pythonflex 0.2__tar.gz → 0.2.2__tar.gz

{pythonflex-0.2 → pythonflex-0.2.2}/.gitignore

@@ -15,3 +15,4 @@ bfg-*.jar
 examples/output/
 src/benchmarkcr/examples/output/
 .aider*
+.vscode

{pythonflex-0.2 → pythonflex-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pythonflex
-Version: 0.2
+Version: 0.2.2
 Summary: pythonFLEX is a benchmarking toolkit for evaluating CRISPR screen results against biological gold standards. The toolkit computes gene-level and complex-level performance metrics, helping researchers systematically assess the biological relevance and resolution of their CRISPR screening data.
 Author-email: Yasir Demirtaş <tyasird@hotmail.com>
 Requires-Python: >=3.9

{pythonflex-0.2 → pythonflex-0.2.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pythonflex"
-version = "0.2"
+version = "0.2.2"
 description = "pythonFLEX is a benchmarking toolkit for evaluating CRISPR screen results against biological gold standards. The toolkit computes gene-level and complex-level performance metrics, helping researchers systematically assess the biological relevance and resolution of their CRISPR screening data."
 readme = "README.md"
 authors = [

{pythonflex-0.2 → pythonflex-0.2.2}/src/pythonflex/utils.py

@@ -5,9 +5,23 @@ import joblib
 import numpy as np
 import pandas as pd
 
-# Constants
+# Constants - ADD .parquet to valid extensions
 TMP_ROOT = ".tmp"
-VALID_EXTS = {".feather", ".npy", ".pkl"}
+VALID_EXTS = {".feather", ".parquet", ".npy", ".pkl"}
+
+# Minimal fix - just patch the problematic save
+original_to_feather = pd.DataFrame.to_feather
+def safe_to_feather(self, path, **kwargs):
+    try:
+        return original_to_feather(self, path, **kwargs)
+    except ValueError as e:
+        if "feather does not support serializing" in str(e):
+            # FIXED: Better path handling
+            parquet_path = os.path.splitext(path)[0] + '.parquet'
+            self.to_parquet(parquet_path, **kwargs)
+        else:
+            raise
+pd.DataFrame.to_feather = safe_to_feather
 
 # Helper to sanitize names (make filesystem-safe)
 def _sanitize(name):
@@ -54,7 +68,7 @@ def dsave(data, category, name=None, path=None):  # 'path' ignored for compatibi
         save_func(tmp_path)
     os.replace(tmp_path, target)  # Atomic move
 
-# Load function
+# Load function - FIXED: Added parquet support
 def dload(category, name=None, path=None):  # 'path' ignored for compatibility
     dir_path = os.path.join(TMP_ROOT, _sanitize(category))
 
@@ -72,6 +86,8 @@ def dload(category, name=None, path=None):  # 'path' ignored for compatibility
             try:
                 if filename.endswith(".feather"):
                     out[k] = pd.read_feather(full_path)
+                elif filename.endswith(".parquet"):  # ADDED
+                    out[k] = pd.read_parquet(full_path)
                 elif filename.endswith(".npy"):
                     out[k] = np.load(full_path, mmap_mode="r")  # MMap for perf
                 elif filename.endswith(".pkl"):
@@ -81,20 +97,28 @@ def dload(category, name=None, path=None):  # 'path' ignored for compatibility
                 os.remove(full_path)  # Delete corrupted file
         return out
 
-    # Load specific name (try extensions in order)
-    for ext in VALID_EXTS:
+    # Load specific name (try extensions in order - PREFER PARQUET over FEATHER)
+    # Check parquet first since it's more reliable for complex data
+    preferred_order = [".parquet", ".feather", ".npy", ".pkl"]
+    
+    for ext in preferred_order:
+        if ext not in VALID_EXTS:
+            continue
         target = _safe_path(category, name, ext)
         if os.path.exists(target):
             try:
                 if ext == ".feather":
                     return pd.read_feather(target)
+                elif ext == ".parquet":
+                    return pd.read_parquet(target)
                 elif ext == ".npy":
                     return np.load(target, mmap_mode="r")  # MMap for perf
                 elif ext == ".pkl":
                     return joblib.load(target, mmap_mode="r")  # MMap for perf
-            except (EOFError, ValueError, OSError):
-                print(f"Warning: '{target}' is corrupted. Deleting and returning {{}}...")
-                os.remove(target)
-                return {}
-    return {}
-
+            except (EOFError, ValueError, OSError) as e:
+                print(f"Warning: '{target}' is corrupted ({e}). Trying next format...")
+                os.remove(target)  # Delete corrupted file
+                continue  # Try next format instead of returning {}
+    
+    print(f"Warning: No valid file found for {category}/{name}")
+    return {}

pythonflex-0.2/.vscode/settings.json

@@ -1,5 +0,0 @@
-{
-    "python-envs.defaultEnvManager": "ms-python.python:conda",
-    "python-envs.defaultPackageManager": "ms-python.python:conda",
-    "python-envs.pythonProjects": []
-}