make compatible with pyranges v1 module renamed to pyranges1

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyrle"
-version = "0.0.42"
+version = "0.0.43"
 description = "Numeric run length encoding for Python."
 readme = "README.md"
 authors = [{ name = "Endre Bakken Stovner", email = "endbak@pm.me" }]

pyrle/methods.py

@@ -1,3 +1,4 @@
+import logging
 import os
 from collections import defaultdict
 
@@ -9,6 +10,7 @@
 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):
     """
@@ -179,16 +181,20 @@ def to_ranges_df_no_strand(rle, k):
 
 
 def to_ranges(grles, nb_cpu=1):
-    import pyranges as pr# type: ignore
+    try:
+        import pyranges1 as pr # type: ignore
+    except ModuleNotFoundError:
+        import pyranges as pr  # type: ignore
 
     func = to_ranges_df_strand if grles.stranded else to_ranges_df_no_strand
 
-    dfs = {k: func(v, k) for k, v in grles.items()}
+    dfs_list = [func(v, k) for k, v in grles.items()]
 
-    try:  # new pyranges
-        return pr.from_dfs(dfs)
-    except:  # legacy pyranges
-        return pr.PyRanges(pd.concat(dfs.values()))
+    try:
+        return pr.PyRanges(pd.concat(dfs_list))
+    except Exception:
+        logger.exception("It was not possible to return a PyRanges object. Returning a pandas Dataframe.")
+        return pd.concat(dfs_list)
 
 
 def _to_ranges(rle):

pyrle/rle.py

@@ -297,7 +297,10 @@ def __getitem__(self, val):
             return df
         elif "PyRanges" in str(type(val)):  # hack to avoid isinstance(key, pr.PyRanges) so that we
             # do not need a dep on PyRanges in this library
-            import pyranges as pr  # type: ignore
+            try:
+                import pyranges1 as pr  # type: ignore
+            except ModuleNotFoundError:
+                import pyranges as pr  # type: ignore
 
             val = val.drop().df
             if val.empty:

pyrle/rledict.py

@@ -87,9 +87,9 @@ class RleDict:
     Rle of length 10 containing 6 elements (avg. length 1.667)
     Unstranded RleDict object with 2 chromosomes.
 
-    >>> import pyranges as pr
-    >>> gr = pr.data.chipseq()
-    >>> df = pr.data.chipseq_background().df
+    >>> import pyranges1 as pr
+    >>> gr = pr.example_data.chipseq
+    >>> df = pr.example_data.chipseq_background
     >>> cs = RleDict(gr, stranded=True)
     >>> bg = RleDict(df, stranded=True)
 
@@ -257,7 +257,10 @@ def __getitem__(self, key):
             # do not need a dep on PyRanges in this library
 
             import pandas as pd
-            import pyranges as pr  # type: ignore
+            try:
+                import pyranges1 as pr  # type: ignore
+            except ModuleNotFoundError:
+                import pyranges as pr  # type: ignore
 
             if not len(key):
                 return pd.DataFrame(columns="Chromosome Start End ID Run Value".split())

tests/hypothesis_helper.py

@@ -5,7 +5,10 @@
 from hypothesis.extra.numpy import arrays
 import hypothesis.strategies as st
 
-from pyranges import PyRanges
+try:
+    from pyranges1 import PyRanges
+except ModuleNotFoundError:
+    from pyranges import PyRanges
 
 import numpy as np
 

tests/test_hypothesis_coverage.py

@@ -11,7 +11,10 @@
 from io import StringIO
 
 from pyrle import Rle
-import pyranges as pr
+try:
+    import pyranges1 as pr  # type: ignore
+except ModuleNotFoundError:
+    import pyranges as pr  # type: ignore
 
 import pandas as pd
 import numpy as np