",
     "make_calypso_task_group_from_config",
     "make_diffcsp_task_group_from_config",
     "make_lmp_task_group_from_config",
+    "normalize_lmp_task_group_config",
     "variant_task_group",
-    "NPTTaskGroup",
-    "ExplorationStage",
-    "ExplorationTask",
-    "BaseExplorationTaskGroup",
-    "ExplorationTaskGroup",
 ]

dpgen2/exploration/task/calypso/__init__.py

@@ -4,3 +4,10 @@
     calypso_run_opt_str_end,
     make_calypso_input,
 )
+
+__all__ = [
+    "calypso_check_opt_str",
+    "calypso_run_opt_str",
+    "calypso_run_opt_str_end",
+    "make_calypso_input",
+]

dpgen2/exploration/task/lmp/__init__.py

@@ -1,3 +1,7 @@
 from .lmp_input import (
     make_lmp_input,
 )
+
+__all__ = [
+    "make_lmp_input",
+]

dpgen2/flow/__init__.py

@@ -1,3 +1,7 @@
 from .dpgen_loop import (
     ConcurrentLearning,
 )
+
+__all__ = [
+    "ConcurrentLearning",
+]

dpgen2/op/__init__.py

@@ -45,3 +45,23 @@
 from .select_confs import (
     SelectConfs,
 )
+
+__all__ = [
+    "CollRunCaly",
+    "CollectData",
+    "DiffCSPGen",
+    "PrepCalyDPOptim",
+    "PrepCalyInput",
+    "PrepCalyModelDevi",
+    "PrepDPTrain",
+    "PrepLmp",
+    "PrepRelax",
+    "RunCalyDPOptim",
+    "RunCalyModelDevi",
+    "RunDPTrain",
+    "RunLmp",
+    "RunLmpHDF5",
+    "RunRelax",
+    "RunRelaxHDF5",
+    "SelectConfs",
+]

dpgen2/superop/__init__.py

@@ -16,3 +16,12 @@
 from .prep_run_lmp import (
     PrepRunLmp,
 )
+
+__all__ = [
+    "ConcurrentLearningBlock",
+    "PrepRunCaly",
+    "PrepRunDPTrain",
+    "PrepRunDiffCSP",
+    "PrepRunFp",
+    "PrepRunLmp",
+]

dpgen2/utils/__init__.py

@@ -45,3 +45,31 @@
 from .step_config import (
     step_conf_args,
 )
+
+__all__ = [
+    "BinaryFileInput",
+    "bohrium_config_from_dict",
+    "chdir",
+    "dflow_config",
+    "dflow_s3_config",
+    "dump_object_to_file",
+    "find_slice_ranges",
+    "gen_doc_step_dict",
+    "get_artifact_from_uri",
+    "get_iteration",
+    "get_last_iteration",
+    "get_last_scheduler",
+    "get_subkey",
+    "init_executor",
+    "load_object_from_file",
+    "matched_step_key",
+    "normalize_step_dict",
+    "print_keys_in_nice_format",
+    "run_command",
+    "set_directory",
+    "setup_ele_temp",
+    "sort_slice_ops",
+    "step_conf_args",
+    "upload_artifact_and_print_uri",
+    "workflow_config_from_dict",
+]