pythonflex 0.2.2__tar.gz → 0.2.4__tar.gz

{pythonflex-0.2.2 → pythonflex-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pythonflex
-Version: 0.2.2
+Version: 0.2.4
 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-0.2.2 → pythonflex-0.2.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pythonflex"
-version = "0.2.2"
+version = "0.2.4"
 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-0.2.2 → pythonflex-0.2.4}/src/pythonflex/utils.py

@@ -1,27 +1,13 @@
 import os
-import re  # For sanitization (built-in, minimal regex)
+import re
 import tempfile
 import joblib
 import numpy as np
 import pandas as pd
 
-# Constants - ADD .parquet to valid extensions
+# Constants
 TMP_ROOT = ".tmp"
-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
+VALID_EXTS = {".parquet", ".npy", ".pkl"}  # Removed .feather
 
 # Helper to sanitize names (make filesystem-safe)
 def _sanitize(name):
@@ -40,36 +26,36 @@ def _safe_path(category, name=None, ext=".pkl"):
     safe_name = _sanitize(name) if name else "data"
     return os.path.join(dir_path, f"{safe_name}{ext}")
 
-# Save function
-def dsave(data, category, name=None, path=None):  # 'path' ignored for compatibility with old code
+# Save function - Parquet for DataFrames
+def dsave(data, category, name=None, path=None):
     # If data is dict and no name, recurse on each item
     if name is None and isinstance(data, dict):
         for k, v in data.items():
             dsave(v, category, k)
         return
 
-    # Choose best extension based on type
+    # Choose format based on type
     if isinstance(data, pd.DataFrame):
-        ext = ".feather"
-        save_func = lambda p: data.to_feather(p)
+        ext = ".parquet"
+        save_func = lambda p: data.to_parquet(p)
     elif isinstance(data, np.ndarray):
         ext = ".npy"
         save_func = lambda p: np.save(p, data, allow_pickle=False)
     else:
         ext = ".pkl"
-        save_func = lambda p: joblib.dump(data, p, compress=0)  # Add compress=3 if needed
+        save_func = lambda p: joblib.dump(data, p, compress=0)
 
     target = _safe_path(category, name, ext)
 
     # Atomic save: Write to temp file, then rename
-    with tempfile.NamedTemporaryFile(dir=os.path.dirname(target), delete=False) as tf:
+    with tempfile.NamedTemporaryFile(dir=os.path.dirname(target), delete=False, suffix=ext) as tf:
         tmp_path = tf.name
-        tf.close()  # Close so save_func can write
+        tf.close()
         save_func(tmp_path)
-    os.replace(tmp_path, target)  # Atomic move
+    os.replace(tmp_path, target)
 
-# Load function - FIXED: Added parquet support
-def dload(category, name=None, path=None):  # 'path' ignored for compatibility
+# Load function - Parquet for DataFrames
+def dload(category, name=None, path=None):
     dir_path = os.path.join(TMP_ROOT, _sanitize(category))
 
     if not os.path.exists(dir_path):
@@ -81,44 +67,35 @@ def dload(category, name=None, path=None):  # 'path' ignored for compatibility
         for filename in os.listdir(dir_path):
             if not any(filename.endswith(ext) for ext in VALID_EXTS):
                 continue
-            k = os.path.splitext(filename)[0]  # Key from filename (without ext)
+            k = os.path.splitext(filename)[0]
             full_path = os.path.join(dir_path, filename)
             try:
-                if filename.endswith(".feather"):
-                    out[k] = pd.read_feather(full_path)
-                elif filename.endswith(".parquet"):  # ADDED
+                if filename.endswith(".parquet"):
                     out[k] = pd.read_parquet(full_path)
                 elif filename.endswith(".npy"):
-                    out[k] = np.load(full_path, mmap_mode="r")  # MMap for perf
+                    out[k] = np.load(full_path, mmap_mode="r")
                 elif filename.endswith(".pkl"):
-                    out[k] = joblib.load(full_path, mmap_mode="r")  # MMap for perf
+                    out[k] = joblib.load(full_path, mmap_mode="r")
             except (EOFError, ValueError, OSError):
                 print(f"Warning: '{full_path}' is corrupted. Skipping...")
-                os.remove(full_path)  # Delete corrupted file
+                os.remove(full_path)
         return out
 
-    # 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
+    # Load specific name - try extensions in order
+    for ext in VALID_EXTS:
         target = _safe_path(category, name, ext)
         if os.path.exists(target):
             try:
-                if ext == ".feather":
-                    return pd.read_feather(target)
-                elif ext == ".parquet":
+                if ext == ".parquet":
                     return pd.read_parquet(target)
                 elif ext == ".npy":
-                    return np.load(target, mmap_mode="r")  # MMap for perf
+                    return np.load(target, mmap_mode="r")
                 elif ext == ".pkl":
-                    return joblib.load(target, mmap_mode="r")  # MMap for perf
+                    return joblib.load(target, mmap_mode="r")
             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 {}
+                os.remove(target)
+                continue
     
     print(f"Warning: No valid file found for {category}/{name}")
     return {}