merge pandas tests with initialize, replace biocgenerics with biocutils

docs/tutorial.md

@@ -442,10 +442,10 @@ rank = gr.rank()
 
 ## Combine `GenomicRanges` objects by rows
 
-Use the `combine` generic from [biocgenerics](https://github.com/BiocPy/generics) to concatenate multiple GenomicRanges objects.
+Use the `combine` generic from [biocutils](https://github.com/BiocPy/generics) to concatenate multiple GenomicRanges objects.
 
 ```python
-from biocgenerics.combine import combine
+from biocutils.combine import combine
 combined_gr = combine(gr, gr1, gr2, ...)
 ```
 
@@ -524,7 +524,7 @@ grlb = GenomicRangesList(ranges=[b, a], names=["b", "c"])
 grlc = grla.combine(grlb)
 
 # or use the combine generic
-from biocgenerics.combine import combine
+from biocutils.combine import combine
 cgrl = combine(grla, grlb)
 ```
 

tests/test_gr_initialize.py

@@ -56,3 +56,34 @@ def test_from_pandas():
     assert len(g_src) == 1
     assert g_src.names is not None
     assert g_src.strand is not None
+
+
+def test__from_pandas_should_fail():
+    with pytest.raises(Exception):
+        df_gr = pd.DataFrame(
+            {
+                "starts": range(100, 110),
+                "ends": range(110, 120),
+                "strand": ["-", "+", "+", "*", "*", "+", "+", "+", "-", "-"],
+                "score": range(0, 10),
+                "GC": [random() for _ in range(10)],
+            }
+        )
+
+        GenomicRanges.from_pandas(df_gr)
+
+
+# def test_gr_empty():
+#     gr = GenomicRanges(number_of_rows=100)
+
+#     assert gr is not None
+#     assert isinstance(gr, GenomicRanges)
+#     assert len(gr) == 100
+#     assert gr.shape == (100, 0)
+
+#     gre = GenomicRanges.empty()
+
+#     assert gre is not None
+#     assert isinstance(gre, GenomicRanges)
+#     assert len(gre) == 0
+#     assert gre.shape == (0, 0)

tests/test_grl_methods.py

@@ -1,7 +1,7 @@
 import pytest
 import pandas as pd
 from genomicranges import GenomicRanges, GenomicRangesList
-from biocgenerics.combine import combine
+from biocutils.combine import combine
 from biocframe import BiocFrame
 from random import random
 import genomicranges

tests/test_names_generic.py

@@ -1,7 +1,7 @@
 import pandas as pd
 from genomicranges import GenomicRanges
-from biocgenerics.rownames import rownames
-from biocgenerics.colnames import colnames
+from biocutils.rownames import rownames
+from biocutils.colnames import colnames
 from random import random
 import genomicranges