- Fix AttributeError: module 'pyranges' has no attribute 'from_dfs'…

… causing to_ranges function to return a pandas Dataframe instead of PyRanges object (pyranges#9)

- Logging exception in case the to_ranges function fails at creating the pr.PyRanges object
- adding Exception (PEP 8: E722)

CHANGELOG.txt

@@ -1,3 +1,7 @@
+# 0.0.38 (08.04.2024) (@Isy89)
+- Fix `AttributeError: module 'pyranges' has no attribute 'from_dfs'` causing to_ranges function to return a pandas 
+  Dataframe instead of PyRanges object (#9)
+
 # 0.0.37 (18.05.23)
 - remove option to return 32-bit PyRanges
 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyrle"
-version = "0.0.39"
+version = "0.0.40"
 description = "Numeric run length encoding for Python."
 readme = "README.md"
 authors = [{ name = "Endre Bakken Stovner", email = "[email protected]" }]

pyrle/methods.py

@@ -1,3 +1,4 @@
+import logging
 import os
 from collections import defaultdict
 
@@ -9,6 +10,8 @@
 from pyrle import rledict as rd  # type: ignore
 from pyrle.src.coverage import _coverage  # type: ignore
 
+logger = logging.getLogger(__name__)
+
 
 class suppress_stdout_stderr(object):
     """
@@ -179,14 +182,15 @@ def to_ranges_df_no_strand(rle, k):
 
 
 def to_ranges(grles, nb_cpu=1):
-    import pyranges as pr# type: ignore
+    import pyranges as pr  # type: ignore
 
     func = to_ranges_df_strand if grles.stranded else to_ranges_df_no_strand
 
     func.remote = func
 
     def get(x):
         return x
+
     dfs, keys = [], []
     for k, v in grles.items():
         result = func.remote(v, k)
@@ -196,8 +200,9 @@ def get(x):
     dfs = {k: v for (k, v) in zip(keys, get(dfs))}
 
     try:
-        return pr.from_dfs(dfs)
-    except:
+        return pr.PyRanges(dfs)
+    except Exception:
+        logger.exception("It was not possible to return a PyRanges object. Returning a pandas Dataframe.")
         return pd.concat(dfs.values())