Merge remote-tracking branch 'origin/celltype_annotation_automl' into celltype_annotation_automl

Author: xingzhongyu

examples/atlas/get_result_web.py

@@ -1,7 +1,7 @@
 import argparse
-from functools import partial
 import json
 import os
+from functools import partial
 from pathlib import Path
 
 import numpy as np
@@ -120,18 +120,19 @@ def spilt_web(url: str):
         print("No match found")
 
 
-def get_metric(run,metric_col):
+def get_metric(run, metric_col):
     """Extract metric value from wandb run.
-    
+
     Parameters
     ----------
     run : wandb.Run
         Weights & Biases run object
-        
+
     Returns
     -------
     float
         Metric value or negative infinity if metric not found
+
     """
     if metric_col not in run.summary:
         return float('-inf')  # Return -inf for missing metrics to handle in comparisons
@@ -140,7 +141,7 @@ def get_metric(run,metric_col):
 
 def get_best_method(urls, metric_col="test_acc"):
     """Find the best performing method across multiple wandb sweeps.
-    
+
     Parameters
     ----------
     urls : list
@@ -163,11 +164,11 @@ def get_best_method(urls, metric_col="test_acc"):
 
     # Track run statistics
     run_states = {"all_total_runs": 0, "all_finished_runs": 0}
-    
+
     for step_name, url in zip(step_names, urls):
         _, _, sweep_id = spilt_web(url)
         sweep = wandb.Api(timeout=1000).sweep(f"{entity}/{project}/{sweep_id}")
-        
+
         # Update run statistics
         finished_runs = [run for run in sweep.runs if run.state == "finished"]
         run_states.update({
@@ -182,10 +183,10 @@ def get_best_method(urls, metric_col="test_acc"):
         best_run = max(sweep.runs, key=partial(get_metric, metric_col=metric_col)) if goal == "maximize" else \
                    min(sweep.runs, key=partial(get_metric, metric_col=metric_col)) if goal == "minimize" else \
                    None
-                   
+
         if best_run is None:
             raise RuntimeError("Optimization goal must be either 'minimize' or 'maximize'")
-            
+
         if metric_col not in best_run.summary:
             continue
         if all_best_run is None:
@@ -323,10 +324,10 @@ def get_new_ans(tissue):
 
 def write_ans(tissue, new_df, output_file=None):
     """Process and write results for a specific tissue type to CSV.
-    
+
     Handles merging of new results with existing data, including conflict detection
     for metric values.
-    
+
     Parameters
     ----------
     tissue : str
@@ -335,6 +336,7 @@ def write_ans(tissue, new_df, output_file=None):
         New results to be written
     output_file : str, optional
         Output file path. Defaults to 'sweep_results/{tissue}_ans.csv'
+
     """
     if output_file is None:
         output_file = f"sweep_results/{tissue}_ans.csv"
@@ -345,7 +347,7 @@ def write_ans(tissue, new_df, output_file=None):
 
     # Reset index to ensure Dataset_id is a regular column
     new_df = new_df.reset_index(drop=True)
-    
+
     # Process new data by merging rows with same Dataset_id
     new_df_processed = pd.DataFrame()
     for dataset_id in new_df['Dataset_id'].unique():

examples/atlas/sc_similarity_examples/sim_query_atlas.py

@@ -76,18 +76,19 @@ def is_match(config_str):
 
 def is_matching_dict(yaml_str, target_dict):
     """Compare YAML configuration with target dictionary.
-    
+
     Parameters
     ----------
     yaml_str : str
         YAML configuration string to parse
     target_dict : dict
         Target dictionary to compare against
-        
+
     Returns
     -------
     bool
         True if dictionaries match, False otherwise
+
     """
     # Parse YAML string
     yaml_config = yaml.safe_load(yaml_str)
@@ -107,18 +108,19 @@ def is_matching_dict(yaml_str, target_dict):
 
 def get_ans(query_dataset, method):
     """Get test accuracy results for a given dataset and method.
-    
+
     Parameters
     ----------
     query_dataset : str
         Dataset identifier
     method : str
         Method name to analyze
-        
+
     Returns
     -------
     pandas.DataFrame or None
         DataFrame containing test accuracy results, None if results don't exist
+
     """
     result_path = f"{file_root}/tuning/{method}/{query_dataset}/results/atlas/best_test_acc.csv"
     if not os.path.exists(result_path):
@@ -137,33 +139,33 @@ def get_ans(query_dataset, method):
 
 def get_ans_from_cache(query_dataset, method):
     """Get cached test accuracy results for atlas datasets.
-    
+
     Parameters
     ----------
     query_dataset : str
         Query dataset identifier
     method : str
         Method name to analyze
-        
+
     Returns
     -------
     pandas.DataFrame
         DataFrame containing test accuracy results from cache
+
     """
     # Get best method from step2 of atlas datasets
     # Search accuracy according to best method (all values should exist)
-    ans = pd.DataFrame(index=[method], 
-                      columns=[f"{atlas_dataset}_from_cache" for atlas_dataset in atlas_datasets])
-    
+    ans = pd.DataFrame(index=[method], columns=[f"{atlas_dataset}_from_cache" for atlas_dataset in atlas_datasets])
+
     sweep_url = re.search(r"step2:([^|]+)",
-                         conf_data[conf_data["dataset_id"] == query_dataset][method].iloc[0]).group(1)
+                          conf_data[conf_data["dataset_id"] == query_dataset][method].iloc[0]).group(1)
     _, _, sweep_id = spilt_web(sweep_url)
     sweep = wandb.Api().sweep(f"{entity}/{project}/{sweep_id}")
-    
+
     for atlas_dataset in atlas_datasets:
         best_yaml = conf_data[conf_data["dataset_id"] == atlas_dataset][f"{method}_best_yaml"].iloc[0]
         match_run = None
-        
+
         # Find matching run configuration
         for run in sweep.runs:
             if isinstance(best_yaml, float) and np.isnan(best_yaml):
@@ -172,14 +174,13 @@ def get_ans_from_cache(query_dataset, method):
                 if match_run is not None:
                     raise ValueError("Multiple matching runs found when only one expected")
                 match_run = run
-                
+
         if match_run is None:
             logger.warning(f"No matching configuration found for {atlas_dataset} with method {method}")
         else:
-            ans.loc[method, f"{atlas_dataset}_from_cache"] = (
-                match_run.summary["test_acc"] if "test_acc" in match_run.summary else np.nan
-            )
-    
+            ans.loc[method, f"{atlas_dataset}_from_cache"] = (match_run.summary["test_acc"]
+                                                              if "test_acc" in match_run.summary else np.nan)
+
     return ans
 
 

examples/atlas/test_get_result_web.py

@@ -108,7 +108,7 @@ def test_write_ans(tmp_path):
     # 测试冲突情况的处理
     write_ans(tissue, conflict_df, output_file=output_file)
     final_df = pd.read_csv(output_file)
-    
+
     # 验证新值被更新
     assert final_df[final_df['Dataset_id'] == 'dataset1']['method1_best_res'].iloc[0] == 0.7