Use relaxed_combine_rows when merging mcols (#99)

* As noted in #98, using `relaxed_combine_rows` allows to perform operations on granges objects that may contain different metadata columns.  
* Set numpy version to < 2.0; since a few operations are incompatible with the new release
* Add tests

setup.cfg

@@ -52,7 +52,7 @@ install_requires =
     biocframe>=0.5.11
     iranges[optional]>=0.2.6
     biocutils>=0.1.3
-    numpy
+    numpy<2.0.0
 
 [options.packages.find]
 where = src

src/genomicranges/GenomicRanges.py

@@ -2848,7 +2848,7 @@ def _combine_GenomicRanges(*x: GenomicRanges) -> GenomicRanges:
         seqnames=ut.combine_sequences(*[y._seqnames for y in x]),
         strand=ut.combine_sequences(*[y._strand for y in x]),
         names=all_names,
-        mcols=ut.combine_rows(*[y._mcols for y in x]),
+        mcols=ut.relaxed_combine_rows(*[y._mcols for y in x]),
         seqinfo=merge_SeqInfo([y._seqinfo for y in x]),
         metadata=x[0]._metadata,
         validate=False,

src/genomicranges/GenomicRangesList.py

@@ -873,7 +873,7 @@ def _combine_grl(*x: GenomicRangesList):
         ranges=ut.combine_sequences(*[y._ranges for y in x]),
         range_lengths=ut.combine_sequences(*[y._range_lengths for y in x]),
         names=all_names,
-        mcols=ut.combine_rows(*[y._mcols for y in x]),
+        mcols=ut.relaxed_combine_rows(*[y._mcols for y in x]),
         metadata=x[0]._metadata,
         validate=False,
     )

tests/test_gr_methods_basic.py

@@ -3,6 +3,7 @@
 import numpy as np
 from genomicranges import GenomicRanges
 from biocframe import BiocFrame
+import biocutils as ut
 from iranges import IRanges
 from random import random
 import genomicranges
@@ -102,3 +103,44 @@ def test_export():
         "chr3",
     ]
     assert df["strand"].tolist() == ["-", "+", "+", "*", "*", "+", "+", "+", "-", "-"]
+
+
+def test_combine():
+    g_src = GenomicRanges(
+        seqnames=["chr1", "chr2", "chr1", "chr3", "chr2"],
+        ranges=IRanges(
+            start=[101, 102, 103, 104, 109], width=[112, 103, 128, 134, 111]
+        ),
+        strand=["*", "-", "*", "+", "-"],
+    )
+
+    g_tgt = GenomicRanges(
+        seqnames=[
+            "chr1",
+            "chr2",
+            "chr2",
+            "chr2",
+            "chr1",
+            "chr1",
+            "chr3",
+            "chr3",
+            "chr3",
+            "chr3",
+        ],
+        ranges=IRanges(start=range(101, 111), width=range(121, 131)),
+        strand=["*", "-", "-", "*", "*", "+", "+", "+", "-", "-"],
+        mcols=BiocFrame(
+            {
+                "score": range(0, 10),
+                "GC": [random() for _ in range(10)],
+            }
+        ),
+    )
+    assert g_src is not None
+    assert g_tgt is not None
+
+    out: GenomicRanges = ut.combine_sequences(g_src, g_tgt)
+
+    assert out is not None
+    assert len(out) == 15
+    assert len(out.get_mcols().get_column_names()) == 2

tests/test_gr_set_ops.py

@@ -70,3 +70,43 @@ def test_intersect():
     assert (out.start == np.array([9])).all()
     assert (out.width == np.array([2])).all()
     assert (out.strand == np.array([-1])).all()
+
+
+def test_intersect():
+    g_src = GenomicRanges(
+        seqnames=["chr1", "chr2", "chr1", "chr3", "chr2"],
+        ranges=IRanges(
+            start=[101, 102, 103, 104, 109], width=[112, 103, 128, 134, 111]
+        ),
+        strand=["*", "-", "*", "+", "-"],
+    )
+
+    g_tgt = GenomicRanges(
+        seqnames=[
+            "chr1",
+            "chr2",
+            "chr2",
+            "chr2",
+            "chr1",
+            "chr1",
+            "chr3",
+            "chr3",
+            "chr3",
+            "chr3",
+        ],
+        ranges=IRanges(start=range(101, 111), width=range(121, 131)),
+        strand=["*", "-", "-", "*", "*", "+", "+", "+", "-", "-"],
+        mcols=BiocFrame(
+            {
+                "score": range(0, 10),
+                "GC": [random() for _ in range(10)],
+            }
+        ),
+    )
+    assert g_src is not None
+    assert g_tgt is not None
+
+    out = g_src.intersect(g_tgt)
+
+    assert out is not None
+    assert len(out) == 3