Fix coercion to pandas when IRanges contains mcols (#46)

Add tests and update changelog.

Author: jkanche

.pre-commit-config.yaml

@@ -17,13 +17,13 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
 
-- repo: https://github.com/PyCQA/docformatter
-  rev: v1.7.5
-  hooks:
-    - id: docformatter
-      additional_dependencies: [tomli]
-      args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
-      # --config, ./pyproject.toml
+# - repo: https://github.com/PyCQA/docformatter
+#   rev: v1.7.5
+#   hooks:
+#     - id: docformatter
+#       additional_dependencies: [tomli]
+#       args: [--in-place, --wrap-descriptions=120, --wrap-summaries=120]
+#       # --config, ./pyproject.toml
 
 - repo: https://github.com/psf/black
   rev: 24.8.0

CHANGELOG.md

@@ -1,10 +1,11 @@
 # Changelog
 
-## Version 0.2.10
+## Version 0.2.10 - 0.2.12
 
 - Added a numpy vectorized version of finding gaps (tldr: not fast compared to the traditional version). May be needs a better implementation
 - Added NCLS based intersection operation (based on what pyranges does in their internals)
 - Added tests for intersection operations.
+- Fixed and issue when coercing `IRanges` containing mcols.
 
 ## Version 0.2.8 - 0.2.9
 

src/iranges/IRanges.py

@@ -2220,7 +2220,7 @@ def to_pandas(self) -> "pandas.DataFrame":
         output = pd.DataFrame({"starts": _starts, "widths": _widths, "ends": _ends})
 
         if self._mcols is not None and self._mcols.shape[1] > 0:
-            output = pd.concat([output, self._mcols.to_pandas()])
+            output = pd.concat([output, self._mcols.to_pandas()], axis=1)
 
         if self._names is not None:
             output.index = self._names

tests/test_IRanges_pandas.py

@@ -24,3 +24,14 @@ def test_pandas_export():
     assert y is not None
     assert isinstance(y, pd.DataFrame)
     assert set(y.columns.tolist()).issubset(["starts", "ends", "widths"])
+
+
+def test_pandas_with_mcols():
+    x = IRanges(
+        [1, 2, 3, 4], [4, 5, 6, 7], mcols=BiocFrame({"temp": ["a", "t", "g", "c"]})
+    )
+
+    y = x.to_pandas()
+    assert y is not None
+    assert isinstance(y, pd.DataFrame)
+    assert set(y.columns.tolist()).issubset(["starts", "ends", "widths", "temp"])