[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

dpti/aitools/codebase/collect_py_files_context.py

@@ -1,55 +1,60 @@
 # %%
 
-import os
-import json
 import argparse
+import json
 from pathlib import Path
-from typing import Dict, List
+from typing import Dict
+
 
 def collect_python_files(directory: str) -> Dict[str, str]:
     """
-    Collect paths and contents of all Python files in the specified directory
-    
+    Collect paths and contents of all Python files in the specified directory.
+
     Args:
         directory: Directory path to scan
-    
-    Returns:
-        Dictionary containing file paths and their contents
+
+    Returns
+    -------
+    Dictionary containing file paths and their contents
     """
     python_files = {}
     base_dir = Path(directory).name
-    
+
     # Use Path object for directory traversal
     for file_path in Path(directory).rglob("*.py"):
         # Skip __pycache__ directory
         if "__pycache__" in str(file_path):
             continue
-            
+
         try:
             # Read file content
-            with open(file_path, 'r', encoding='utf-8') as f:
+            with open(file_path, encoding="utf-8") as f:
                 content = f.read()
-                
+
             # Convert to relative path and include base directory
             relative_path = str(file_path.relative_to(directory))
             full_path = f"{base_dir}/{relative_path}"
             python_files[full_path] = content
-            
+
         except Exception as e:
-            print(f"Error reading file {file_path}: {str(e)}")
-            
+            print(f"Error reading file {file_path}: {e!s}")
+
     return python_files
 
-def group_by_directory(files: Dict[str, str], max_files_per_group: int = 20) -> Dict[str, Dict[str, str]]:
+
+def group_by_directory(
+    files: Dict[str, str], max_files_per_group: int = 20
+) -> Dict[str, Dict[str, str]]:
     """
-    Group files by their directory structure
-    
+    Group files by their directory structure.
+
     Args:
         files: Dictionary of file paths and contents
         max_files_per_group: Maximum number of files per group
-    
-    Returns:
-        Dictionary of grouped files
+
+    Returns
+    -------
+    Dictionary of grouped files
     """
     # First group by directory
     dir_groups = {}
@@ -58,92 +63,101 @@ def group_by_directory(files: Dict[str, str], max_files_per_group: int = 20) ->
         if dir_name not in dir_groups:
             dir_groups[dir_name] = {}
         dir_groups[dir_name][file_path] = content
-    
+
     # Merge small groups and split large groups
     final_groups = {}
     current_group = {}
     current_group_size = 0
     group_index = 1
-    
+
     for dir_name, dir_files in dir_groups.items():
         # If adding this directory's files would exceed the limit
-        if current_group_size + len(dir_files) > max_files_per_group and current_group_size > 0:
+        if (
+            current_group_size + len(dir_files) > max_files_per_group
+            and current_group_size > 0
+        ):
             # Save current group and start a new one
             final_groups[f"group_{group_index}"] = current_group
             current_group = {}
             current_group_size = 0
             group_index += 1
-        
+
         # Add files to current group
         current_group.update(dir_files)
         current_group_size += len(dir_files)
-    
+
     # Don't forget to save the last group
     if current_group:
         final_groups[f"group_{group_index}"] = current_group
-    
+
     return final_groups
 
+
 def save_grouped_json(groups: Dict[str, Dict[str, str]], output_base: str) -> None:
     """
-    Save each group to a separate JSON file
-    
+    Save each group to a separate JSON file.
+
     Args:
         groups: Grouped files dictionary
         output_base: Base name for output files
     """
     output_base = Path(output_base)
     base_name = output_base.stem
     parent_dir = output_base.parent
-    
+
     for group_name, group_files in groups.items():
         output_file = parent_dir / f"{base_name}_{group_name}.json"
         wrapper = {
             "project_files": {
                 "description": f"Python source files collection - {group_name}",
                 "base_directory": Path().absolute().name,
-                "files": group_files
+                "files": group_files,
             }
         }
-        
-        with open(output_file, 'w', encoding='utf-8') as f:
+
+        with open(output_file, "w", encoding="utf-8") as f:
             json.dump(wrapper, f, ensure_ascii=False, indent=2)
         print(f"Saved {len(group_files)} files to {output_file}")
 
+
 def main():
     parser = argparse.ArgumentParser(
-        description='Collect Python files content into JSON for context'
+        description="Collect Python files content into JSON for context"
     )
     parser.add_argument(
-        '-d', '--directory',
-        default='../../../dpti/',
-        help='Directory to scan (default: current directory)'
+        "-d",
+        "--directory",
+        default="../../../dpti/",
+        help="Directory to scan (default: current directory)",
     )
     parser.add_argument(
-        '-o', '--output',
-        default='build/python_files_context.json',
-        help='Output JSON file base name (default: python_files_context.json)'
+        "-o",
+        "--output",
+        default="build/python_files_context.json",
+        help="Output JSON file base name (default: python_files_context.json)",
     )
     parser.add_argument(
-        '-n', '--num-files',
+        "-n",
+        "--num-files",
         type=int,
         default=20,
-        help='Maximum number of files per group (default: 20)'
+        help="Maximum number of files per group (default: 20)",
     )
-    
+
     args = parser.parse_args()
-    
+
     # Collect Python files
     python_files = collect_python_files(args.directory)
-    
+
     # Group files
     groups = group_by_directory(python_files, args.num_files)
-    
+
     # Save grouped files
     save_grouped_json(groups, args.output)
-    
+
     print(f"\nTotal files collected: {len(python_files)}")
     print(f"Split into {len(groups)} groups")
 
+
 if __name__ == "__main__":
     main()

dpti/workflows/analyze/compare_ti_plot.py

@@ -35,7 +35,7 @@ def plot_free_energy_comparison(
 
     Returns
     -------
-        base64 encoded string of the plot image
+    base64 encoded string of the plot image
     """
     plt.figure(figsize=(12, 8))
     plt.rcParams.update({"font.size": 14})
@@ -175,7 +175,7 @@ def analyze_align_different_temp_starting_points(result_info: dict) -> str:
 
     Returns
     -------
-        base64 encoded string of the plot image
+    base64 encoded string of the plot image
     """
     pass
 
@@ -192,7 +192,7 @@ def compare_multiple_runs(result_files: list, labels: Optional[list] = None) ->
 
     Returns
     -------
-        base64 encoded string of the plot image
+    base64 encoded string of the plot image
     """
     # Create figure with two subplots
     fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(12, 16), height_ratios=[1, 1])
@@ -348,10 +348,10 @@ def plot_multiple_phase_comparison(
 
     Returns
     -------
-        Dict containing base64 encoded plot images:
-        - 'all_comparisons': Plot showing all N*M comparisons
-        - 'statistical_distribution': Plot showing distribution and mean
-        - 'mean_comparison': Plot showing mean values with error bars
+    Dict containing base64 encoded plot images:
+    - 'all_comparisons': Plot showing all N*M comparisons
+    - 'statistical_distribution': Plot showing distribution and mean
+    - 'mean_comparison': Plot showing mean values with error bars
     """
     import base64
     from itertools import product

tests/workflows/flows/test_flow_instance_method.py

@@ -32,7 +32,7 @@ def create_workflow_flow(workflow_class, method_name, **flow_kwargs):
 
     Returns
     -------
-        装饰后的flow函数
+    装饰后的flow函数
     """
 
     @flow(**flow_kwargs)